A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

Abl_X(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Calculate the x-derivative of the gradient image.
Abl_Y(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Calculate the y-derivative of the gradient image.
abs(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Absolute values of the image elements.
abs(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Absolute values of the image elements.
abs_diff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Absolute difference of the elements of two images
absDiff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Absolute difference of two images.
AbstractAssociationDistribution<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for association distributions that allow sampling of the association variables for a set of observations in a multi-target tracking framework.
AbstractAssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, DataAssociationFactory) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
Constructor
AbstractMultiObservationDistribution<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for multi target observation distributions.
AbstractMultiObservationDistribution(AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<S>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
Constructor to set the condition conditionX, and the factories of multi state and multi observation variables
AbstractMultiObservationDistributionIndep<S extends Copyable<?>,T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for multi target observation distributions.
AbstractMultiObservationDistributionIndep(AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<S>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Constructor to set the condition conditionX, and the factories of multi state and multi observation variables
AbstractMultiState<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
Abstract class to hold the states of multiple targets.
AbstractMultiState(AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Constructor that assigns a factory
AbstractMultiStateFactory<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
Factory class for creating new multi state objects
AbstractMultiStateFactory(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Constructor with specification of the variables of a single state
AbstractMultiStateTransitionDistribution<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class for multi-target state transition distributions.
AbstractMultiStateTransitionDistribution(AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
Constructor to set the condition X, and the factories of multi state and multi observation variables
AbstractMultiStateTransitionDistributionIndep<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
Abstract class of multi-target state transition distribution with independent targets.
AbstractMultiStateTransitionDistributionIndep(AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
 
accept(File) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
 
accept(File) - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
acceptStacks(File) - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
acot(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the arcus cotangens of value in radian.
ActinAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Operator for analyzing actin filament structures in 2D images.
ActinAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Default constructor.
ActinAnalyzer2D.CellMaskFormat - Enum in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Format of cell segmentation data.
ActinAnalyzer2D.FeatureType - Enum in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Type of features to characterize local structure.
ActinFeatureExtractorEigenStructures - Class in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Operator for extracting Eigen structures as features for the ActinAnalyzer2D.
ActinFeatureExtractorEigenStructures() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Default constructor.
ActinFeatureExtractorHaralickMeasures - Class in de.unihalle.informatik.MiToBo.apps.actinAnalysis
Operator for extracting Haralick texture measures from cooccurrence matrices as features for the ActinAnalyzer2D.
ActinFeatureExtractorHaralickMeasures() - Constructor for class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Default constructor.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Fires a PropertyChangeEvent with property CheckBoxPanel.CHECK_CHANGED_PROPERTY if a checkbox value was changed
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Assigns the reader options to the option variables when a file selection is approved by the file chooser.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Assigns the writer options to the option variables when a file selection is approved by the file chooser.
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Assigns the selected radio button string and fires a PropertyChangeEvent with property RadioButtonPanel.SELECTION_CHANGED_PROPERTY
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
 
activeSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Array with active snakes.
activityArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Array of active snakes, suitable for masking snakes in optimization.
adaptedGamma - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
The new and adapted gamma values for all snake points.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Gamma adaptation using fixed decreasing factor for all gamma values.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
No gamma adaptation is made.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
Gamma adaptation using a point wise adaptation, depending on the current snake and the external energy force.
adaptGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Method for gamma adaptation.
add(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
add(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Append a border (at the end) to the set of borders.
add(MTBContour2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Append a contour (at the end) to the set of contours.
add(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
add histogram data to this MTBHistogram object.
add(MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Append a polygon (at the end) to the set of polygons.
add(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Append a region (at the end) to the set of regions.
add(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Add a region set to this bag
add(MTBRegion3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Append a region (at the end) to the set of regions.
add(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Appends the specified element to the end of this list.
add(MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Appends the specified element to the end of this list.
add(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Add the elements of two images
add(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Add the elements two images
add(TrackEvaluator.TrackEvaluatorResult) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
addBordersToRoiManager(MTBBorder2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of 2D borders to the ROI manager.
addChild(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Add a new child to the node.
addContoursToRoiManager(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of 2D contours to the ROI manager.
addCurrentInfo(double, DataAssociation, AbstractMultiState<T>, Set<Short>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Add sample info of the current time step
addData(Vector<Vector<Point2D.Double>>, Vector<Vector<Line2D.Double>>, int[], Vector<Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Add data to the current neurite object.
addEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Add a edge to MTBGraph.
addElementAt(int, MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Inserts the specified element at the specified position in this list.
addElementAt(int, MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Inserts the specified element at the specified position in this list.
addEnergy(T, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Append another energy to the list.
addEnergy(T) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Append another energy to the list with default weight 1.0.
addEnergy(MTBLevelsetEnergyDerivable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Append another energy to the list.
addEnergy(MTBLevelsetEnergyDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Append another energy to the list with default weight 1.0.
addEnergy(MTBSnakeEnergyComputable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Append another energy to the list.
addEnergy(MTBSnakeEnergyComputable) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Append another energy to the list with default weight 1.0.
addEnergy(MTBSnakeEnergyDerivable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Append another energy to the list.
addEnergy(MTBSnakeEnergyDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Append another energy to the list with default weight 1.0.
addFile(String) - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Adds a file to the list of the node.
addFirst(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Inserts the specified element at the beginning of this list.
addImage(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
addIndepGaussian(GaussianDistribution, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Add an independent Gaussian state distribution
addInEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Add a incoming MTBGraphEdge to the MTBGraphNode
addInner(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Add an inner border to the existing border object.
addInner(MTBBorder2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Add a inner contour to the existing contour object.
addInnerContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Adding the possible inner contours to the outer contour of a region.
addLast(MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Appends the specified element to the end of this list.
addNewResult(SegResult_Complete) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
 
addNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Add a node to MTBGraph.
addOutEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Add a outgoing MTBGraphEdge to the MTBGraphNode
addPixel(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Add a 2D point to the existing border.
addPixel(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Append a point to the region from the given coordinates.
addPixel(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Append a point to the region from the given point object.
addPoint(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
addPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Appends a new point to the end of the polygon.
addPoint(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Append a 3D point to the region.
addPoint(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Append a point to the region from the given coordinates.
addPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Overwrites Polygon2D method.
addPolygonsToRoiManager(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of polygons to the ROI manager.
addPolygonToRoiManager(MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds the given polygon to the ROI manager.
addRegionsToRoiManager(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Adds a set of 2D regions to the ROI manager.
addResult(FeatureCalculatorResult[]) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Adds result data to the object.
addSegmentationResult(SegResult_Particles) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
addSubgraph(MTBGraph, Color) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Specify a subgraph that is to be painted in the given color.
addSubgraphAdjaceny(AdjacencyMatrix<T>, Color) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Specify a subgraph that is to be painted in the given color.
AdjacencyMatrix<T extends Comparable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for the adjacency matrix of a graph.
adjmatrix - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
adjMatrix - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
adoptSliceLabels(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy slice labels from src to this
ALDMetaInfo - Annotation Type in de.unihalle.informatik.Alida.admin.annotations
Annotation for adding meta data to Alida classes.
ALDMetaInfo.ExportPolicy - Enum in de.unihalle.informatik.Alida.admin.annotations
Class export policy.
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Update function for alpha values.
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
alphaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
Update function for alphas.
analyzeIntensities(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeShapes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeTrajectories(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Bitwise logical AND of two images.
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Bitwise logical AND of two images.
angle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Orientation of the filter.
angleDiff360(double, double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
 
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Angular sampling step size.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Angular sampling interval.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Sampling step size for orientations.
angleSampling - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Sampling step size for orientations considered.
applyNiblackThresholdWholeImage(ImageProcessor, double, double, ImagePlus) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Deprecated. 
approxFunction - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Helper to calculate values of approximated Dirac impulse function.
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Region sizes.
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Region sizes.
areAssociated(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
Determine if target and observation are associated.
areAssociated(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Ask if the specified target and observation are associated
areRegionsInManagerAvailable() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Returns true if there are regions available in ROI manager.
ArrayToColorMapImage - Class in de.unihalle.informatik.MiToBo.color.visualization
This operator visualizes a 2D array using a specified color mapping.
ArrayToColorMapImage() - Constructor for class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Default constructor.
ArrayToColorMapImage(double[][]) - Constructor for class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Constructor.
ArrayToColorMapImage.RangeColor - Enum in de.unihalle.informatik.MiToBo.color.visualization
Possible colors to colorize value ranges.
assocDistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
assocfactory - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
factory for the data association object
AssociationDistribution<S extends TargetID,T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
Association distribution to sample association variables for a set of observations based on a model of how observations are formed.
AssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Constructor.
AssociationDistribution(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Constructor where the maximum number of observations in the time series is specified to avoid some re-computations.
AssociationDistributionNN<S extends TargetID,T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
Association distribution to sample association variables for a set of observations based on a model of how observations are formed.
AssociationDistributionNN(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Constructor.
AssociationDistributionNN(Random, AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>, LogProbabilityDensityFunction, LogProbabilityDensityFunction, LogProbabilityMassFunction, LogProbabilityMassFunction, double, int, int, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Constructor where the maximum number of observations in the time series is specified to avoid some re-computations.
AssociationDistributionNN.AType - Enum in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
assocObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
aTrousDWT(MTBImage, int, MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
A trous DWT
availableCodecs(Class<? extends IFormatWriter>) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Get available codecs of a specific writer class.
availableQualities(Class<? extends IFormatWriter>) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Get available qualities of a specific writer class.
avgsize_cells - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Average size of cells.
avgsize_nuclei - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Average size of nuclei.
avgsize_particles - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Average size of particles.
AwtColorDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Data I/O provider for Cmdline-OpRunner for java.awt.Color objects.
AwtColorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
 
AwtColorDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Data I/O provider for GUI-OpRunner for java.awt.Color objects.
AwtColorDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
AwtColorDataIOSwing.ColorChooserButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
 
AwtColorDataIOSwing.ColorChooserButton(Color) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
AwtColorDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Xmlbeans provider for java.awt.Color objects.
AwtColorDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 

B

backwardDifferencing_X(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_X(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
backwardDifferencing_Y(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_Y(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
backwardDifferencing_Z(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method
backwardDifferencing_Z(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by backward euler method, explicit define fallback-strategy
BasicMorphology - Class in de.unihalle.informatik.MiToBo.morphology
class implementing basic morphological operations (for use with grayscale as well as with binary images)
BasicMorphology() - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
BasicMorphology(MTBImage, MTBStructuringElement) - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
BasicMorphology(Integer, BasicMorphology.opMode, BasicMorphology.maskShape) - Constructor for class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
Constructor to create new BasicMorphology object with mask size, mode and shape of the structuring element.
BasicMorphology.maskShape - Enum in de.unihalle.informatik.MiToBo.morphology
 
BasicMorphology.opMode - Enum in de.unihalle.informatik.MiToBo.morphology
 
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Update function for beta values.
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
betaUpdate(SnakeOptimizerSingle, double[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
Update function for betas.
BG_PHASE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Level set function value to represent the background phase
bgLabel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
binaryImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
binMask - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Binary segmentation mask.
binMask - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Binary segmentation mask.
binning(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
change the binning of the histogram
binomial(int, int) - Static method in class de.unihalle.informatik.MiToBo.math.MathX
Binomial coefficient of n over k
borderDist - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Safety distance along image borders.
borderSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
The set of borders represented as a Vector.
BordersOnLabeledComponents - Class in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Class to extract borders from connected components.
BordersOnLabeledComponents() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Standard constructor.
BordersOnLabeledComponents(MTBImageByte, MTBRegion2DSet, MTBBorder2D.BorderConnectivity, BordersOnLabeledComponents.BorderType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Constructor.
BordersOnLabeledComponents.BorderType - Enum in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Possible types of borders to be extracted.
BoundEnsure(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Test the image boundary.
BoundExpand(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Expand the image boundary.
BoundShrink(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Shrink the image boundary.
boxWhiskerChart - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Resulting box-whisker chart.
BoxWhiskerChartPlotter - Class in de.unihalle.informatik.MiToBo.visualization.plots
Operator that generates box-whisker plots using JFreeChart.
BoxWhiskerChartPlotter() - Constructor for class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Default constructor.
boxWhiskerCharts - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Box-whisker plot of the group-wise cluster distributions.
buildSkeletonGraph(int, int, int, int, MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Build the skeleton graph from a given binary skeleton image and a given starting point to build up the graph.
BYTE_TO_DEGREE - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Constants to convert from [0-255] to [0-359] and vice versa.

C

C - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Covariance matrix calculated from mean-free data.
C2DtoMTB(C2DPolygon) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Converts a C2D polygon to the MiToBo polygon data type.
calcAverageSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the average size of the set.
calcCentre(Vector<MTBPoint3D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the centroid (not yet normalized by volume) of a given vector of points.
calcContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get all inner- and outer-contours for the given regions.
calcEnergy(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Calculates the absolute energy value for the given segmentation.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Calculates normalized snake energy.
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Calculates length term of snake energy at a certain position for the current snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Calculates snake energy (non-normalized!).
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Calculates energy at a certain position for the current snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Calculates the current energy of the snake.
calcEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
calcEnergy(SnakeOptimizerSingle, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Calculates energy at a certain snake point.
calcEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Calculates the energy of the current snake.
calcExteriorMean() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Calculates the average intensity in the background of the segmentation.
calcFeatures(double[][]) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Extracts Haralick features from given matrix.
CalcGlobalThreshOtsu - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
This class implements routines to calculate Otsu's threshold from given grayscale images.
CalcGlobalThreshOtsu() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Default constructor.
CalcGlobalThreshOtsu(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Default constructor with input image as argument.
CalcGlobalThreshOtsu(MTBImageHistogram) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Default constructor with input histogram as argument.
calcGVF() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Calculate the GVF field with the given number of iterations on the given input image.
calcInteriorEnergy(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Calculates the interior part of energy value for the given segmentation.
calcMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Function calculating actual matching, to be implemented by subclasses.
calcMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
 
calcMatching_mainTest() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Checks whether a valid solution has been found.
calcMatching_stageOne() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Implements stage one: searching for new candidate matches.
calcMatching_stageThree() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Implements stage three: decrease scores to generate new zero entries.
calcMatching_stageTwo(int, int) - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Implements stage two: extracting exchange chain.
calcMatrix(FeatureCalculatorHaralickMeasures.HaralickDirection) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Extracts the co-occurence matrix for the given distance and direction.
calcMaxSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the maximum size of the set.
calcMean(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the mean value of an array of double.
calcMedian(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the median value of an array of double.
calcMinMax(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the min and max value.
calcMinSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the minimum size of the set.
calcPotential_approxLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Calculates an approximation of the potential of the field by gradient descent.
calcPotential_exactLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Calculates the potential of the field by solving a LSE with least squares.
calcPotential_exactLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Exact least squares reconstruction of the potential.
calcPotential_gradientDescent(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Reconstruct potential via gradient descent.
calcPotential_incrementalLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Reconstructs the potential of the vector field incrementally.
calcPotential_incrLeastSquares(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Calculates a rough approximation of the potential of the field in linear time.
CalcSegmentationStatistics - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Operator for doing statistical calculations on segmentations of images.
CalcSegmentationStatistics() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor without arguments.
CalcSegmentationStatistics(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor.
CalcSegmentationStatistics(MTBImage, MTBSegmentationInterface) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor.
CalcSegmentationStatistics(MTBImage, MTBSegmentationInterface, Vector<CalcSegmentationStatistics.CalcTargets>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Default constructor.
CalcSegmentationStatistics.CalcTargets - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Statistical numbers provided by this class.
calcSnakeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Calculates total snake energy.
calcSnakeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Calculates total snake energy.
CalcStructureStatistics - Class in de.unihalle.informatik.MiToBo.segmentation.evaluation
Extracts statistics from cell and structure segmentation results.
CalcStructureStatistics() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Default constructor.
CalcStructureStatistics(MTBImageByte, MTBImageByte, MTBImageByte, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Deprecated. 
CalcStructureStatistics(MTBImageByte, MTBImageByte, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Default constructor.
CalcStructureStatistics.StructureCountMode - Enum in de.unihalle.informatik.MiToBo.segmentation.evaluation
Mode how to assign structures to cell regions.
calculateCovarianceMatrixAndEigenstuff() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Calculates covariance matrix and eigenvalues and -vectors.
calculateMeanFreeData() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Computes the average data vector and makes data mean-free.
calcVariance(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the variance of an array of double.
calibration - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
calibration object (from ImageJ)
cbbox - Variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
container for arrangement of checkboxes
cbs - Variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
checkbox components
cdf - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
cumulative distribution function, used for sampling
cDOF - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
degrees of freedom of the continuous variables of a single state
cellContours - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Set of detected cell boundaries.
CellMigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Operator for segmenting, tracking and analyzing 2D image sequences of fluorescently labeled cells
CellMigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
CellMigrationAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
CellSegmentationPostprocessing - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
operator for doing common postprocessing tasks on already segmented cell images
CellSegmentationPostprocessing() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
CellSegmentationPostprocessing(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
CellSegmenter - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
base class for cell segmentation
CellSegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
CellSegmenter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
cellSizes - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Array indexed with snake IDs containing region sizes of snake interiors.
cellsResult - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Result for cell/cytoplasm channel.
CellTrackerBipartite - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
This operator assigns unique labels to regions representing individual cells in the input binary image sequence
CellTrackerBipartite() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
CellTrackerBipartite(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
cgal_isClockwiseOriented(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.  
cgal_isConvex(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.  
cgal_isCounterclockwiseOriented(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.  
cgal_isSimple(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated. Checks if a polygon is simple.
cgal_makePolySimple(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated. Simplifies the given polygon.
cgal_orientation(double[], double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.  
cgal_signedArea(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated. Calculates the signed area of a polygon.
chainMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Helper matrix for exchange chain extraction: 0 = unselected, 1 = selected.
changePhase(int, int, int, byte) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Change a pixel/voxel to a new phase.
changePhase(int, int, byte) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Change a pixel to a new phase.
channel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
channelIdx - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
chartTitle - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Title of the chart.
chartTitle - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Title of the chart.
ChaudhuriMatchedFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D Matched filter.
ChaudhuriMatchedFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Default constructor.
CHECK_CHANGED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
property string that is fired when the state of any checkbox is changed
CheckBoxPanel - Class in de.unihalle.informatik.MiToBo.gui
A panel with a titled border and a set of checkboxes that can be reconfigured easily.
CheckBoxPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Constructor
chi - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
childs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
List of nodes that are childs of the given node.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
2D map with class labels.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
2D map with class labels.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
2D map marking the region enclosed by the snake.
cleanNeurites(MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to clean up the extracted neurites, due to multiple features along a NSG path or feature shifts at the start point due to different NSG lengths.
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Remove all regions from this set
clear() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Deletes all(!)
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Remove all radiobuttons from the panel.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Remove all radiobuttons from the panel.
clearPanel() - Method in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
Remove all entries from the panel.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
generate a clone of this object
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Override java.lang.Object.clone() to create and return a copy of this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Clones this object.
clone() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Clones this object.
close() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Close the displayed ImagePlus
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Close all windows openened by this operator (for clean-up).
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
closeWindows() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
clusterNum - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Number of clusters to be used in feature clustering.
clutterdistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
spatial clutter distribution
cmdTools.cellAnalysis - package cmdTools.cellAnalysis
 
cmdTools.mtb_imagetools - package cmdTools.mtb_imagetools
 
cmdTools.tracking.multitarget - package cmdTools.tracking.multitarget
 
cmdTools.visualization - package cmdTools.visualization
 
codec - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
codec - Variable in class mtb_io.Save_Image_MTB
codec option if available
codpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
colMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Array containing column marks.
color2int(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
colorArray - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Array with colors for visualization.
colorArray - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Array containing pseudo-colors for snake visualization.
colorNegative - Variable in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Color for negative values.
colorPlot() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Plots the field in colored image.
colorPositive - Variable in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Color for positive values.
cols - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Number of columns of the table.
compare(GraphNodeID, GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
compare(GraphNodeID, GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
compareTo(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
 
compareTo(GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
compareTo(GraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
ComponentPostprocess - Class in de.unihalle.informatik.MiToBo.morphology
Methods for post-processing components/pixels in binary images.
ComponentPostprocess() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Default constructor.
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Default constructor.
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Deprecated.  
ComponentPostprocess(MTBImage, ComponentPostprocess.ProcessMode, int, int, int, double) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Deprecated.  
ComponentPostprocess.ProcessMode - Enum in de.unihalle.informatik.MiToBo.morphology
Processing mode identifiers.
comppanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
compression - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
compression - Variable in class mtb_io.Save_Image_MTB
compression option if available
computeESS() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Compute effective sample size (ESS).
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Derive N_n^k from X, see Han et al.
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4
 
computeN() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8
 
computeSigmaScales() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Compute scaling factors of noise sigma for wavelet scales (these scaling factors are estimated using a gaussian noise image with sigma=1 to measure noise in the wavelet scales)
computeSubgraphs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Compute subgraphs with greedyGourmet algorithm.
ConditionalDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for conditional densities, e.g. p(x|y)
condX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
multi state condition on the density
condX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
multi state condition on the density
configButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Configuration button.
configureCollectionApplicationOps() - Static method in class mitoboRunner.Grappa_Editor
Configure collection of operators belonging to the application set.
configureCollectionStandardOps() - Static method in class mitoboRunner.Grappa_Editor
Configure collection of operators belonging to the standard set.
configureSnakes(double, int, double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Configures basic snake parameters.
confWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Configuration window.
connectivity - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Connectivity of border pixels.
contains(double, double, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Determines if a point lies inside a polygon or on its boundary.
contains(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Test if a point is inside the region or not.
containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Checks if a given point is part of the segment.
containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Checks if given point lies inside of the polygon.
containsPoint(MTBPolygon2D, double, double) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if a point lies inside of the polygon.
ContourOnLabeledComponents - Class in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Class to segment contours from a binary image using the contour following algorithm.
ContourOnLabeledComponents() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Standard constructor.
ContourOnLabeledComponents(MTBImageByte, MTBRegion2DSet, ContourOnLabeledComponents.ContourType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Constructor.
ContourOnLabeledComponents(MTBRegion2DSet, ContourOnLabeledComponents.ContourType, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Constructor.
ContourOnLabeledComponents.ContourType - Enum in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
The possible type of contours for segmentation.
conv(MTBImage, MTBImage[], int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Convolve input image with an 'a trous' kernel (zeros inserted) given the original kernel and scale j
convert(Object, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
convertContourToSnake(MTBContour2D) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Converts a contour into a snake.
convertRangeColorToHue(ArrayToColorMapImage.RangeColor) - Static method in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Converts given color to hue value.
convertRegionsToSnakes(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Converts the regions of a label/binary image into a set of snakes.
convertRegionToSnake(MTBRegion2D) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Converts a region into a snake.
convertType(MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Create an image of given type from this image's values.
convertType(MTBOperator, MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Create an image of given type from this image's values.
convertType(MTBImage, MTBImage.MTBImageType, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Create an image of given type from this image's values.
convolve(MTBImage, MTBImage, int[], boolean, MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Convolve an image with a specified kernel.
coordinatesNeighborNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
For each neighbor in the neighborhood this vector holds coordinates of all other pixels in the neighborhood which are connected to the neighbor under consideration with regard the the neighborhood definition.
coordinatesNeighborNeighborsByCoord - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
As coordinatesNeighborNeighbors this array give for each neighbor in the neighborhood coordinates of its neighbors (i.e. neighborneighbors).
coordinatesNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
For each neighbor in the neighborhood this gives their coordinates in a 3x3x3 array center around the current pixel (of which the neighborhood is represented).
copy() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
copy() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
copy() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilterIndep
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
Not implemented, always returns null
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Copy this multi-state
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
 
copy() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.Copyable
 
copy() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
Copyable<T> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for objects that can be copied (deep copy is assumed).
copyPhysicalProperties(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy physical properties like stepsizes and units from sourceImg to this.
copyTo(MTBLevelsetFunctionPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
copy this object to another one
correctGamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
cost - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Cost of the MTBGraphEdge.
cot(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the cotangens of value.
counterClockwiseSnakePointOrderRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to indicate if snakes are required to be sorted counter-clockwise.
countInner() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get the number of inner borders included.
cov - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
covariance matrix
covs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
create2DTrajectoryImage(boolean, boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
create3DTrajectoryImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
createCircularElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createDataAssociation() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
 
createDataAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
 
createDataAssociation() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociationFactory
Create a new data association object
createDataAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociationFactory
Create a new data association object for given number of targets/states and observations
createDynamicModels() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
createEmptyMultiState() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Create an empty multi state object
createEmptyMultiState() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
createEnergy(MTBLevelsetMembership, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
Create a proper length energy asked for by the level set function.
createEnergy(MTBImage, MTBLevelsetMembership, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
Create a proper length energy asked for by the level set function.
createFileChooser() - Method in class mtb_io.Save_Image_MTB
Create a file chooser configured for image writing, adding a panel for image writer options
createGaussianNoiseImage(double, double, double, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Create an image with Gaussian noise
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBWrapperDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
Generic reading of table models.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing
 
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
GUI element for reading sets of snake energies.
createGUIElement(Field, Class<?>, Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
Generic reading of segmentation objects.
createHorizontalLineElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createImageFromWindow() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
 
createInitialStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
createMTBImage(ImagePlus) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Factory method to create MTBImage objects.
createMTBImage(int, int, int, int, int, MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Factory method to create MTBImage objects with value 0 at each coordinate.
createMTBImageByte(int, int, int, int, int, byte[][]) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Creates an image of type MTBImage.MTBImageType.MTB_BYTE from the given data array.
createMultiState(double[][], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Create a multi state object initialized by the specified data
createMultiState(Matrix[], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Create a multi state object initialized by the specified data
createMultiState(double[][], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
createMultiState(Matrix[], T[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
createObservationModel() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
createOverlayImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
createProgressionImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
createQuadraticElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createRandomRegion2D(int, int, int, Random) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Create a random connected 2D region of size maxArea in a hypothetical image of a random size between 1 and maxArea.
createRectangularElement(int, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createVerticalLineElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
CropImage - Class in de.unihalle.informatik.MiToBo.tools.image
Crop an image part.
CropImage() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.CropImage
Constructor.
cumulate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
calculate the cumulative histogram
cumulateOnly() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
calculate the cumulative histogram without changing the sum of absolute frequencies (normalizing factor), because cumulate() calls initialize() and thus destroys this normalizing factor
currentOverlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Overlap mask of current snake configuration, updated in each iteration.
currentSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Current set of snakes.
cweights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
CytoplasmAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.cytoplasm2D
Operator to segment cell contours from a given single-layer image.
CytoplasmAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Default constructor.
CytoplasmAnalyzer2D(MTBImage, MTBPolygon2DSet, SnakeOptimizerCoupled, CytoplasmAnalyzer2D.DetectMode, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Default constructor.
CytoplasmAnalyzer2D.DetectMode - Enum in de.unihalle.informatik.MiToBo.apps.cytoplasm2D
Operator mode.

D

data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
MTBGraphNode data.
data - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
The data contained in the table.
data - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Data to display.
data - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Data to display.
DataAssociation - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for data association objects.
DataAssociationExclusive - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A class that represents exlusive data association.
DataAssociationExclusive() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
Constructor
DataAssociationExclusiveFactory - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Factory class for exclusive data association objects
DataAssociationExclusiveFactory() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusiveFactory
 
DataAssociationFactory - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
Interface for data association object factories
DataConverter<S,T> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
An operator class to convert between data types.
DataConverter() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
dataDim - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Dimensionality of the input data.
dataObject - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Data object associated with the given node.
de.unihalle.informatik.Alida.admin.annotations - package de.unihalle.informatik.Alida.admin.annotations
 
de.unihalle.informatik.MiToBo.apps.actinAnalysis - package de.unihalle.informatik.MiToBo.apps.actinAnalysis
Provides tools and applications for quantifying actin filament structures in microscopy images of cells.
de.unihalle.informatik.MiToBo.apps.cells2D - package de.unihalle.informatik.MiToBo.apps.cells2D
 
de.unihalle.informatik.MiToBo.apps.cytoplasm2D - package de.unihalle.informatik.MiToBo.apps.cytoplasm2D
 
de.unihalle.informatik.MiToBo.apps.datatypes.cellImages - package de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
 
de.unihalle.informatik.MiToBo.apps.neurites2D - package de.unihalle.informatik.MiToBo.apps.neurites2D
 
de.unihalle.informatik.MiToBo.apps.neurons2D - package de.unihalle.informatik.MiToBo.apps.neurons2D
 
de.unihalle.informatik.MiToBo.apps.nuclei2D - package de.unihalle.informatik.MiToBo.apps.nuclei2D
 
de.unihalle.informatik.MiToBo.apps.particles2D - package de.unihalle.informatik.MiToBo.apps.particles2D
 
de.unihalle.informatik.MiToBo.apps.scratchAssay - package de.unihalle.informatik.MiToBo.apps.scratchAssay
 
de.unihalle.informatik.MiToBo.apps.singleCellTracking2D - package de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
de.unihalle.informatik.MiToBo.apps.xylem - package de.unihalle.informatik.MiToBo.apps.xylem
 
de.unihalle.informatik.MiToBo.clustering - package de.unihalle.informatik.MiToBo.clustering
 
de.unihalle.informatik.MiToBo.color.conversion - package de.unihalle.informatik.MiToBo.color.conversion
 
de.unihalle.informatik.MiToBo.color.visualization - package de.unihalle.informatik.MiToBo.color.visualization
 
de.unihalle.informatik.MiToBo.core.batch.provider.input.swing - package de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
 
de.unihalle.informatik.MiToBo.core.batch.provider.output.swing - package de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
 
de.unihalle.informatik.MiToBo.core.dataconverter - package de.unihalle.informatik.MiToBo.core.dataconverter
 
de.unihalle.informatik.MiToBo.core.dataio - package de.unihalle.informatik.MiToBo.core.dataio
 
de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline - package de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
 
de.unihalle.informatik.MiToBo.core.dataio.provider.swing - package de.unihalle.informatik.MiToBo.core.dataio.provider.swing
 
de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components - package de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components
 
de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans - package de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
 
de.unihalle.informatik.MiToBo.core.datatypes - package de.unihalle.informatik.MiToBo.core.datatypes
Provides basic datatypes for MiToBo.
de.unihalle.informatik.MiToBo.core.datatypes.defines - package de.unihalle.informatik.MiToBo.core.datatypes.defines
 
de.unihalle.informatik.MiToBo.core.datatypes.images - package de.unihalle.informatik.MiToBo.core.datatypes.images
Contains MiToBo image data types.
de.unihalle.informatik.MiToBo.core.datatypes.neurites - package de.unihalle.informatik.MiToBo.core.datatypes.neurites
 
de.unihalle.informatik.MiToBo.core.datatypes.wrapper - package de.unihalle.informatik.MiToBo.core.datatypes.wrapper
Provides wrapper for for input and output datatypes for MiToBo operators.
de.unihalle.informatik.MiToBo.core.exceptions - package de.unihalle.informatik.MiToBo.core.exceptions
Defines MiToBo exceptions.
de.unihalle.informatik.MiToBo.core.grappa - package de.unihalle.informatik.MiToBo.core.grappa
 
de.unihalle.informatik.MiToBo.core.gui - package de.unihalle.informatik.MiToBo.core.gui
 
de.unihalle.informatik.MiToBo.core.helpers - package de.unihalle.informatik.MiToBo.core.helpers
 
de.unihalle.informatik.MiToBo.core.imageJ - package de.unihalle.informatik.MiToBo.core.imageJ
Provides convenience classes for interaction with ImageJ system.
de.unihalle.informatik.MiToBo.core.operator - package de.unihalle.informatik.MiToBo.core.operator
Provides basis classes for MiToBo operator concept.
de.unihalle.informatik.MiToBo.enhance - package de.unihalle.informatik.MiToBo.enhance
Provides classes for image preprocessing and improvement (no filters!).
de.unihalle.informatik.MiToBo.features - package de.unihalle.informatik.MiToBo.features
Provides operators for calculating features from given images, e.g., statistical indicators or texture measures.
de.unihalle.informatik.MiToBo.features.statistical - package de.unihalle.informatik.MiToBo.features.statistical
Provides operators for calculating statistical image features, e.g., average intensities or variances, or moments of the intensity distribution.
de.unihalle.informatik.MiToBo.features.texture - package de.unihalle.informatik.MiToBo.features.texture
Provides operators for calculating texture features from given images, e.g., Haralick measures.
de.unihalle.informatik.MiToBo.fields - package de.unihalle.informatik.MiToBo.fields
Provides classes for calculating gradient vector flow fields, image gradient fields, potential fields and other possible fields from different data sources.
de.unihalle.informatik.MiToBo.filters.linear - package de.unihalle.informatik.MiToBo.filters.linear
Provides classes implementing linear systems.
de.unihalle.informatik.MiToBo.filters.linear.anisotropic - package de.unihalle.informatik.MiToBo.filters.linear.anisotropic
 
de.unihalle.informatik.MiToBo.filters.nonlinear - package de.unihalle.informatik.MiToBo.filters.nonlinear
Provides classes implementing nonlinear image filters.
de.unihalle.informatik.MiToBo.filters.vesselness - package de.unihalle.informatik.MiToBo.filters.vesselness
Provides various operators for enhancing vessel-like structures in images.
de.unihalle.informatik.MiToBo.gui - package de.unihalle.informatik.MiToBo.gui
 
de.unihalle.informatik.MiToBo.io.dirs - package de.unihalle.informatik.MiToBo.io.dirs
Provides classes for dealing with directories.
de.unihalle.informatik.MiToBo.io.files - package de.unihalle.informatik.MiToBo.io.files
Provides classes for handling (non-)image files.
de.unihalle.informatik.MiToBo.io.images - package de.unihalle.informatik.MiToBo.io.images
Provides classes for handling image files.
de.unihalle.informatik.MiToBo.io.tools - package de.unihalle.informatik.MiToBo.io.tools
Contains helper classes for image I/O.
de.unihalle.informatik.MiToBo.math - package de.unihalle.informatik.MiToBo.math
Provides mathematical functionality.
de.unihalle.informatik.MiToBo.math.distributions.impl - package de.unihalle.informatik.MiToBo.math.distributions.impl
 
de.unihalle.informatik.MiToBo.math.distributions.interfaces - package de.unihalle.informatik.MiToBo.math.distributions.interfaces
 
de.unihalle.informatik.MiToBo.math.images - package de.unihalle.informatik.MiToBo.math.images
Provides mathematical operations on images.
de.unihalle.informatik.MiToBo.math.optimization - package de.unihalle.informatik.MiToBo.math.optimization
 
de.unihalle.informatik.MiToBo.math.statistics - package de.unihalle.informatik.MiToBo.math.statistics
This package contains oeprators for performing statistical analysis of data sets.
de.unihalle.informatik.MiToBo.morphology - package de.unihalle.informatik.MiToBo.morphology
Provides classes for morphological processing of binary images.
de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes - package de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
 
de.unihalle.informatik.MiToBo.segmentation.activecontours.energies - package de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
 
de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions - package de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
 
de.unihalle.informatik.MiToBo.segmentation.basics - package de.unihalle.informatik.MiToBo.segmentation.basics
 
de.unihalle.informatik.MiToBo.segmentation.contours.extraction - package de.unihalle.informatik.MiToBo.segmentation.contours.extraction
Provides classes for performing contour extractions from regions or other image elements.
de.unihalle.informatik.MiToBo.segmentation.evaluation - package de.unihalle.informatik.MiToBo.segmentation.evaluation
 
de.unihalle.informatik.MiToBo.segmentation.levelset.core - package de.unihalle.informatik.MiToBo.segmentation.levelset.core
 
de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable - package de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
 
de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE - package de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
 
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes - package de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
 
de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver - package de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
 
de.unihalle.informatik.MiToBo.segmentation.regions.convert - package de.unihalle.informatik.MiToBo.segmentation.regions.convert
 
de.unihalle.informatik.MiToBo.segmentation.regions.filling - package de.unihalle.informatik.MiToBo.segmentation.regions.filling
Provides operators for filling wholes in binary 2D/3D regions.
de.unihalle.informatik.MiToBo.segmentation.regions.labeling - package de.unihalle.informatik.MiToBo.segmentation.regions.labeling
Provides classes to perform region labeling to find connected components in binarized images.
de.unihalle.informatik.MiToBo.segmentation.regions.mser - package de.unihalle.informatik.MiToBo.segmentation.regions.mser
 
de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes - package de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Provides basic datatypes for MiToBo explicit active contours (snakes).
de.unihalle.informatik.MiToBo.segmentation.snakes.energies - package de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Provides classes with energies to be used with MiToBo snakes.
de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt - package de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Provides classes with parameter adaptation for energies to be used with MiToBo snakes.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Provides classes for performing snake-based segmentation on images.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Provides classes for calculating several update strategies of the snake step size gamma.
de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination - package de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Provides classes for calculating several termination strategies of the snake optimization.
de.unihalle.informatik.MiToBo.segmentation.thresholds - package de.unihalle.informatik.MiToBo.segmentation.thresholds
Provides classes for thresholding grayscale and color images.
de.unihalle.informatik.MiToBo.tools - package de.unihalle.informatik.MiToBo.tools
 
de.unihalle.informatik.MiToBo.tools.image - package de.unihalle.informatik.MiToBo.tools.image
 
de.unihalle.informatik.MiToBo.tools.strings - package de.unihalle.informatik.MiToBo.tools.strings
 
de.unihalle.informatik.MiToBo.tools.system - package de.unihalle.informatik.MiToBo.tools.system
 
de.unihalle.informatik.MiToBo.topology - package de.unihalle.informatik.MiToBo.topology
 
de.unihalle.informatik.MiToBo.tracking.multitarget.algo - package de.unihalle.informatik.MiToBo.tracking.multitarget.algo
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatools - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
 
de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces - package de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces
 
de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts - package de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts
 
de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl - package de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
de.unihalle.informatik.MiToBo.tracking.multitarget.eval - package de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
de.unihalle.informatik.MiToBo.transforms - package de.unihalle.informatik.MiToBo.transforms
 
de.unihalle.informatik.MiToBo.visualization.drawing - package de.unihalle.informatik.MiToBo.visualization.drawing
Provides operators to visualize data types.
de.unihalle.informatik.MiToBo.visualization.plots - package de.unihalle.informatik.MiToBo.visualization.plots
 
debug - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
Debug flag for internal use only.
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Bit mask for debug output on System.out.
debug - Static variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
debug flag
DEFAULT_erodeSize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default size of the structuring element to erode the image
DEFAULT_hueThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default hue threshold
DEFAULT_linkageMode - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default linkage mode for growing
DEFAULT_minAreaAfterOpening - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
DEFAULT_minAreaPostProcessing - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Minimum area of a region in post processing.
DEFAULT_minAreaSeedRegions - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default minimum area for a region to be further eroded
DEFAULT_minCompactness - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
DEFAULT_neighbourhood - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default neighborhood for growing
DEFAULT_openingSESize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default size of structuring element for opening (post processing)
DEFAULT_satThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default saturation threshold
DEFAULT_seOpeningSize - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
DEFAULT_xThresh - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default intensity threshold
defaultfps - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
DEGREE_TO_BYTE - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
delimiter - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Delimiter to be used when exporting the model.
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
delta_t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
DeltaApproxHelper - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Class calculating approximations to the Dirac impulse function.
DeltaApproxHelper(double, DeltaApproxHelper.ApproxVersion) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Default constructor.
DeltaApproxHelper.ApproxVersion - Enum in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Available approximations for the Heaviside function and its derivatives.
deltaApproximator - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Helper to calculate approximated values for the Dirac function.
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Calculate differences of energy if the pixel/voxel (x,y,z) is changed from its current phase in the level set function phi supplied from current phase to newPhase.
deltaE(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Calculate differences of energy if the pixel/voxel (x,y,z) changes its phase in the levelest function phi supplied as argument and assumed to be associated with this energy object.
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
deltaE(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Time step size in iterative optimization.
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
denoise(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Denoise wavelet coefficients using Jeffrey's noninformative prior for a given sigma of noise
denoiseDWTJeffreys(MTBImage[], double, double[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Denoise wavelet coefficients using Jeffrey's noninformative prior [..]
denormalize() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Denormalizes the snake coordinates.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Depth of the input image and levelset function.
depth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Depth of the input image.
desiredImageClass - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Class of image to be returned.
detectedRegions - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
detectionMode - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Operator mode to run.
DetectMSERs - Class in de.unihalle.informatik.MiToBo.segmentation.regions.mser
Implementation of maximally stable extremal regions based on ImgLib2.
DetectMSERs() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Default constructor.
DetectMSERs.Thresholding_Direction - Enum in de.unihalle.informatik.MiToBo.segmentation.regions.mser
Modes for direction of intensity thresholding.
detectWithLocalContrastEnhancement() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detect nuclei by first improving image contrast.
detectWithNiblack() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detects nuclei based on Niblack thresholding.
detectWithOtsu_erodedilate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detects nuclei based on Otsu thresholding and a combination of erosion/ dilation.
detectWithOtsu_openclose() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detects nuclei based on Otsu thresholding and a combination of opening and closing.
determineSubspaceDimension() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Determines desired sub-space dimensionality according to selected mode.
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mtb_segmentation.Threshold_Image
 
directed - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
True if MTBGraph is directed.
directions - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Set of directions.
directions - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Directions for calculating cooccurrence matrices.
DirectoryTree - Class in de.unihalle.informatik.MiToBo.io.dirs
This class implements a data structure for representing directory trees.
DirectoryTree(String) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Standard constructor.
DirectoryTree(String, boolean) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Constructor.
DirectoryTreeNodeData - Class in de.unihalle.informatik.MiToBo.io.dirs
Implements class TreeNodeData for DirectoryTree.
DirectoryTreeNodeData(String) - Constructor for class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Default constructor.
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
disableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Deactivates the configuration window to prohibit value changes.
disableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Disable energy calculations completely.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Disable kernel normalization.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Disable kernel normalization.
disableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Disable kernel normalization.
disableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Do not save intermediate results.
disableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Deactivates writing of intermediate results.
disableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Disable display of intermediate results.
disableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Deactivates display of intermediate results.
dispImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Image for displaying intermediate/final results.
dispImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Image for showing/saving intermediate results.
DisplayImage - Class in cmdTools.visualization
A simple commandline tool to display image files using MiToBo's image reader.
DisplayImage() - Constructor for class cmdTools.visualization.DisplayImage
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
dispose() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
dispose() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Disposes this window and all sub-components.
distance - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Distance.
distance - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Distance.
distance(MTBPoint3D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Compute the Euclidean distance between this 3D point object and the given 3D point object.
distance(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Compute the Euclidean distance between this 3D point object and the given location.
DistanceTransform - Class in de.unihalle.informatik.MiToBo.morphology
Class to calculate a distance map / field from a binary image using the Champfer-algorithm from G.
DistanceTransform() - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Standard constructor.
DistanceTransform(MTBImageByte, DistanceTransform.DistanceMetric, DistanceTransform.ForegroundColor) - Constructor for class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Constructor to create a new DistanceTransform object.
DistanceTransform.DistanceMetric - Enum in de.unihalle.informatik.MiToBo.morphology
Several distance metrics.
DistanceTransform.ForegroundColor - Enum in de.unihalle.informatik.MiToBo.morphology
Color of binary image foreground.
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Divide the elements of two images (img1/img2)
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Divide the elements of two images (img1/img2)
doDimensionReduction() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Does the actual dimension reduction by data projection into sub-space.
DOF - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
doFeatureCalculation - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Flag for calculating features.
doIsotropicCalcutations(boolean) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Set flag for isotropic calculations.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Here the main work should be done.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Performs one single optimization step, i.e. iterates once over all points.
doIteration() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Performs one single optimization step.
doNormalization - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
do normalization?
doPCA - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Perform PCA in second stage?
doResampleSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns true if snake should be resampled during optimization.
doResampling - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Flag to enable/disable snake resampling.
dotGlobalAttributes - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
dotGraphFilename - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Called method to temporary view the selected set of borders from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Called method to temporary view the selected set of contours from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Called method to temporary view the selected set of polygons from the Roi-Manager into the current image.
draw(Graphics) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Called method to temporary view the selected set of regions from the Roi-Manager into the current image.
drawBordersToImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Draws result contours to an image.
drawLine2D(Line2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Draws a 2D line into the neuron image.
drawLine2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Draws a 2D line into the current slice of the image.
drawLine2D(Line2D.Double, Point2D.Double, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Draws a 2D line into the neuron image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPixels(ImageProcessor) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Called method to draw the selected entry from the Roi-Manager into the current image.
drawPoint2D(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Draws a point at given position into the x-y-plane.
drawPolygon(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw a polygon into an image (in red color).
drawPolygon(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw a polygon into an image.
drawPolygon(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Draw snake into an image.
DrawPolygon2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A class to visualize 2D polygons.
DrawPolygon2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Default constructor.
DrawPolygon2DSet(MTBPolygon2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Simple constructor.
DrawPolygon2DSet(MTBPolygon2DSet, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Complete constructor.
drawPolygonPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw polygon points into an image (in red color and as crosses).
drawPolygonPoints(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Draw polygon points into an image.
drawPolygonPoints(MTBImage, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Draw snake points into an image (as crosses).
DrawRegion2DSet - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A class to visualize 2D regions.
DrawRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Default constructor where NO parameters are set.
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Simple constructor to create the most common region image types: see DrawType
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Simple constructor to create the most common region image types: see DrawType
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Simple constructor to draw the most common region image types to a given image:
DrawRegion2DSet.DrawType - Enum in de.unihalle.informatik.MiToBo.visualization.drawing
Type of image to be drawn: LABEL_IMAGE: draw gray value image where regions are labeled by their index in the set + 1 ID_IMAGE: draw gray value image where regions are labeled by their region id (see MTBRegion2D.id) MASK_IMAGE: draw a mask image with equal gray values for all regions COLOR_IMAGE: draw a mask with colored regions TRANSPARENT_IMAGE: draw a mask with colored regions, but the regions are transparent to show the underlying intensity structure of the given target image CONTOURS: draw contours of the regions in a given colour
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
drawSample(int, T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IndependentSamplingDistribution
Generate a new sample from this density by drawing only one independent variable for a given realization x.
drawSample() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.SamplingDistribution
Generate a new sample from this density.
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
 
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistributionIndep
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
drawSample() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
drawSample(int, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
 
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
drawSampleDebug(DataAssociation, OutputStream) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
 
drawSpot(MTBImage, MTBRegion2D, int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Draw region to an image at time=t and channel=c with specified color.
drawSpots - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
drawSqare(MTBImage, MTBRegion2D, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Draw square to an image at time=t and channel=c with specified color and size=2*radius+1.
DrawTracks2D - Class in de.unihalle.informatik.MiToBo.visualization.drawing
Draw trajectories of tracked observations over time.
DrawTracks2D() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Constructor.
drawTrajectories - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
drawTrajectories(Matrix, Matrix, int, int, int, MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
Draw trajectory between two points at the given and all later timepoints until t_last
duplicate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Duplicates the object.
duplicate(MTBOperator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Duplicates the object.
duplicate(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
DynamicColorLUT - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A color lookup table that generates colors dynamically and randomly for indices that do not exist.
DynamicColorLUT() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Constructor with a (seeded) random generator and channel offset = 20.
DynamicColorLUT(Random) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Constructor for a specific random generator and channel offset = 20..
DynamicColorLUT(Random, int) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Constructor for a specific random generator and a given channel offset

E

E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Return the complete energy for the level set function phi.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
 
E(int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
Get energy term a pixel (x,y) for phi. 2D only
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
 
E(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
Get energy term a voxel (x,y,z) for phi.
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
E(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
edgeData - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Data of the MTBGraphEdge, included in a vector object.
edges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Vector of included graph edges.
eigenVals - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Set of computed eigenvalues.
eigenVects - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Matrix of eigenvectors, each column containing a vector.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get a border by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get a contour by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Get a polygon by index.
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Get a region by index
elementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Get a region by index
elementMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Matrix for elements markers: 0 = no mark, 1 = starred, 2 = primed
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
enableComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Reactivates the configuration window to allow for value changes.
enableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Enable energy calculation in each iteration.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Enable kernel normalization.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Enable kernel normalization.
enableNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Enable kernel normalization.
enableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Save intermediate results.
enableSaveIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Activates writing of intermediate results to disc.
enableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Enable display of intermediate results.
enableShowIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Activates display of intermediate results.
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
List of snake energies.
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Current energy of the snake.
energyCalculationRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Flag for invoking energy calculations.
energyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Set of energies to apply.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Set of energies.
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
 
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
 
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
List of snake energies to be used in segmentation.
energyWeightsNormed - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
List of normalized energy weights.
energyWeightsNormed - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
List of normalized energy weights.
entriespanel - Variable in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
panel to hold all the entries
epsilon - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.defines.MTBConstants
Accuracy for numerical calculations.
epsilon - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Epsilon value for approximation of Heaviside function.
equals(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Test if this object and img are of same type, have same size and same values
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
 
equals(MTBLevelsetFunctionPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
are these two LevelSets equal?
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
equalSize(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Test if this object and img have the same size in x-, y-, z-, t- and c-dimension
equalWeights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
equalWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Returns true if all particle weights are equal
EraseLargeComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function to remove large components from a binary image.
eraseNonCompactComponents(MTBImageByte, double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function to remove all non compact/circular components of a binary image.
EraseRoundComponents(MTBImageByte, double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Remove components with small eccentricity.
EraseSmallComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function to remove small components from a binary image.
essPercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
esspercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Estimate internal parameters (if any) for the level set function phi assumed to be associated with this energy object.
estimateParams(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
evaltime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
time that elapsed for evaluation
EvalTracks - Class in cmdTools.tracking.multitarget
Commandline tools to compare observation-files, i.e. the target-IDs of the individual observation, to evaluate the quality of target-association in one file with respect to the other that is interpreted as groundtruth.
EvalTracks() - Constructor for class cmdTools.tracking.multitarget.EvalTracks
 
EvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for distributions that can be evaluated for each realization x of its random variable X.
evaluateFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
 
evaluateGradientOfFunction(double[]) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
 
examineDataset() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Extracts number of samples and their dimension from dataset.
exclude - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
excludeMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Mask to exclude image pixels from calculations.
executeOperator(ALDOperatorLocation) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
 
expectedWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Expected width of vessels.
ExponentialDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
Exponential distribution.
ExponentialDistribution(double) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
Constructor for exponential distribution lambda*exp(-lambda*x) if x >= 0.
extensions - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
extractBorders() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Extract requested borders for given input data.
extractCentroids() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
extract centroids from labeled regions
extractCentroids(MTBImage, boolean, double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
extractParticles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
extractProfiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 

F

F - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
state-transition matrix
factorial(int) - Static method in class de.unihalle.informatik.MiToBo.math.MathX
Calculates the factorial of the given natural number.
factorialVals - Static variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Pre-computed factorial values.
factory - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
factory that holds information how a target's state is composed
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
multi state factory for condition variable, used for validity checks
factoryX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
multi state factory for condition variable, used for validity checks
factoryZ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
factoryZ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
multi state factory for observation variable, used for validity checks
FeatureCalculator - Class in de.unihalle.informatik.MiToBo.features
Super class for operators calculating features on images.
FeatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Default constructor.
FeatureCalculatorHaralickMeasures - Class in de.unihalle.informatik.MiToBo.features.texture
Calculates set of Haralick co-occurrence texture features from an image.
FeatureCalculatorHaralickMeasures() - Constructor for class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Default constructor.
FeatureCalculatorHaralickMeasures.HaralickDirection - Enum in de.unihalle.informatik.MiToBo.features.texture
Directions available for matrix calculations.
FeatureCalculatorHaralickMeasuresResult - Class in de.unihalle.informatik.MiToBo.features.texture
Class representing the result of statistical feature calculations.
FeatureCalculatorHaralickMeasuresResult(double[]) - Constructor for class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
Default constructor.
FeatureCalculatorIntensityStats - Class in de.unihalle.informatik.MiToBo.features.statistical
Calculates statistical features on images tile-wise, based on FeatureCalculator.
FeatureCalculatorIntensityStats() - Constructor for class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
Default constructor.
FeatureCalculatorIntensityStatsResult - Class in de.unihalle.informatik.MiToBo.features.statistical
Class representing the result of statistical feature calculations.
FeatureCalculatorIntensityStatsResult(ImageStatistics.StatValue, double) - Constructor for class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
Default constructor.
FeatureCalculatorResult - Interface in de.unihalle.informatik.MiToBo.features
Interface for result data returned from classes extending FeatureCalculator.
featureDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Feature directory.
featureType - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Type of features to apply.
field - Variable in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Vector field the potential is reconstructed for.
FieldOperations2D - Class in de.unihalle.informatik.MiToBo.fields
Class implements several operations on a 2D vector field.
FieldOperations2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Standard constructor.
FieldOperations2D(MTBVectorField2D, MTBImageDouble, FieldOperations2D.FieldOperation) - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Constructor to create a new field operation operator.
FieldOperations2D(MTBVectorField2D, FieldOperations2D.FieldOperation) - Constructor for class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Constructor to create a new field operation operator.
FieldOperations2D.FieldOperation - Enum in de.unihalle.informatik.MiToBo.fields
Several operation types on a 2D vector field.
filename - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
fileName - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
fileName - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
FilenameGenerator - Class in de.unihalle.informatik.MiToBo.tools
Utility operator to generate a filename from a given filename.
FilenameGenerator() - Constructor for class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
fileNameOut - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
FilePathManipulator - Class in de.unihalle.informatik.MiToBo.io.tools
Class providing helpers to manipulate file and directory paths.
FilePathManipulator() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
 
fill(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
fill(MTBImage, Color) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
fillBlack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
fillHoles(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
FillHoles2D - Class in de.unihalle.informatik.MiToBo.segmentation.regions.filling
Operator to fill holes in connected components of binary or label image.
FillHoles2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Default constructor.
FillHoles2D(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Constructor with input image.
fillImage(MTBImage, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Fill the specified image with a gray value.
fillImage(MTBImage, Color, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Fill the image with a RGB color value.
fillPanel(String[], boolean[]) - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
Adds checkboxes to the panel according the entries array.
fillPanel(String[], String) - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Adds radio buttons to the panel according the choices array.
fillPanel(HashMap<String, Component>) - Method in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
Add the components in the HashMap to the panel.
fillWhite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
fillWhite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
 
filter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
The current state distribution of targets in this sample estimated by a prediction filter
filterImage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
findMiddleScale(double, double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Numerically finds the middle scale between to given scales.
findNextPoint(Point2D.Double, int, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Find direction to next pixel in specific direction from the last pixel.
findPrefixes(Vector<String>) - Static method in class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis
Helper to recursively extract common prefixes.
FirstOrderMoment<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for classes that provide a first order moment.
FLAG_LENGTH - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Bit mask for length energies for debugging purposes.
FluorescentCellSegmenter - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
This operator is for segmenting images or image sequences containing fluorescently labeled cells
FluorescentCellSegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
FluorescentCellSegmenter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
FNclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FNtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FNtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FNtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
Converts an java.awt.Color object to a string-representation in the format "rINT:bINT:gINT:aINT".
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
 
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
Format the given object value to a string
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
Get a string representing the seed of the specified Random generator.
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
 
forwardDifferencing_X(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
forwardDifferencing_Y(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
forwardDifferencing_Z(int, int, int, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method, explicit define fallback-strategy
FPclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
fps - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
fps - Variable in class mtb_io.Save_Image_MTB
frames per second option if available
fpsfield - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
FPtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FPtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
FPtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
frequency - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Filter frequency.
fromXMLType(MTBXMLMatrixType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Obtain a JAMA matrix from its xml-beans type
fromXMLType(MTBXMLMultiStateMMIDType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Obtain a MultiState object from its xml-beans representation
fromXMLType(MTBXMLMultiStateMMIDVectorType) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Obtain a Vector> object from its xml-beans representation

G

GaborFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D Gabor filter.
GaborFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Default constructor.
GaborFilter2D.KernelPart - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Allows to request kernel masks for real and complex parts independently.
GaborFilter2D.ResultType - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Reponse mode.
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
gammaAdaptive - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Vector containing the current gamma values (step sizes).
GammaCorrection2D - Class in de.unihalle.informatik.MiToBo.enhance
Gamma correction on a 8- oder 16-bit image for one- or multi-channel images.
GammaCorrection2D() - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Standard constructor.
GammaCorrection2D(MTBImage, double, int) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Constructor to create a new gamma correction 2D operator.
GammaCorrection2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
No gamma value is set.
gammaUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Gamma update strategy.
gauss2poisson(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Transforms image with gaussian noise to image with poisson noise J.
GaussFilter - Class in de.unihalle.informatik.MiToBo.filters.linear
Multidimensional Gauss filter class.
GaussFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor with default parameters sigmaX=1, sigmaY=1, sigmaZ=0, sigmaT=0, sigmaC=0, kernelTruncation=3, sigmaInterpretation=PHYSICALSIZE.
GaussFilter(MTBImage, double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor for Gaussian filtering in x- and y-dimension.
GaussFilter(MTBImage, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor for Gaussian filtering in x-, y- and z-dimension.
GaussFilter(MTBImage, double, double, double, double, double, MTBImageWindow.BoundaryPadding, double, GaussFilter.SigmaInterpretation) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Constructor for Gaussian filtering.
gaussFilter() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
compute the Gaussian filter
GaussFilter.SigmaInterpretation - Enum in de.unihalle.informatik.MiToBo.filters.linear
Indicator how to interpret the specified standard deviations: - PIXEL: Sigma is given in pixels - PHYSICALSIZE: Sigma is given in terms of the physical pixel size (see MTBImage.getStepsizeX/Y/Z/T, in c-dimension always pixel interpretation is used)
gaussian - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
multivariate gaussian density object for evaluation
gaussian - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
multivariate gaussian density object for evaluation
GaussianDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A multivariate Gaussian distribution.
GaussianDistribution(int) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Constructor for a Gaussian distribution of dimension DOF with the zero vector as mean, the unity matrix as covariance matrix and a new random generator for sampling
GaussianDistribution(int, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Constructor for a Gaussian distribution of dimension DOF with the zero vector as mean, the unity matrix as covariance matrix and a given random generator for sampling
GaussianDistribution(Matrix, Matrix) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Gaussian distribution with given mean, covariance and a new random generator for sampling
GaussianDistribution(Matrix, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Gaussian distribution with given mean, covariance and random generator for sampling
gaussians - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
GaussMixDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A multivariate Gaussian mixture distribution.
GaussMixDistribution(GaussianDistribution[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
Constructor with equally weighted Gaussian components
GaussMixDistribution(GaussianDistribution[], double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
Constructor for weighted Gaussian components
gaussmixtures - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
gaussnoise - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
GaussPDxFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D linear filter implementing first partial derivative of a Gaussian in x.
GaussPDxFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Default constructor.
GaussPDxxFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
2D filter implementing second partial derivative of Gaussian in x.
GaussPDxxFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Default constructor.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Standard deviation of the Gaussian.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Standard deviation of the Gaussian.
gaussStdDev - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Standard deviation of the Gaussian.
gaussStdDevX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Standard deviation of the Gaussian in x.
gaussStdDevY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Standard deviation of the Gaussian in x.
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
 
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
generateHelpMenu() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
generateNextStates(MultiState<MotionModelID>, LinearTransformGaussNoise[]) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
generateObservations(MultiState<MotionModelID>, LinearTransformGaussNoise, MultiStateFactory<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
generateSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates segmentation objects given specified data.
GenericDiscreteDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A generic discrete distribution
GenericDiscreteDistribution(double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
Constructor.
GenericDiscreteDistribution(double[], Random, boolean) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
Constructor.
genInfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Get a region by index
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
 
get(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Get a region by index
get(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Get the function value at position (x,y,z).
get(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
get the value of this function at the position of the predecessor of ( x, y, z )
get2DInterface(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates 2D segmentation.
get2DMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates a synthetic 2D mask according to given specification.
get3DInterface(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates 3D segmentation.
get3DMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generates a synthetic 3D mask according to given specification.
get3SigClippedStdDev(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get the standard deviation (sigma) of an image only using values clipped by 3*sigma from a first estimate of sigma
getActivityArray() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Returns current activity array.
getActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get flag for thresholding only the actual slice (true) or the whole image (false)
getAllEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get all edges of the node.
getAllInner() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get all inner contours from the contour object.
getAllInnerBorders() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get all inner borders from the border object.
getAllPaths(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of all paths of the neurite skeleton graph.
getAllPixels(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all pixels of the neurite skeleton graph from the nodes and edges.
getAllTiles() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Generates and returns array of all tiles.
getAlpha() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get snake length term weight alpha.
getAlpha() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get weighting factor for snake length term.
getAlphaDecrease() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Get the fix alpha decrease value.
getAnalyzedImages() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get vector of analyzed images.
getArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return the area of the region in pixels.
getAreaFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Get area fraction.
getAreaFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Get area fraction.
getArithmeticOperation() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getAssociatedObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
getAssociatedObservations(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the indices of all observations that are associated with the specified state.
getAssociatedTargets(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
getAssociatedTargets(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the indices of all targets that are associated with the specified observation.
getAvailableCodecs() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Return available codecs for movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
getAvailableCompression() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the available compression methods for the specified file format.
getAvailableQualities() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Return available qualities for quicktime movie writers (see Bio-Formats package loci.formats.out.QTWriter) represented by a hashmap.
getAverageMean(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getAverageStdDev(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getAvgConeWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each neurite growth cone.
getAvgNeuriteWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each complete neurite branch.
getAvgShaftWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each neurite shaft.
getBackground(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.LabelAreasToRegions
 
getBeta() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get snake curvature term weight beta.
getBeta() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get weighting factor for snake curvature term.
getBetaDecrease() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Get the fix beta decrease value.
getBGValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get background value
getBinaryImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the image for binary mode.
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Generates binary mask for inside part of the polygon.
getBinaryMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get a binary mask of the represented segmentation.
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Generates binary mask for inside part of the snake.
getBinaryResultMap() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Returns the final binary map.
getBinIndex(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
determines the index of the histogram bin, to which a value is assigned, if histogram value range and binning were specified at creation
getBinMidpoint(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
determines the value midpoint of a histogram bin for given bin index, if
histogram value range and binning were specified at creation
getBinValue(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getBorder() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to get the border object from the current 2D region, for example to visualize the regions.
getBorderSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Get 2D border set from Roi.
getBorderSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads a ROI manager selection into a set of borders.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get value of Parameter argument boundaryPadding.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get value of Parameter argument boundaryPadding.
getBoundaryPadding() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get value of Parameter argument boundaryPadding.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Calculates the axes-parallel bounding box of the contour.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Calculates the axes-parallel bounding box of the snake.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates the axes-parallel bounding box of the region.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculates the axes-parallel bounding box of the region.
getBrancheCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of neurite branches.
getBranchLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get lengths of neurite branches along the complete neurite skeleton graph.
getBranchNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all branch nodes of the MTBNeuriteSkelGraph.
getBthImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get black top-hat image.
getBthMaskSize() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get mask size of black top-hat.
getC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getCalibration() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the calibration object.
getCandidates() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns set of detected candidate peaks.
getCConditionalProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the probability of the associations at time t conditional on the previous associations and all observations up to time t.
getCellAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns average size of detected cells.
getCellCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns number of detected cells.
getCellSizes() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns sizes of snake interiors.
getCenterOfMass_X() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return x-coordinate of the center of mass.
getCenterOfMass_Y() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return y-coordinate of the center of mass.
getCenterX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getCenterY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getCentralMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate central moment of the region of order p,q.
getCentralMoment(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
 
getCentre() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the center of the region as 3D point.
getCentreX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the x-coordinate of the center of the region.
getCentreY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the y-coordinate of the center of the region.
getCentreZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the z-coordinate of the center of the region.
getChaincode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Calculates chaincode from the outer contour.
getChannel() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the image channel.
getChannelB() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get a reference to the blue channel image.
getChannelG() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get a reference to the green channel image.
getChannelR() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get a reference to the red channel image.
getChannelsAreRGBFlag() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get flag if RGB color channels are interpreted as real image channels.
getChart() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Get reference to resulting chart.
getChart() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Get reference to resulting chart.
getChartObject() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
Returns the chart object associated with the button.
getChartShowButton() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel
Returns the button object associated with the panel.
getChilds() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Returns Vector with child nodes.
getChosenColor() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
getCircularity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates circularity of given region (1 for perfect circle, else smaller).
getCJointProb() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the joint probability of all associations up to 'current time' (see getCurrentTime) conditional on all observations up to that time.
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getClass(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the class label of position (x,y).
getClass(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the class label of position (x,y,z).
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getClass(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getCLogConditionalProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the log of probability of the associations at time t conditional on the previous associations and all observations up to time t.
getCLogJointProb() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the natural log of joint probability of all associations up to 'current time' (see getCurrentTime) conditional on all observations up to that time.
getCodec() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get codec option
getCodec() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the codec (quicktime only)
getColor() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the uniform color of the regions in a color image (COLOR_IMAGE only).
getColor(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Get the color for a given key.
getColorImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get image of randomly colored regions, if the create-color-image-flag was set to true.
getColumnCount() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getColumnName(int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getCompactness() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
calculates compactness value according to
Carlos Martinez-Ortiz. "2D and 3D Shape Descriptors".
getCompactnessThreshold() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the actual value of compactness threshold.
getComplexKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Generates the sinus filter mask of the complex part of the Gabor filter.
getCompression() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get compression option
getCompression() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the compression type
getCOMx() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the center of mass of the snake in x-direction.
getCOMy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the center of mass of the snake in y-direction.
getCondition() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
getCondition() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.ConditionalDistribution
Get conditional variable
getCondition() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
getCondition() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
 
getConeAreas() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get areas of growth cone regions.
getConeLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get length of the growth cone region along the neurite skeleton graph without neurite shaft areas.
getConeRoundness() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get roundness of growth cone regions, 1 means a perfect circle.
getConeSpineCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of spines (filopodia-like protrusions) per growth cones.
getConfigValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given environment property.
getConnectivity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Query the connectivity of pixels within border.
getContinuousDOF() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get continuous dimensions of target state in continuous
getContinuousDOF() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Get number of continuous state variables
getContour() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get a Contour2D copy of this object.
getContour() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to get the contour object from the current 2D region.
getContour2DAsXml(MTBContour2D, MTBXMLContour2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Copy the information of contour into the corresponding xml element xmlContour.
getContour2DFromXml(MTBXMLContour2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get a new MTBContour2D from the information of the xmlContour.
getContourLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Calculates the length of the outer contour using it's chaincode.
getContours() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns extracted contours.
getContourSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Get 2D contour set from Roi.
getContourSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads a ROI manager selection into a set of contours.
getContourType() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the current contour type.
getCorrCircularity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculates corrected circularity of given region (1 for perfect circle, else smaller).
getCorrectGamma() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get flag to use gamma correction.
getCorrelationImages() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Compute the correlation images as specified by the parameters.
getCorrelationThreshold() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get threshold for thresholding wavelet correlation images
getCost() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get edge cost as double value.
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Returns the covariance matrix
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
getCovariance() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.SecondOrderCentralMoment
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
getCovariance() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
getCreateColorImageFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the flag that determines the creation of an image with randomly colored regions.
getCreateLabelImageFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the flag that determines the creation of an image with region labels.
getCurGamma() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Returns current gamma vector.
getCurrentMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Extracts currently selected mode, i.e. data source.
getCurrentOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Get the current overlap mask.
getCurrentSlice() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the current slice.
getCurrentSlice(MTBOperator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the current slice.
getCurrentSliceCoords() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the current slice coordinates (z,t,c) (for functions that work on a slice only, this has nothing to do with the ij.ImageStack's current slice)
getCurrentSliceIndex() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the current slice index (for functions that work on a slice only, this has nothing to do with the ij.ImageStack's current slice)
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the slice label of the slice specified by the current slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the slice label of the slice specified by the actual slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the slice label of the slice specified by the actual slice index
getCurrentSliceLabel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the slice label of the slice specified by the actual slice index
getCurrentSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns a copy of the current snake.
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns a copy of the current snake(s).
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Returns a copy of the set of current snakes.
getCurrentSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns a set with current snake(!).
getCurrentTime() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the current time index, i.e. the time index that was assigned to the latest added information
getCurrentZStackCoords() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the current z-stack coordinates. [0]=t-coordinate, [1]=c-coordinate.
getCurvature(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Curvature at point (x,y,z).
getCurvature(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
compute the curvature at at nearest contourpoint to (x,y,z) if x or y are not in the boundaries it returns 0 if z is not in the boundaries it returns the 2d cuvature
getCytoplasmResult() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns reference to cytoplasm/cell boundary detection result.
getData(Class<?>) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get data for current MTBGraphEdge.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get data of MTBGraphNode.
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Returns a reference to the data associated with the node.
getDataLabels() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Get assigned labels.
getDebug() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of debug.
getDebug() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of debug.
getDebug() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of debug.
getDefaultValue(Boolean, Boolean, ALDOpParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorParameterPanel
 
getDefinedSpineLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get length to define a neurite branch as spine (filopodia-like protrusions).
getDelimiter() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Returns the currently chosen delimiter.
getDeltaApproximator() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get reference to delta function approximator.
getDeltaT() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get step size.
getDenoise() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get the denoising flag. true if denoising is activated.
getDerivative(MTBSegmentationInterface, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the energy derivative value at position (x,y,z).
getDerivative(MTBSegmentationInterface, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Returns the energy derivative value at position (x,y,z).
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
getDerivative(MTBLevelsetFunctionDerivable, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Get the energy derivative value, i.e. velocity, for position (x,y,z).
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Updates the fitting term based on new region average values.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Updates matrix A given weights for the internal energy term.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Updates matrix A given weights for the internal energy term.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Updates the region coupling energy term in matrix A.
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
getDerivative_MatrixPart(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Returns the linear matrix part of this energy for snake optimization.
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
getDerivative_VectorPart(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Returns the vector part of this energy for snake optimization.
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
getDerivativeWithoutDelta(MTBLevelsetFunctionDerivable, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Get the energy derivative value, i.e. velocity, for position (x,y,z).
getDerivativeX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Partial derivative in x direction at position (x,y,z).
getDerivativeX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve x-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Get x-derivative of the distance map at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Get x-derivative of negative absolute gradient value to the power of two (external energy) at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get x-derivative of external snake energy at given position.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Get x-derivative of external snake energy at given position using central differences.
getDerivativeX(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get x-derivative of external snake energy at given position.
getDerivativeX_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get x-derivative of external snake energy at given position on a normalizes image coordinates in range [width*scale, height*scale].
getDerivativeXX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in x direction at position (x,y,z).
getDerivativeXX(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in x direction 2 times at nearest contourpoint to (x,y,z)
getDerivativeXY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in x-y direction at position (x,y,z).
getDerivativeXY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in x and y direction at nearest contourpoint to (x,y,z)
getDerivativeXZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in x-z direction at position (x,y,z).
getDerivativeXZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in x and z direction at nearest contourpoint to (x,y,z)
getDerivativeY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Partial derivative in y direction at position (x,y,z).
getDerivativeY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve y-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Get y-derivative of the distance map at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Get y-derivative of negative absolute gradient value to the power of two (external energy) at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get y-derivative of external snake energy at given position.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Get y-derivative of external snake energy at given position using central differences.
getDerivativeY(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get y-derivative of external snake energy at given position.
getDerivativeY_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get y-derivative of external snake energy at given position on a normalizes image coordinates in range [width*scale, height*scale].
getDerivativeYY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in y direction at position (x,y,z).
getDerivativeYY(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in y direction 2 times at nearest contourpoint to (x,y,z)
getDerivativeYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in y-z direction at position (x,y,z).
getDerivativeYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in y and z direction at nearest contourpoint to (x,y,z)
getDerivativeZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Partial derivative in z direction at position (x,y,z).
getDerivativeZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
retrieve z-derivation at nearest contourpoint to ( x, y, z ), calculated by forward euler method
getDerivativeZZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Second partial derivative in z direction at position (x,y,z).
getDerivativeZZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
computes the the derivation in z direction 2 times at nearest contourpoint to (x,y,z)
getDescription() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
 
getDescription() - Method in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
getDestinationImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get value of Input argument DestinationImage.
getDetectedNeurites() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get vector of detected neurite sets for each image.
getDetectedNeuritesSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get set of detected neurites.
getDetectedParticles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get regions of detected particles.
getDetectionResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get the result table of the detected neurites.
getDetectorMode() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get current detector mode.
getDetectors() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Get a reference to configured detectors' vector.
getDiagonalNeighbors() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get value of Parameter argument DiagonalNeighbors.
getDiagonalNeighborsFlag() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the neighborhood flag.
getDiffX_image() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Calculate the image from the first order partial derivative in x-direction from the vectors U.
getDiffY_image() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Calculate the image from the first order partial derivative in y-direction from the vectors V.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns the dimension of the given membership.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Returns the dimension of the given membership.
getDimension() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the dimension of the segmentation.
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getDimension() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the dimension of the given membership.
getDimensionality() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns the dimension of the result object.
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getDimensionality() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getDimensionOfScope() - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
 
getDirection(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get direction of the vector at position (x,y) in the vector field, relative to the x-axis.
getDirName() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Get directory for processing.
getDistanceImage() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the calculated distance map image.
getDistanceMap() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the calculated distance map.
getDistImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns calculated distance map.
getDistMetric() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the used distance metric.
getDoErosion() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of doErosion.
getDomainXMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal x coordinate represented in class map.
getDomainXMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal x coordinate represented in class map.
getDomainYMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal y coordinate represented in visibility map.
getDomainYMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal y coordinate represented in class map.
getDrawType() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the kind of region image drawn by the operator
getEccentricity() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate eccentricity of the region in range [0,1]. 1 means a sustained region.
getEdgeNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get number of included MTBGraphEdges.
getEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get all edges of the MTBGraph.
getEigenvalues() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Get calculated eigenvalues in ascending order.
getEigenvects() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Get calculated eigenvectors, one vector per column, in ascending order.
getElapsedTime() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Returns the elapsed time since last reset (or invoking the constructor) in seconds
getElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the element at the specified position in this list.
getElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Returns the element at the specified position in this list.
getEllipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns set of initial snake ellipses.
getEndCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of end points.
getEndNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all end nodes of the MTBNeuriteSkelGraph.
getEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Returns a reference to the list of energies.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get external snake energy label.
getEnergy(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns the energy with given index.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns element i of the energy list.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns element i of the energy list.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of energy.
getEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of energy.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns element i of the energy list.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns element i of the energy list.
getEnergyDerivativeMaxVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the maximum possible derivative value this energy may yield.
getEnergyDerivativeMaxVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Returns the maximum possible derivative value this energy may yield.
getEnergyDerivativeMinVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the minimum possible derivative value this energy may yield.
getEnergyDerivativeMinVal() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Returns the minimum possible derivative value this energy may yield.
getEnergyLabel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get energy label for external energy, used for optimization.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns the list of energies.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns the list of level set energies.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns list of energies with actual type.
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
 
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get set of energies.
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns a reference to the set of energies.
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
getEnergySet() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
getEnergyValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Get current energy value for the snake.
getEntireTargetIDs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the targetIDs of all targets that ever existed up to current time.
getEntropyImage() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getEnvVarValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given environment variable.
getEpsilon() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get epsilon for Heaviside function approximation.
getErodeSize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of erodeSize.
getErodeSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The size of the eroding element.
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
getError() - Method in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Returns the complete exception message as string.
getESSPercentage() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
If this percentage of number of samples is below the current effective sample size (ESS), the samples are resampled.
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
 
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBException
 
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
 
getExcluded() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getExcluded() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
getExcludeMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the current exclude mask.
getExistingTargetIDs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
getExistingTargetIDs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the targetIDs of all targets existing at time t.
getExtension(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Get extension from filename if any.
getExtractedNeurites() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get extracted neurites as result of the NeuriteExtraction2D operator.
getFactory() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get associated factory
getFactoryMethod() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getFeatureLines() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding feature lines of borders between soma and neurite shafts and neurite shafts and growth cones.
getFeaturePoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding feature points of borders between soma and neurite shafts and neurite shafts and growth cones.
getFGValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get foreground value
getFieldSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
getFieldSizeX() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the field size in x-direction.
getFieldSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
getFieldSizeY() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the field size in y-direction.
getFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Collect all files in the directory tree including their complete paths.
getFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Get the list of all files inside the directory.
getFileName() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the filename of the image that has to be read.
getFileName() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get image filename
getFileName(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Returns the file name without leading directories or file description (extension).
getFilterImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get flag to use gaussian filter.
getFilterMode() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get filter mode to define relation of foreground to background.
getFilterResponseStack() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Get individual filter responses.
getFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the first element in this list.
getfirstFeatureAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get first feature of neurite corresponding feature points from borders between soma and neurite shafts.
getForeground() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the used foreground color.
getForegroundSum() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getFps() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the frames per second for movie writers (*.avi,*.mov).
getFramesPerSecond() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get fps option
getGamma() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get gamma correction value.
getGamma() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the gamma value.
getGammaToAuto() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get if gamma should be calculated automatically or not.
getGaussianKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Generates the Gaussian part of the Gabor kernel for a given orientation.
getGaussKernelC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in c-dimension for given parameters, null if sigma is zero in c-dimension
getGaussKernelT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in t-dimension for given parameters, null if sigma is zero in t-dimension
getGaussKernelX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in x-dimension for given parameters, null if sigma is zero in x-dimension
getGaussKernelY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in y-dimension for given parameters, null if sigma is zero in y-dimension
getGaussKernelZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get Gaussian kernel image (non-normalized) in z-dimension for given parameters, null if sigma is zero in z-dimension
getGaussMixture(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getGenericEnergyList() - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns list of energies converted to generic type.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns the list of energies.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns the list of energies.
getGenericEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns the list of energies.
getGradientMode() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get the used gradient mode for field calculation.
getGradientMode(GradientFieldCalculator2D.GradientMode) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set the used gradient mode for field calculation.
getGraphCost() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get total amount of the graph costs.
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the gray value of the regions in a mask image (MASK_IMAGE only).
getGrownRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Returns a MTBImageByte image after growing.
getGrowthConeRegions() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get regions of the separated growth cones.
getGVF() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get the calculated Gradient Vector Flow field.
getH() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Get current h-parameter (max height of the h-domes).
getHeight() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get skeleton graph image size in y direction.
getHeight() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get image height.
getHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get height of level set function.
getHistogram() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
getHistoryLink(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Gets the port to which the object is currently linked in history.
getHueMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Get the hue channel image.
getHueThresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Return the treshold for the hue channel.
getIcon() - Method in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
Get reference to the icon.
getID() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return the ID of the region.
getID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the ID of the region.
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBLevelsetException
 
getIdentString() - Method in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBSnakeException
 
getIgnoreInvalidStackSpecification() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the flag to ignore an invalid stack specification.
getImageCount() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the number of (multi-dimensional) images stored in the specified file.
getImageFiles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get vector of all image files included in the experiment folder for detection.
getImageID(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the ID of the imageIdx-th image in the file, if available
getImageJPropValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given ImageJ preference.
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
 
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
 
getImageName() - Method in interface de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Interface
Returns the name of the processed image.
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
 
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Note: Returned string might be null if the result is associated with a single cell rather than a complete image!
getImageName() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Note: Returned string might be null if the result is associated with a single cell rather than a complete image!
getImageName(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the name of the imageIdx-th image in the file, if available
getImageObject() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
Returns the image object associated with the button.
getImagePart(int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of a part of this image as new MTBImage.
getImagePart(MTBOperator, int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of a part of this image as new MTBImage.
getImagePart(MTBImage, int, int, int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Get a copy of a part of this image as new MTBImage
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get an ImagePlus object.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get an ImagePlus object.
getImageShowButton() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel
Returns the button object associated with the panel.
getImageSizeX() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the image size in x-direction.
getImageSizeY() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the image size in y-direction.
getImageType() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get output image type.
getImageType() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the datatype of the resulting image
getImg() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get reference to the (input) image.
getInConst() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getIndex() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
The index of this channel.
getIndexMap() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Get map of indices of maximal responses.
getIndexOfImageToRead() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the index of the image that has to be read from the file.
getInEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get input edges for node.
getInfo() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getInImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getInImg() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Input argument inImg.
getInImg() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get the input image.
getInImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of inImg.
getInImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Get input image.
getInImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Input argument inImg.
getInImg1() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getInImg2() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getInitAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Get the initial alpha value.
getInitBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Get the initial beta value.
getInitBinImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of initBinImg.
getInitialSegmentation() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getInitialSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Get initial segmentation.
getInitialSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns initial snake.
getInitLabelImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of initLabelImg.
getInitSegImageByte() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Return the resulting initial segmentation image.
getInner(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get a specific inner border.
getInner(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get a specific inner contour from the contour object.
getInnerContourLengthMin() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get the minimum number of pixels in the inner contour (length of the contour).
getInnerCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Get the number of inner contours including in the contour object.
getInputDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get directory of input images.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get multichannel fluorescence input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get input image
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get uneven illuminated input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get low contrast input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get the underlying input image of the gradient field..
getInputImage() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
getInputImage() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Get value of inImg.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Returns the input image, null if not set.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get reference to the current input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns input image.
getInputImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get input image
getInputImage() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getInputImagePlus() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get ImagePlus that has to be stored to disk
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Get input image.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get input image
getInputMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get input mode.
getInputMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get MTBImage that has to be stored to disk
getInputMTBImgRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Returns the input image, null if not set.
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the input regions.
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the regions that have to be drawn
getInputRegs() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Get set of input regions.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
Get singleton instance.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Single access point for singleton functionality.
getIntensityNormalizationMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Request mode for normalizing image intensities.
getIntermediateLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
getIntermediateLS() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of intermediateLS.
getIntersection(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the point of intersection between the segments.
getInvalidImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of invalidImage.
getInvalidImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of invalidImg.
getInvalidTilesNum() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Get number of invalid tiles.
getInverseCovariance() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
getIterationCount() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the current iteration count.
getIterationsPerSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Returns the total number of iterations per snake.
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
getJmax() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get Jmax
getJmax() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get Jmax (maximum scale 2^Jmax - 1)
getJmin() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get Jmin
getJVMPropValue(String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This function reads out the value of a given JVM property.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Calculates kernel for given angle and pre-defined sigma and length.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Calculates kernel for given angle and pre-defined sigmas.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Calculates Gaussian derivative kernel for given parameters.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Calculates Gaussian derivative kernel for given parameters.
getKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Calculates kernel for the given orientation.
getKernelImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get convolution kernel (image).
getKernelMask() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Get mask of valid kernel elements.
getKernelNormalization() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get value of Parameter argument kernelNormalization.
getKernelOrigin() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get value of Parameter argument kernelOrigin.
getKernels() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get smoothing kernels
getKernelTruncation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get kernel truncation factor.
getKey(HashMap<Integer, String>, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Obtain the key for a given value of a HashMap, if available.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns label mask with segmentation result.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns label image of detected nuclei.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns gray-scale label image with nuclei regions.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns a label image visualizing the segmentation.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Get reference to the current Label image.
getLabelImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get image of region labels (of type MTB_INT), if the create-label-image-flag was set to true.
getLabelImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of labelImg.
getLabelMostInRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
getLabelsInRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
getLambda() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
getLargestNonEmptyBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getLast() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the last element in this list.
getLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
getLevel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Return the tree level (level identifier).
getLinkageMode() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getLogFaculty(int) - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty
log(n!)
getLogFacultyFraction(int, int) - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty
log(n1!
getLongestCommonPrefixes(Vector<String>) - Static method in class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis
Extracts the set of all prefixes shared by at least two strings in the given set.
getLongestPath(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of the longest path of the neurite skeleton graph.
getLowerBound() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Get lower bound of the normalization to range [lowerBound, upperBound].
getMagImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Calculate the gradient magnitude image from the vectors U and V.
getMagnitude(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get magnitude of the vector at position (x,y) in the vector field.
getMajorAxisLength() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
calculation of the length of the major axis of the ellipse best fitting
using moments of the region
getMask() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns binary mask with segmentation result.
getMask() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns binary mask with segmentation result.
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getMask(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Gets the mask of the specified class (0 Background, 255 Foreground)
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getMask(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getMaskFromNuclei(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
getMaskRadiusC() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusC.
getMaskRadiusT() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusT.
getMaskRadiusX() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusX.
getMaskRadiusY() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusY.
getMaskRadiusZ() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument maskRadiusZ.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Get value of masksize.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Returns the given mask size, 0 if not set.
getMasksize() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get current masksize.
getMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Returns result matrix with matching result.
getMax() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
The maximum value of this channel.
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Get the maximum value for parameter alpha.
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
getMaxAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Get the maximum value for parameter beta.
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
getMaxBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
getMaxFragmentDistance() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get maximum neuron fragment distance in pixel.
getMaxFragmentDistance() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum fragment distance , in pixel.
getMaximalComponentDist() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the maximal component distance for linking.
getMaximalComponentSize() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the maximal valid component size for component removal.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of maxIter.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Get maximum iteration count.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Get maximum iteration count.
getMaxIter() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Get maximum iteration count.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get maximum number of iterations to stop detection.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum number of iterations to finish snake optimization,
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of maxIterations.
getMaxIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get maximal number of iterations.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns the maximal label used in the membership representation.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Returns the maximal label used in the membership representation.
getMaxLabel() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the maximal label used in the segmentation representation.
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getMaxLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the maximal label used in the membership representation.
getMaxLevels() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Returns maximum number of levels in iterative mode.
getMaxN() - Method in class de.unihalle.informatik.MiToBo.math.LogFaculty
 
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get maximum length of a spine (filopodia-like protrusion) in pixel.
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum length of a spine, in pixel.
getMaxSpineLength() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get maximum length of a spine (filopodia-like protrusion) in pixel.
getMaxValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getMaxValueBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getMaxVoronoiExpandDist() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the maximal distance of pixels considered in Voronoi expansion.
getMaxWeight() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getMean() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
Returns the mean vector.
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
getMean() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
getMean() - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.FirstOrderMoment
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
getMean() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
getMeanKernelC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in c-dimension for given parameters, null if size is zero in c-dimension
getMeanKernelT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in t-dimension for given parameters, null if size is zero in t-dimension
getMeanKernelX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in x-dimension for given parameters, null if size is zero in x-dimension
getMeanKernelY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in y-dimension for given parameters, null if size is zero in y-dimension
getMeanKernelZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get mean kernel image (non-normalized) in z-dimension for given parameters, null if size is zero in z-dimension
getMeans() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Returns the average region intensities last calculated.
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
 
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
 
getMeasurementUnit() - Method in interface de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Interface
Returns the unit of measurements.
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
 
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
 
getMeasurementUnit() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
 
getMemorizedMatrixA() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Returns matrix carrying always the values of the last iteration, or null before first run.
getMin() - Method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
The minimum value of this channel.
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Get the minimum value for parameter alpha.
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
getMinAlpha() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
getMinAreaAfterErosion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getMinAreaAfterOpening() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getminAreaSeedRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Get the minimum value for parameter beta.
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
getMinBeta() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
getMinCompactness() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getMinimalComponentSize() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the minimal valid component size for component removal.
getMinMaxCoordinates() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Extracts the extreme coordinates of the region in each dimension.
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get minimum and maximum value of the image as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get minimum and maximum value of the image (all channels) as double
getMinMaxDouble() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get minimum and maximum value of the image as double
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get minimum and maximum value of the image as int
getMinMaxInt() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get minimum and maximum value of the image as int
getMinRegionArea() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getMinRegionSize() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get the minimum size of detected regions.
getMinSize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of minSize.
getMinSizeFraction() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of minSizeFraction.
getMinWeight() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getMode() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get the desired operator mode.
getModification() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getMoelculeImg() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the input image with the fluorescence labeled molecules.
getMoleculeChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get molecule channels, used for extraction.
getMoleculeChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get molecule channels, used for molecular profile extraction.
getMolecules() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get names of molecules for each image channel.
getMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate moment of the region of order p,q.
getMoment(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
 
getMorphOp() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get morphological operation for illumination correction, default is closing.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get minimum fraction of point motion to stop detection.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get minimum motion fraction of snake control points, to finish snake optimization.
getMotionFraction() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Get motion fraction.
getMSERs() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Returns set of detected MSERs.
getMTBImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a bi-level MTBImageByte of the level set function.
getMTBImageLabel() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a MTBImageByte of the level set function.
getMultiphase() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of multiphase.
getNarrowBandWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get width of narrow band.
getNarrowIterator() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
get an iterator through narrow band
getNeighbors() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get all neighbors of the current node.
getNeighbourhood() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getNeurite() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
getNeuriteColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get neurite region color (RGB) for result image.
getNeuriteColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get neurite region color (RGB) for result image.
getNeuriteDetector() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get current neurite detector.
getNeuriteGraph() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding skeleton graph.
getNeuriteImage(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Visualize the neurites skeleton graphs and regions.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get neurite mask size in pixel.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get maximum neurite mask size, in pixel.
getNeuriteMaskSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get neurite mask size in pixel.
getNeuriteRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite corresponding region.
getNeuriteSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the input set of neurites.
getNeuriteSet() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get the input set of neurites.
getNeuriteShaftArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get area of neurite shaft region (without growth cone).
getNeuriteShaftRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite shaft region (without growth cone).
getNeuriteStack(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Visualize the neurites skeleton graphs and regions.
getNeuriteWidths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get average widths of each neurite branch, including the average widths of the whole branches, the shafts and the growth cones.
getNeuronChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get neuron channels, used for detection.
getNeuronChannles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get neuron channels, used for detection.
getNeuronColor() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get binary neuron color.
getNeuronImage() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get input image of the binary neuron.
getNewConfigWin(ALDOperator) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
 
getNewConfigWin(ALDOperator) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorGUIExecutionProxy
 
getNewIndent(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Return a new indentation string.
getNiblackConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get niblack constant.
getNiblackConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get Niblack thresholding constant.
getNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Return the node object containing the data.
getNodeNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get number of included MTBGraphNodes.
getNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Get all nodes of the MTBGraph.
getNodes() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getNodes() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Get graph nodes
getNodeType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
 
getNoiseCovariance() - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
getNorm() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the Euclidean norm of the segment.
getNormalCentralMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate normalized central moment of the region of order p,q.
getNormalizationMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns energy normalization mode.
getNormalizedCumulativeHistogram(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Create a normalized cumulative histogram from an image
getNormedMagImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Normalize the gradient magnitude values into a range of [0,1].
getNRSCandidates() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns possible peak locations from NucleusRegionSeperator.
getNRSDistImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns distance image calculated intermediately.
getNRSEllipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Creates and returns a set of polygons as starting regions for snake analysis based on hypothesized ellipses from nucleus information
getNRSResultAreas() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns set of result regions from region separator.
getNRSResultCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns set of detected region centers from region separator.
getNRSVoronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Creates and returns a set of polygons as starting regions for the snakes.
getNucDetector() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detector for nuclei.
getNucleiAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns average size of detected nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get image channel of nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get channel number, including the labeled nuclei.
getNucleiChannel() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get nuclei channel number.
getNucleiCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns number of detected nuclei.
getNucleiRegions() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Returns set of detected regions.
getNucleiRegions() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detected nuclei regions.
getNucleiResult() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns nuclei detection result.
getNucleusRatio() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get ratio of nucleus pixels which should be included in an intact neuron region
getNucleusRatio() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get ratio of nucleus pixels which should be included in an intact neuron region
getNucleusSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get minimum nucleus size of nuclei regions
getNucleusSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get minimum nucleus size of nuclei regions
getNumberChannels() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns the number of image channels available.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Returns the number of classes represented in the membership.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Returns the number of classes represented in the membership.
getNumberOfClasses() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the number of classes represented by the segmentation.
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getNumberOfClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns the number of classes represented in the membership.
getNumberOfInEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get number of incoming edges for MTBGraphNode.
getNumberOfMSERs() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Returns number of detected MSERs.
getNumberOfOutEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get number of outgoing edges for MTBGraphNode.
getNumberOfStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get number of states
getNumberOfStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
getNumEntries() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getNumericalValue(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns a numerical value representing the requested result component.
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getNumericalValue(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get number of iterations for the GVF field.
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of numIterations Explanation: Number of iterations performed
getNumIterations() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of numIterations Explanation: Number of iterations performed
getNumOfComponents() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getNumOfImages() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
 
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getNumOfIndeps() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
getNumOfParticles() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get number of particles
getNumPhases() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return .e. number phases.
getObjectsMeans(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getObjectsStdDevs(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getObservationDistribution() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
getObservationDistribution() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilterIndep
 
getObservationMatrices() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
getObservations() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
getObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get the observations of time t.
getOldId() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Get previous index of snake point from the previous snake.
getOpeningSESize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getOperation() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Return UserTime or RealTime depending on mode of operation
getOperationType() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the operation type which should be applied to the input vector field.
getOpIdentifier() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Method returns an identifier characterizing the operator.
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getOpIdentifier() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getOpMode() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of opMode.
getOrientation(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Deprecated. 
getOrientation() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate orientation of principal axis of the MTBRegion2D, using the atan2 function.
getOtsuRegs() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns set of regions resulting from Otsu thresholding.
getOtsuThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Get the resulting threshold.
getOutEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get outgoing edges for node.
getOuterContours(MTBRegion2DSet, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Calculate the outer contours of the given regions in a image.
getOutImageType() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get the type of image object that is created as result image.
getOutputDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get directory of output results.
getOutputImage() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get medialness filter image.
getOutputObservations() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get a copy of the input observations with IDs set corresponding to the tracking results after GreedyGourmetPartitioning of the track graph constructed from the RBMCDA samples.
getOutputType() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get output image type
getOverwrite() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the overwrite permission flag
getParent() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Get the parent of this node.
getPartChannel() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get particle channel number.
getPartDetector() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detector for particles.
getPartialDiffX() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in x-direction using central differences.
getPartialDiffX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of partial derivative in x-direction at point with given index.
getPartialDiffX_forward() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in x-direction using forward differences.
getPartialDiffX_sobel() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in x-direction using Sobel.
getPartialDiffY() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in y-direction using central differences.
getPartialDiffY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of partial derivative in y-direction at point with given index.
getPartialDiffY_forward() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in y-direction using forward differences.
getPartialDiffY_sobel() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Calculate first order partial derivative in y-direction using Sobel.
getParticle(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get idx-th particle
getParticleAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns average size of detected particles.
getParticleChannel() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get image channel including particles.
getParticleCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns number of detected particles.
getParticleDetector() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Get particle detector.
getParticleDetector2D() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
getParticleRegions() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get detected particle regions.
getParticleResult(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns number of detected particles per channel.
getParticles() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get particles
getPath() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Request path associated with the node.
getPdf(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getPerCellAvgSize() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns detected particle average size per cell.
getPerCellCount() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Returns detected particles per cell.
getPhase(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel/voxel
getPhase(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel/voxel, z coordinate defaults to zero
getPhaseCheckXY(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel checking limits of all coordinates.
getPhaseCheckXYZ(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return phase for a pixel/voxel checking limits of all coordinates.
getPhi() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Get current level set function.
getPhi() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of phi.
getPhiColorImage2D(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get visualization of current level set function in red-blue color map.
getPhiImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get visualization of current level set function.
getPixelInside() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return number of pixels of all object phases.
getPixelOutside() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return number of pixels of background phase.
getPointAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get a specific 2D point belonging to the border object.
getPointDist(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Deprecated. 
getPointNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get the number of points of the border object.
getPointNum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Get the number of points from the polygon.
getPoints() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Get all points belonging to the border object.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Get polygon points.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Return all points of the region.
getPoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the points which are included in the 3D region.
getPoisson2Gauss() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
getPolygon() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Get a Polygon2D copy of this object.
getPolygon2DAsXml(MTBPolygon2D, MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Copy the information of polygon into the corresponding xml element xmlPolygon.
getPolygon2DFromXml(MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
* Get a new Polygon2D from the information of the xmlPolygon .
getPolygonSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Get 2D polygon set from Roi.
getPolygonSetFromRoiFile(String, boolean) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads an ImageJ roi file into a set of polygons/snakes.
getPolygonSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads ROI manager selections into a set of polygons/snakes.
getPotential() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Returns a copy of the potential field (for faster access!).
getPotential() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Get the energy potential field from this external energy.
getPrecisionClutter() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPrecisionTrackEnd() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPrecisionTrackSegment() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPrecisionTrackStart() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getPredecessorOnContour(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
gets the value of the nearest contourpoint to point (x,y,z)
getPreferredSize() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
getPreserveTopology() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of preserveTopology.
getPreserveTopology() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of preserveTopology.
getPreviousEnergyValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Get old energy value for the snake at last iteration.
getPreviousSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns the previous snake.
getProcessedChannel() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Get the processed channel.
getProcessMode() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get current process mode.
getProfile() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Get profile data of the neurite region.
getProfilePoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
getProfiles() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Get the resulting set of neurite profiles.
getProfileSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
getQuality() - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Get quality option
getQuality() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get the quality (quicktime only)
getRadiusImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Returns supplemental radius image, null if not generated.
getRandom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the random number generator which is responsable to draw each region in a random color (COLOR_IMAGE only).
getRankOpMode() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Parameter argument rankOpMode.
getRealKernel(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Generates the cosine filter mask of the complex part of the Gabor filter.
getRecallClutter() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getRecallTrackEnd() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getRecallTrackSegment() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getRecallTrackStart() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
getReduceC() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Parameter argument reduceC.
getReducerMethod() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Parameter argument reducerMethod.
getReduceT() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Parameter argument reduceT.
getReduceX() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Parameter argument reduceX.
getReduceY() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Parameter argument reduceY.
getReduceZ() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Parameter argument reduceZ.
getRegCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns the centers of the nuclei sorted to their original regions.
getRegion(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Method to get the included region in a 2D contour as Region2D object.
getRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Get a Region2D copy of this object.
getRegion() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Return the 2D region.
getRegionID() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the region id.
getRegionMeans() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get average intensity array indexed with class labels for first channel.
getRegionMeansAllChannels() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get average intensity array indexed with class labels for all channels.
getRegions(MTBImage, int) - Static method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.LabelAreasToRegions
 
getRegions(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.LabelAreasToRegions
 
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Get 2D region set from Roi.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the region set.
getRegionSet() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
getRegionSetFromRoiFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads an ImageJ roi file into a set of regions.
getRegionSetFromRoiFile(String, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads an ImageJ roi file into a set of regions.
getRegionSetFromRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reads a ROI manager selection into a set of regions.
getRegionSizes() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get array of region areas indexed with class labels for first channel.
getRegionsTree(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Build a tree of regions from binarized images.
getRegionVars() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get intensity variance array indexed with class labels for first channel.
getRegionVarsAllChannels() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Get intensity variance array indexed with class labels for all channels.
getREngine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get JRI R engine to run R as a single thread.
getREngine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get R engine.
getResampleConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get snake point resampling constant.
getResampleConstant() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get constant for snake point resampling.
getResponseStack() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Returns stack with intermediate (non-binary) results.
getResult() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns the result data object of the calculator.
getResult() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getResult() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getResult() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get result data.
getResultAreas() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns separated regions sorted according to original regions.
getResultBorders() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Get result borders.
getResultCellImg() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Returns (optional) result image with cell contours.
getResultCenters() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns centers of result regions.
getResultContourImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of ResultContourImage.
getResultContours() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the calculated contours.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Get the result data, i.e. mask and related quantitative data.
getResultData() - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Returns result data object.
getResultData() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Get the transformed dataset.
getResultDataAreaFractions() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with area fractions per cell.
getResultDataArray() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Returns extracted result data.
getResultDataAvgSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with average size per cell.
getResultDataCellSizes() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with areas per cell.
getResultDataCounts() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with counts per cell.
getResultDataTotalSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Returns result data object with total structure size per cell.
getResultDir() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get directory of intermediate and final results.
getResultIdentifier(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Method returns an identifier characterizing the related component of the result.
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getResultIdentifier(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Get the result label image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Returns result image, i.e. the segmentation mask.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns RGB color image overlayed with nuclei contours.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Returns result image, i.e. the segmentation mask.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Returns the result color image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Get the gamma corrected image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Get illumination corrected result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Returns result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get contrast enhanced result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get image with result data.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get result image of the operation on the vector field.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Get result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Get the result image after applying operator.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Get the resulting h-dome image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
Returns the opened image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Get value of resultImg.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Returns the eroded image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Returns the opened image, null if not available.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Get the result image after applying the operator.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Get result image with extracted borders.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the binary image with the calculated contours.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of ResultImage.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of resultImage.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get image with segmentation result overlay.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Get the resulting image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Returns the result image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get the result image
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Get the resulting thresholded image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the resulting region image.
getResultImagePlus() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get resulting image that was read from disk.
getResultImageStack() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns stack with result segmentation images.
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
getResultImageType() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
getResultImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Get value of resultImg.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get resulting image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Get value of Output argument resultImg.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Get result image.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get result image
getResultImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Get value of Output argument resultImg.
getResultingRegions() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Get the resulting regions.
getResultingRegionsets() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
getResultMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get binary mask of segmentation result.
getResultMTBImage() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Returns the converted image, null if not available.
getResultMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get resulting image that was read from disk.
getResultRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Returns the result RGB color.
getResults() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get resulting regions (each detetection corresponds to a region)
getResultSnakeImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns image with snakes contours.
getResultSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the set of result snakes.
getResultsTable() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get the result table of the detected neurites.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get final result table of morphology measurements.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Get particle statistics.
getResultTable() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Get result table.
getResultValue() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
Get result value;
getResultVec() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
 
getResultVesselMap() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Get result.
getResultXylemRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Return the binary image after the post processing of the grown region image.
getRGBResult() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Get RGB values.
getRGBValue() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
getRoot() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Access the root node.
getRoundnessThreshold() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Returns the currently active roundness threshold.
getRowCount() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getRuntime() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getSample(double[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
getSample(double[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Returns a sample in the range [0, 1] from a cumulative distribution given by the array cdf
getSampleConditionalProb(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the probability of the associations of i-th sample at the time t conditional on previous associations and all observations up to time t.
getSampleInfo(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the sample info object of the i-th sample.
getSampleInfo() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Get the info object of this RBMCDA-sample
getSampleJointProb(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the joint probability of all associations of the i-th sample conditional on all observations, normalized by all samples' probabilities.
getSampleJointProbs() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get the joint probability of all associations of all samples conditional on all observations, normalized by all samples' probabilities.
getSampleObservations(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
Get a copy of the observations with IDs set corresponding to the i-th sample's tracking results.
getSatMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Get the saturation channel image.
getSatTresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getSaveIntermediateResultPath() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Returns path where to save intermediate results.
getScaleDown() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get the scaling factor of the snake.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Get scaling factor.
getScaleFactor() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Get scaling factor.
getScaleFactor() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Get scaling factor.
getScaleFactor() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Get scaling factor.
getScaleIntervalSize() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get the size of the scale interval for correlation images
getScaleMax() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get maximum of scales.
getScaleMin() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get minimum of scales.
getScaleNum() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get number of scales.
getScratchArea() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getScratchFeatures() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getsecondFeatureAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get second feature of neurite corresponding feature points from borders between neurite shafts and growth cones.
getSeedPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
coarse segementation of input frame to localize cells
getSeedPoints(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
coarse segmentation of input frame to localize cells
getSeedRegions() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
getSeErosionSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getSegDim() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get target dimension.
getSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the generated segmentation object.
getSegmentationMode() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Returns mode activated during segmentation.
getSegmentLength() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns desired segment length for resampling.
getSelection() - Method in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Get the currently selected radio button string
getSelections() - Method in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
 
getSelections() - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Returns a hash map with the absolute filename as key and the indices of images selected from the corresponding file.
getSeOpeningSize() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getSettings() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
getShaftLengths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get neurite shaft lengths of all branches without growth cone areas.
getShape() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get the selected shape.
getShapeDimX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get extent of shape in x dimension.
getShapeDimY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get extent of shape in y dimension.
getShapeDimZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get extent of shape in z dimension.
getShapeForErosion() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getShapeForOpening() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
getShapeMaskSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get size of shape mask in x dimension.
getShapeMaskSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get size of shape mask in y dimension.
getShapeMaskSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get size of shape mask in z dimension.
getShapePosX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get position of shape in x dimension.
getShapePosY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get position of shape in y dimension.
getShapePosZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get position of shape in z dimension.
getShortestPath(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of the shortest path of the neurite skeleton graph.
getSigmaC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in c-dimension.
getSigmaInterpretation() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get the mode of how sigmas are interpreted.
getSigmaT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in t-dimension.
getSigmaX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in x-dimension.
getSigmaY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in y-dimension.
getSigmaZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Get standard deviation (sigma) in z-dimension.
getSignedArea() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Calculates the signed area of simple (!)
getSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getSize() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
count number of elements
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of c(hannel)-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeC() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of c(hannel)-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in c-dimension
getSizeC() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in c-dimension.
getSizeDilation() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of sizeDilation.
getSizeOpening() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of sizeOpening.
getSizePhase(byte) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return the size, i.e. number of pixel/voxels of a phase.
getSizeStack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of the underlying (ImageJ) stack which corresponds to the number of slices
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of t(ime)-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of t(ime)-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in t-dimension
getSizeT() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in t-dimension.
getSizeTH() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of sizeTH.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in x-dimension
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the expansion in x-direction of the region.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getSizeX() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in x-dimension.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getSizeX() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the size of the segmentation domain in x direction.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return X size of the level set function.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get width of level set function.
getSizeX() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in y-dimension
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the expansion in y-direction of the region.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getSizeY() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in y-dimension.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getSizeY() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the size of the segmentation domain in y direction.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return Y size of the level set function.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get height of level set function.
getSizeY() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get size of z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getSizeZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get size of z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get window size in z-dimension
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Calculate the expansion in z-direction of the region.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Get standard deviation (size) in z-dimension.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getSizeZ() - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the size of the segmentation domain in z direction.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return Z size of the level set function.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Get depth of level set function.
getSizeZ() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getSkeletonGraphNodes() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get all nodes of the MTBNeuriteSkelGraph as MTBNeuriteSkelGraphNodes.
getSlice(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the specified slice.
getSlice(MTBOperator, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get a copy of the specified slice.
getSlice(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Get a copy of the specified slice
getSliceLabel(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the slice label of the slice specified by (z,t,c)
getSmallestNonEmptyBin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getSnakeAsXml(MTBSnake, MTBXMLSnakeType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Copy the information of snake into the corresponding xml element xmlSnake.
getSnakeIterCount() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get number snake iteration counts, used for optimization.
getSnakeNumber() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the number of snakes currently managed.
getSnakePoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get snake points as vector of SnakePoint2D objects.
getSnakes() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Returns the result snakes.
getSndPartialDiffX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of 2nd order partial derivative in x-direction.
getSndPartialDiffY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get approximation of 2nd order partial derivative in y-direction.
getSpacing() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of spacing.
getSpacingIntermediate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of spacingIntermediate.
getSpineCount() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Get number of spines (filopodia-like protrusions).
getSpinePaths() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the pixels of all spine paths of the neurite skeleton graph.
getSrcNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get source node of the MTBGraphEdge.
getStackWithIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns a stack with intermediate segmentation results.
getStartFrame() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
getStartNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get the start node of the MTBNeuriteSkelGraph.
getStateContinuous(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get the continuous part of the idx-th state (indices start from 0)
getStateContinuous(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
getStateDiscrete(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Get the discrete part of the idx-th state (indices start from 0)
getStateDiscrete(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
getStdDev() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getStdDev(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get standard deviation of the image
getStepSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get step size of snake movement.
getStepSize() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get step size of snake point movement.
getStepsizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the stepsize in t-dimension (timestep)
getStepsizeT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the stepsize in t-dimension (timestep)
getStepsizeT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the stepsize in t-dimension (timestep)
getStepsizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the physical size of a voxel (stepsize) in x-dimension
getStepsizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the physical size of a voxel (stepsize) in y-dimension
getStepsizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the physical size of a voxel (stepsize) in z-dimension
getStepsizeZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the physical size of a voxel (stepsize) in z-dimension
getStepsizeZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the physical size of a voxel (stepsize) in z-dimension
getString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
 
getSubtreeFileList() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Collects the list of all files inside this directory AND inside all subdirectories.
getSum() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getSynthMask(SegmentationInitializer.SegmentationDimension) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Generate synthetic mask.
getT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getTableEntry(int) - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Returns entry in requested field as string representation.
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
getTableEntry(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
getTargetImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Get the target image to which the regions are drawn, if one was specified.
getTargetImageType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getTgtNode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Get target node of the MTBGraphEdge.
getTheta() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get coefficient to relate vessel radius and scale.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get threshold to be applied to image.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Get value of threshold.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get threshold.
getThresholdImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Get image for thresholding
getThresTH() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of thresTH.
getTile(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns tile with given indices.
getTileCols() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns number of tiles and colums, respectively, in x-dimension.
getTileCountX() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get number of tiles in x-direction.
getTileCountY() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Get number of tiles in x-direction.
getTileRows() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Returns number of tiles and rows, respectively, in y-dimension.
getTitle() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the image's title
getTitle() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get title string
getTitle() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get title of underlying image
getTitleRunning(String) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return a unique title for the copy of an image, i.e. a running number is appended/incremented.
getTotalNumberOfEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get total number of edges for MTBGraphNode.
getTrack(short) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
Get track of target given by targetID up to current time, where targetID may be 0 to obtain the clutter observations (which do not form a track).
getTrackImage() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
getTrajectories() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
getTransformMatrix() - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
getTransitionMatrices() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get MiToBo image type
getType() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get data type
getType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get underlying data type
getType() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get input image type.
getTypeMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return the maximum value that the current type can handle
getTypeMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return the minimum value that the current type can handle
getTypeName(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Deprecated. 
getU() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get vector U of the field.
getUnitT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the t-dimension
getUnitT() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the t-dimension
getUnitT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the t-dimension
getUnitX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the x-dimension
getUnitX() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the x-dimension
getUnitX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the x-dimension
getUnitY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the y-dimension
getUnitY() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the y-dimension
getUnitY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the y-dimension
getUnitZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the unit of the z-dimension
getUnitZ() - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the unit of the z-dimension
getUnitZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the unit of the z-dimension
getUpperBound() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Get upper bound of the normalization to range [lowerBound, upperBound].
getUseThresh() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Get adaptive thresholding tag.
getUWT() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Get the UWT coefficient images.
getV() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get vector V of the field.
getValue(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get RGB value from the specified position.
getValue(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get RGB value from the specified position in the actual slice.
getValue(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
getValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
Returns the double value.
getValue() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
getValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper
Calculate approximated value for given parameter value.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Returns the distance value from the distance map at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Returns the negative absolute gradient value to the power of 2 (the external energy) at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Returns the value of the external energy at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Returns the value of the external energy at the given position.
getValue(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Returns the value of the external energy at the given position.
getValue_norm(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Returns the value of the external energy at the given position on a normalizes image coordinates in range [width*scale, height*scale].
getValueAt(int, int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
getValueB(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get blue value from the specified position.
getValueB(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get blue value from the specified position in the actual slice.
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current slice at coordinate (x,y,z) as an Double
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the value of the actual slice at coordinate (x,y) as a Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueDouble(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueDouble(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the value of the actual slice at coordinate (x,y) as an Double
getValueDouble(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the value of the 5D image at coordinate (x,y,z,t,c) as a Double
getValueG(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get green value from the specified position.
getValueG(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get green value from the specified position in the actual slice.
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current z-stack coordinate (x,y,z) as an Integer
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the value of the current slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the 5D image at coordinate (x,y,z,t,c) No test of coordinate validity
getValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the voxel value of the actual z-stack at coordinate (x,y,z) No test of coordinate validity
getValueInt(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Get the value of the actual slice at coordinate (x,y) as an Integer
getValueInt(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the value of the 5D image at coordinate (x,y,z,t,c) as an Integer
getValuePotential(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Returns value of potential at specified position.
getValueR(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get red value from the specified position.
getValueR(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Get red value from the specified position in the actual slice.
getValues() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get the double values of the given image.
getValueU(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get value from vector U at position (x,y).
getValueV(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Get value from vector V at position (x,y).
getVariance() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the operation based 2D vector field.
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get the resulting 2D vector field.
getVectorField() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get calculated GVF vector field..
getVectorFieldImage() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Get the operation based 2D vector field image.
getVersion() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
 
getVisibilityMapHeight() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns height of the visibility map.
getVisibilityMapWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns width of the visibility map.
getVisibilityMapXMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal x coordinate represented in visibility map.
getVisibilityMapXMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal x coordinate represented in visibility map.
getVisibilityMapYMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal y coordinate represented in visibility map.
getVisibilityMapYMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal y coordinate represented in visibility map.
getVolume() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Return the volume of the 3D region (number of points within the region).
getVolume() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
Get volume of the hypercube where p(x) > 0
getVoronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns set of snake polygons resulting from Voronoi tesselation.
getVoronoiImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Get voronoi tesselation image.
getVoronoiStack() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Get stack of voronoi tesselation images.
getVotesAdjacency(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getVotesClutter(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getVotesTarget(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get weight of idx-th particle
getWeight(int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns the weight of the energy with given index.
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
getWeight(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the pixel weight of position (x,y).
getWeight(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Returns the pixel weight of position (x,y,z).
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns element i of the weight list.
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns element i of the weight list.
getWeight(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getWeight(PartitGraphNodeID, PartitGraphNodeID) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
getWeight(T, T) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Get weight of edge from nodeSrc to nodeTgt.
getWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
getWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get particle weights
getWeights() - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Returns the list of weights.
getWeights() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Returns the list of weights.
getWidth() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Get skeleton graph image size in x direction.
getWidth() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get image width.
getWidth() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Get width of level set function domain.
getWindowPosition() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the current window position
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns working image.
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
getWorkingImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
getWthImage() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get white top-hat image.
getWthMaskSize() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Get mask size of white top-hat.
getX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Return coordinate of x-dimension.
getX() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
getXMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the maximal x-coordinate of the domain of this border set.
getXMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the maximal x-coordinate of the domain of this contour set.
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns maximal x coordinate of the domain.
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getXmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getXMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the minimal x-coordinate of the domain of this border set.
getXMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the minimal x-coordinate of the domain of this contour set.
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns minimal x coordinate of the domain.
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getXmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getXML() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the XML file description string if one was available.
getXMTBImg() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Get the value channel image.
getXThresh() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
The Intensity/Brighntness/Value-Parameter (depending on the used input image type).
getXylemImage() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Return the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
getXylemImage() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Return the input xylem image.
getY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Return coordinate of y-dimension.
getY() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
getYMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the maximal y-coordinate of the domain of this border set.
getYMax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the maximal y-coordinate of the domain of this contour set.
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns maximal x coordinate of the domain.
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getYmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getYMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the minimal y-coordinate of the domain of this border set.
getYMin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the minimal y-coordinate of the domain of this contour set.
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Returns minimal y coordinate of the domain.
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
getYmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Return coordinate of z-dimension.
getZ() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
getZmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getZmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
GradientFieldCalculator2D - Class in de.unihalle.informatik.MiToBo.fields
Class to calculate a gradient vector field of a given image.
GradientFieldCalculator2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Standard constructor.
GradientFieldCalculator2D(MTBImage, GradientFieldCalculator2D.GradientMode) - Constructor for class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Constructor.
GradientFieldCalculator2D.GradientMode - Enum in de.unihalle.informatik.MiToBo.fields
Provided calculation modes for calculation the gradient image.
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one pixel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
calculate the gradient magnitude of the forward difference of the heaviside function corresponding to the level set for one voxel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE
Calculate the gradient magnitude of the foreard difference of the heavyside function corresponding to the level set for one voxel
gradMagHeaviside(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
calculate the gradient magnitude of the foreward difference of the heavyside function corresponding to the level set for one voxel
graph - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
GraphNodeID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A graph node object to hold a nodeID as well as a subgraphID
GraphNodeID(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
Constructor (subgraphID=0)
GraphNodeID(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
Constructor to assign the node to a subgraph
GraphvizWriter<T extends Comparable<?> & Comparator<?>> - Class in de.unihalle.informatik.MiToBo.io.files
Write graph to file using the DOT-language for visualization using graphviz tools.
GraphvizWriter() - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Empty constructor
GraphvizWriter(AdjacencyMatrix<T>, String) - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Constructor for specifying the graph by an adjacency matrix
GraphvizWriter(MTBGraph, String) - Constructor for class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Constructor for specifying the graph by MTBGraph
Grappa_Editor - Class in mitoboRunner
ImageJ plugin for running the Alida/MiToBo graphical editor "Grappa".
Grappa_Editor() - Constructor for class mitoboRunner.Grappa_Editor
 
GreedyGourmetPartitioning - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
greedyGourmet graph partitioning algorithm following:
J.
GreedyGourmetPartitioning(MatchingAdjacencyMatrix, boolean, double) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Constructor.
groundtruthObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
groundtruthToSampleTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
GVFFieldCalculator2D - Class in de.unihalle.informatik.MiToBo.fields
Class to calculate a special 2D vector field, a Gradient Vector Flow Field (GVF) with its x- and y-flows from the given image.
GVFFieldCalculator2D() - Constructor for class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Standard constructor.
GVFFieldCalculator2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Constructor.

H

H - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
state-to-observation-space linear transform matrix
H - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
 
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Check if energies are given.
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
hasEnergies() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
hashCode() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
 
hashtableToString(Hashtable<Integer, Vector<Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
hashtableToString(Hashtable<Integer, Vector<Double>>, String, Hashtable<Integer, Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
hasImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
hasOneCC() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Checks if the neighborhood represented in X has exactly one connected component of entries set to true using the neighborhood definition as as represented in the neighborhood arrays of the class.
HDomeTransform3D - Class in de.unihalle.informatik.MiToBo.morphology
H-dome transform in 3D (straightforward use with 2D-images).
HDomeTransform3D() - Constructor for class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Constructor
HDomeTransform3D(MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Constructor
header - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
Header defines.
headerStrings - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Header defines.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Height of the filter mask.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Height of segmentation domain.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Height of the input image and levelset function.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Height of the input image.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Height of the given image for the energy.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Function to update object state after setting new point list.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Function to update object state after setting new point list.
hookPointsUpdated() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Function to update object state after setting new point list.
hsiInput - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Input HSI values.
HSIToRGBPixelConverter - Class in de.unihalle.informatik.MiToBo.color.conversion
Operator to convert a single HSI value to RGB.
HSIToRGBPixelConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Default constructor.
HSIToRGBPixelConverter(double[]) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Constructor.
HSVToRGBPixelConverter - Class in de.unihalle.informatik.MiToBo.color.conversion
Class to convert values from HSV color space into other color spaces like RGB or so.
HSVToRGBPixelConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Standard constructor.
HSVToRGBPixelConverter(double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Constructor to create a HSVconverter object
HUE_UNDEFINED - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
 
hybridGrayscaleReconstruct(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Implements the fast hybrid grayscale reconstruction algo of [Vincent93].
HyperStackParticleDetectorUWT2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D
A particle detector that runs the ParticleDetectorUWT2D given as input (with all parameters set) over all slices of the input image for a given channel.
HyperStackParticleDetectorUWT2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
HyperStackParticleDetectorUWT2D(MTBImage, ParticleDetectorUWT2D, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
HysteresisThresholding - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
Hysteresis thresholding on gray-scale images.
HysteresisThresholding() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Standard constructor.

I

icov - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
inverse covariance matrix
ID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
Target ID
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Depth of working image.
ignoreButtonPress(boolean) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image height.
IlluminationCorrection - Class in de.unihalle.informatik.MiToBo.enhance
This class corrects the uneven illumination (e.g. background gradient) of especially gray value bright filed or DIC images.
IlluminationCorrection() - Constructor for class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Standard constructor.
IlluminationCorrection(MTBImage, BasicMorphology, MTBImage.MTBImageType) - Constructor for class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Constructor to create a new IlluminationCorrection object.
image_channel - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Channel of the image that was processed.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Name of the image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Name of the analyzed image.
image_name - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Name of the analyzed image.
ImageArithmetics - Class in de.unihalle.informatik.MiToBo.math.images
Image arithmetics class for MTBImage objects.
ImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Create empty ImageArithmetics object.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Constructor for arithmetic operations considering two images.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Constructor for arithmetic operations considering one image and a constant.
ImageArithmetics.ArithOp - Enum in de.unihalle.informatik.MiToBo.math.images
Arithmetic operations:
ADD, SUB, MULT, DIV, MIN, MAX, AND, OR, ABS_DIFF require two input images,
ADD_CONST, MULT_CONST, POW_CONST require one input image and a constant
INV, ABS require one input image only
imageClosed(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
ImageContrastReducer - Class in de.unihalle.informatik.MiToBo.tools.image
Contrast-reduction of images by reducing number of gray-scale values.
ImageContrastReducer() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Default constructor.
ImageContrastReducer.ResultValueMode - Enum in de.unihalle.informatik.MiToBo.tools.image
Modes for choosing result values.
ImageContrastReducer.TargetContrast - Enum in de.unihalle.informatik.MiToBo.tools.image
Available target contrast modes.
ImageConvert - Class in cmdTools.mtb_imagetools
Commandline tool to convert image formats and datatypes.
ImageConvert() - Constructor for class cmdTools.mtb_imagetools.ImageConvert
 
ImageConverter - Class in de.unihalle.informatik.MiToBo.tools.image
Plugin to convert images that are represented by MTBImage.
ImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Constructor.
ImageConverter(MTBImage, MTBImage.MTBImageType, boolean, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Constructor
ImageDimensionReducer - Class in de.unihalle.informatik.MiToBo.tools.image
 
ImageDimensionReducer() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Constructor
ImageDimensionReducer(MTBImage, boolean, boolean, boolean, boolean, boolean, ImageDimensionReducer.ReducerMethod) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Constructor
ImageDimensionReducer.ReducerMethod - Enum in de.unihalle.informatik.MiToBo.tools.image
Methods for dimension reduction.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Input image directory.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Input image directory.
imageDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Input image directory.
ImageFilter - Class in de.unihalle.informatik.MiToBo.io.tools
Class to filter the files by a file chooser.
ImageFilter() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
ImageFilter(String[]) - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
imageIndex - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
ImageIOUtils - Class in de.unihalle.informatik.MiToBo.io.tools
A class of utility functions used by the MiToBo's image-IO classes
ImageIOUtils() - Constructor for class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
 
imageOpened(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
ImageReaderMTB - Class in de.unihalle.informatik.MiToBo.io.images
Image reader operator to create MTBImage or ImagePlus objects from image files while reading and restoring image history from corresponding history files (.mph).
ImageReaderMTB() - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
ImageReaderMTB(String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Constructor of an image reader instance by filename.
ImageReaderMTB.OutImageType - Enum in de.unihalle.informatik.MiToBo.io.images
Specifies the image object that is constructed by the reader
ImageReaderOptionsPane - Class in de.unihalle.informatik.MiToBo.gui
A panel for image reader options that is used as accessory in a JFileChooser
ImageReaderOptionsPane(JFileChooser) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Constructor that will install this reader options panel to the specified JFileChooser
ImageStatistics - Class in de.unihalle.informatik.MiToBo.math.images
Class offering statistical calculations on objects of type MTBImage.
ImageStatistics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
Default constructor.
ImageStatistics(MTBImage, ImageStatistics.StatValue) - Constructor for class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
Constructor with image argument.
ImageStatistics.StatValue - Enum in de.unihalle.informatik.MiToBo.math.images
Statistical values that could be calculated.
ImageToTilesSplitter - Class in de.unihalle.informatik.MiToBo.tools.image
Operator to split an image into tiles and save them to disk.
ImageToTilesSplitter() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
Empty constructor.
imageUpdated(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
ImageValueTools - Class in de.unihalle.informatik.MiToBo.tools.image
An operator class for different simple operations on the values of an image like inversion, filling with a constant value, etc.
ImageValueTools() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
ImageValueTools(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Constructor.
ImageValueTools.ImageValueModification - Enum in de.unihalle.informatik.MiToBo.tools.image
Available image value modification methods.
ImageWriterMTB - Class in de.unihalle.informatik.MiToBo.io.images
Image writer operator to store MTBImage or ImagePlus to disk along with the image history (.mph) file.
ImageWriterMTB() - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
ImageWriterMTB(MTBImage, String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Image file output operator for MTBImage objects.
ImageWriterMTB(ImagePlus, String) - Constructor for class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Image file output operator for ImagePlus objects.
ImageWriterOptionsPane - Class in de.unihalle.informatik.MiToBo.gui
A panel for image writer options that is used as accessory in a JFileChooser
ImageWriterOptionsPane(JFileChooser) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Constructor that will install this writer options panel to the specified JFileChooser
img - Variable in class mtb_io.Save_Image_MTB
 
ImgClose - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological closing on 2D binary/grayscale images.
ImgClose() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgClose
Default constructor.
ImgClose(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgClose
Constructor.
ImgDilate - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological dilation on 2D binary/grayscale images.
ImgDilate() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Default constructor.
ImgDilate(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Constructor.
ImgErode - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological erosion on 2D binary/grayscale images.
ImgErode() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgErode
Default constructor.
ImgErode(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgErode
Constructor.
ImgOpen - Class in de.unihalle.informatik.MiToBo.morphology
This class implements morphological opening on 2D binary/grayscale images.
ImgOpen() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Default constructor.
ImgOpen(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Constructor.
imgReadInfo(IFormatReader) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Create a string of image reading information
imgStatsOp - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Operator to calculate energy parameters.
ImgThresh - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
Image thresholding operator with lower threshold (threshold and upper threshold (upperThreshold.
ImgThresh(MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Constructor for thresholding using 255 as foreground and 0 as background value.
ImgThresh(MTBImage, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Constructor for thresholding using 'fgValue' as foreground and 'bgValue' as background value.
ImgThresh() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
ImgThreshNiblack - Class in de.unihalle.informatik.MiToBo.segmentation.thresholds
Image binarization based on local Niblack thresholding.
ImgThreshNiblack() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Default constructor.
ImgThreshNiblack(MTBImage, ImgThreshNiblack.Mode, double, double, int, int, double, MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Constructor.
ImgThreshNiblack.Mode - Enum in de.unihalle.informatik.MiToBo.segmentation.thresholds
Niblack processing mode.
ImgTophat - Class in de.unihalle.informatik.MiToBo.morphology
This class implements the tophat operator.
ImgTophat() - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Default constructor.
ImgTophat(MTBImage, ImgTophat.tophatMode, int) - Constructor for class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Constructor with parameters.
ImgTophat.tophatMode - Enum in de.unihalle.informatik.MiToBo.morphology
Available operating modes.
imgWriteInfo(String, IFormatWriter, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Create a string of image writing information
imp - Variable in class mtb_io.Save_Image_MTB
 
includeMask(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
incrPositionC() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the c-dimension
incrPositionC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the c-dimension
incrPositionT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the t-dimension
incrPositionT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the t-dimension
incrPositionX() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the x-dimension
incrPositionX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the x-dimension
incrPositionY() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the y-dimension
incrPositionY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the y-dimension
incrPositionZ() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 1 in the z-dimension
incrPositionZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Increment the window's position by 'increment' in the z-dimension
IndependentlyEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities p(X) with independent variables in X, that can be evaluated for each element in the realization x of its random variable X.
IndependentSamplingDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities with independent variables, where components of a sample can be drawn independently.
inEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Vector of incoming edges of the MTBGraphNode.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Single-layer input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
inImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Input image to calculate features for.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Image to work on.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Image to work on.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Input image to be segmented.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Image to process.
inImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Input image.
init() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Initializes the operator, i.e. allocates memory.
init() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Method to properly initialize instances of this class.
init() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Method to properly initialize instances of this class.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Initialize the energy object.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Initialization routine which is called once before the energy is actually used.
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE
Here potentially anisotropic grids may be reflected setting weights accordingly
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
init(MTBImage, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
Initialize the energy object.
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Initialize the updater according to associated energy object.
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
init(MTBSnakeEnergyCD_KassCurvature) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Initialize the updater according to associated energy object.
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
init(MTBSnakeEnergyCD_KassLength) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
 
init(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Initializing routine which is called once before the gamma adaptation is actually used.
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
 
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Initializing routine which is called once before the termination is actually used.
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
 
init(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
 
initAlpha - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
Initial alpha value of the internal Kass energy.
initBeta - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
Initial beta value of the Kass curvature energy.
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
initEnergy(LevelsetSolverDerivatives) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
initEnergy(LevelsetSolverDerivatives) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Initializes the energy object according to given solver settings.
initEnergy(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
initEnergy(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
 
initEnergy(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
initEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Init routine which is called once before the energy is actually used.
initEnergy(SnakeOptimizerCoupled) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Init routine which is called once before the energy is actually used.
initEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Init routine which is called once before the energy is actually used.
initGenerator - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Operator to generate initialization for the level set function.
initialGammas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Initial step size in snake optimization.
initializeWithPrevious(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
initialSegmentation - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Initial segmentation for initializing level set function.
initialSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Initial snakes for cells, e.g. nuclei contours.
initialSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set of initial snake contours.
initNeighbors(float) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
This initializes all relevant arrays containing information on neighbors where dist defines the neighborhood, e.g.
initNewTab(ALDGrappaWorkbenchGraph) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
 
initOperatorWorkflow(ALDOperatorLocation) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorGUIExecutionProxy
 
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Initializes the optimizer.
initOptimizer() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Initializes the optimizer.
initReader() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Initialize the reader (this method is called in the constructor)
initReloadedTab(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
 
initReloadedWorkflow(mxGraph, ALDWorkflow) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
 
initSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Runs initializer to calculate initial segmentation.
initWorkbench() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaFrame
 
inMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
inner - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set of inner borders if available.
inputArray - Variable in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Input array to visualize.
inputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Input image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Input image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Image to process.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Input image to be processed.
inputImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Image to segment.
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
inRange - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Dynamic range of image intensities.
insertData(Vector<Object[]>) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Appends a set of results to the table, i.e. adds a new row at the end.
insertState(Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Insert an additional state
insertState(Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
int2Color(int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
IntegrableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for distributions with distribution functions that can be evaluated for each realization x of its random variable X.
IntensityAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
IntensityAnalyzer(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
intermediatePhiColorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Color image to visualize intermediate segmentation results.
intermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
List of intermediate result segmentations.
intermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set of intermediate segmentation results, required for stack generation.
intermediateResultSamplingRate - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
intermediateResultStack - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
intNormMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Mode for normalizing image intensities.
inv(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Inverts the image.
inv(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Invert the image.
INVALID_PHASE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Level set function value to represent invalid pixels
inverseATrousDWT(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
inverseATrousDWT(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Inverse a trous DWT
invert() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
inverts the values of the structuring element
invert(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
invertImage(MTBImage, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Invert the specified image.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Flag to invert filter mask.
invertMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Flag to invert filter mask.
invisibleRegionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
irop - Variable in class mtb_io.Open_Image_MTB
 
isAppliedComponentwise() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Return operator mode.
isBGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Test if background pixels keep their original pixel values
isClockwiseOriented(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if polygon is oriented counter-clockwise.
isClosed - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Indicates if the polygon is closed or not.
isClosed() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Returns true if the polygon forms a closed polygon.
isConvertableToNumericalData() - Method in interface de.unihalle.informatik.MiToBo.features.FeatureCalculatorResult
Indicates if result data can be 'condensed' to numerical values, e.g., for visualization purposes.
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStatsResult
 
isConvertableToNumericalData() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasuresResult
 
isConvex() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if polygon is convex.
isConvex(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if a polygon is convex.
isCounterClockwiseOriented(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if polygon is oriented counter-clockwise.
isDirected() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Directed or undirected graph?
isDirected() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
isDirected() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Returns true if graph has directed edges, false if undirected
isEmpty() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns true if this collection contains no elements.
isEmpty() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Returns true if this collection contains no elements.
isFGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Test if foreground pixels keep their original pixel values
isForwardTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Test if parameter object is set to (forward) transform (image to wavelet)
isHueUndefined(float) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the hue channel is undefined which is true is saturation is zero or undefined which in turn is encoded as zero.
isHueUndefined(int) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the hue channel is undefined which is true is saturation is zero or undefined which in turn is encoded as zero.
isInverseTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Test if parameter object is set to Inverse Transform (wavelet to image)
iSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Total area/volume of working image.
isOrderedClockwise() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if points are ordered clockwise.
isOrderedCounterClockwise() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if points are ordered counter-clockwise.
isotropicCalcs - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Flag for isotropic calculations.
isotropicCalcs - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Flag for isotropic calculations.
isRegionBinaryMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Check for region input mode.
isRegistered(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Checks if an object is registered in the database.
isSaturationUndefined(float) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the saturation channel is undefined which is true if the x channel is zero.
isSaturationUndefined(int) - Static method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Return true if the saturation channel is undefined which is true if the x channel is zero.
isScaleValues() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get flag if values are scaled to match the range of output type values if necessary
isSilent(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
should results be saved without user interaction
isSimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Check if polygon is simple, i.e. has no self-overlaps.
isSimple(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Checks if a polygon is simple.
isValid(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
returns true, if pixel/voxel is valid.
isValidType(MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Deprecated. 
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
isVisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
True, if position (x,y) is visible.
isVisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
True, if position (x,y,z) is visible.
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
is this pixel visible?
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
isVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Get visibility of a certain pixel position.
itCounter - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Iteration counter.
iteration - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Iteration counter.
iterationsPerSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Number of iterations done for each snake.
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
 
iterator() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Returns a iterator for the coordinatesNeighbors in the order as defined
iteratorOffsets() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Returns a iterator for the pixelOffsets in the order as defined
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image width.
iwop - Variable in class mtb_io.Save_Image_MTB
a panel for image writer options (set as accessory of a JFileChooser)

J

jfc - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
jfc - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
jMode - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Mode for joining results from different orientations.
join(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Join a region with this region.
junitTest - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Internal flag for interrupting recursive calls in unit testing.

K

kernelSize - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Size of the (squared) kernel window.
keyPressed(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
KMeans - Class in de.unihalle.informatik.MiToBo.clustering
Clustering of (feature) vectors with k-means based on Weka library.
KMeans() - Constructor for class de.unihalle.informatik.MiToBo.clustering.KMeans
Default constructor.
kNearestObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Stores for each observation the k-nearest observations that will be associated after the corresponding observation.
kNearestObservations(int, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Get the (k) nearest observations for each observation in this.Z, i.e. for each observation z_m all following observations z_{m:M} are sorted by Euklidean distance and stored in an array.
kPart - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Variable to configure which part of kernel mask is calculated.

L

L - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
LabelAreasToRegions - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
LabelAreasToRegions() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.LabelAreasToRegions
 
labelComponents(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Sequential component labeling
LabelComponentsSequential - Class in de.unihalle.informatik.MiToBo.segmentation.regions.labeling
Sequential component labeling for binarized 2D images to find connected components.
LabelComponentsSequential() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Constructor
LabelComponentsSequential(MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Constructor
labelImage - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Label mask.
labelImage - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Gray-scale label image of nuclei regions.
labelImage(MTBImage, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
labelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Input image to process.
labelNeighbors(MTBImage, MTBImage, boolean[][], int, int, double, double) - Static method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Function for recursive labeling of foreground pixels.
lambda - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
lambda - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
mean=variance of the distribution
lambda_in - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Weighting factor for inner region fit.
lambda_out - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Weighting factor for outer region fit.
lambdaBirth - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
lambdaBirth - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
lambdaClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
lambdaClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
lambdaDeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
lambdaDeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
lastDir - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
For convenience: always open last directory for saving.
lastM - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Number of observations in last call of drawSample()
lastN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Number of targets in last call of drawSample()
lastSample - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Last sample that was sampled
length - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Expected length of vessel segments.
letNewbornTargetIDsStartFrom(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Specify the starting target-ID for newborn targets
letTargetsDie() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Let targets die randomly using the specified distribution of target death and the internal random generator.
LevelsetSegmentationNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Operator intended as user interface for level set segmentation using nonPDE optimization and optionally topology preserving.
LevelsetSegmentationNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Default constructor.
LevelsetSolveNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements a level set solver which may optionally perserve the topology using non PDE optimization.
LevelsetSolveNonPDE(MTBGenericEnergyNonPDE, MTBLevelsetMembership, int, int, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Constructor.
LevelsetSolveNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Constructor
LevelsetSolver - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Generic super class for level set solvers.
LevelsetSolver() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Default constructor.
LevelsetSolverDerivatives - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Level set solver using variational calculus.
LevelsetSolverDerivatives() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Default constructor.
LevelsetSolverPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
Solver for level set segmentation problems based on PDEs.
LevelsetSolverPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Default constructor.
LevelsetSolverPDE.VelocityExpansionMode - Enum in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver
Available modes for expanding zero level velocities.
LinearFilter - Class in de.unihalle.informatik.MiToBo.filters.linear
Generic linear filter operation class
LinearFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Empty constructor
LinearFilter(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Constructor
LinearFilter(MTBImage, MTBImage, int[], boolean, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Constructor
LinearTransformGaussNoise - Class in de.unihalle.informatik.MiToBo.math
A linear transform with additive Gaussian noise.
LinearTransformGaussNoise(Matrix, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
LinkAdjacentComponents(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function for linking adjacent components/regions in a binary image.
LinkAdjacentPixels(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Function for linking adjacent pixels in a binary image.
llimits - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
LocallyAdaptiveContrastEnhancement - Class in de.unihalle.informatik.MiToBo.enhance
This class implements contrast enhancement for microscopy images.
LocallyAdaptiveContrastEnhancement() - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Default constructor.
LocallyAdaptiveContrastEnhancement(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Constructor with given image.
LocallyAdaptiveContrastEnhancement(MTBImage, double, int) - Constructor for class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Constructor with given image and parameters.
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
log_p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
log_p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
log_p - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
log_p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
log_p(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.LogEvaluatableDistribution
Evaluate natural logarithm of p(X) at location x. log(P(X=x))
log_p(T, int) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.LogIndependentlyEvaluatableDistribution
Evaluate log(p_i(X)) at x_i
log_p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
log_p(AbstractMultiState<S>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state j in X
log_p(AbstractMultiState<S>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state i in X
log_p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
 
log_p(DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
This method is here only valid for the latest DataAssociation sampled with drawSample().
log_p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
log_p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
log_p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
log_p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
log_p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
log_p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
log_pzc - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
storage for the log likelihood values of the observations for possible associations to avoid recomputation
logarithmize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
calculate the logarithmic (base e) histogram; entries smaller than one become zero!
logBinom - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Binomial distribution of number of observations associated to existing targets
LogEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for distributions that can be evaluated for each realization x of its random variable X.
logFac - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
An object to compute and store log(n!)
logfactor - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
log of the normalization factor
LogFaculty - Class in de.unihalle.informatik.MiToBo.math
Class to compute the logarithm of the faculty of an integer n.
LogFaculty(int) - Constructor for class de.unihalle.informatik.MiToBo.math.LogFaculty
Constructor to precompute log(0!)
LogIndependentlyEvaluatableDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities p(X) with independent variables in X, that can be evaluated (natural logarithm) for each element in the realization x of its random variable X.
logMuValues - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) values of mu to avoid recomputation
logNuValues - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) values of nu to avoid recomputation
logp(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
logP_C - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) probability of the current set of association variables given observations and previous associations
logP_MN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
(log) propability of M observations given N existing targets and the current model configuration
logPofRegion(MTBRegion2D, MTBImage, MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
LogProbabilityDensityFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for multivariate distributions that allow evaluation of the natural logarithm of their probability density function.
LogProbabilityMassFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for univariate distributions based on log-probability mass functions
logSumP(double, double) - Static method in class de.unihalle.informatik.MiToBo.math.MathX
Natural logarithm of the sum of two values P1 and P2 when only their natural logarithms log(P1) and log(P2) are given.

M

M - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
number of observations
m_currentC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
current c-coordinate, for 3D only access functions
m_currentSliceIdx - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Index of the current slice.
m_currentT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
current t-coordinate, for 3D only access functions
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
image data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
image data
m_dataB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the ImagePlus pixel data (blue channel)
m_dataG - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the ImagePlus pixel data (green channel)
m_dataR - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the ImagePlus pixel data (red channel)
m_img - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
the underlying ImagePlus object
m_imgStack - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
reference to the ImageStack object of the underlying ImagePlus object
m_impulator - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
source image on which the window is applied
m_level - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Tree level (level identifier).
M_max - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Maximum number of observations in the time series
m_padMode - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
padding mode for nonexistent values (outside the underlying image), see static finals
m_posC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current c-position of the window in the source image
m_posT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current t-position of the window in the source image
m_posX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current x-position of the window in the source image
m_posY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current y-position of the window in the source image
m_posZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
current z-position of the window in the source image
m_reg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
2D region object.
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of c-dimension
m_sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in c-dimension
m_sizeStack - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
stacksize
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of t-dimension
m_sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in t-dimension
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of x-dimension
m_sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in x-dimension
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of y-dimension
m_sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in y-dimension
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
size of z-dimension
m_sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
size of the window in z-dimension
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
slice labels
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
slice labels
m_sliceLabels - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
slice labels
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Vector of installed StatusListener objects.
m_title - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
image title
m_type - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
MiToBo image type
mahalanobis(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
main(String[]) - Static method in class cmdTools.cellAnalysis.ParticleDetector2D
 
main(String[]) - Static method in class cmdTools.mtb_imagetools.ImageConvert
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.EvalTracks
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.ObservationSeriesGenerator
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
 
main(String[]) - Static method in class cmdTools.tracking.multitarget.RBMCDATracker
 
main(String[]) - Static method in class cmdTools.visualization.DisplayImage
 
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4
Test
main(String[]) - Static method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8
Test
makePolySimple(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Simplifies the given polygon.
makeReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
makeReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
makeReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
makeReport() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
makeSimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Makes the polygon simple, i.e. removes self-overlaps.
makeSimple() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
mapHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Height of class map.
mapIndexToValue(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
mapMaxX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal x coordinate of class map.
mapMaxY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal y coordinate of class map.
mapMinX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal x coordinate of class map.
mapMinY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal y coordinate of class map.
mapWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Width of class map.
markov - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Markov matrix probability of dynamic model switching: A matrix with size (#dynamicmodels x #dynamicmodels).
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Directory with (cell) masks.
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Directory with (cell) masks.
maskDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Directory with (cell) masks.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Format of provided cell masks.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Format of provided cell masks.
maskFormat - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Format of provided cell masks.
MatchingAdjacencyMatrix - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts
Abstract class of an adjacency matrix for graph matching, i.e. graph nodes are associated to different partitions.
MatchingAdjacencyMatrix() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.MatchingAdjacencyMatrix
 
MatchingBipartite - Class in de.unihalle.informatik.MiToBo.math.optimization
Base class for bipartite matching algorithms.
MatchingBipartite() - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Default constructor.
MatchingBipartite_HungarianAlgorithm - Class in de.unihalle.informatik.MiToBo.math.optimization
Bipartite matching with Hungarian algorithm.
MatchingBipartite_HungarianAlgorithm() - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Default constructor.
MatchingBipartite_HungarianAlgorithm(double[][], MatchingBipartite_HungarianAlgorithm.ScoreInterpretation) - Constructor for class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Default constructor with parameters.
MatchingBipartite_HungarianAlgorithm.ScoreInterpretation - Enum in de.unihalle.informatik.MiToBo.math.optimization
Matrix scores interpretation.
MathHelper - Class in de.unihalle.informatik.MiToBo.apps.xylem
 
MathX - Class in de.unihalle.informatik.MiToBo.math
Math class with functions that are not provided by Java's Math class.
MathX() - Constructor for class de.unihalle.informatik.MiToBo.math.MathX
 
matrixScore - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Score interpretation.
matrixSize - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Number of rows and columns, respectively.
max(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Pixelwise maximum
max(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Pixelwise maximum
MAX_ALLOWED_NUM_PHASES - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Maximal number of phases which may be represented including background phase.
MAX_VALUE - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constant used in SDF calculations.
maxAngle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Maximal orientation where to end.
maxAssociatedTargetID() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
maxAssociatedTargetID() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the maximum target id associated by this data association object
maxDistNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
maxDistNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Maximum distance of neighboring observations
maxEnergyVal - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Maxmimum value of energy, dependent on number of snakes and rho.
maxExpansion - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Maximum expansion by Voronoi dilation.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
maxLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Maximal label appearing in the label list.
maxLabel - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Maximal label appearing in the label list.
maxLevels - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Maximum number of levels to perform.
maxNumNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
maxNumNeighbors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Maximum number of neighboring observations
maxTargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
maxTargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
The maximum target ID that occurred in this sample up to the current time step
maxWeight - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
maxWeights - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
maxWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Expected width of thick vessels.
mean - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
mean vector
mean - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
mean - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Average vector of input dataset.
mean - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
MeanFilter - Class in de.unihalle.informatik.MiToBo.filters.linear
Multidimensional mean filter
MeanFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor with default parameters sizeX=1, sizeY=1, sizeZ=0, sizeT=0, sizeC=0, kernelTruncation=3, sizeInterpretation=PHYSICALSIZE.
MeanFilter(MTBImage, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor for mean filtering in x- and y-dimension.
MeanFilter(MTBImage, Integer, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor for mean filtering in x-, y- and z-dimension.
MeanFilter(MTBImage, Integer, Integer, Integer, Integer, Integer, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Constructor for mean filtering.
meanFilter() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
compute the mean filter
meanFilterSize - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Size of mean filter for Gaussian derivative image.
meanfreeData - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Normalized, i.e., mean-free, dataset.
meanfreeDataMatrix - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Normalized, i.e., mean-free, data matrix.
meaningfulNodes(MTBTreeNode, MTBImage[], MTBImageHistogram[], int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get the most meaningful regions from a (sub)tree.
meanOfRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
means - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Average intensities.
means - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Average intensities.
means_compl - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Average intensities of non-regions.
meanX - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
MedialnessMultiScaleFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
2D multi-scale medialness filter for vessel segmentation.
MedialnessMultiScaleFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Standard constructor.
MedialnessMultiScaleFilter2D(MTBImage, Integer, Double, Double, Double, MedialnessMultiScaleFilter2D.FilterMode, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Constructor to create a new 2D multi-scale medialness filter.
MedialnessMultiScaleFilter2D.FilterMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness
Settings.
MFFDOGFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
MF-FDOG filter for vessel segmentation.
MFFDOGFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Default constructor.
MFFDOGFilter2D.VesselMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness
Detection scenario mode.
MFFDOGMultiScaleFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
MF-FDOG multi-scale filter for vessel segmentation.
MFFDOGMultiScaleFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Default constructor.
Mica2D - Class in de.unihalle.informatik.MiToBo.apps.cells2D
Operator for integrated cell image analysis.
Mica2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Default constructor.
Mica2D(MTBImage, int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Default constructor.
Mica2DTableModel - Class in de.unihalle.informatik.MiToBo.apps.cells2D
Implementation of a TableModel for the Granule Detector result table.
MigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
Operator for analyzing the movement pattern of cells as well as changes in morphology and fluorescence intensity
MigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
MigrationAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
MigrationAnalyzer(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
min(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Pixelwise minimum
min(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Pixelwise minimum
minAngle - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Minimal orientation from where to start.
minAreaGrowth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Lower threshold for region growth.
minIntensityVariance - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Minimum admissible variance in new snake interior fractions..
minMN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Minimum of number of observations and number of targets
minSeedSize - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
minWidth - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Expected width of thin vessels.
MiToBo_Runner - Class in mitoboRunner
ImageJ plugin to start the Swing-based Alida/Mitobo operator runner.
MiToBo_Runner() - Constructor for class mitoboRunner.MiToBo_Runner
 
mitoboRunner - package mitoboRunner
 
MixtureDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A distribution represented by a mixture of distributions
MixtureDistribution(ProbabilityDensityFunction[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
MixtureDistribution(ProbabilityDensityFunction[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
Constructor
mmID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
motion-model-ID
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Mode for detecting vessels.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Scenario for detecting vessels.
mode - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Scenario for detecting vessels, i.e. relation of foreground to background.
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
MotionModelID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A target-ID class that additionally hold a "motion model"-ID.
MotionModelID(short, byte) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
Constructor.
MotionModelID(MTBXMLMotionModelIDType) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
Constructor with the corresponding XML-Type.
MPH_EXTENSION - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Default extension of MiToBo processing history file.
MPMFFilter2D - Class in de.unihalle.informatik.MiToBo.filters.vesselness
Multiscale Production of the Matched Filter (MPMF) implementation.
MPMFFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Default constructor.
MPMFFilter2D.VesselMode - Enum in de.unihalle.informatik.MiToBo.filters.vesselness
Detection scenario mode.
mtb_io - package mtb_io
Provides plugins for MiToBo image I/O.
mtb_segmentation - package mtb_segmentation
Provides plugins for image segmentation in general.
MTBActiveContourEnergy - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for active contour energies.
MTBActiveContourEnergy_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
Active contour energy implementing Chan-Vese region fitting.
MTBActiveContourEnergy_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Default constructor.
MTBActiveContourEnergy_CVRegionFit(MTBImage, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Default constructor with arguments.
MTBActiveContourEnergy_MeanSep - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
Active contour energy based on region mean separation.
MTBActiveContourEnergy_MeanSep() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Default constructor.
MTBActiveContourEnergy_MeanSep(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Default constructor with parameter.
MTBActiveContourEnergyComputable - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for active contour energies used in non-PDE contexts.
MTBActiveContourEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for active contour energies used in PDE contexts.
MTBActiveContourException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
MiToBo exception thrown in context of segmentation with active contours.
MTBActiveContourException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException
Default constructor.
MTBActiveContourException.ExceptionType - Enum in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
Possible exception types.
MTBAwtPoint2DDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio
Data I/O class for Point2D.Double.
MTBAwtPoint2DDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
MTBBorder2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Datatype to represent borders of components.
MTBBorder2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Standard constructor.
MTBBorder2D(Vector<Point2D.Double>, MTBBorder2D.BorderConnectivity) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Constructor to create an 2D border object from a 2D point vector.
MTBBorder2D.BorderConnectivity - Enum in de.unihalle.informatik.MiToBo.core.datatypes
Kind of neighborhood to be applied to border pixels.
MTBBorder2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 2D borders.
MTBBorder2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Standard constructor.
MTBBorder2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Construct an empty set of borders with given extent of domain.
MTBBorder2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBBorder2DSet in the ImageJ ROI-Manager.
MTBBorder2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Constructor of super class.
MTBBorder2DSetROI(MTBBorder2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBBorder2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBBorder2DSet.
MTBChooseOpNameFrame - Class in de.unihalle.informatik.MiToBo.core.gui
Main window for selecting MiToBo annotated operators for running.
MTBChooseOpNameFrame() - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
Constructor.
MTBConstants - Class in de.unihalle.informatik.MiToBo.core.datatypes.defines
Constants globally defined for MiToBo.
MTBConstants() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.defines.MTBConstants
 
MTBContour2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to create 2D contour objects with a vector of points, belonging to the contour.
MTBContour2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Standard constructor.
MTBContour2D(Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Constructor to create an 2D contour object from a 2D point vector.
MTBContour2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 2D contours living in a common domain which is a rectangular subset of R x R.
MTBContour2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Standard constructor.
MTBContour2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Construct an empty set of contours with given extent of domain.
MTBContour2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBContour2DSet in the ImageJ ROI-Manager.
MTBContour2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Constructor of super class.
MTBContour2DSetROI(MTBContour2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBContour2DSet.
MTBCVFittingEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
A class to implement the fitting term of the Chan-Vese energy for level sets using a non PDE approach to optimization.
MTBCVFittingEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Construct an energy object for the level set function phi realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Construct an energy object realizing the fitting term of the Chan-Vese energy.
MTBCVFittingEnergyNonPDE(MTBImage, MTBLevelsetMembership, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Construct an energy object with the initial level set function phi realizing the fitting term of the Chan-Vese energy to segment img.
MTBDataIOFile - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
DataIO provider (for commandline-OpRunner) for classes that can only be read from and written to file.
MTBDataIOFile() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
MTBDataIOFile.MTBDataIOFileButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
 
MTBDataIOFile.MTBDataIOFileButton(Class<?>, Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile.MTBDataIOFileButton
 
MTBDataIOFileSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Data I/O provider for GUI-OpRunner supporting MiToBo container classes Provides data I/O for the following classes:
MTBRegion2DSetBag
MTBRegion2DSet
MTBRegion3DSet
MTBPolygon2DSet
MTBContour2DSet
MTBBorder2DSet
Note that some of the classes allow for interaction with the ROI manager of ImageJ, i.e. the class MTBPolygon2DSet.
MTBDataIOFileSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
MTBDataIOFileSwing.InputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Input mode for data.
MTBDataIOFileSwing.OutputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Output mode for data.
MTBDataIOFileXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
DataIO provider for xmlbeans for classes that can only be read from and written to file.
MTBDataIOFileXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
MTBDatatypeException - Exception in de.unihalle.informatik.MiToBo.core.exceptions
MiToBo exception type related to problems with data types in general.
MTBDatatypeException(MTBDatatypeException.DatatypeExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException
Default constructor.
MTBDatatypeException.DatatypeExceptionType - Enum in de.unihalle.informatik.MiToBo.core.exceptions
Possible exception types.
MTBDoubleData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper
A double to be used as input or output for MTB operators.
MTBDoubleData(Double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
Construct an empty double data object from the given double value.
MTBEnergySumNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
 
MTBEnergySumNonPDE(String, Vector<MTBGenericEnergyNonPDE>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
Construct an energy object for a level set function realizing the sum of energies in the vector energies.
MTBEnergySumNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
Construct an energy object for a level set function realizing the sum of energies.
MTBEnvironmentConfig - Class in de.unihalle.informatik.MiToBo.core.helpers
This class extends the super class with routines to access ImageJ properties.
MTBEnvironmentConfig() - Constructor for class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
 
MTBException - Exception in de.unihalle.informatik.MiToBo.core.exceptions
MiToBo specific exception type.
MTBException() - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBException
 
MTBGammaFixed - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class for gamma adaptation with a fixed decreasing factor for all gamma values.
MTBGammaFixed() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Default constructor.
MTBGammaFixed(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Constructor with fixed decreasing factor for adaptation.
MTBGammaNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class which is not changing the gamma values.
MTBGammaNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
Standard constructor.
MTBGammaPtWiseExtEner - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class for gamma adaptation depending on the external energy values for each snake control point.
MTBGammaPtWiseExtEner() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
Standardconstructor
MTBGammaUpdate - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize
Class for adaptive step size calculation of the snake step size gamma.
MTBGammaUpdate() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
 
MTBGenericEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
The base class for energies intended for a nonPDE level set approach.
MTBGenericEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
 
MTBGraph - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements an (un-) directed MTBGraph.
MTBGraph() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Standard constructor.
MTBGraph(boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Constructor to create an empty undirected or directed MTBGraph.
MTBGraph(Vector<MTBGraphNode<?>>, Vector<MTBGraphEdge>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Constructor to create an undirected or directed MTBGraph with the given nodes and edges.
MTBGraphEdge - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements MTBGraphEdges for the MTBGraph.
MTBGraphEdge(MTBGraphNode<?>, MTBGraphNode<?>, Vector<?>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Constructor to create a new MTBGraphEdge.
MTBGraphEdge(MTBGraphNode<?>, MTBGraphNode<?>, Vector<?>, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Constructor to create a new MTBGraphEdge.
MTBGraphNode<T> - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements MTBGraphNodes for the MTBGraph.
MTBGraphNode(T) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Constructor to create a new MTBGraphNode object.
MTBGrappaFrame - Class in de.unihalle.informatik.MiToBo.core.grappa
Main frame of Grappa graphical editor for MiToBo.
MTBGrappaFrame(Collection<ALDOperatorLocation>, Collection<ALDOperatorLocation>) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaFrame
Default constructor
MTBGrappaWorkbench - Class in de.unihalle.informatik.MiToBo.core.grappa
Main frame of Grappa in MiToBo context.
MTBGrappaWorkbench(MTBGrappaFrame) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
Default constructor
MTBGrappaWorkbenchTab - Class in de.unihalle.informatik.MiToBo.core.grappa
Grappa workflow graph.
MTBGrappaWorkbenchTab(MTBGrappaWorkbench, ALDGrappaWorkbenchGraph) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
Default constructor
MTBGrappaWorkbenchTab(ALDGrappaWorkbench, mxGraph, ALDWorkflow) - Constructor for class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
Constructor to setup tab from given (reloaded) workflow.
MTBIcon - Class in de.unihalle.informatik.MiToBo.core.helpers
Singleton class to provide access to MiToBo icon in graphical environments.
MTBIcon() - Constructor for class de.unihalle.informatik.MiToBo.core.helpers.MTBIcon
Default constructor.
MTBImage - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Abstract wrapper class for easy access to hyperstacks.
MTBImage(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Constructor.
MTBImage() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Constructor for initializing an empty image (dimension sizes = -1).
MTBImage.FactoryMethod - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images
methods to create new image from an existing one. used in MTBImageFactory
MTBImage.MTBImageFactory - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
A class for creating MTBImages which implements the MTBOperator.
MTBImage.MTBImageFactory() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
MTBImage.MTBImageFactory(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Duplicate constructor
MTBImage.MTBImageFactory(MTBImage, MTBImage.MTBImageType, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Convert constructor
MTBImage.MTBImageFactory(MTBImage, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Get slice constructor
MTBImage.MTBImageFactory(MTBImage, int, int, int, int, int, int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
Create a new image from the specified image part
MTBImage.MTBImageType - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images
MiToBo image types
MTBImageArithmetics - Class in de.unihalle.informatik.MiToBo.math.images
This class that provides convenience functions for the ImageArithmetics class.
MTBImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Constructor.
MTBImageArithmetics(MTBOperator) - Constructor for class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Constructor with calling operator.
MTBImageByte - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Wrapper class for easy access to Byte (hyper)stacks.
MTBImageByte(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Constructor
MTBImageByte(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Constructor
MTBImageByte(byte[][], int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Constructor
MTBImageConverter - Class in de.unihalle.informatik.MiToBo.core.dataconverter
Convert a MTBImage to any other image and any image type to a MTBImage.
MTBImageConverter() - Constructor for class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
MTBImageDataIO - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Implementation of ALDDataIOCmdline interface for MitoBo images.
MTBImageDataIO() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
 
MTBImageDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Implementation of ALDDataIOCmdline interface for MitoBo images.
MTBImageDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Default constructor.
MTBImageDataIOSwing.ImageShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Button to display an image on demand.
MTBImageDataIOSwing.ImageShowButton(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
Constructor.
MTBImageDataIOSwing.ImageShowPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel containing the button to display an image on demand.
MTBImageDataIOSwing.ImageShowPanel(MTBImageDataIOSwing.ImageShowButton, String) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowPanel
Constructor.
MTBImageDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Implementation of ALDDataIOCmdline interface for MitoBo images via xmlbeans provider.
MTBImageDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
 
MTBImageDouble - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for easy access to Double (hyper)stacks.
MTBImageDouble(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Constructor
MTBImageException - Exception in de.unihalle.informatik.MiToBo.core.exceptions
MiToBo exception type related to problems with its image data types.
MTBImageException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
Default constructor.
MTBImageFloat - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Wrapper class for easy access to Float (hyper)stacks.
MTBImageFloat(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Constructor
MTBImageFloat(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Constructor
MTBImageHistogram - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class for generating intensity histograms of objects from class MTBImage.
MTBImageHistogram(MTBImage, int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a histogram for the given input image
with specification of binning and value range
all MTBImage types except RGB type are supported
MTBImageHistogram(MTBImage, MTBImage, int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a histogram for the given input image only for the pixels specified by a binary mask
all MTBImage types except RGB type are supported
with specification of binning and value range
MTBImageHistogram(MTBImage, MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a new MTBHistogram object from the given MTBImage
the histogram ranges from the smallest image value to the largest image value
MTBImageHistogram(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a new MTBHistogram object from the given MTBImage
the histogram ranges from the smallest image value to the largest image value
MTBImageHistogram(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
construct a new MTBHistogram object from the given MTBImage
number of bins is 256 and the histogram ranges from the smallest
image value to the largest image value
MTBImageHistogram(double[], int, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
Construct new histogram from array of values.
MTBImageInt - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for easy access to Int (hyper)stacks.
MTBImageInt(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Constructor
MTBImageManipulator - Interface in de.unihalle.informatik.MiToBo.core.datatypes.images
 
MTBImageRGB - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for easy access to RGB (hyper)stacks.
MTBImageRGB(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Constructor
MTBImageRGB(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Constructor
MTBImageSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
A set of MTBImages stored in a vector.
MTBImageSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
MTBImageSet(MTBImage[]) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
MTBImageShort - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Wrapper class for easy access to Short (hyper)stacks.
MTBImageShort(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Constructor
MTBImageShort(int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Constructor
MTBImageTileAdapter - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Adapter class to support tile-wise processing of images.
MTBImageTileAdapter(MTBImage, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Default constructor.
MTBImageTileAdapter(MTBImage, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Default constructor.
MTBImageTileAdapter.TileIterator - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Iterates from top-left to bottom-right over the tiles of an image.
MTBImageTileAdapter.TileIterator(MTBImageTileAdapter) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
Default constructor.
MTBImageWindow - Class in de.unihalle.informatik.MiToBo.core.datatypes.images
Class for windowing a MTBImage.
MTBImageWindow(int, int, int, int, int, MTBImageManipulator, MTBImageWindow.BoundaryPadding) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Create a new window on a given source MTBImageManipulator (i.e.
MTBImageWindow.BoundaryPadding - Enum in de.unihalle.informatik.MiToBo.core.datatypes.images
Padding of image: Method of how to obtain pixel values outside the image domain
MTBIntegerData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper
an Integer wrapper class to be used as input or output for MTB operators
MTBIntegerData(Integer) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
MTBIteratorImageData - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBIteratorImageData() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
MTBIteratorImageData.MTBImageIteratorImageDataPanel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
GUI element class for image batch iterator.
MTBIteratorImageData.MTBImageIteratorImageDataPanel(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Default constructor.
MTBJFreeChartDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Implementation of ALDDataIOSwing interface for JFreeChart objects.
MTBJFreeChartDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
Default constructor.
MTBJFreeChartDataIOSwing.ChartShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Button to display a chart on demand.
MTBJFreeChartDataIOSwing.ChartShowButton(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
Constructor.
MTBJFreeChartDataIOSwing.ChartShowPanel - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Panel containing the button to display an image on demand.
MTBJFreeChartDataIOSwing.ChartShowPanel(MTBJFreeChartDataIOSwing.ChartShowButton, String) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowPanel
Constructor.
MTBLengthEnergyFW2D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 2D images and a two phase level set function.
MTBLengthEnergyFW2D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
Constructor
MTBLengthEnergyFW2D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
Constructor
MTBLengthEnergyFW2DMPNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 2D images and a multi phase leve lset function.
MTBLengthEnergyFW2DMPNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
constructor
MTBLengthEnergyFW2DMPNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
constructor
MTBLengthEnergyFW2DNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 2D images.
MTBLengthEnergyFW2DNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
constructor
MTBLengthEnergyFW2DNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DNonPDE
constructor
MTBLengthEnergyFW3D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 3D images and a two phase levelset function.
MTBLengthEnergyFW3D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
constructor
MTBLengthEnergyFW3D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
constructor
MTBLengthEnergyFW3DMPNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 3D images and a multi phase level set function.
MTBLengthEnergyFW3DMPNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE
constructor
MTBLengthEnergyFW3DMPNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DMPNonPDE
constructor
MTBLengthEnergyFW3DNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using forward differences for 3D images.
MTBLengthEnergyFW3DNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
constructor
MTBLengthEnergyFW3DNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3DNonPDE
constructor
MTBLengthEnergyFWNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Base class of length energies using forward differences.
MTBLengthEnergyFWNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
constructor
MTBLengthEnergyFWNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFWNonPDE
constructor
MTBLengthEnergyKB2D2P4NNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using length approximation due to Kolmogorov/Boykov for tw0 phases and 4 neighborhood.
MTBLengthEnergyKB2D2P4NNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE
constructor
MTBLengthEnergyKB2D2P4NNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2P4NNonPDE
constructor
MTBLengthEnergyKB2D2PNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Implements the (standard) length energy using length approximation due to Kolmogorov/Boykov for two phases.
MTBLengthEnergyKB2D2PNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
constructor
MTBLengthEnergyKB2D2PNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
constructor
MTBLengthEnergyKBNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Base class of length energies using forward differences.
MTBLengthEnergyKBNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
constructor
MTBLengthEnergyKBNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKBNonPDE
constructor
MTBLengthEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
An class for energies for a nonPDF level set approach based on different length energies of the phases boundaries.
MTBLengthEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Constructor
MTBLengthEnergyNonPDE(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Constructor
MTBLevelEnergyDerivable_Area - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Level set energy minimizing area enclosed by the zero level.
MTBLevelEnergyDerivable_Area() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
Default constructor.
MTBLevelEnergyDerivable_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Implementation of Chan-Vese energy for level set functions.
MTBLevelEnergyDerivable_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
Default constructor.
MTBLevelEnergyDerivable_CVRegionFit(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
Constructor with given image.
MTBLevelEnergyDerivable_Length - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Energy minimizing the length of a level set's isocontour.
MTBLevelEnergyDerivable_Length() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
Default constructor.
MTBLevelsetEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable
Interface specifying level set energies to be used with techniques of the calculus of variations.
MTBLevelsetException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
MiToBo exception thrown inside snake segmentation framework.
MTBLevelsetException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBLevelsetException
Default constructor.
MTBLevelsetFunctionDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Level set function supporting optimization based on variational calculus.
MTBLevelsetFunctionDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
 
MTBLevelsetFunctionPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
Class representing a 3-dimensional level set function.
MTBLevelsetFunctionPDE(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Create a new levelset function.
MTBLevelsetFunctionPDE(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constructor to init empty function with safety border.
MTBLevelsetFunctionPDE(int, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(boolean, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(boolean, int, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
create a new levelsetfunction, setting a default handle for derivations on borders
MTBLevelsetFunctionPDE(int, int, int, MTBSegmentationInterface, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constructor to build a level set function from a segmentation object.
MTBLevelsetFunctionPDE(int, int, int, MTBSegmentationInterface, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Constructor to build a level set function from a segmentation object.
MTBLevelsetFunctionPDE.SortedList<EType> - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
A genric class representing a sorted list
MTBLevelsetFunctionPDE.SortedList() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
create empty SortetList
MTBLevelsetFunctionPDE.SortedListElement<EType> - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes
internal representation of elements
MTBLevelsetFunctionPDE.SortedListElement(EType, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
MTBLevelsetMembership - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
A class to hold a level set function where only the memership to a phase is required and represented.
MTBLevelsetMembership(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructs a two phase level set function which is initialiazed with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int, int, int, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructs a two phase level set function which is initialiazed with a circle or sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
MTBLevelsetMembership(int, int, int, MTBImage, int, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a two phase level set function from an image via thresholding.
MTBLevelsetMembership(MTBLevelsetMembership) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Creates a copy of phi.
MTBLevelsetMembership(int, int, Vector<MTBRegion2D>, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for given size which is initialized from a list of 2D regions for a 2D level set function.
MTBLevelsetMembership(int, int, MTBRegion2DSet, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for given size which is initialized from a MTBRegion2DSet for a 2D level set function.
MTBLevelsetMembership(MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for a two phase level set function from a label image.
MTBLevelsetMembership(MTBImage, MTBImage, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Constructor for a level set function from a label image.
MTBLineSegment2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Enhanced 2D line segments.
MTBLineSegment2D(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Constructor.
MTBMeijeringFittingEnergyNonPDE - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
class that implements the energy functional introduced in O.
MTBMeijeringFittingEnergyNonPDE() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
constructor
MTBMeijeringFittingEnergyNonPDE(MTBImage, MTBLevelsetMembership) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
constructor
MTBNeurite2D - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
Class for neurite objects.
MTBNeurite2D(MTBNeuriteSkelGraph, Vector<Vector<Point2D.Double>>, Vector<Vector<Line2D.Double>>, MTBRegion2D, int, int[], Vector<Vector<Double>>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Constructor to generate a new neurite object.
MTBNeurite2DProfile - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
Container class for storing neurite profile data and associated additional information for a single neurite region.
MTBNeurite2DProfile() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
MTBNeurite2DProfile(MTBNeurite2D, double[], Vector<Vector<Point2D.Double>>, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Constructor to create a new MTBNeuriteProfile object from the given MTBRegion2D.
MTBNeurite2DProfileSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
A set of neurite profiles organized as linked list.
MTBNeurite2DProfileSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Constructor to create a new set of neurite profiles.
MTBNeurite2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes.neurites
Class to represent a set of MTBNeurite2D objects.
MTBNeurite2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Constructor to create a new set of neurites.
MTBNeuriteSkelGraph - Class in de.unihalle.informatik.MiToBo.core.datatypes
The class implements a neurite skeleton graph (NSG), based on the skeleton of a neurite region.
MTBNeuriteSkelGraph() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Standard constructor.
MTBNeuriteSkelGraph(int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Constructor that creates an empty directed MTBNeuriteSkelGraph with defined maximum spine length.
MTBNeuriteSkelGraph(Vector<MTBNeuriteSkelGraphNode<Point2D.Double>>, Vector<MTBGraphEdge>, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Constructor to create an directed MTBNeuriteSkelGraph with the given MTBSkeletonGraphNodes and MTBGraphEdges.
MTBNeuriteSkelGraphException - Exception in de.unihalle.informatik.MiToBo.core.datatypes
Exception handling for MTBSkeletonGraph.
MTBNeuriteSkelGraphException() - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
MTBNeuriteSkelGraphException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
MTBNeuriteSkelGraphNode<T> - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class implements a MTBSkeletonGraphNode, which is a type of the MTBGraphNode.
MTBNeuriteSkelGraphNode(T, MTBNeuriteSkelGraphNode.MTBSkeletonNodeType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
Constructor to create a new MTBGraphNode object.
MTBNeuriteSkelGraphNode.MTBSkeletonNodeType - Enum in de.unihalle.informatik.MiToBo.core.datatypes
Type of the MTBGraphNode
MTBOperator - Class in de.unihalle.informatik.MiToBo.core.operator
Abstract super class for all MiToBo operators.
MTBOperator() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
Default constructor.
MTBOperatorConfigurationFrame - Class in de.unihalle.informatik.MiToBo.core.gui
Frame to configure.
MTBOperatorConfigurationFrame(ALDOperator) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
Constructs a control frame for an operator object.
MTBOperatorControlFrame - Class in de.unihalle.informatik.MiToBo.core.gui
This frame is used to display and modify the input parameters of an ALDOperator.
MTBOperatorControlFrame(ALDOperator, ALDOperatorGUIExecutionProxy) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
Construct a JFrame to intantiate and configure an operator opName and use executeOperator to execute this operator if requested by the user.
MTBOperatorControllable - Class in de.unihalle.informatik.MiToBo.core.operator
Operator class with inherent event handling for execution control.
MTBOperatorControllable() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorControllable
Default constructor.
MTBOperatorGUIExecutionProxy - Class in de.unihalle.informatik.MiToBo.core.gui
Manager for executing single MiToBo operator and workflow objects via GUI.
MTBOperatorGUIExecutionProxy(ALDOperatorLocation) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorGUIExecutionProxy
Default constructor.
MTBOperatorParameterPanel - Class in de.unihalle.informatik.MiToBo.core.gui
Implementation of panels for MiToBo operator parameters.
MTBOperatorParameterPanel(ALDOperator, Parameter.ExpertMode, boolean, ALDSwingValueChangeListener) - Constructor for class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorParameterPanel
Default constructor.
MTBPlotHistogram - Class in de.unihalle.informatik.MiToBo.visualization.drawing
A class to visualize 2D polygons.
MTBPlotHistogram() - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
Default constructor.
MTBPlotHistogram.HistogramFrame - Class in de.unihalle.informatik.MiToBo.visualization.drawing
 
MTBPlotHistogram.HistogramFrame(double[]) - Constructor for class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram.HistogramFrame
 
MTBPoint3D - Class in de.unihalle.informatik.MiToBo.core.datatypes
The Point3D class defines a point representing a location in (x, y, z) coordinate space.
MTBPoint3D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Standardconstructor to create an new empty 3D point object.
MTBPoint3D(double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Construct a new 3D point with the given coordinates.
MTBPoint3D(MTBPoint3D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Construct a new 3D point from the given 3D point.
MTBPoint3D(MTBXMLPoint3DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Construct a new MTBPoint3D from a 3D-point object constructed from xml-representation.
MTBPolygon2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Polygon datatype with double precision.
MTBPolygon2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Default constructor.
MTBPolygon2D(double[], double[], boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Construct polygon from coordinate arrays.
MTBPolygon2D(Vector<Point2D.Double>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Construct from point list.
MTBPolygon2D_GeoPolygonsWrapper - Class in de.unihalle.informatik.MiToBo.core.datatypes
Wrapper class for C2DPolygon functions from GeoPolygons library.
MTBPolygon2D_GeoPolygonsWrapper() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
 
MTBPolygon2DException - Exception in de.unihalle.informatik.MiToBo.core.datatypes
Exception handling for Polygon2D object.
MTBPolygon2DException() - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Standardconstructor.
MTBPolygon2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Constructor for new MTBPolygon2DException with specific message output.
MTBPolygon2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
Data type to represent a set of MTBPolygon2D.
MTBPolygon2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Standard constructor
MTBPolygon2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Construct an empty set of polygons with given extent of domain.
MTBPolygon2DSet(Vector<MTBPolygon2D>, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Construct polygon set from given vector.
MTBPolygon2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBPolygon2DSet in the ImageJ ROI-Manager.
MTBPolygon2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Constructor of super class.
MTBPolygon2DSetROI(MTBPolygon2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBPolygon2DSet.
MTBPortHashAccess - Class in de.unihalle.informatik.MiToBo.core.operator
Interface to the port database of the Alida / MiToBo operator history.
MTBPortHashAccess() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Constructor without function.
MTBRegion2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to implement a 2D region object. the region is stored in a vector of 2D double points with its x- and y-coordinate.
MTBRegion2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct a new empty MTBRegion2D object.
MTBRegion2D(Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct a new MTBRegion2D from the given points.
MTBRegion2DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 2D regions living in a common domain which is a rectangular subset of R x R.
MTBRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Standard constructor.
MTBRegion2DSet(double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct an empty set of regions with given extent of domain
MTBRegion2DSet(Vector<MTBRegion2D>, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct an empty set of regions with given extent of domain
MTBRegion2DSet(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a set of regions from a xml-file that was written by the write method of this class.
MTBRegion2DSet(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a set of regions from a label image.
MTBRegion2DSet(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a set of regions from a label image.
MTBRegion2DSet(MTBXMLRegion2DSetType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct a new MTBRegion2DSet from a region set object that was constructed from a xml-representation.
MTBRegion2DSetBag - Class in de.unihalle.informatik.MiToBo.core.datatypes
A datatype to store multiple MTBRegion2D sets
MTBRegion2DSetBag() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Constructor to create an empty bag of region sets
MTBRegion2DSetBag(int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Constructor to create an empty bag of region sets with the given capacity
MTBRegion2DSetBag(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Construct a bag of region sets from a xml-file that was written by the write method of this class.
MTBRegion2DSetBag(MTBXMLRegion2DSetBagType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Construct a bag of region sets from a xml-object created by the toXMLType method of this class.
MTBRegion2DSetROI - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class to visualize and handle a MTBRegion2DSet in the ImageJ ROI-Manager.
MTBRegion2DSetROI(Roi) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Constructor of super class.
MTBRegion2DSetROI(MTBRegion2DSet, String) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Constructor to create a new Roi-Manager-Object, based on a MTBRegion2DSet.
MTBRegion3D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to create a 3D region object.
MTBRegion3D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D object.
MTBRegion3D(Vector<MTBPoint3D>) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D object from the given points.
MTBRegion3D(Vector<MTBPoint3D>, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D object from the given points and set its id
MTBRegion3D(MTBXMLRegion3DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Construct a new MTBRegion3D from a 3D-region in xml-representation.
MTBRegion3DSet - Class in de.unihalle.informatik.MiToBo.core.datatypes
A set of 3D regions living in a common domain which is a rectangular subset of R x R.
MTBRegion3DSet(double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an empty set of regions with given extent of domain
MTBRegion3DSet(int, double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an empty set (with memory allocated for N elements) of regions with given extent of domain
MTBRegion3DSet(Vector<MTBRegion3D>, double, double, double, double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an empty set of regions with given extent of domain
MTBRegion3DSet(MTBXMLRegion3DSetType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct set of 3D-regions from an xml-representation
MTBRegion3DSet(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct a set of 3D-regions from a xml-file that was written by the write method of this class.
MTBRegionInterface - Interface in de.unihalle.informatik.MiToBo.core.datatypes
Interface for regions in MiToBo to enable unified handling.
MTBRegionSetInterface - Interface in de.unihalle.informatik.MiToBo.core.datatypes
Interface for region sets in MiToBo to enable unified handling.
MTBSegmentation2D - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Class for representing 2D segmentations of image data.
MTBSegmentation2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Default constructor with empty segmentation.
MTBSegmentation2D(int, int, int, int[][], boolean[][], double[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Constructor.
MTBSegmentation2D(int, int, int, byte[][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Constructor.
MTBSegmentation3D - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Class for representing 3D segmentations of image data.
MTBSegmentation3D(int, int, int, int, int[][][], boolean[][][], double[][][]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Constructor.
MTBSegmentationInterface - Interface in de.unihalle.informatik.MiToBo.segmentation.basics
Interface for representing 2D and 3D segmentations of image data.
MTBSegmentationInterface.SegmentationDimension - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Segmentation dimension datatype.
MTBSet_ActiveContourEnergy - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for sets of active contour energies.
MTBSet_ActiveContourEnergyDataIOCmdline - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Class for loading/saving sets of PDE energies for command line interfaces.
MTBSet_ActiveContourEnergyDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
Default constructor
MTBSet_ActiveContourEnergyDataIOSwing - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Class for loading/saving sets of PDE energies in GUI contexts.
MTBSet_ActiveContourEnergyDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
MTBSet_ActiveContourEnergyDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Class for loading/saving sets of PDE energies for command line interfaces.
MTBSet_ActiveContourEnergyDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
MTBSet_LevelEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Container data type for derivable level set energies.
MTBSet_LevelEnergyDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Default contructor for empty set.
MTBSet_LevelEnergyDerivable(Vector<MTBLevelsetEnergyDerivable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Constructor for a given vector of energies.
MTBSet_LevelEnergyDerivable(Vector<MTBLevelsetEnergyDerivable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Constructor with energies and weights.
MTBSet_SnakeEnergyComputable - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Container data type for snake energies in nonPDE approaches.
MTBSet_SnakeEnergyComputable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Default contructor for empty set.
MTBSet_SnakeEnergyComputable(Vector<MTBSnakeEnergyComputable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Constructor for a given vector of energies.
MTBSet_SnakeEnergyComputable(Vector<MTBSnakeEnergyComputable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Constructor with energies and weights.
MTBSet_SnakeEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Container data type for snake energies in PDE approaches.
MTBSet_SnakeEnergyDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Default contructor for empty set.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Constructor for a given vector of energies.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Constructor with energies and weights.
MTBSetWeightedEnergy<T> - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Container data type for energies in PDE approaches.
MTBSetWeightedEnergy() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Default contructor for empty set.
MTBSetWeightedEnergy(Vector<T>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Constructor for a given vector of energies.
MTBSetWeightedEnergy(Vector<T>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Constructor with energies and weights.
MTBSnake - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Active Contour (Snake) datatype.
MTBSnake() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Standard constructor to create a new and empty snake object.
MTBSnake(Vector<MTBSnakePoint2D>, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Constructor to create a new Snake object.
MTBSnake(Vector<MTBSnakePoint2D>, boolean, double, boolean) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Constructor to create a new Snake object.
MTBSnakeEnergyCD_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Snake energy based on Chan-Vese region fitting.
MTBSnakeEnergyCD_CVRegionFit() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Default constructor.
MTBSnakeEnergyCD_CVRegionFit(MTBImage, double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Default constructor.
MTBSnakeEnergyCD_KassCurvature - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Curvature energy of the pioneering paper of Kass et al.
MTBSnakeEnergyCD_KassCurvature() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Default constructor.
MTBSnakeEnergyCD_KassCurvature(double, MTBSnakeEnergyCD_KassCurvature_ParamAdapt) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Constructor with dynamic parameter updater.
MTBSnakeEnergyCD_KassCurvature_ParamAdapt - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Parameter adaptation for Kass et al. curvature penalty.
MTBSnakeEnergyCD_KassCurvature_ParamAdapt() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
 
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Fixed value parameter adaptation for Kass et al. curvature energy.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Default constructor.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Construct a new updater for the internal energy using a fixed value.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Dummy parameter adaptation for Kass et al. curvature energy.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
Default constructor.
MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
Construct a new updater.
MTBSnakeEnergyCD_KassLength - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Internal length penalty energy of the pioneering paper of Kass et al.
MTBSnakeEnergyCD_KassLength() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Default constructor.
MTBSnakeEnergyCD_KassLength(double, MTBSnakeEnergyCD_KassLength_ParamAdapt) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Constructor with dynamic parameter updater.
MTBSnakeEnergyCD_KassLength_ParamAdapt - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Parameter adaptation for Kass et al. length penalty.
MTBSnakeEnergyCD_KassLength_ParamAdapt() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
 
MTBSnakeEnergyCD_KassLength_ParamAdaptFix - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Parameter adaptation for Kass et al. length penalty energy by fixed value.
MTBSnakeEnergyCD_KassLength_ParamAdaptFix() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Default constructor.
MTBSnakeEnergyCD_KassLength_ParamAdaptFix(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Construct a new updater for the internal energy using a fixed value.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt
Dummy parameter adaptation for Kass et al. length penalty energy.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
Default constructor.
MTBSnakeEnergyCD_KassLength_ParamAdaptNone(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
Construct a new updater.
MTBSnakeEnergyCD_OverlapPenalty - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Energy to avoid overlaps of snakes in joint optimization of multiple snakes.
MTBSnakeEnergyCD_OverlapPenalty() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Default constructor.
MTBSnakeEnergyCD_OverlapPenalty(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Default constructor.
MTBSnakeEnergyCDIB_Distance - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Class for external energy from a distance transform (distance map / field).
MTBSnakeEnergyCDIB_Distance() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
MTBSnakeEnergyCDIB_Distance(MTBImageByte, DistanceTransform.DistanceMetric, DistanceTransform.ForegroundColor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Constructor to create a new SnakeExternalEnergyDistance object.
MTBSnakeEnergyCDIB_Gradient - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
External snake energy based on local intensity gradients.
MTBSnakeEnergyCDIB_Gradient() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Constructor to create a new SnakeExternalEnergyGradient object.
MTBSnakeEnergyCDIB_Gradient(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Constructor to create a new SnakeExternalEnergyGradient object.
MTBSnakeEnergyCDIB_GVF2D - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Class for external energy of a GVF field energy vector.
MTBSnakeEnergyCDIB_GVF2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Default constructor.
MTBSnakeEnergyCDIB_GVF2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Constructor to create a new SnakeExternalEnergyGVF2D object.
MTBSnakeEnergyCDIB_Intensity - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
External snake energy based on image intensities.
MTBSnakeEnergyCDIB_Intensity() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Default constructor.
MTBSnakeEnergyCDIB_Intensity(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Constructor to create a new SnakeExternalEnergyIntensity object.
MTBSnakeEnergyCDImageBased - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Interface class for snake energies that are purely image-based.
MTBSnakeEnergyCDImageBased() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
MTBSnakeEnergyComputable - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Super class for all energies to be used with greedy snakes in MiToBo.
MTBSnakeEnergyCoupled - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Super class for energies working simultaneously on multiple snakes.
MTBSnakeEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Super class for all energies to be used with PDE snakes in MiToBo.
MTBSnakeException - Exception in de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions
MiToBo exception thrown inside snake segmentation framework.
MTBSnakeException(MTBActiveContourException.ExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBSnakeException
Default constructor.
MTBSnakePoint2D - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Class to implement 2D snake points with a special structure: (snake points means control points of the snake, on which the snake energy is calculated and optimized) - every snake point has an old index (position) within the snake, if the point does not exists before, the old index is set to -1 by default - every snake point has a Point2D.Double object for point coordinates
MTBSnakePoint2D() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Standard constructor to create a new SnakePoint2D
MTBSnakePoint2D(double, double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Constructor to create a new SnakePoint2D with x- and y-coordinates for the point.
MTBSnakePoint2D(Point2D.Double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Constructor to create a new SnakePoint2D from the specified Point2D.Double object.
MTBStringData - Class in de.unihalle.informatik.MiToBo.core.datatypes.wrapper
Class to implement string objects to be used as input or output to MTB operators.
MTBStringData(String) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
Construct a new MTBStringData object from the given string.
MTBStructuringElement - Class in de.unihalle.informatik.MiToBo.core.datatypes
class representing a 2D flat (, i.e. without different gray values) structuring element
for the use with morphological operations
values are stored in a recatangular 2D array (rows: 1st dimension, columns: 2nd dimension)
whereas onValue represents set locations and 0 represents unset locations
MTBStructuringElement(int[][], int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
creates structuring element from given 2D-array
MTBStructuringElement(int[][]) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
creates structuring element from given 2D-array, center is assumed to be at the center of the array
MTBStructuringElement() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
create quadratic 3x3 structuring element
MTBSummarizerImageData - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerImageData() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
 
MTBSummarizerRegion2DSet - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
 
MTBSummarizerSegResultParticlesMultiChannel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MitoBo images.
MTBSummarizerSegResultParticlesMultiChannel() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
 
MTBSummarizerTableModel - Class in de.unihalle.informatik.MiToBo.core.batch.provider.output.swing
Implementation of ALDBatchInputIteratorSwing for MTBTableModel.
MTBSummarizerTableModel() - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
 
MTBTableModel - Class in de.unihalle.informatik.MiToBo.gui
Table model for MiToBo data tables.
MTBTableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Default constructor.
MTBTableModel(int, int, Vector<String>) - Constructor for class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Constructor with given header strings.
MTBTableModelDataIO - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Class for loading/saving MTBTableModel data objects via commandline.
MTBTableModelDataIO() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
 
MTBTableModelDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Class for loading/saving MTBTableModel data objects.
MTBTableModelDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
MTBTableModelDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Class for loading/saving MTBTableModel data objects via xmlbeans provider.
MTBTableModelDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
 
MTBTableWindow - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components
GUI window for displaying tables in MiToBo.
MTBTableWindow(MTBTableModel) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow
Default constructor.
MTBTableWindow.DataTabFileFilter - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components
Internal class that realizes a FileFilter for text files where MiToBo table data is stored.
MTBTableWindow.DataTabFileFilter() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.components.MTBTableWindow.DataTabFileFilter
 
MTBTermAreaDiff - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check upon snake termination by the area within the snake.
MTBTermAreaDiff() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Default constructor.
MTBTermAreaDiff(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Constructor with area fraction below the snake iteration is terminated or if a maximum number of iterations is reached.
MTBTermAreaDiffSlidingOffset - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check upon snake termination by area change within the snake.
MTBTermAreaDiffSlidingOffset() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Default constructor.
MTBTermAreaDiffSlidingOffset(double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
MTBTermination - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Class for checking termination criteria of the current snake iteration.
MTBTermination() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
 
MTBTermMaxIterations - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check upon snake termination by a given number of maximal iterations of the snake.
MTBTermMaxIterations() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Default constructor.
MTBTermMaxIterations(int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Constructor with maximum number of iterations on which the snake optimization is terminated.
MTBTermMotionDiff - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination
Check on snake termination by motion difference.
MTBTermMotionDiff() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Default constructor.
MTBTermMotionDiff(double, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Constructor with motion fraction factor and maximum iteration count.
MTBtoC2D(MTBPolygon2D) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D_GeoPolygonsWrapper
Converts a MiToBo polygon to C2D data type.
MTBTopologicalNumber - Class in de.unihalle.informatik.MiToBo.topology
An abstract class to compute topological numbers given a neighborhood.
MTBTopologicalNumber() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
 
MTBTopologicalNumber.PixelOffsetIterator - Class in de.unihalle.informatik.MiToBo.topology
 
MTBTopologicalNumber.PixelOffsetIterator() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
MTBTopologicalNumber.Point3D - Class in de.unihalle.informatik.MiToBo.topology
This class is used as a light weight 3D point implementation
MTBTopologicalNumber.Point3D(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
MTBTopologicalNumber.Point3D() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
MTBTopologicalNumber2D - Class in de.unihalle.informatik.MiToBo.topology
An abstract class to compute topological numbers for the 2D case.
MTBTopologicalNumber2D() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
 
MTBTopologicalNumber2DN4 - Class in de.unihalle.informatik.MiToBo.topology
Class to compute topological numbers for the 2D case.
MTBTopologicalNumber2DN4() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN4
Construct a class for this neighborhood definitions
MTBTopologicalNumber2DN8 - Class in de.unihalle.informatik.MiToBo.topology
Class to compute topological numbers for the 2D case.
MTBTopologicalNumber2DN8() - Constructor for class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2DN8
Construct a class for this neighborhood definition
MTBTree - Class in de.unihalle.informatik.MiToBo.core.datatypes
This class implements a simple tree data structure.
MTBTree(MTBTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Constructor for the tree.
MTBTree(MTBTreeNode) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Constructor for the tree for a given root node.
MTBTreeNode - Class in de.unihalle.informatik.MiToBo.core.datatypes
This class implements the nodes of class 'Tree'.
MTBTreeNode(MTBTreeNodeData) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Constructor for a TreeNode.
MTBTreeNodeData - Class in de.unihalle.informatik.MiToBo.core.datatypes
Abstract class to define properties for data objects associated with TreeNodes.
MTBTreeNodeData() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
 
MTBTreeNodeRegion2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to create a TreeNodeData object for a 2D region (MTBRegion2D).
MTBTreeNodeRegion2D(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Construct a new MTBTreeNodeRegion2D from the given 2D region object.
MTBVectorField2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Class to represent several kinds of vector fields.
MTBVectorField2D() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
MTBVectorField2D(double[], double[], int, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
 
MTBVersionProviderReleaseFile - Class in de.unihalle.informatik.MiToBo.core.operator
Info class which provides MiToBo plugins with version information from release file in a jar archive.
MTBVersionProviderReleaseFile() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
 
MTBWrapperDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Class for loading/saving primitive datatypes in Alida.
MTBWrapperDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
 
MTBWrapperDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio
Class for loading/saving wrapper datatypes in MiToBo.
MTBWrapperDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.MTBWrapperDataIOSwing
 
MTBWrapperDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Class for loading/saving primitive datatypes in Alida.
MTBWrapperDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
 
mu - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
weight of the length term
mu - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Distribution of the number of clutter observations
mult(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Multiply the elements of two images
mult(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Multiply the elements of two images
MultiChannelParticleAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Operator for detecting sub-cellular structures in a given image.
MultiChannelParticleAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Empty constructor.
MultiChannelParticleAnalyzer2D(MTBImage, Vector<ParticleDetector>) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Default constructor.
MultiChannelParticleAnalyzer2D.ResultImageMode - Enum in de.unihalle.informatik.MiToBo.apps.particles2D
Display mode of the result image.
MultiObsDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi observation density, which assumes independence of the single observations with multivariate Gaussian noise.
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateLinTransDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateLinTransDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
MultiObsDistributionIndepGaussMix<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi observation density, which assumes independent Gaussian mixtures as the underlying distributions.
MultiObsDistributionIndepGaussMix(Random, Matrix, Vector<GaussMixDistribution>, AbstractMultiState<T>, AbstractMultiStateFactory<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
MultiObservationGenerator - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Operator to create a (time) series of observations which can be used for evaluation of multi target tracking algorithms.
MultiObservationGenerator() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
MultiObservationGenerator.GeneratorInfo - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
 
MultiObservationGenerator.GeneratorInfo() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
MultiObservationTrackerRBMCDAIMM - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Tracking of multiple targets using Rao-Blackwellized Monte Carlo Data Association (RBMCDA) for observation-to-target association and Interacting Multiple Models (IMM) filters for target state estimation.
MultiObservationTrackerRBMCDAIMM() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
MultiState<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Multi-target state implementation.
MultiStateDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi state density, which assumes independence of the single states with multivariate Gaussian noise.
MultiStateDistributionIndepGaussians(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
MultiStateDistributionIndepGaussians(AbstractMultiState<T>, Matrix, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Constructor with identical covariance matrices for all states
MultiStateDistributionIndepGaussians(AbstractMultiState<T>, Vector<Matrix>, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Constructor with different covariance matrix for each state
MultiStateFactory<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Multi-target state factory implementation.
MultiStateFactory(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiStateFactory
 
MultiStateIO - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatools
File-IO for (vectors of) MultiState objects.
MultiStateIO() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO
 
MultiStateLinTransDistributionIndepGaussians<T extends Copyable<?>> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
A simple multi state-transition density, which assumes independence of the single states and multivariate Gaussian process noise.
MultiStateLinTransDistributionIndepGaussians(Random, Matrix, Matrix, AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiStateLinTransDistributionIndepGaussians(Random, Matrix[], Matrix[], AbstractMultiState<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiStateLinTransDistributionIndepGaussians(Random, Matrix, Matrix, MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiStateLinTransDistributionIndepGaussians(Random, Matrix[], Matrix[], MultiStateDistributionIndepGaussians<T>, AbstractMultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
MultiTargetIMMFilter - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Multi-target Interacting Multiple Models (IMM) filter for varying number of targets.
MultiTargetIMMFilter(MultiTargetIMMFilter) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Copy constructor.
MultiTargetIMMFilter(Vector<GaussMixDistribution>, LinearTransformGaussNoise, LinearTransformGaussNoise[], Matrix, double, ExponentialDistribution, GaussMixDistribution, Matrix, AbstractMultiStateFactory<MotionModelID>, AbstractMultiStateFactory<MotionModelID>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Constructor that initializes the internal random generator with seed 1.
MultiTargetIMMFilter(Vector<GaussMixDistribution>, LinearTransformGaussNoise, LinearTransformGaussNoise[], Matrix, double, ExponentialDistribution, GaussMixDistribution, Matrix, AbstractMultiStateFactory<MotionModelID>, AbstractMultiStateFactory<MotionModelID>, Random) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
Constructor.
MultiTargetPredictionFilter<T extends Copyable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Interface for multi-target prediction filters
MultiTargetPredictionFilterIndep<T extends Copyable<?>> - Interface in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Interface for multi-target prediction filters with independent targets
MultiTargetRBMCDA<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.algo
Rao-Blackwellized Monte Carlo Data Association following:
S.
MultiTargetRBMCDA(Random, RBMCDASample<T>, int, AssociationDistribution<T, T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
MultiTargetRBMCDA(Random, RBMCDASample<T>[], AssociationDistribution<T, T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
myX - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.
myY - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.

N

N - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
number of targets
name - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Name of the energy.
narrow - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Pixels in narrow-band.
narrowBandWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
naString - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
nearZero(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Checks if a pixel belongs to the zero level.
neuriteColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
neuriteDetection(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Main method for 2D neurite detection.
NeuriteDetector2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The Neurite Detector 2D application offers advanced functionality to detect neurites in 2D fluorescence microscope images of neurons.
NeuriteDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Standard constructor.
NeuriteDetector2D(String, Integer, int, double, Integer[], double, int, NeuriteDetector2D.NeuriteDetector2DMode, NeuriteDetector2DAlgos.DetectorExternalEnergy, double, double, double, double, int, int, int, int, Color, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Constructor
NeuriteDetector2D.NeuriteDetector2DMode - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D
Different detection modes.
NeuriteDetector2DAlgos - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The class implements the basic algorithm for neurite detection based on a 2D multichannel fluorescence image.
NeuriteDetector2DAlgos() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Standard constructor.
NeuriteDetector2DAlgos(MTBImage, int, int, double, int[], double, int, String, String, NeuriteDetector2DAlgos.DetectorExternalEnergy, double, double, double, double, int, int, int, int, Color, MTBTableModel, Boolean, Rengine) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Constructor.
NeuriteDetector2DAlgos.DetectorExternalEnergy - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D
Label for different external energies of the snake which can be used by the detector.
NeuriteDetector2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurites2D
Exception handling for 2D neurite detection.
NeuriteDetector2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
NeuriteDetector2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
NeuriteExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The Neurite Extractor 2D application offers advanced functionality to extract neurite regions in 2D binary neuron images of neurons.
NeuriteExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Standard constructor.
NeuriteExtractor2D(MTBImageByte, NeuriteExtractor2D.NeuronColor, int, int, Rengine, String) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Constructor to create a new neurite extraction object.
NeuriteExtractor2D.NeuronColor - Enum in de.unihalle.informatik.MiToBo.apps.neurites2D
Color of binary neuron image foreground.
NeuriteExtractor2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurites2D
Exception handling for 2D neurite extraction.
NeuriteExtractor2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
NeuriteExtractor2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
NeuriteMolProfExtractor2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
The Neurite Molecular Profile Extractor 2D application offers advanced functionality to extract molecular intensity profiles of multichannel fluorescence images along detected neurite regions.
NeuriteMolProfExtractor2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Standard constructor
NeuriteMolProfExtractor2D(MTBImage, Integer[], MTBNeurite2DSet, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Constructor to create a new neurite profile extraction operator.
NeuriteParticleDetector2D - Class in de.unihalle.informatik.MiToBo.apps.neurites2D
This operator detects particles of a neuron image, for example from FISH analysis.
NeuriteParticleDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Standardconstructor.
NeuriteParticleDetector2D(Integer, ParticleDetectorUWT2D, MTBNeurite2DSet, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Constructor.
NeuronAnalyzer2D - Class in de.unihalle.informatik.MiToBo.apps.neurons2D
The Neuron Analyzer 2D application offers advanced functionality to analyze 2D fluorescence microscope images of neurons.
NeuronAnalyzer2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Standard constructor.
NeuronAnalyzer2D(NeuriteDetector2D, Boolean, String[], Integer[], Boolean, NeuriteParticleDetector2D, Boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Constructor.
NeuronAnalyzer2D_ - Class in mitoboRunner
ImageJ plugin to directly start the neuron analyzer 2D operator.
NeuronAnalyzer2D_() - Constructor for class mitoboRunner.NeuronAnalyzer2D_
 
NeuronAnalyzer2DException - Exception in de.unihalle.informatik.MiToBo.apps.neurons2D
Exception handling for 2D neuron analyzer.
NeuronAnalyzer2DException() - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
NeuronAnalyzer2DException(String) - Constructor for exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
newborndistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
spatial distribution of observations from newborn targets
newbornStateDistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
newbornStateFromObs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
newtargetID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Target-ID to start from for newborn targets
next() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
 
next - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
next() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
nf - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
nInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
node - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Reference to the associated node of the tree.
nodeID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
The node's ID
nodeIsSrc(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
 
nodeIsTgt(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
 
nodes - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Vector of included graph nodes.
noiseCov - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
noNeighborsOldAlgo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Normalization factor for scaling matrix entries.
normalize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
normalize the histogram
normalize(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Normalizes the snake coordinates.
normalizedFilterResponse(double, double) - Static method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Computes the (ideal) filter response to the Gaussian derivative kernel.
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
Normalize the external energy in a range [0.0, 1.0].
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Normalization of the GVF field. !!!
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Normalize the external energy in a range [-1.0, 1.0].
normalizeEnergy() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Normalize the external energy in a range [-1.0, 1.0].
normalizeInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Normalizes image intensities according to normalization mode of operator.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Flag to normalize sum of kernel elements to zero.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Flag to normalize sum of kernel elements to zero.
normalizeMask - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Flag to normalize sum of kernel elements to zero.
normalizeOnly() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
normalize the histogram without changing the sum of absolute frequencies (normalizing factor), because normalize() calls initialize() and thus destroys this normalizing factor.
normalizeWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
Normalize weights
normalizeWeights() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Normalize the particle weights to sum to 1.
normfactor - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
normalization factor
normFromTo(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
normImageFromTo(MTBImage, double, double, double, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Normalize the image values to range [lowerBound, upperBound].
normImageTo(MTBImage, double, double, MTBOperator) - Static method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
Normalize the image values to range [lowerBound, upperBound].
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Mode for normalizing energies.
normTo(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
normValues() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Normalize the values in the gvf field in a range of [-1,1].
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
nTimesteps - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
nu - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Distribution of the number of observations from newborn targets
NuclearParticleDetector2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
This class detects nuclei and particles inside these nuclei and gives some statistics about particles, like particle number per nuclei, particle size, sum of intensities, etc.
NuclearParticleDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Standard constructor.
NuclearParticleDetector2D(MTBImageByte, Integer, Integer, Boolean, Double, Boolean, NucleusDetector2D, ParticleDetectorUWT2D) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
nucleiRegions - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Set of detected regions.
nucleusChannelID - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Index of the nucleus channel, if -1 it is unknown or image has only one.
NucleusDetector2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Operator for segmenting cell nuclei in 2D images.
NucleusDetector2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Default constructor.
NucleusDetector2D(MTBImage, NucleusDetector2D.NuclDetectMode, ImgThreshNiblack, boolean, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Constructor.
NucleusDetector2D.NuclDetectMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D
Available modes for nuclei segmentation in 2D images.
nucleusResult - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Result for nucleus channel.
NucleusSeparator2D - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Class provides routines for separating conglomerates of cell nuclei in 2D.
NucleusSeparator2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Empty constructor.
NucleusSeparator2D(MTBImage, NucleusSeparator2DAlgos) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Default constructor.
NucleusSeparator2D.ResultImageMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D
Display mode of the result image.
NucleusSeparator2DAlgos - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Common super class for all nucleus separators.
NucleusSeparator2DAlgos() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Empty constructor.
NucleusSeparator2DBeamCut - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Class provides routines for separating conglomerates of cell nuclei in 2D.
NucleusSeparator2DBeamCut() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Default constructor
NucleusSeparator2DBeamCut(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Constructor.
NucleusSeparator2DBeamCut(MTBImage, NucleusSeparator2DBeamCut.NuclSeparateMode) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Constructor.
NucleusSeparator2DBeamCut.NuclSeparateMode - Enum in de.unihalle.informatik.MiToBo.apps.nuclei2D
Available modes for nuclei separation in 2D images.
NucleusSeparator2DPeakSearch - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Operator for separating merged nuclei regions in images.
NucleusSeparator2DPeakSearch() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Default constructor.
NucleusSeparator2DPeakSearch(MTBImageShort) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Constructor with input image.
NucleusSeparator2DPeakSearch(MTBImageShort, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Constructor with gray-scale and binary image.
NucleusSeparator2DPeakSearch_RegionSeparator - Class in de.unihalle.informatik.MiToBo.apps.nuclei2D
Operator to analyze a given binary image or a set of nuclei regions.
NucleusSeparator2DPeakSearch_RegionSeparator() - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Default constructor.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Constructor with input image.
NucleusSeparator2DPeakSearch_RegionSeparator(MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Constructor with region set.
number_cells - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Count of detected cells.
number_channels - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Number of channels in the image.
number_nuclei - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Count of detected nuclei.
number_particles - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Count of detected particles.
numberOfEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Number of edges in the MTBGraph.
numberOfNodes - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Number of nodes in the MTBGraph.
numberToString(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
numClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numClutterInput - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of clutter observations in input observations
numClutterTracker - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of clutter observations in tracking results
numDeadTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numNewbornTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numOfNodes() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
numOfNodes() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Get number of graph nodes
numOfObservationAssocs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
numOfObservationAssocs(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the number of observations that are associated with the specified target
numOfTargetAssocs(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
numOfTargetAssocs(int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Get the number of targets that are associated with the specified observation
numRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Number of represented regions.
numRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Number of represented regions.
numSamples - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
numTargetInput - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of target observations in input observations
numTargetTracker - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
number of target observations in tracker results

O

obsAssocAdjacency - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
obsConflict(Matrix, MultiState<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
obsdistrib - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
observation/measurement likelihood P(z_m^t | c_m, Z^{1:t-1}, c_{1:m-1}
obsDomainAreaRatio - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
ObservationAdjacency - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
An adjacency matrix for observations in a time series used for greedyGourmet-partitioning.
ObservationAdjacency(Vector<MultiState<MotionModelID>>, RBMCDASampleInfo<MotionModelID>[]) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
Constructor that initializes the adjacency matrix with the given observations and sets edge weights according to the information from RBMCDA-samples
ObservationAdjacency(Vector<MultiState<MotionModelID>>, DataAssociationExclusive[][]) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
Deprecated. 
ObservationAdjacency(ObservationAdjacency) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
observations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
observations - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
ObservationSeriesGenerator - Class in cmdTools.tracking.multitarget
Commandline tool to create a (time) series of observations which can be used for evaluation of multi-target tracking algorithms.
ObservationSeriesGenerator() - Constructor for class cmdTools.tracking.multitarget.ObservationSeriesGenerator
 
ObservationsInfo - Class in cmdTools.tracking.multitarget
Commandline tool to print information about a (time) sequence of observations and optionally their association to targets/clutter.
ObservationsInfo() - Constructor for class cmdTools.tracking.multitarget.ObservationsInfo
 
observationsToRegions(boolean, Vector<MultiState<MotionModelID>>, double, double, double, double) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
Convert observations to regions.
observationsToTracks(Vector<MultiState<MotionModelID>>, HashMap<Integer, Vector<Integer>>) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
Obtain observations assigned to each target from observations with assigned target IDs
offer(EType, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
add an element to List
offsetsNeighborNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
As for the neighbors this vector is in analogy to coordinatesNeighborNeighbors and gives for each neighborneighbor the offset instead of coordinates.
offsetsNeighbors - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
In analogy to coordinatesNeighbors this array hold the offsets of the neighbors.
oFilter - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Oriented filter to apply.
oldId - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Old index (position) of the point within the snake.
omemeta - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
omePixelType(MTBImage.MTBImageType) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Get the OME pixel type corresponding to the specified MTB image type
omexml - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
Open_Image_MTB - Class in mtb_io
Plugin for image open dialog
Open_Image_MTB() - Constructor for class mtb_io.Open_Image_MTB
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Invokes analysis procedure on given image.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetector
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellMigrationAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector

operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower

operate() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
operate() - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Creates a MTBImage with three channels, the same size as the original one and converts each rgb pixel to a hsx pixel, where x stands for Inentsity or Brightness or Value depending on the mode set.
operate() - Method in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
 
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
 
operate() - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
 
operate() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
This function calls the actual Gauss filtering method.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
This function calls the actual mean filtering method.
operate() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
operate() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
operate() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageStatistics
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgClose
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
This function does the actual work, i.e. optimization of the energy.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Methode that runs the operator.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
This method does the actual work.
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
 
operate() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
operate() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
operate() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
 
operate() - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
 
optimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Current snake optimizer with all its parameters and fields like the current snake, old snake, gamma values and energies.
optimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Current snake optimizer with all its parameters and fields.
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Bitwise OR of the elements of two images
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Bitwise logical OR of two images.
ordinalToType(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Return the corresponding MTBImageType for its index in the enum.
OrientedFilter2D - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Base class for anisotropic linear filters in 2D.
OrientedFilter2D() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Default constructor.
OrientedFilter2DBatchAnalyzer - Class in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Base class for applying oriented filters in different orientations.
OrientedFilter2DBatchAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Default constructor.
OrientedFilter2DBatchAnalyzer.JoinMode - Enum in de.unihalle.informatik.MiToBo.filters.linear.anisotropic
Method for joining the results from the various orientations.
ostream - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
outDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Output and working directory.
outDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Output and working directory.
outDir - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Output and working directory.
outEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Vector of outgoing edges of the MTBGraphNode.
outImageType - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
outIntermediateResultsStack - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image stack with intermediate result images.
outIntermediateResultsStackInterval - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Interval for saving intermediate results in stack.
outIntermediateResultsStackWanted - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to request a stack of intermediate result images.
outputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
outputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
outSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Result contours.
outSnakesImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image with final snake contours overlayed.
overlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Mask to indicate overlap regions between snakes.
overlapMaskRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Flag to indicate if overlap mask is required by at least one energy.
OverwriteException - Exception in de.unihalle.informatik.MiToBo.io.images
Special exception for the ImageWriterMTB operator.
OverwriteException(ALDOperatorException.OperatorExceptionType, String) - Constructor for exception de.unihalle.informatik.MiToBo.io.images.OverwriteException
 

P

P(Double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
p(Integer) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
p - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
p(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
p(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.EvaluatableDistribution
Evaluate p(X) at location x.
p(T, int) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IndependentlyEvaluatableDistribution
Evaluate p_i(X) at x_i
P(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.IntegrableDistribution
Evaluate probability distribution function P(X <= x)
p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
p(AbstractMultiState<S>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state j in X
p(AbstractMultiState<S>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
Evaluate the density independently for observation i in Z conditional on state i in X
p(AbstractMultiState<S>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistributionIndep
 
p(DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
This method is here only valid for the latest DataAssociation sampled with drawSample().
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
p(AbstractMultiState<T>, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussMix
 
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
p(AbstractMultiState<T>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
p(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
P_D - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Probability of target detection
P_t - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
The final transformation matrix to be used for dimension reduction.
parent - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Parent node
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
A java.awt.Color object is created from a string, which holds color information in the following format:

"rINT:bINT:gINT[:aINT]"

where INT is an integer value in the range [0,255].
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
 
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
Method to parse MTB wrapper data from a string.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
Convert a string to a Random generator.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
 
ParticleDetector - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Common super class for all particle detectors.
ParticleDetector() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetector
Empty constructor.
ParticleDetector2D - Class in cmdTools.cellAnalysis
Commandline tool for particle detection based on the undecimated wavelet transform.
ParticleDetector2D() - Constructor for class cmdTools.cellAnalysis.ParticleDetector2D
 
ParticleDetectorUWT2D - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Detector for spotlike structures (bright on dark background) in 2D based on the undecimated wavelet transform.
ParticleDetectorUWT2D() - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Constructor.
ParticleDetectorUWT2D(MTBImage, int, int, double, int, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Constructor with non-default parameters.
ParticleDetectorUWT2D(MTBImage, int, int, double, int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Constructor that sets the poisson2gauss flag to true
ParticleDetectorUWT2D.UWTRunner - Class in de.unihalle.informatik.MiToBo.apps.particles2D
Thread class to run UWT wavelet transformation threaded.
ParticleDetectorUWT2D.UWTRunner(UndecimatedWaveletTransform) - Constructor for class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner
Default constructor.
ParticleDistribution<G extends Copyable<? extends G>> - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A distribution represented by weighted particles
ParticleDistribution() - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor where all fields are initialized by null.
ParticleDistribution(Random, G[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor with equally weighted particles that must be specified.
ParticleDistribution(Random, G[], double[]) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor with equally weighted particles that must be specified.
ParticleDistribution(Random, SamplingDistribution<G>, int) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Constructor that samples numParticles from density.
particleRegions - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
List of detected regions.
particleResults - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Detection results for particles.
particles - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
PartitGraphNodeID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A graph node object for multipartite graphs to store a partitionID, a nodeID as well as a subgraphID.
PartitGraphNodeID(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
Constructor to specify partitionID and nodeID (subgraphID=0)
PartitGraphNodeID(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
Constructor to specify partitionID, nodeID and subgraphID
partitionID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
The node's partitionID
PCA - Class in de.unihalle.informatik.MiToBo.math.statistics
This class implements the Karhunen-Loeve transformation, also known as PCA.
PCA() - Constructor for class de.unihalle.informatik.MiToBo.math.statistics.PCA
Default constructor.
PCA.ReductionMode - Enum in de.unihalle.informatik.MiToBo.math.statistics
Available modes for determining the sub-space dimensionality.
Pdeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
pdeath - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
pDetect - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
pDetect - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
pdetector - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
pdfs - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
perCellAvgSize - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Average particle size per cell (optional).
perCellCount - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Particle counts per cell (optional).
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Level set function.
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
The level set function.
phi_0 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
phi_1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
physicalPixelSize_from_OME(Calibration, IMetadata, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Set the calibration of an image from the OME meta data of image of index imageIdx
physicalPixelSize_to_OME(Calibration, IMetadata, int) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Set OME meta data for image of index imageIdx using information from a Calibration object
PI_HALF - Static variable in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
 
plotImageToBackground() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Copies the input image as background into the output frame.
plotSnakeToImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
pmf - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
probability mass function
pobs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
observation distribution: independent Gaussian mixtures for each target
point2DDiff(Point2D.Double, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Substract two Point2D.Double .
point2DSum(Point2D.Double, Point2D.Double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Sums up two Point2D.Double .
pointHashtableToString(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointHashtableToStringX(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointHashtableToStringY(Hashtable<Integer, Vector<Point2D.Double>>, String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointNum - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
The number of border points.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set of border pixels.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
List of polygon points.
pointVectorToString(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointVectorToStringX(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
pointVectorToStringY(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
poisson2gauss(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Transforms image with poisson noise to image with gaussian noise J.
PoissonDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
Poisson distribution.
PoissonDistribution(double, Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
Constructor for Poisson distribution with parameter lambda (=mean=variance)
poll() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedList
retrieve element with highest priority
Polygon2D_Cgal - Class in de.unihalle.informatik.MiToBo.core.datatypes
Deprecated. 
Polygon2D_Cgal() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Deprecated.  
popUpChart() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing.ChartShowButton
Shows the chart to the user.
popUpImage(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Shows an image to the user.
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Raise image values to the power of 'constant'
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Raise image values to the power of 'exponent'
predecessors - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Map of precursors on contour for each pixel in narrow-band.
predict() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
predict() - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilter
Prediction step method
predict() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
predict(LinearTransformGaussNoise) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
predictIndep(int, LinearTransformGaussNoise) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
predictors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
dynamic models
prepareMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Preprocess the matrix.
preprocess(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
preprocess(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
preSegmentation() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Method for pre-segmentation.
prev - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
previousEnergy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Snake energy in previous iteration (for change assessment).
previousSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Old snake of previous iteration (for evolution assessment).
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Print the whole MTBGraph with all its nodes and edges.
print() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Print the neurite skeleton graph informations.
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Print this energy object - including the value of the energy for phi assumed to be associated with this energy object.
print(MTBLevelsetMembership, PrintStream, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
print() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Print information of this class to stdout
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Recursively prints the data contained in the nodes of the tree.
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Method to print the data associated with the node.
printData() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
 
printData() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
 
printHelp() - Static method in class cmdTools.cellAnalysis.ParticleDetector2D
 
printHelp(String, String) - Static method in class cmdTools.mtb_imagetools.ImageConvert
 
printHelp() - Static method in class cmdTools.visualization.DisplayImage
 
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Print current parameter settings to standard output device.
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Print important parameters to standard output stream.
printParams() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Print important parameters to standard output stream.
printPoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Prints points of snake to standard output stream.
printReadabeTimeInfo(long) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
printTree() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Prints tree data.
priority - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
ProbabilityDensityFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for multivariate distributions that allow evaluation of their probability density function.
ProbabilityMassFunction - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for univariate distributions based on probability mass functions
processedRegionsToBinImage(MTBImage, MTBRegion2DSet, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Create a binary image from given regions.
projector - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
observation model
propertyChange(PropertyChangeEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Changes the available options of the reader option panel according to the selected files
propertyChange(PropertyChangeEvent) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Changes the available options of the writer option panel according to the selected file filter of the file chooser
propertyChange(PropertyChangeEvent) - Method in class mtb_io.Open_Image_MTB
 
propertyChange(PropertyChangeEvent) - Method in class mtb_io.Save_Image_MTB
Process the WRITER_OPTIONS_APPROVED_PROPERTY event of the ImageWriterOptionsPane to assign the writer options when the file chooser closed by approving the file selection (and thereby writer options).
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBWrapperDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.AwtColorDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBTableModelDataIO
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBWrapperDataIOCmdline
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
Interface method to announce class for which IO is provided for
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
Interface method to announce class for which IO is provided for field is ignored.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
Interface method to announce class for which IO is provided for.
psi - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
pstate - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
state distribution: independent Gaussian mixtures for each target
putValue(int, int, int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new RGB value at the specified position.
putValue(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new RGB value at the specified position in the actual slice.
putValueB(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new blue value at the specified position.
putValueB(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new blue value at the specified position in the actual slice.
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y,z) using a Double
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueDouble(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueDouble(int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the value of the actual slice at coordinate (x,y) using a Double
putValueDouble(int, int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the value of the 5D image at coordinate (x,y,z,t,c) using a Double
putValueG(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new green value at the specified position.
putValueG(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new green value at the specified position in the actual slice.
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y,z) using an Integer
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the value of the current slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageManipulator
Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the 5D image at coordinate (x,y,z,t,c)
putValueInt(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the voxel value of the actual z-stack at coordinate (x,y,z)
putValueInt(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Set the value of the actual slice at coordinate (x,y) using an Integer
putValueInt(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the value of the 5D image at coordinate (x,y,z,t,c) using an Integer
putValueR(int, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new red value at the specified position.
putValueR(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Put a new red value at the specified position in the actual slice.

Q

Q - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
Gaussian process noise covariance matrix
qsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
qsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
quality - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
quality - Variable in class mtb_io.Save_Image_MTB
quality option if available
qualpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
qxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
qxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
qxy_ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
qxy_ - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 

R

R - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
Gaussian measurement noise covariance matrix
RadioButtonPanel - Class in de.unihalle.informatik.MiToBo.gui
A panel with a titled border and a set of radio buttons that can be reconfigured easily.
RadioButtonPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Constructor
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
random generator for sampling
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
rand - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
random generator for sampling
rand - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
randomColor(Random) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
RandomGeneratorDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline
Data I/O provider for ALDOpRunner (commandline) for java.util.Random objects.
RandomGeneratorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.RandomGeneratorDataIOCmdline
 
RandomGeneratorDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio
Data I/O provider for GUI-OpRunner for java.util.Random objects.
RandomGeneratorDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing
 
RandomGeneratorDataIOXmlbeans - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans
Xmlbeans provider forjava.util.Random objects.
RandomGeneratorDataIOXmlbeans() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
rankOp(MTBImage, RankOperator.RankOpMode, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Compute the rank operation of a gray-valued image, stack or hyperstack
RankOperator - Class in de.unihalle.informatik.MiToBo.filters.nonlinear
Rank operator class to compute Median, Minimum or Maximum filter for hyperstack, stack and plain images.
RankOperator() - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Constructor
RankOperator(MTBImage, RankOperator.RankOpMode, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Constructor
RankOperator(MTBImage, RankOperator.RankOpMode, int, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Constructor
RankOperator.RankOpMode - Enum in de.unihalle.informatik.MiToBo.filters.nonlinear
Defines the operation
rbbox - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
vertical box to place the radio buttons on the panel
rbgroup - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
the logical group of radio buttons
RBMCDASample<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
Representation of a RBMCDA-sample.
RBMCDASample() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Constructor.
RBMCDASample(MultiTargetPredictionFilterIndep<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Constructor with an initial prediction filter.
RBMCDASampleInfo<T extends TargetID> - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
RBMCDA-sample info object.
RBMCDASampleInfo() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
RBMCDASampleInfo(int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
RBMCDASampleInfo(RBMCDASampleInfo<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
RBMCDATracker - Class in cmdTools.tracking.multitarget
Commandline tool for multi-target tracking with RBMCDA-framework described in [Gress,Posch, "
RBMCDATracker() - Constructor for class cmdTools.tracking.multitarget.RBMCDATracker
 
read(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Read a contour set from an xml file filename and set the MTB polygon set accordingly.
read(MTBXMLContour2DSetType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Read a contour set from an xml object xmlContourSet and set the MTB polygon set accordingly.
read(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Read a polygon set from an xml file filename and set the MTB polygon set accordingly.
read(MTBXMLPolygon2DSetType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Read a polygon set from an xml object xmlPolygon2DSet and set the MTB polygon set accordingly.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBWrapperDataIOSwing
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
readData(Field, Class<?>, ALDXMLObjectType, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Gets the data from the configuration window.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Extracts current data.
reader - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
READER_OPTIONS_APPROVED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
Property change when writer options are approved (i.e. when filechooser selection is approved)
readFromBinFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Reads a vector field from a file in binary format.
readImagePlus(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Read image imageIdx from the specified file and return it as ImagePlus object.
readMTBImage(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Read image imageIdx from the specified file and return it as MTBImage object.
readMultiStates(String) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO
Read a vector of MultiState objects from a file with xml-beans representation.
readResolve() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperator
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Init function for deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Function for proper initialization of deserialized objects.
readResolve() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Function for proper initialization of deserialized objects.
recursiveProcessing() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBImageIteratorImageDataPanel
Query flag for recursive processing.
Region2DSetFromLabelimage - Class in de.unihalle.informatik.MiToBo.segmentation.regions.convert
Operator to convert 2D label image to a MTBRegionsSet2D.
Region2DSetFromLabelimage() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Default constructor.
regionBinaryMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
The set of regions represented as a Vector.
regionSet - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
regionsToBinImage(MTBImage, MTBImage, Vector<MTBRegion2D>) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Create binary image from a set of regions.
regionsToObservations(boolean, MTBRegion2DSetBag) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
Convert regions to observations
regionToFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Write the coordinates of the included 3D points into a text file.
register(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Registers the object to the database.
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
remove() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter.TileIterator
 
remove(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Delete the given region object from the set, if contained.
remove(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Remove a region set from this bag
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Remove a region set from this bag by its index
remove() - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.PixelOffsetIterator
 
removeChild(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Remove child node.
removeEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Remove the specified edge from the graph
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Delete the i-th border from the set.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Delete the i-th contour from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Delete the i-th region from the set
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Removes the element at the specified position in this list.
removeElementAt(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Removes the element at the specified position in this list.
removeExtension(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Remove extension from filename if any.
removeFirst() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Removes and returns the first element from this list.
removeImage(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
removeIndepGaussian(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Remove independent Gaussian state distribution (at index i)
removeInEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Remove a incoming MTBGraphEdge from the MTBGraphNode.
removeLast() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Removes and returns the last element from this list.
removeLeadingDirectories(String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.FilePathManipulator
Remove all leading pathname components from a filename.
removeNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Remove the specified node from the graph as well as the edges connected to it.
removeOutEdge(MTBGraphEdge) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Remove a outgoing MTBGraphEdge from the MTBGraphNode.
removeState(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Remove the idx-th state (indices start from 0)
removeState(int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
replacementPattern - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
replacementString - Variable in class de.unihalle.informatik.MiToBo.tools.FilenameGenerator
 
report - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
ReportGenerator - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
ReportGenerator() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
requiresCounterClockwiseContourSorting() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Ask energy if contour points need to sorted counter-clockwise.
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Ask energy if contour points need to sorted counter-clockwise.
requiresCounterClockwiseContourSorting() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Ask energy if contour points need to sorted counter-clockwise.
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
requiresOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Ask energy if an overlap mask for all snakes jointly optimized is required.
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Ask energy if an overlap mask for all snakes jointly optimized is required.
requiresOverlapMask() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Ask energy if an overlap mask for all snakes jointly optimized is required.
resample(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Method to re-sample the line segments of the polygon in a range of a given segment length.
resample() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Resample this distribution and equalize weights
resample(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to re-sample the line segments of the snake in a range of a given segment length.
resampleSegLength - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Target length of snake segments in resampling.
resampleSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Resamples the snake using the specified segment length.
reset() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Reset time
reset() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
resetPotential() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Resets the potential, next access to it will enforce recalculation.
resizeMatrices() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Resize parameter matrices.
responseStack - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Stack with filter responses of all orientations.
restoreConfigWins() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
 
resultCellImg - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Input image with snake contours overlayed (optional).
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Result data object.
resultImage - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Result segmentation image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Resulting binarized image.
resultImagePlus - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
resultImageStack - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
(Optional) stack of result images with segmentation masks/overlays.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Result label image of separated nuclei.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Filtered image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Result image.
resultingRegionsets - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
resultMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
resultMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Result matrix containing final matching.
resultMTBImage - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
resultObj - Variable in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Result data object, e.g., an image, a histogram, a vector, ....
resultSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
resultType - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Desired type of result.
resultValueMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Result value mode.
resultVector - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Name of the analyzed image.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Final vessel map.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Resulting binary vessel map.
resultVesselMap - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Resulting binary vessel map.
reversePolypoints() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Changes the ordering of the polygon points.
reversePolypoints() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Overwrite reversePolypoints method of Polygon2D.
rgbOutput - Variable in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Output RGB values.
RGBToHSXConverter - Class in de.unihalle.informatik.MiToBo.color.conversion
Converts an image of type MTBImageRGB ( RGB color space ) into an image with HSX( hue saturation intensity/brightness/value ) color space.
RGBToHSXConverter() - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Default constructor.
RGBToHSXConverter(MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Constructor.
RGBToHSXConverter.ColorChannel - Enum in de.unihalle.informatik.MiToBo.color.conversion
Supported Color Channels.
RGBToHSXConverter.Mode - Enum in de.unihalle.informatik.MiToBo.color.conversion
The way of converting an image from rgb to hsi.
RoiManagerAdapter - Class in de.unihalle.informatik.MiToBo.core.imageJ
Convenience functions for interaction with ImageJ's ROI manager.
root - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Root node of the tree.
rowMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Array containing row marks.
rows - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Number of rows of the table.
rsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
rsize - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
run() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D.UWTRunner
 
run(String) - Method in class mitoboRunner.Grappa_Editor
 
run(String) - Method in class mitoboRunner.MiToBo_Runner
 
run(String) - Method in class mitoboRunner.NeuronAnalyzer2D_
 
run(String) - Method in class mitoboRunner.ScratchAssayAnalyzer_
 
run(String) - Method in class mitoboRunner.Snake_Optimizer
 
run(String) - Method in class mitoboRunner.Xylem_Detector
 
run(String) - Method in class mtb_io.Open_Image_MTB
 
run(ImageProcessor) - Method in class mtb_io.Save_Image_MTB
 
run(ImageProcessor) - Method in class mtb_segmentation.Threshold_Image
 
rxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
rxy - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 

S

sampleCount - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Number of data samples in input data.
sampleEnergyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
SamplingDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities from which samples can be drawn.
SATURATION_UNDEFINED - Static variable in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
To cope with undefined saturation/hue-values, we use the following scheme.
save(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
write the histogram data into a text file
Save_Image_MTB - Class in mtb_io
Plugin for image save dialog
Save_Image_MTB() - Constructor for class mtb_io.Save_Image_MTB
 
saveExtEnergy(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Save the gvf field in a MATLAB like file.
saveIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set flag to save intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Flag for saving intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to enable/disable saving of intermediate results.
saveIntermediateResultsPath - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Path where to save intermediate results.
saveIntermediateResultsPath - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Path to where intermediate results should be stored.
saveProfileSet(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Saves the given profile data list with N profiles to the given file.
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Save intermediate results.
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Save intermediate results.
saveTable(File) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Saves the contents of the table to given file, TSV format.
saveTilesToFiles(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Saves all tiles to the given path.
saveToBinFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Saves the vector field to a file in binary format.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
Scaling factor for normalization Still experimental
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Scaling factor for image coordinates.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Scaling factor for image coordinates.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Scaling factor to rescale image coordinates in range [0,1] or several ranges to the original coordinates range like [1000, 1000] in a image of size 1000 x 1000.
scaleFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Scale factor for snake normalization.
scaleValues(int, int, double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Method to scale the intensity values (range [curMin, curMax]) of the image to a given range [scaleMin, scaleMax].
scalprod(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the scalar product of the given segment to this one.
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Matrix containing pairwise scores of bipartite sets.
ScratchAssayAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay
class for analyzing the scratch area in several scratch assay images
ScratchAssayAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
ScratchAssayAnalyzer(String, int, int, ScratchAssayAnalyzer.ScratchOrientation, boolean, ScratchAssayAnalyzer.InputType, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
ScratchAssayAnalyzer.InputType - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssayAnalyzer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssayAnalyzer_ - Class in mitoboRunner
ImageJ plugin to directly start the scratch assay analyzer.
ScratchAssayAnalyzer_() - Constructor for class mitoboRunner.ScratchAssayAnalyzer_
 
ScratchAssaySegmenter - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay
class for segmenting the wound area of a scratch assay image

First the image is smoothed.
ScratchAssaySegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
ScratchAssaySegmenter(MTBImage, int, int, boolean, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
ScratchAssaySVMTrainer - Class in de.unihalle.informatik.MiToBo.apps.scratchAssay
class for training and cross validating a support vector machine for classification of scratch assay
images into images containing a scratch and those that don't
ScratchAssaySVMTrainer() - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
ScratchAssaySVMTrainer(String, String, int, int, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
ScratchAssaySVMTrainer.KERNEL_TYPE - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssaySVMTrainer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssaySVMTrainer.ValidationMethod - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
SecondOrderCentralMoment<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for classes that provide a second order central moment.
seedImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
segDim - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
segment(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
segment cells in a single frame of the input image
segment(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
SegmentationInitializer - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Operator for initializing objects of type MTBSegmentationInterface.
SegmentationInitializer() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Default constructor.
SegmentationInitializer.InputMode - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Available data sources.
SegmentationInitializer.SegmentationDimension - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Available dimensions for segmentations.
SegmentationInitializer.ShapeType - Enum in de.unihalle.informatik.MiToBo.segmentation.basics
Available shape types.
SegmentationInitializerDataIOSwing - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Class for loading/saving objects of type SegmentationInitializer.
SegmentationInitializerDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
SegmentationInitializerDataIOSwing.ConfigureSegmentationButton - Class in de.unihalle.informatik.MiToBo.segmentation.basics
GUI element for configuring segmentations.
SegmentationInitializerDataIOSwing.ConfigureSegmentationButton(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Constructor.
SegmentationInitializerDataIOSwing.SegmentationConfigWin - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Segmentation configuration window.
SegmentationInitializerDataIOSwing.SegmentationConfigWin(Field, Class<?>, Object, ALDParameterDescriptor) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Default constructor.
segMode - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Mode how the channel of the image was treated during segmentation.
segObject - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
SegResult_Complete - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Complete segmentation result from multi-channel image.
SegResult_Complete(String, int, SegResult_Complete.SegmentationMode, SegResult_Cytoplasm) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Default constructor.
SegResult_Complete.SegmentationMode - Enum in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Indicator for segmentation mode.
SegResult_Cytoplasm - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Cell boundary segmentation result from single-layer image.
SegResult_Cytoplasm(String, MTBPolygon2DSet, MTBImageByte, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Deprecated. 
SegResult_Cytoplasm(String, MTBPolygon2DSet, MTBImageByte, int, int[], double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Default constructor.
SegResult_Interface - Interface in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Interface for unified handling of segmentation results extracted by particle, cell or nucleus detectors.
SegResult_Nuclei - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Nuclei segmentation result from a single image channel.
SegResult_Nuclei(String, int, MTBImageByte, MTBImage, MTBRegion2DSet, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Default constructor.
SegResult_Particles - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Particle detection result for a single channel of an image.
SegResult_Particles(String, int, MTBRegion2DSet, MTBImageByte, int, double) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Default constructor.
SegResult_ParticlesMultiChannel - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Particle detection result for a multi-channel image.
SegResult_ParticlesMultiChannel(String) - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Default constructor.
SegResultEnums - Class in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Defines of enumeration types used in conjunction with cell image analysis.
SegResultEnums() - Constructor for class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums
 
SegResultEnums.MeasureUnit - Enum in de.unihalle.informatik.MiToBo.apps.datatypes.cellImages
Unit for measurements.
selection - Variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
string/label of the selected radio button
SELECTION_CHANGED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
Property change of the panel when a selection is changed
selectLargeRegions(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
seriesIndices - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
seriesIndices - Variable in class mtb_io.Open_Image_MTB
 
seriesnames - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
seriespanels - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
set(int, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
 
set(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
assign a value to the matrix at position ( x, y, z )
setActivityArray(boolean[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Specify set of active snakes.
setActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Only actual slice is thresholded, this will force the output image type to be of the same type as the input image (or destination image type)
setAdjacencyMatrix(AdjacencyMatrix<T>) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set the main graph's adjacency matrix
setAngle(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Set orientation of filter.
setAngleSampling(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Set angular sampling interval.
setArithmeticOperation(ImageArithmetics.ArithOp) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
setAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Set an association between target and observation.
setBGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Tell the thresholder to use the original pixel value for background pixels
setBGValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set value of Parameter argument BGValue.
setBinaryImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set the binary image.
setBinValue(int, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
set the bin value at i-th position
setBorderExclusion(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
should border touching objects be excluded
setBorderType(BordersOnLabeledComponents.BorderType) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set border type to be extracted.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set value of Parameter argument boundaryPadding.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set value of Parameter argument boundaryPadding.
setBoundaryPadding(MTBImageWindow.BoundaryPadding) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set value of Parameter argument boundaryPadding.
setBthMaskSize(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Set mask size of black top-hat.
setC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setCalibration(Calibration) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the calibration object (see getCalibration() for further information).
setChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
setChannel(int) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set the image channel.
setChannelsAreRGBFlag(Boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set flag if RGB color channels are interpreted as real image channels.
setChannelsToCopy(int[]) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify list of channels to copy to result stack.
setChosenColor(Color) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing.ColorChooserButton
 
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setClass(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set the label of position (x,y) to c.
setClass(int, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set the label of position (x,y,z) to c.
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Deprecated. 
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Deprecated. 
setClass(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Deprecated. 
setClass(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Deprecated. 
setClosed() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Set polygon closed.
setClusterNum(int) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Specify number of clusters.
setCodec(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the codec (quicktime only).
setColor(String) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawPolygon2DSet
Specify color in which to draw the snakes.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the uniform color of the regions in a color image (COLOR_IMAGE only).
setColor(int, int) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DynamicColorLUT
Set the color for given key.
setColorArray(int[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Specify pseudo-colors for snake visualization.
setColorImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Add the label image to the parameter object
setColumnName(int, String) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Sets the header of column to specified string.
setCompactnessThreshold(double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set the compactness threshold for eliminating non compact components.
setCompression(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the compression type
setCondition(Double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.PoissonDistribution
 
setCondition(T) - Method in interface de.unihalle.informatik.MiToBo.math.distributions.interfaces.ConditionalDistribution
Set the conditional variable
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiObservationDistribution
 
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractMultiStateTransitionDistribution
 
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiObsDistributionIndepGaussians
 
setCondition(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
 
setConnectivity(MTBBorder2D.BorderConnectivity) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set the connectivity.
setConnectivity(MTBBorder2D.BorderConnectivity) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Specify connectivity for extracted border pixels.
setContourType(ContourOnLabeledComponents.ContourType) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the contour type.
setCorrectGamma(Boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set flag to use gamma correction.
setCorrelationThreshold(double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set threshold for thresholding wavelet correlation images
setCountMode(CalcStructureStatistics.StructureCountMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Specify mode how to assign structures to cells.
setCovariance(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
setCreateBinaryMasks(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Enable/disable creation of binary masks.
setCreateColorImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set the flag that determines the creation of an image with randomly colored regions.
setCreateLabelImageFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set the flag that determines the creation of an image with region labels.
setCurrentSlice(MTBImageManipulator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy the values of the source to the current slice
setCurrentSliceCoords(int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the current slice for functions that work on a slice only (this has nothing to do with the ij.ImageStack's current slice)
setCurrentSliceIndex(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the current slice for functions that work on a slice only (this has nothing to do with the ij.ImageStack's current slice) Stack indices range from 0 to N-1 (unlike ImageJ, where stack indices range from 1 to N)
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the slice label of the slice specified by the current slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Set the slice label of the slice specified by the actual slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Set the slice label of the slice specified by the actual slice index
setCurrentSliceLabel(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the slice label of the slice specified by the actual slice index
setCurrentZStackCoordinates(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the current z-stack coordinates for functions that work on (spatial) 3D only.
setData(Vector<?>, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set data for current MTBGraphEdge with the given cost.
setData(Vector<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set data for current MTBGraphEdge.
setData(HashMap<String, HashMap<String, LinkedList<Double>>>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set the data to plot.
setData(HashMap<String, HashMap<String, Double>>) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set the data to plot.
setDataset(double[][]) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Specify an input dataset.
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of debug.
setDebug(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of debug.
setDebug(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of debug.
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
setDebug(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Set debug bit mask
setDefaultFps(int) - Method in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Set a default fps to show in the option panel, e.g. if the fps can be determined from some image metadata
setDelimiter(ALDTableWindow.TableModelDelimiter) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Configure the delimiter to be used when exporting the table.
setDelta(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set distance between threshold images to be compared.
setDeltaT(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setDeltaT(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set the time between two frames
setDeltaX(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setDeltaX(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set pixel length in x-direction
setDeltaY(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setDeltaY(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set pixel length in y-direction
setDenoise(boolean) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set the denoising flag. true to activate denoising.
setDestinationImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set value of Input argument DestinationImage.
setDetectionMode(CytoplasmAnalyzer2D.DetectMode) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify detection mode.
setDiagonalNeighbors(boolean) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
If true 8-neighborhood, i.e. diagonal neighbors, will be used in mode 'VORONOI_EXPAND' for Voronoi dilation.
setDiagonalNeighborsFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set the neighborhood flag.
setDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Directions to be analyzed.
setDistance(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify distance for calculating cooccurrence matrices.
setDistance(int) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Specify distance to be used in calculations.
setDistmet(DistanceTransform.DistanceMetric) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Specify the metric for the distance transformation.
setDistMetric(DistanceTransform.DistanceMetric) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set the distance metric.
setDoErosion(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of doErosion.
setDoGauss(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify if cell channel is to be smoothed prior to detection.
setDotGlobalAttributes(String[]) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set global attributes of the graph e.g. the style of the nodes etc.
setDrawType(DrawRegion2DSet.DrawType) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the kind of region image to be drawn
setElementAt(MTBBorder2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Set the i-th border of the set.
setElementAt(MTBContour2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Set the i-th contour from the set.
setElementAt(int, MTBPolygon2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Set a polygon at i-th position of the set.
setElementAt(MTBRegion2D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Set the i-th region from the set
setElementAt(MTBRegion3D, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Set the i-th region from the set
setElementAt(int, MTBNeurite2DProfile) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Replaces the element at the specified position in this list with the specified element.
setElementAt(int, MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Replaces the element at the specified position in this list with the specified element.
setEnergy(MTBGenericEnergyNonPDE) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of energy.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Sets list of energies.
setEnergyList(Vector<T>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Specify a new set of energies, all weights are reset to 1.0.
setEnergyList(Vector<MTBActiveContourEnergy>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Specify a new set of energies, all weights are reset to 1.0.
setEqualWeightsFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Set the "equal weights"-flag
setErodeSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of erodeSize.
setErodSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the size of the eroding element in pixel.
setESSPercentage(double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
Set percentage of number of samples used to determine if resampling is required, i.e. if it is below the current effective sample size (ESS).
setExcluded(Vector<Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
setExcludeList(int[]) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Specify attributes to be excluded.
setExcludeMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Specify exclude mask.
setExcludeMask(boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set exclude mask.
setFactor(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setFactoryMethod(MTBImage.FactoryMethod) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setFeatureOperators(Vector<FeatureCalculator>) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Set feature operators.
setFG_Value(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
set the intensity value of the remaining foreground regions
setFGOriginalValue() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Tell the thresholder to use the original pixel value for foreground pixels
setFGValue(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set value of Parameter argument FGValue.
setFieldSizeX(int) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the field size in x-direction.
setFieldSizeY(int) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the field size in y-direction.
setFilename(String) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set the filename for output
setFileName(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set the filename of the image that has to be read.
setFileName(String) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set image filename
setFill(Color) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setFill(double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setFilterImage(Boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set flag to use gaussian filter.
setFilterMode(MedialnessMultiScaleFilter2D.FilterMode) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set filter mode to define relation of foreground to background.
setFlagIsotropicCalculations(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Enable/disable isotropic calculations.
setFlagThrinkMatrix(boolean) - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
Flag for thrinking matrix if possible.
setForeground(DistanceTransform.ForegroundColor) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set the foreground color.
setForwardTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Toggle computation of the (forward) transform (image to wavelet)
setFps(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the frames per second for movie writers (*.avi,*.mov).
setFrequency(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify frequency.
setGamma(Double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set gamma correction value.
setGamma(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
setGamma(double) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set the gamma value.
setGammaToAuto(boolean) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set if gamma should be calculated automatically or not.
setGaussSigma(double) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify sigma for Gaussian smoothing.
setGraph(MTBGraph) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set the main graph using MTBGraph
setGrayValue(Double) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the gray value of the regions in a mask image (MASK_IMAGE only).
setGroundtruthObservations(Vector<MultiState<MotionModelID>>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
setGrownRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setH(double) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Set current h-parameter (max height of the h-domes).
setHaralickDirections(Vector<FeatureCalculatorHaralickMeasures.HaralickDirection>) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Set directions for which to calculate cooccurence matrices.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Specify height of filter mask.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set image height.
setHigherThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Specify higher threshold.
setHistogram(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
setHistoryLink(Object, ALDPort) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Sets the port to which the object is to be linked in history.
setHSIInput(double[]) - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSIToRGBPixelConverter
Specify HSI value to be converted.
setHueMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the hue channel image.
setHueThresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setID(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Set the ID of the region.
setID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Set the ID of the region.
setIgnoreBorderFlag(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Set flag to include/ignore structures along image border.
setIgnoreInvalidStackSpecification(boolean) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the flag to ignore an invalid stack specification.
setImageDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify input image directory.
setImageDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify input image directory.
setImageJPref(String, String, String) - Static method in class de.unihalle.informatik.MiToBo.core.helpers.MTBEnvironmentConfig
This functions sets a given property to the specified value.
setImagePart(MTBImageManipulator, int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set a part of this image to the values of the source
setImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Set output image type.
setImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the resulting image's datatype.
setImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set the image domain image
setInConst(double) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setIndexOfImageToRead(int) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set the index of the image that has to be read from the file.
setInfo(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Specify gray-scale input image.
setInImg(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Specify binary input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Input argument inImg.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
Set input image for morphological operation.
setInImg(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set the input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of inImg.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Set input image.
setInImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Input argument inImg.
setInImg1(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setInImg2(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setInitalSegmentation(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setInitBinImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of initBinImg.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify set of initial snakes.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify initial snakes.
setInitialSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Specify initial snakes.
setInitLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of initLabelImg.
setInitMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
setInitSegImageByte(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setInner(Vector<MTBBorder2D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Set the inner borders of the border object.
setInner(Vector<MTBBorder2D>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Set the inner contours of the contour object.
setInnerContourLengthMin(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set the minimum number of pixels in the inner contour (length of the contour).
setInputData(MTBTableModel) - Method in class de.unihalle.informatik.MiToBo.clustering.KMeans
Specify input data.
setInputGrayScaleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Specify input gray-scale image.
setInputGrayScaleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Specify input gray-scale image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Set the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Set uneven illuminated input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Specify the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Set low contrast input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.FeatureCalculator
Sets the input image to work on.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set the underlying input image of the gradient field.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Set input image to analyze.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify the input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Set the input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set input image.
setInputImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the current input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set a new input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set input image to process.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Specify an input image for the segmentation.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set input image
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Set input image.
setInputImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setInputImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set ImagePlus to store to disk
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Set input image.
setInputImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set input image
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Specify label input image.
setInputLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Specify label input image.
setInputMode(SegmentationInitializer.InputMode) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set input mode.
setInputMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set MTBImage to store to disk
setInputMTBImgRGB(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the input image.
setInputObservations(Vector<MultiState<MotionModelID>>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set input regions.
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the the input regions.
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the input regions to be drawn
setInputRegs(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Specify set of input regions.
setIntensityImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setIntermediateLS(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
 
setIntermediateResultDirectory(String) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Set intermediate result directory.
setIntermediateResultPath(String) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set path for intermediate results.
setInvalidImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of invalidImg.
setInvalidTilesNum(int) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Set number of invalid tiles.
setInverseTransform() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set computation of the inverse transform (wavelet to image)
setInvert() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Enable/disable inversion of mask.
setInvertMask(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Enable/disable inversion of mask.
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setInvisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y) invisible.
setInvisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y,z) invisible.
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setInvisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setInvisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setJmax(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set Jmax
setJmax(int) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set Jmax (maximum scale 2^Jmax - 1)
setJmin(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set Jmin
setKernelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set convolution kernel (image).
setKernelNormalization(boolean) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set value of Parameter argument kernelNormalization.
setKernelOrigin(int[]) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set value of Parameter argument kernelOrigin.
setKernelPart(GaborFilter2D.KernelPart) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify which kernel part should be generated.
setKernels(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set smoothing kernels
setKernelSize(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify size of the kernel.
setKernelTruncation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set kernel truncation factor.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Set label image of detected nuclei.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set the label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
Set Label image.
setLabelImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Set image of region labels
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of labelImg.
setLabelImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Specify label input image.
setLambda(double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ExponentialDistribution
 
setLength(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify length of vessels.
setLevel(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Set the tree level (level identifier).
setLinkageMode(XylemGrower.GrowingMode) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setLocation(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinates of current 3D point object.
setLocation(double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Overwrites Java Point2D method.
setLocation(Point2D) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Overwrites Java Point2D method.
setLocation(Point2D.Double, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Sets the location of this SnakePoint2D to the same coordinates as the specified Point2D.Double object.
setLocation(double, double, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Sets the location of this SnakePoint2D to the specified double coordinates.
setLowerThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Specify lower threshold.
setMad(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.
setMad(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Sets maximal allowed discrepancy of direct connection to actual profile between two peaks.
setMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify binary mask of nuclei.
setMask(MTBImage) - Method in class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Set optional exclude mask.
setMask(BasicMorphology.maskShape, int) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
setMask(MTBStructuringElement) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
setMaskDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify input mask directory.
setMaskDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify input mask directory.
setMaskFormat(ActinAnalyzer2D.CellMaskFormat) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify input mask format.
setMaskFormat(ActinAnalyzer2D.CellMaskFormat) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify input mask format.
setMaskRadiusC(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusC.
setMaskRadiusT(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusT.
setMaskRadiusX(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusX.
setMaskRadiusY(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusY.
setMaskRadiusZ(int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument maskRadiusZ.
setMax_d2c(float) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets factor to adjust maximal allowed distance from lower to upper peak.
setMax_d2c(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Sets factor to adjust maximal allowed distance from lower to upper peak.
setMaxAngle(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify maximal angle to apply.
setMaxAreaChange(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
setMaxDistance(double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
setMaximalComponentDistance(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set maximal component/pixel distance for linking.
setMaximalComponentSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set maximal component size for erasing large components.
setMaximalInstabilityScore(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set maximal instability score.
setMaximalSize(long) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set maximal size of valid regions.
setMaximalVoronoiExpansionDistance(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set radius of dilation mask in Voronoi expansion.
setMaxIter(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of maxIter.
setMaxIteration(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
setMaxIterations(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of maxIterations.
setMaxLevels(int) - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Specify maximum number of levels for iterative mode.
setMaxSpineLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set maximum length of a spine (filopodia-like protrusion) in pixel.
setMaxWeight(double) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Specify the maximum weight in the graph.
setMean(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
setMeanFreeData(boolean) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Set flag to indicate if data is already mean-free.
setMeasure(ImageStatistics.StatValue) - Method in class de.unihalle.informatik.MiToBo.features.statistical.FeatureCalculatorIntensityStats
 
setMeasurementUnit(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify unit for measurements.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Specify how to measure lengths and areas.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Specify units in which to measure areas.
setMeasureUnits(SegResultEnums.MeasureUnit) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Specify units in which to measure areas.
setMedianMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
setMinAngle(int) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify minimal angle to apply.
setMinAreaAfterErosion(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setMinAreaAfterOpening(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setminAreaSeedRegions(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setMinCompactness(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setMinimalBorderLength(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
Set the minimal border length.
setMinimalComponentSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set minimal component size for erasing small components.
setMinimalDiversity(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set minimal diversity.
setMinimalRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Specify minimal size of regions considered.
setMinimalSize(long) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set minimal size of valid regions.
setMinimumObjectArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
set the minimum area (number of pixels) a region must have in order to be kept
setMinRegionArea(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setMinRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set the minimum size of detected regions.
setMinSeedSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
setMinSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of minSize.
setMinSizeFraction(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of minSizeFraction.
setMinTrackLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setMinTrackLength(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set minimum track length
setMode(BasicMorphology.opMode) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
setModification(ImageValueTools.ImageValueModification) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setMorphOp(BasicMorphology) - Method in class de.unihalle.informatik.MiToBo.enhance.IlluminationCorrection
Set morphological operation for illumination correction, default is closing.
setMultiphase(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of multiphase.
setNarrowBandWidth(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Set width of narrow band.
setNegativeColor(ArrayToColorMapImage.RangeColor) - Method in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Color for negative values.
setNeighbourhood(XylemGrower.Neighbourhood) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setNeurite(MTBNeurite2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
setNeuriteSet(MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Set the input set of neurites.
setNeuronColor(NeuriteExtractor2D.NeuronColor) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set binary neuron color.
setNeuronImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set input image of the binary neuron.
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
 
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
 
setNewObservations(AbstractMultiState<S>, AbstractMultiObservationDistributionIndep<S, T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
 
setNode(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeData
Sets the node the object is associated with.
setNode(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
 
setNodeType(MTBNeuriteSkelGraphNode.MTBSkeletonNodeType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
 
setNormFromTo(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setNormTo(double, double) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
setNucDetector(NucleusDetector2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set detector for nuclei.
setNucleiAvgSize(double) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify average size of nuclei.
setNucleiChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set nuclei channel number.
setNucleiCount(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify number of segmented nuclei regions.
setNucleiMask(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Specify nuclei mask.
setNucleiRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify set of regions.
setNucleiResult(SegResult_Nuclei) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Set nuclei detection result.
setNucleusChannel(int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify image channel containing nuclei (just for reference).
setNumberOfComponents(int) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Number of sub-space components if reduction mode is NUMBER_COMPONENTS.
setNumIterations(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set number of iterations for the GVF field.
setNumIterations(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of numIterations Explanation: Number of iterations performed
setNuriteMaskSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set neurite mask size in pixel.
setObjectsEightConnected(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
are regions to be considered 8-connected (4-connected otherwise)
setObjectsEightConnected(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
setOldId(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
Set old index of current snake point within the snake.
setOpen() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Set polygon opened (not closed).
setOpeningSESize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setOperationType(FieldOperations2D.FieldOperation) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
 
setOpMode(NucleusSeparator2DBeamCut.NuclSeparateMode) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of opMode.
setOrientedFilter(OrientedFilter2D) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Specify the oriented filter to apply.
setOutImageType(ImageReaderMTB.OutImageType) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set the type of image object that is created as result image.
setOutputDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify output directory.
setOutputDir(ALDDirectoryString) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify output directory.
setOutputType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set output image type
setOverwrite(boolean) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the overwrite permission flag
setParent(MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Set the parent of this node.
setPartChannel(Integer) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set particle channel number.
setPartDetector(ParticleDetectorUWT2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Set detector for particles.
setParticle(int, G) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Set idx-th particle
setParticleImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Set particle image for particle detector.
setParticleResult(SegResult_Particles, int) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Set particle counts per channel.
setPath(String) - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Specify path associated with the node.
setPdf(int, ProbabilityDensityFunction) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussMixDistribution
 
setPdf(int, ProbabilityDensityFunction) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
setPerCellAvgSize(HashMap<Integer, Double>) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Sets particle average sizes per cell.
setPerCellCount(HashMap<Integer, Integer>) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Sets particle counts per cell.
setPercentageOfVariance(double) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Fraction of variance to be represented in the sub-space if the reduction mode is PERCENTAGE_VARIANCE.
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Set all points of the polygon from the specified point vector object.
setPoints(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Overwrite Polygon2D method to set all points of the snake from the specified point vector object.
setPoisson2Gauss(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set flag if input image with poisson noise is to be transformed to image with gaussian noise following J.
setPositionC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'c' in the c-dimension
setPositionT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 't' in the t-dimension
setPositionX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'x' in the x-dimension
setPositionY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'y' in the y-dimension
setPositionZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position to 'z' in the z-dimension
setPositiveColor(ArrayToColorMapImage.RangeColor) - Method in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Color for positive values.
setPreserveTopology(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of preserveTopology.
setPreserveTopology(Boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of preserveTopology.
setProfile(double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Pass profile data to the profile.
setProfilePoints(Vector<Vector<Point2D.Double>>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Set the points of the neurite region where the profiles are calculated from.
setQuality(Integer) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set the quality (quicktime only).
setRandom(Random) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set a random number generator to draw each region in a random color (COLOR_IMAGE only).
setRankOpMode(RankOperator.RankOpMode) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Parameter argument rankOpMode.
setReduceC(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Parameter argument reduceC.
setReducerMethod(ImageDimensionReducer.ReducerMethod) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Parameter argument reducerMethod.
setReduceT(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Parameter argument reduceT.
setReduceX(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Parameter argument reduceX.
setReduceY(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Parameter argument reduceY.
setReduceZ(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Parameter argument reduceZ.
setReductionMode(PCA.ReductionMode) - Method in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Specify the mode for selecting the sub-space dimensionality.
setRegionBinaryMode(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Specify region input mode.
setRegionID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Set the region id.
setRegionSet(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set the region set.
setREngine(Rengine) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Set R engine.
setResultCellImg(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Specify (optional) result image with cell contours.
setResultContourImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of ResultContourImage.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Set value of resultImg.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of ResultImage.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Set the resulting image.
setResultImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set resulting image
setResultImageStack(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Set stack with result segmentation images.
setResultImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
setResultImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
setResultImg(MTBImageShort) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Set value of resultImg.
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Set value of Output argument resultImg.
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set result image
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Set value of Output argument resultImg.
setResultingRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
Attach the vector of resulting regions.
setResultMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Set resulting image
setResults(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set detected regions
setResultsTable(MTBTableModel) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setResultType(GaborFilter2D.ResultType) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify result type.
setResultValueSelectionMode(ImageContrastReducer.ResultValueMode) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Set value selection mode.
setRevisionFile(String) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Set the name of the revision file.
setRoundnessThreshold(double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set roundness threshold for eliminating round components.
setSampling(int) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify angular sampling.
setSatMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the saturation channel image.
setSatTresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setSaveIntermediateResultPath(String) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set path where to save intermediate results.
setSavePath(String) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets the path to where intermediate snake results are to be written.
setSaveSnakes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
(De)activates saving of iteration step results.
setScaleDown(boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setScaleFactor(MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
set the scale factor if normalization is requested.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Set the scaling factor.
setScaleFactor(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Set the scaling factor.
setScaleFactor(double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Set the scaling factor.
setScaleFactor(double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Set the scaling factor.
setScaleIntervalSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Set the size of the scale interval for correlation images
setScaleMax(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set maximum of scales.
setScaleMin(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set minimum of scales.
setScaleNum(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set number of scales.
setScaleValues(boolean) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set flag if values are scaled to match the range of output type values if necessary
setSeedImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
setSeedPointImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
setSeErosionSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setSegDim(SegmentationInitializer.SegmentationDimension) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set target dimension.
setSegmentation(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Specifiy image segmentation.
setSegmentationDomain(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Specify the domain of the underlying segmentation.
setSeOpeningSize(int) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setShape(SegmentationInitializer.ShapeType) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Specify shape for synthetic initialization.
setShapeDimX(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set extent of shape in x dimension.
setShapeDimY(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set extent of shape in y dimension.
setShapeDimZ(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set extent of shape in z dimension.
setShapeForErosion(BasicMorphology.maskShape) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setShapeForOpening(BasicMorphology.maskShape) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 
setShapeMaskSizeX(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set size of shape mask in x dimension.
setShapeMaskSizeY(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set size of shape mask in y dimension.
setShapeMaskSizeZ(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set size of shape mask in z dimension.
setShapePosX(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set position of shape in x dimension.
setShapePosY(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set position of shape in y dimension.
setShapePosZ(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set position of shape in z dimension.
setShowSnakes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
(De)activates displaying of intermediate results during snake-iterations.
setSigmaC(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in c-dimension.
setSigmaInterpretation(GaussFilter.SigmaInterpretation) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set the mode of how sigmas are interpreted.
setSigmaT(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in t-dimension.
setSigmaX(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify Gaussian standard deviation in x.
setSigmaX(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in x-dimension.
setSigmaY(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D
Specify Gaussian standard deviation in y.
setSigmaY(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in y-dimension.
setSigmaZ(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
Set standard deviation (sigma) in z-dimension.
setSizeC(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeC(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in c-dimension.
setSizeDilation(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of sizeDilation.
setSizeOpening(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of sizeOpening.
setSizeT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeT(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in t-dimension.
setSizeTH(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of sizeTH.
setSizeX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeX(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in x-dimension.
setSizeY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeY(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in y-dimension.
setSizeZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeZ(Integer) - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
Set standard deviation (size) in z-dimension.
setSlice(MTBImageManipulator, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Copy the value of source to the specified slice
setSliceLabel(String, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the slice label of the slice specified by (z,t,c)
setSnakeIterations(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets number of iterations for snake optimization.
setSnakePoints(Vector<MTBSnakePoint2D>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Set all points of the snake from the specified SnakePoint2D vector object.
setSource(MTBImageManipulator) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set a new source for the window.
setSpacing(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of spacing.
setSpacingIntermediate(Integer) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Set value of spacingIntermediate.
setSrcNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set source node of the MTBGraphEdge.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
Specify standard deviation of Gaussian.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
Specify standard deviation of Gaussian.
setStandardDeviation(double) - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
Specify standard deviation of Gaussian.
setStartFrame(int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
setStartNode(MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Set a new start node.
setState(int, Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
Set the idx-th state (indices start from 0)
setState(int, Matrix, T) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
setStepsizeT(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the stepsize in t-dimension (timestep)
setStepsizeT(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the stepsize in t-dimension (timestep)
setStepsizeX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the physical size of a voxel (stepsize) in x-dimension
setStepsizeX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the physical size of a voxel (stepsize) in x-dimension
setStepsizeY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the physical size of a voxel (stepsize) in y-dimension
setStepsizeY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the physical size of a voxel (stepsize) in y-dimension
setStepsizeZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the physical size of a voxel (stepsize) in z-dimension
setStepsizeZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the physical size of a voxel (stepsize) in z-dimension
setString(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
Set the string data of the MTBStringData object.
setSuppressor(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Sets threshold to suppress peak analysis close to scraggy contours.
setSuppressor(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Sets threshold to suppress peak analysis close to scraggy contours.
setSVMFile(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
sets the path to a svm model file used for classification
setSVMFile(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
setSVMParameters(svm_parameter) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
setT(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setTargetContrast(ImageContrastReducer.TargetContrast) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Set target contrast.
setTargetImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Set target image.
setTargetImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
Specify a target image to which the regions are drawn, specify 'null' to create a new image
setTargetImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setTargets(Vector<CalcSegmentationStatistics.CalcTargets>) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Specify targets to calculate.
setTgtNode(MTBGraphNode<?>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Set target node of the MTBGraphEdge.
setTheta(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set coefficient to relate vessel radius and scale.
setThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set threshold for threshold mode.
setThreshold(Double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSegmentationNonPDE
Set value of threshold.
setThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set threshold
setThresholdImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
Set image for thresholding.
setThresholdingDirection(DetectMSERs.Thresholding_Direction) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs
Set direction of threshold compuations.
setThresTH(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of thresTH.
setTickLabelSize(int) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set size of tick labels on both axes.
setTickLabelSize(int) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set size of tick labels on both axes.
setTileShiftX(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify shift of tiles in x-direction.
setTileShiftX(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify shift of tiles in x-direction.
setTileShiftY(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify shift of tiles in y-direction.
setTileShiftY(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify shift of tiles in y-direction.
setTileSizeX(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify size of tiles in x-direction.
setTileSizeX(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify size of tiles in x-direction.
setTileSizeY(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Specify size of tiles in y-direction.
setTileSizeY(int) - Method in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Specify size of tiles in y-direction.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the image's title.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the images title
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set title of chart plot.
setTitle(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set title of chart plot.
setU(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set vector U of the field.
setU(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set value on (x,y) for vector U of the field.
setUnitAngle(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set unit of angles
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set unit of time
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the t-dimension
setUnitT(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the t-dimension
setUnitX(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the x-dimension
setUnitX(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the x-dimension
setUnitXY(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
setUnitXY(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
set unit of space
setUnitY(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the y-dimension
setUnitY(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the y-dimension
setUnitZ(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the unit of the z-dimension
setUnitZ(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Set the unit of the z-dimension
setup(String, ImagePlus) - Method in class mtb_io.Save_Image_MTB
 
setup(String, ImagePlus) - Method in class mtb_segmentation.Threshold_Image
 
setupEnergyTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Inits the table for sampled energy values.
setupEnergyTable() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Inits the table for sampled energy values.
setupParamConfigPanel() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
setupParamConfigPanel() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
setUseThresh(Boolean) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D
Set adaptive thresholding tag.
setUWT(MTBImageSet) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set UWT coefficient images
setV(double[], int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set value on (x,y) for vector V of the field.
setV(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Set value on (x,y) for vector V of the field.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBWrapperDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing
 
setValue(Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
Set the value of the double datat object.
setValue(Integer) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
sets the value for this object
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.ConfigureSegmentationButton
Set new values.
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Updates current initializer configuration.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
setValueAt(Object, int, int) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
 
setVectorField(MTBVectorField2D) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the operation based 2D vector field.
setVectorFieldImage(MTBImageDouble) - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Set the operation based 2D vector field image.
setVesselMode(MFFDOGFilter2D.VesselMode) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify detection scenario.
setVisibilityMask(boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Set the valid mask from external mask data.
setVisibilityMask(boolean[][][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Set the valid mask from external.
setVisibilityMask(boolean[][], int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Set the valid mask from external mask data.
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setVisible(int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y) visible.
setVisible(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Set position (x,y,z) visible.
setVisible(boolean[][][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Set visibility of positions.
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setVisible(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setVoronoiImg(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Specify an image to be filled with voronoi data.
setVotesAdjacency(int, int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setVotesClutter(int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setVotesTarget(int, int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setWeight(int, double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
setWeight(int, double) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Set weight for particle specified by idx.
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
 
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
 
setWeight(int, int, double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Sets the pixel weight of position (x,y) to c.
setWeight(int, int, int, double) - Method in interface de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface
Sets the pixel weight of position (x,y,z) to c.
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
 
setWeight(int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setWeight(int, int, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
setWeight(PartitGraphNodeID, PartitGraphNodeID, double) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
setWeight(T, T, double) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.AdjacencyMatrix
Set weight of edge from nodeSrc to nodeTgt.
setWeightAsEdgeThickness(boolean) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
Set flag how edge weights are visualized.
setWeights(double[]) - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
setWeights(Vector<Double>) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergy
Sets the weights for the energies.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
Specify new weights.
setWeights(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
Specify new weights.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Set image width.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set image width.
setWidth(Double) - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Specify width of vessels.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set image width.
setWidth(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set image width.
setWindowPosition(int, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Set the window's position in the source image.
setWthMaskSize(Integer) - Method in class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Set mask size of white top-hat.
setX(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setX(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinate of x-dimension.
setX(int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
setXAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set label of x-axis.
setXAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set label of x-axis.
setXML(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the XML file description string if one was available
setXMTBImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter
Set the value channel image.
setXThresh(double) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the Intensity/Brighntness/Value-Parameter (depending on the used input image type).
setXylemImage(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the Hue/Saturation/{Intensity|Brightness|Value}-MTBImage.
setXylemImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Set the input xylem image - this must be an 8bit image.
setXylemResultRegions(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Set the binary image after the morphological processing on the grown region image.
setY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setY(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinate of y-dimension.
setY(int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
setYAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Set label of y-axis.
setYAxisLabel(String) - Method in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Set label of y-axis.
setZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setZ(double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Set coordinate of z-dimension.
setZ(int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber.Point3D
 
sgn(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Signum function.
sgn(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Returns the sign of a value.
shape - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
ShapeAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
ShapeAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
constructor
shapeDimX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeDimY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeDimZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeMaskSizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeMaskSizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapeMaskSizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapePosX - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapePosY - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shapePosZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
shift(double, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Method to shift the whole polygon outward (positive value) ore inward (negative value) to its normal vector from every line segment.
shift(double, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to shift the whole snake outward (positive value) ore inward (negative value) to its normal vector from every line segment.
shiftX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Offset of the tiles in x dimension.
shiftY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Offset of the tiles in y dimension.
show() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Display the image as an ImagePlus.
showAboutBox() - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
 
showIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set flag to display intermediate results.
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Flag for displaying intermediate results.
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
showIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag to enable/disable showing of intermediate results.
showMasksOnly(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set flag indicating whether to show masks or overlays in result stack.
showOverlayImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Display current result contour by overlaying the current snake result onto the input image.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Display input image with current snake overlayed.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Display intermediate results by overlaying the input image with the current snake result.
showTrajectoryMap(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
signDistance(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Transform function into signed distance function.
simplify() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Deprecated. 
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Get the number of borders of this set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the number of contours of this contour set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Get the number of polygons of this polygon set.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Number of region sets in this bag
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Get the number of regions of this region set
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
Returns the number of elements in this list.
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
Returns the number of elements in this list.
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
snake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
The snake on which the algorithm works.
Snake_Optimizer - Class in mitoboRunner
ImageJ plugin to directly start the snake optimizer operator.
Snake_Optimizer() - Constructor for class mitoboRunner.Snake_Optimizer
 
snakeNum - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Number of snakes to be optimized.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Number of snakes currently managed.
snakeOpter - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Snake optimizer.
snakeOpters - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Array of individual snake optimizers.
SnakeOptimizer - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes.
SnakeOptimizer() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Default constructor
snakeOptimizer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Optimizer object for a single snake.
SnakeOptimizer.Snake_status - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Indicates the current (internal) state of the snake calculations.
SnakeOptimizerCoupled - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using multiple parametric snakes.
SnakeOptimizerCoupled() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Default constructor.
SnakeOptimizerCoupled(MTBImage, MTBPolygon2DSet, SnakeOptimizerSingle, boolean[]) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Default constructor.
SnakeOptimizerSingle - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes.
SnakeOptimizerSingle() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Default constructor.
SnakeOptimizerSingle.EnergyNormalizationMode - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Snake normalization mode.
SnakeOptimizerSingle.IntensityNormalizationMode - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image intensity normalization mode.
SnakeOptimizerSingleGreedy - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes with greedy optimization.
SnakeOptimizerSingleGreedy() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
SnakeOptimizerSingleVarCalc - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes.
SnakeOptimizerSingleVarCalc() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Default constructor.
SnakeOptimizerSingleVarCalc(MTBImage, MTBPolygon2DSet, MTBSet_SnakeEnergyDerivable, MTBGammaUpdate, Double, MTBTermination, Boolean, Double) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Default constructor with parameters.
solve() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Solve this level set problem.
spbox - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
splitFilename(String) - Static method in class cmdTools.mtb_imagetools.ImageConvert
 
sqrtSizeMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
sqrtSizeMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
sqrtSizeMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
sqrtSizeMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
src - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Source node of the MTBGraphEdge.
stackedBarChart - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Resulting stacked bar chart.
StackedBarChartPlotter - Class in de.unihalle.informatik.MiToBo.visualization.plots
Operator that generates stacked bar plots using JFreeChart.
StackedBarChartPlotter() - Constructor for class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Default constructor.
stackedBarCharts - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Resulting stacked bar plot of cluster distributions.
stageThreeMin - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Helper to make matrix minimum in stage three externally accessible.
standardization(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
stateConflict(Matrix, MultiState<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
StatisticsFilter - Class in de.unihalle.informatik.MiToBo.filters.nonlinear
class for calculating several statistical values for the neighborhood of the pixels
in an image
StatisticsFilter() - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
StatisticsFilter(MTBImage, StatisticsFilter.FilterMethod, int) - Constructor for class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
StatisticsFilter.FilterMethod - Enum in de.unihalle.informatik.MiToBo.filters.nonlinear
available filtermodes
status - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Status of current snake.
statuslabel1 - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
statuslabel2 - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
statusListeners - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2D
Vector of installed objects of type StatusListener.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Vector of installed StatusListeners.
statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Vector of installed StatusListeners.
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorConfigurationFrame
 
statusUpdated(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorControlFrame
 
statusUpdated(StatusEvent) - Method in class mtb_io.Open_Image_MTB
 
statusUpdated(StatusEvent) - Method in class mtb_io.Save_Image_MTB
 
step() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Do one iteration, update all pixels of levelset function (in narrow band).
StringAnalysis - Class in de.unihalle.informatik.MiToBo.tools.strings
Class providing helpers to analyze (sets of) strings.
StringAnalysis() - Constructor for class de.unihalle.informatik.MiToBo.tools.strings.StringAnalysis
 
stringToType(String) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
For a given String, return the corresponding MTBImageType.
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
Subtract the elements of two images (img1 - img2)
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.images.MTBImageArithmetics
Subtract the elements two images (img1 - img2)
subDim - Variable in class de.unihalle.informatik.MiToBo.math.statistics.PCA
Dimensionality of the sub-space as either specified by the user or automatically determined based on the percentage of variance.
subgraphID - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
The node's subgraphID
subgraphs - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subgraphs_adj - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subgraphs_adj_color - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
subgraphs_color - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
supportConversion(Class<?>, Type[], Class<?>, Type[]) - Method in class de.unihalle.informatik.MiToBo.core.dataconverter.MTBImageConverter
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
supportsStepWiseExecution() - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
SynchronizedImageWindows - Class in de.unihalle.informatik.MiToBo.gui
A class that synchronizes viewing of images for easier comparison.
SynchronizedImageWindows() - Constructor for class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 

T

tableToString() - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Converts the contents of the table to a string array in CSV format (suitable for import in Excel).
targetContrast - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
Target contrast of result image.
targetEnergyRange - Static variable in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Target interval boundaries of energy.
TargetID - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl
A target-ID class.
TargetID(short) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
Constructor.
targetIDtoIdx - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
targetImage - Variable in class de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage
Optional target image for result.
termCriterion - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Termination criterion.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Termination is done when the area difference of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Termination is done when the area difference of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Method to check termination status of the snake.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Termination is done when a maximum number of snake iterations is reached.
terminate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Termination is done when the snake control point motion of the former and the current snake is below a given fraction factor or if a maximum number of iterations is reached.
tgt - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Target node of the MTBGraphEdge.
threshDWTCoeffs(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshDWTJeffreys(MTBImage[], double, double[]) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshHigh - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Upper threshold.
threshImage(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshImgNiblack(MTBImage, double, int) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
threshLow - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.HysteresisThresholding
Lower threshold.
threshold - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
Higher threshold for binarization.
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
threshold(MTBImage, double, double, double, double, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Apply threshold to an MTBImage and create a new thresholded MTBImage.
threshold(MTBImage, MTBImage, double, double, double, double, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Apply threshold to an MTBImage and write results to a destination MTBImage.
Threshold_Image - Class in mtb_segmentation
Plugin for thresholding plain images, stacks and hyperstacks.
Threshold_Image() - Constructor for class mtb_segmentation.Threshold_Image
 
thresholdImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
threshScalingConstant - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D
Threshold scaling constant.
tickLabelSize - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Size of axes' tick labels.
tickLabelSize - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Size of axes' tick labels.
tileColumns - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Number of tile columns.
TileFeatureCalculator - Class in de.unihalle.informatik.MiToBo.features
Calculates features on images tile-wise, based on operators extending FeatureCalculator.
TileFeatureCalculator() - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Default constructor.
TileFeatureCalculator(int, int) - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Constructor with non-default tile sizes.
TileFeatureCalculator(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculator
Constructor with non-default tile sizes.
TileFeatureCalculatorResult - Class in de.unihalle.informatik.MiToBo.features
Result data of the operator TileFeatureCalculator.
TileFeatureCalculatorResult() - Constructor for class de.unihalle.informatik.MiToBo.features.TileFeatureCalculatorResult
Default constructor.
tileRows - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Number of tile rows.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Tile shift in x-direction.
tileShiftX - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Tile shift in x-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Tile size in y-direction.
tileShiftY - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Tile size in y-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Tile size in x-direction.
tileSizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Size of a tile in x-dimension.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D
Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorEigenStructures
Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinFeatureExtractorHaralickMeasures
Tile size in y-direction.
tileSizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageTileAdapter
Size of a tile in y-dimension.
time - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
A variable to store time information
timer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Timer object for time measurements.
TNclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
toArray() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
toByteImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Draw the skeleton graph into a binary image.
toCartesianAsPoint2D(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Converts an angle in degree to its corresponding in cartesian coordinates.
toCartesianAsVector(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Converts an angle in degree to its correspondant in cartesian coordinates.
toImage() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Visualize the skeleton graph as RGB image.
toImage(MTBImageRGB) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Draw the skeleton graph in the given RGB image.
toImage(Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Visualize the neurites skeleton graph as RGB image.
toImage(MTBImageRGB, Color) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Visualize the neurites skeleton graph in the given RGB image.
toMicrons(double, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Convert a value of given space unit to microns.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Draws border with all inner borders to a given image.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to save a region with in a given MTBImage image.
toMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to draw and save the snake in a given MTBImage.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D
Draws a border with all inner borders to a binary image with given size.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to save the region on a binary image with specific width and height.
toMTBImageByte(String, int, int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Method to save the region on a binary image with specific width, height and color.
toMTBImageByte() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Method to save all contours from the regions on a binary image with specific width and height.
toMTBImageByte(String, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Method to draw and save the snake in a binary image.
TopHatContrastEnhancement - Class in de.unihalle.informatik.MiToBo.enhance
This class enhances the contrast by top-hat operations, especially for gray value bright filed or DIC images.
TopHatContrastEnhancement() - Constructor for class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Standard constructor.
TopHatContrastEnhancement(MTBImageByte, Integer, Integer) - Constructor for class de.unihalle.informatik.MiToBo.enhance.TopHatContrastEnhancement
Constructor to create a new IlluminationCorrection object.
topologyPreservation - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
topoNumberIsOne(int[][][], int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Check if topological for the class c is one in the neighborhood nbClassess3D.
topoNumberIsOne(MTBSegmentationInterface, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
Check if topological for the class c is one in the pixel with coordinate (x,y,z) in the segmentation object segmentation.
topoNumberIsOne(int[][][], int) - Method in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber2D
 
toPositiveAngle360(double) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Simple way to convert negative angles to 0-360 degree.
toRGB() - Method in class de.unihalle.informatik.MiToBo.color.conversion.HSVToRGBPixelConverter
Method to convert a single color from HSV color space into RGB color space.
toSeconds(double, String) - Static method in class de.unihalle.informatik.MiToBo.io.tools.ImageIOUtils
Convert a value of given time unit to seconds.
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Returns the String "IMG("title of the image")"
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBDoubleData
 
toString() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
toString() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Return an ascii representation identifying the energy and internal parameters, but not the state.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Return a string representation.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyComputable
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSet_SnakeEnergyDerivable
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
 
toString() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Get an identifier string for the energy object.
toString() - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Get an identifier string for the energy object.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdapt
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptNone
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdapt
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptNone
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaNone
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaPtWiseExtEner
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Method for short adaptation description name.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Method for short termination description name.
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
 
toString() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.GraphNodeID
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.PartitGraphNodeID
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
toSWC(String, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Method to save neurite skeleton graph as SWC file.
totalObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
total number of observations over all frames
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
 
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Generate xml-representation of this 3D-point.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Create a xml representation of this polygon set using MiToBo's xml-scheme MTBXMLPolygon2DSet.xsd
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Construct an object that represents this region by xml.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Create a xml representation of this bag of region sets using MiToBo's xml-scheme MTBRegion2DSetBag.xsd
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
 
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Construct an xml-representation of this set of 3D-regions.
toXMLType(Matrix) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Convert a JAMA matrix to its xml-beans type
toXMLType(MultiState<MotionModelID>) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Convert a MultiState object to its xml-beans representation
toXMLType(Vector<MultiState<MotionModelID>>) - Static method in class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
Convert a Vector> object to its xml-beans representation
toXMLType() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MotionModelID
Convert this object to its XML-representation.
TPclutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
TPtrackend - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
TPtracksegment - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
TPtrackstart - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
traceContour(int, int, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Trace contour, starting at (xS, yS) in direction dS.
TrackAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
class for analyzing movement and shape of already tracked objects in a given label image
TrackAnalyzer(Vector<Trajectory2D>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
TrackAnalyzer(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
trackcolors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
trackcolors - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
trackerOutputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
trackEvalResult - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
TrackEvaluator - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluator(Vector<MultiState<MotionModelID>>, Vector<Vector<MultiState<MotionModelID>>>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
TrackEvaluator.TrackEvaluatorResult - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluator.TrackEvaluatorResult() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
trackgraphs - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
trackImage - Variable in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
trackingtime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
time that elapsed for tracking
TrackVisualizer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
TrackVisualizer(MTBImage, Vector<Trajectory2D>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
trafo - Variable in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
 
Trajectory2D - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
Trajectory2D(int, int, Vector<Point2D.Double>) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
Trajectory2D(int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
Trajectory2D(int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
TrajectoryExtraction2D - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
TrajectoryExtraction2D(MTBImage, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
transform(Matrix) - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
Transform the (column) vector x and add noise sampled from the Gaussian noise distribution.
transform(GaussianDistribution) - Method in class de.unihalle.informatik.MiToBo.math.LinearTransformGaussNoise
Transform the Gaussian distribution gaussian with this transform.
transform(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Compute the h-dome transform
translate(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Translate current coordinates of the 3D point object.
trim(Hashtable<Integer, Vector<Double>>, int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
truncate(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
truncate the histogram to the specified interval
TwoColumnPanel - Class in de.unihalle.informatik.MiToBo.gui
A panel with a titled border and two columns for a variable number of generic components that are placed vertically with an additional label.
TwoColumnPanel(String) - Constructor for class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
Constructor
type - Variable in exception de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException
Type of exception.
typeoftime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 

U

ulimits - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
UndecimatedWaveletTransform - Class in de.unihalle.informatik.MiToBo.transforms
Undecimated wavelet transform (UWT) operator.
UndecimatedWaveletTransform() - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for dimension x, y and z.
UndecimatedWaveletTransform(MTBImage, int, boolean, MTBImage[]) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Constructor.
UndecimatedWaveletTransform(MTBImage, int, boolean) - Constructor for class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Constructor with default Gaussian kernel [1/16, 1/4, 3/8, 1/4, 1/16] for at most dimension x, y (and z if present).
UndecimatedWaveletTransform.TransformationMode - Enum in de.unihalle.informatik.MiToBo.transforms
 
UniformDistribution - Class in de.unihalle.informatik.MiToBo.math.distributions.impl
A multivariate uniform distribution.
UniformDistribution(int, double[], double[], Random) - Constructor for class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
Constructor for uniform distribution with hypercube shape in dimension DOF, given lower and upper limits in the corresponding dimension and a random generator for sampling.
unitAngle - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Particles
Unit in which measurements are provided.
units - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Unit in which measurements are provided.
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
unitVector(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Return the unit vector of vector.
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
unsetActualSliceOnly() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
The whole image is thresholded (default)
unsetAssociation(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.DataAssociationExclusive
Unsets the association of the specified observation and state.
unsetAssociation(int, int) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.interfaces.DataAssociation
Unset the association between target and observation.
UNTITLED - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Title string for new and untitled images
update(AbstractMultiState<MotionModelID>, DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
update(T, DataAssociation) - Method in interface de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetPredictionFilter
Update step method given a multi-target observation
update(AbstractMultiState<T>, DataAssociation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
The DataAssociation object may be null and is interpreted as groundtruth if given.
update(LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
updateAndRepaintWindow() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update and repaint the image window if the image is displayed by ImageJ
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Should be used to create or update ImagePlus data if the MTBImage is not using an ImagePlus to store the data (MTB_INT, MTB_DOUBLE, MTB_RGB).
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageByte
Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageDouble
Creates or updates an ImagePlus of Float type from the MTBImage Double data, can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageFloat
Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
Creates or updates an ImagePlus of Float type from the MTBImage Int data, which can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
Creates or updates an ImagePlus of RGB type from the MTBImage RGB(3 byte-channels) data, can be returned by getImagePlus() or displayed by show()
updateImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
Does nothing, because the underlying ImagePlus is updated immediately when values are changed in the MTBImage
updateImageSize_ImgToProp() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update the image size in the properties hashtable from the image's size
updateIndep(int, LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
updateIndep(int, int, LinearTransformGaussNoise, AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
Update i-th Gaussian component with j-th observation
updateOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Update current overlap mask for all snakes.
updateParameters(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
Updates parameters according to given membership.
updateParameters(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Updates internal parameters according to given segmentation.
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
updateParams(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
 
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
updateParams(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBEnergySumNonPDE
 
updateParams(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Update parameters (if any) of the energy object which depend on the associated level set function.
updateParams(int, int, int, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Update parameters (if any) of the energy object which depend on the associated level set function.
updateParams(int, int, int, byte, MTBLevelsetMembership) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
updatePhysProperties_ImgToProp() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update physical properties (stepsizes, units) in the properties hashtable from its member variables
updatePhysProperties_PropToImg() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Update physical properties (stepsizes, units) of the image (member variables) from its properties hashtable
updateRegions() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Update neurite shaft and growth cone regions, due to changes of this regions by adding features or something else.
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
updateStatus(MTBLevelsetFunctionDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
updateStatus(MTBLevelsetFunctionDerivable) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Function which updates the internal status of the energy.
updateStatus(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
updateStatus(SnakeOptimizerCoupled) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
updateStatus(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
updateStatus(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Update internal state of energy object prior to querying derivatives and so on.
updateStatus(SnakeOptimizerCoupled) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCoupled
Update internal state of energy object prior to querying derivatives and so on.
updateStatus(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Update internal state of energy object prior to usaging it.
useAutoDistanceDetermination(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
useExternalSVM(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
useHeavideApproximation(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
useHeavideApproximation(boolean) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Enable or disable approximation of Heaviside function.
UserTime - Class in de.unihalle.informatik.MiToBo.tools.system
This is a stopwatch to measure elapsed user or real time used.
UserTime() - Constructor for class de.unihalle.informatik.MiToBo.tools.system.UserTime
Creates a new time object and starts the clock.
UserTime(boolean) - Constructor for class de.unihalle.informatik.MiToBo.tools.system.UserTime
Creates a new time object and starts the clock elapsing real time.

V

valid(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
Validity of point (x,y,z).
valid(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
is this pixel valid?
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Area
 
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_CVRegionFit
 
validate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelEnergyDerivable_Length
 
validate() - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.energies.derivable.MTBLevelsetEnergyDerivable
Function to validate configuration of energy object.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NuclearParticleDetector2D
Custom validation of some input parameters.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.ChaudhuriMatchedFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaussPDxxFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
The validation of parameters and inputs.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.linear.MeanFilter
The validation of parameters and inputs.
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.images.ImageArithmetics
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.convert.Region2DSetFromLabelimage
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.CropImage
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageToTilesSplitter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.DrawTracks2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.visualization.drawing.MTBPlotHistogram
 
validMultiState(AbstractMultiState<T>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiStateFactory
Test if the specified multistate is valid for this factory.
value - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE.SortedListElement
 
valueOf(String) - Static method in enum de.unihalle.informatik.Alida.admin.annotations.ALDMetaInfo.ExportPolicy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D.CellMaskFormat
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D.FeatureType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.InputType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage.RangeColor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType
Returns the enum constant of this type with the specified name.
values() - Static method in enum de.unihalle.informatik.Alida.admin.annotations.ALDMetaInfo.ExportPolicy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D.CellMaskFormat
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.actinAnalysis.ActinAnalyzer2D.FeatureType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.InputType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.GrowingMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.Neighbourhood
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower.SortMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.ColorChannel
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.color.conversion.RGBToHSXConverter.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.color.visualization.ArrayToColorMapImage.RangeColor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.InputMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing.OutputMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2D.BorderConnectivity
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.core.exceptions.MTBDatatypeException.DatatypeExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.features.texture.FeatureCalculatorHaralickMeasures.HaralickDirection
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.KernelPart
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.GaborFilter2D.ResultType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.anisotropic.OrientedFilter2DBatchAnalyzer.JoinMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MedialnessMultiScaleFilter2D.FilterMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGFilter2D.VesselMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.filters.vesselness.MPMFFilter2D.VesselMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageArithmetics.ArithOp
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.images.ImageStatistics.StatValue
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.math.statistics.PCA.ReductionMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.CalcTargets
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.InputMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.SegmentationDimension
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializer.ShapeType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.BordersOnLabeledComponents.BorderType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.core.DeltaApproxHelper.ApproxVersion
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE.VelocityExpansionMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.regions.mser.DetectMSERs.Thresholding_Direction
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.ResultValueMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageContrastReducer.TargetContrast
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum de.unihalle.informatik.MiToBo.visualization.drawing.DrawRegion2DSet.DrawType
Returns an array containing the constants of this enum type, in the order they are declared.
vectorDiff(double[], double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Subtract two vectors.
VectorField2DPotentialFinder - Class in de.unihalle.informatik.MiToBo.fields
Routines for reconstructing potential from vector field.
VectorField2DPotentialFinder() - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Standard constructor.
VectorField2DPotentialFinder(MTBVectorField2D) - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Default constructor.
VectorField2DPotentialFinder.PotentialFinderOptFunction - Class in de.unihalle.informatik.MiToBo.fields
Optimization function for gradient-based potential reconstruction.
VectorField2DPotentialFinder.PotentialFinderOptFunction(boolean) - Constructor for class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
Default constructor.
vectorNorm(double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Returns the norm of a vector.
vectorSum(double[], double[]) - Static method in class de.unihalle.informatik.MiToBo.apps.xylem.MathHelper
Sums up two vectors.
vectorToString(Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
vectorToString(int, Vector<Double>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaUpdate
Flag to turn display of additional information on/off.
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermination
Flag to turn display of additional information on/off.
verbosePrintln(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
prints the given text if the verbose flag is set
vExpandMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
 
vidpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
visibilityMapHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Height of visibility map.
visibilityMapWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Width of visibility map.
visible - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Visibility array.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Visibility map for hiding individual pixels.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Visibility map for hiding individual pixels.
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Visibility map for hiding individual pixels.
visibleMapMaxX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal x coordinate of visibility map.
visibleMapMaxY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal y coordinate of visibility map.
visibleMapMinX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal x coordinate of visibility map.
visibleMapMinY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal y coordinate of visibility map.
vol - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
VoronoiExpandComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Dilate components, but avoid merges.
votesClutter - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
votesTarget - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 

W

wantStackWithIntermediateResults(boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Flag for turning on/off generation of stack with intermediate results.
weightAsEdgeThickness - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
weightmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Map of weights for the segmentation.
weightmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation3D
Map of weights for the segmentation.
weights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.MixtureDistribution
 
weights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
weights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
List of energy weights.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentation2D
Width of segmentation domain.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.datatypes.MTBLevelsetFunctionPDE
Width of the input image and levelset function.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.PDE.solver.LevelsetSolverPDE
Width of the input image.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Width of the given image for the energy.
widthLengthTab - Variable in class de.unihalle.informatik.MiToBo.filters.vesselness.MFFDOGMultiScaleFilter2D
Table with vessel widths and lengths to apply.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing.SegmentationConfigWin
Main frame.
workingImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Image on which to actually do the segmentation.
workingMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Local copy of matrix modified during calculations.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Write this contour set into XML file filename.xml Additionally, its processing history is written.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Write this polygon set as xml into file filename.xml Additionally the processing history is written.
write(String, boolean) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Write this polygon set as xml into file filename If flag is set to true, the processing history is written, too.
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Write this region set to disk in XML format using MiToBo's xml-scheme MTBRegion2DSet.xsd
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
Write this bag of region sets to disk in XML format using MiToBo's xml-scheme MTBRegion2DSetBag.xsd
write(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Write this set of 3D-regions to disk in XML format using MiToBo's xml-scheme MTBRegion3DSet.xsd
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerImageData
 
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerRegion2DSet
 
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerSegResultParticlesMultiChannel
 
writeData(ALDBatchRunResultInfo, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.output.swing.MTBSummarizerTableModel
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBWrapperDataIOSwing
 
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBDataIOFile
 
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.cmdline.MTBImageDataIO
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.AwtColorDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBDataIOFileSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBJFreeChartDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.AwtColorDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBDataIOFileXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBImageDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBTableModelDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.MTBWrapperDataIOXmlbeans
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.xmlbeans.RandomGeneratorDataIOXmlbeans
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
writeData(Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOXmlbeans
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.segmentation.basics.SegmentationInitializerDataIOSwing
 
writeImagePlus(String, ImagePlus) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Write ImagePlus to disk
writeMTBImage(String, MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Write an MTBImage to disk
writeMultiStates(Vector<MultiState<MotionModelID>>, String) - Static method in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.MultiStateIO
Write a vector of MultiState objects to file in its xml-beans representation.
WRITER_OPTIONS_APPROVED_PROPERTY - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
Property change when writer options are approved (i.e. when filechooser selection is approved)

X

x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at x-dimension.
X - Variable in class de.unihalle.informatik.MiToBo.topology.MTBTopologicalNumber
8- or 26 neighbors of the current pixel used to determine topological numbers represented as an 3x3x3 array center around the current pixel.
xFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Vector field flow in x-direction.
xFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.
xLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Label of the x-axis.
xLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Label of the x-axis.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Maximal x-coordinate of the domain of this border set.
xMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
xMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Minimal x-coordinate of the domain of this border set.
xMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
xMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
xml - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
File description XML string if available
XMLTypeConverter - Class in de.unihalle.informatik.MiToBo.tools
A class providing static methods to convert specific object to and from their corresponding xml-types provided by xml-beans.
XMLTypeConverter() - Constructor for class de.unihalle.informatik.MiToBo.tools.XMLTypeConverter
 
Xylem_Detector - Class in mitoboRunner
ImageJ plugin to directly start the xylem detector.
Xylem_Detector() - Constructor for class mitoboRunner.Xylem_Detector
 
XylemDetector - Class in de.unihalle.informatik.MiToBo.apps.xylem
This operator implements xylem detection in RGB or HSX images.
XylemDetector() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemDetector
Default Constructor.
XylemGrower - Class in de.unihalle.informatik.MiToBo.apps.xylem
This operators implements region growing for xylem segmentation.
XylemGrower() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
Default Constructor.
XylemGrower(MTBImageByte, MTBImageByte, XylemGrower.GrowingMode) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemGrower
 
XylemGrower.GrowingMode - Enum in de.unihalle.informatik.MiToBo.apps.xylem
The region growing modus.
XylemGrower.Neighbourhood - Enum in de.unihalle.informatik.MiToBo.apps.xylem
The kind of neighbourhood to inspect a pixel.
XylemGrower.SortMode - Enum in de.unihalle.informatik.MiToBo.apps.xylem
Sort Mode for different MTBRegion2D's.
XylemInitialSegmentation - Class in de.unihalle.informatik.MiToBo.apps.xylem
Purpose of this operator is to make an initial segmentation of Xylem Cell Images.
XylemInitialSegmentation() - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
Default constructor.
XylemInitialSegmentation(MTBImageByte) - Constructor for class de.unihalle.informatik.MiToBo.apps.xylem.XylemInitialSegmentation
 

Y

y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at y-dimension.
yFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Vector field flow in y-direction.
yFlow - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The flows of the field in x- and y-direction.
yLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter
Label of the y-axis.
yLabel - Variable in class de.unihalle.informatik.MiToBo.visualization.plots.StackedBarChartPlotter
Label of the y-axis.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Maximal y-coordinate of the domain of this border set.
yMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
yMax - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBBorder2DSet
Minimal y-coordinate of the domain of this border set.
yMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
yMin - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 

Z

z - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at z-dimension.
Z - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
observations
Zadj - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
adjacency votes matrix: which observations are associated (same track) and how many particles vote for these associations

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