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

A - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Optimization matrix A, to be modified by snake energies in each iteration.
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.ImageArithmetics
Absolute values of the image elements.
abs(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Absolute values of the image elements.
abs_diff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Absolute difference of the elements of two images
absDiff(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.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
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing.ColorChooserButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
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.MTBTableModelDataIOSwing.TableModelShowButton
 
actionPerformed(ActionEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
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.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
 
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.
actualSliceOnly - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
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(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.ImageArithmetics
Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Add the elements of two images
add(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Add a constant to each image value
add(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Add the elements two images
add(TrackEvaluator.TrackEvaluatorResult) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
 
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(MTBSnakeEnergyDerivable, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSet_SnakeEnergyDerivable
Append another energy to the list.
addEnergy(MTBSnakeEnergyDerivable) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSet_SnakeEnergyDerivable
Append another energy to the list with default weight 1.0.
addEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Add button for energies.
addFeatures(double, double[]) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
add the given patterns (feature arrays) together with their corresponding label to the existing patterns used to train the SVM
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(MTBContour2D) - 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.MTBContour2D
Add a 2D point to the existing contour.
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.
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.GaussFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
addStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
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.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 java.lang.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
alpha - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
alpha - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Weighting factor for snake length term.
alphaDecrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassLength_ParamAdaptFix
Value by which alpha is decreased in each iteration.
alphaInitial - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Initial weighting factor for the length term, should be > 0.
alphas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Vector of point-specific alpha values.
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.
analyzedImages - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Vector with all analyzed image files.
analyzeIntensities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeIntensities(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeIntensities - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
analyzeShapes - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeShapes(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeShapes - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
analyzeTrajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeTrajectories(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
analyzeTrajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Bitwise logical AND of two images.
and(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Bitwise logical AND of two images.
angle(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
applyComponentWise - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Flag to activate component-wise application, yields a binary result image.
applyMask(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Invokes dilation.
applyMask(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Invokes erosion.
applyMaskBinary(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Applies a dilation mask to the given binary image.
applyMaskBinary(MTBImage, int, int, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Applies an erosion mask to the given binary image.
applyMaskGray(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
Applies a dilation mask to the given intensity image.
applyMaskGray(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgErode
Applies an erosion mask to the given intensity image.
applyNiblackThreshold(MTBImage, int, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
This function implements the conventional (enhanced) Niblack binarization.
applyNiblackThreshold_withLocalVarCheck(MTBImage, int, double, double, int, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
This function implements the conventional Niblack binarization, enhanced with a local variance check.
applyNiblackThresholdMaskwise(MTBImage, int, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Enhanced Niblack binarization applied maskwise to the image, i.e. all pixels inside the mask get the same threshold.
applyNiblackThresholdWholeImage(ImageProcessor, double, double, ImagePlus) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Deprecated. 
applyNiblackThresholdWholeImage(MTBImage, double, double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
This function implements the conventional (enhanced) Niblack binarization.
area - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Size of region in pixels.
areaFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Area fraction factor.
areaFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
Area fraction factor.
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.
areas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
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.
arithmeticOp - Variable in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
assign(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
assign regions from one frame to regions from another frame
assignStructsToCell_com(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Assigns the given set of structure regions to individual cells.
assignStructsToCell_overlap(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Assigns the given set of structure regions to individual cells.
asSnakes - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Flag to either return snakes or polygons.
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
 
AssociationDistributionNN.AType() - Constructor for enum de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.AType
 
AssociationDistributionNN.ObsDistance - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
AssociationDistributionNN.ObsDistance(double, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
AssociationDistributionNN.ProbTreeData - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl
 
AssociationDistributionNN.ProbTreeData() - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
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
auto - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
availableClasses - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
List of available energies.
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.
avgNeuriteWidths - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Vector of neurite widths, containing 3 elements. 1. average width of whole neurite, 2. average width of neurite shaft, and 3. average width of growth cone.
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
Data I/O provider for Cmdline-OpRunner for java.awt.Color objects.
AwtColorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOCmdline
 
AwtColorDataIOSwing - Class in de.unihalle.informatik.MiToBo.core.dataio
Data I/O provider for GUI-OpRunner for java.awt.Color objects.
AwtColorDataIOSwing() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing
 
AwtColorDataIOSwing.ColorChooserButton - Class in de.unihalle.informatik.MiToBo.core.dataio
 
AwtColorDataIOSwing.ColorChooserButton(Color) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing.ColorChooserButton
 

B

B - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
External energy vector, to be modified by snake energies.
background_color - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
 
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.maskShape - Enum in de.unihalle.informatik.MiToBo.morphology
 
BasicMorphology.maskShape() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.maskShape
 
BasicMorphology.opMode - Enum in de.unihalle.informatik.MiToBo.morphology
 
BasicMorphology.opMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.BasicMorphology.opMode
 
beta - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
beta - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Weighting factor for snake curvature term.
betaDecrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.paramAdapt.MTBSnakeEnergyCD_KassCurvature_ParamAdaptFix
Value by which beta is decreased in each iteration.
betaInitial - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Weighting factor for the curvature term, should always be > 0.
betas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Vector of point-specific beta values.
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
 
bgLabel - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
bgValue - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
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
black - Variable in class mtb_segmentation.Threshold_Image
black value for current image
blacklist - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
blackTophat(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
calculates the black tophat transform, i.e. difference of the closing of the image and the image
(also called closing tophat)
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
boundaryPadding - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
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.
boxLinksImagePlus - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Associative list for links between ImagePlus and associated image boxes.
boxLinksMTBImage - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Associative list for links between MTBImages and associated image boxes.
build(int, int, MTBImageByte, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Internal method to create the graph from the skeleton image.
buildMainPanel(Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Build the main panel for configuring the list of energies.
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.
button - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
buttonEdit - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
buttonLoad - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
buttonShow - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
buttonView - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
BWImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 

C

C - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
c - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
c - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
array to hold means of phases, starting with MTBLevelsetMembership.BG_PHASE
c - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
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.
calcDefaultDomain() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Calculates snake bounding box (in non-normalized coordinates!).
calcDM() - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Method to calculate the distance map of the given binary image using the Chamfer-algorithm.
calcEnergy(MTBSegmentationInterface) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_CVRegionFit
 
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
 
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
 
calcEnergy(SnakeOptimizerSingle) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Calculates the energy of the current snake.
calcEnhancedImage(MTBImage, double, int, boolean) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Calculates the new image intensity values of the image.
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.
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.
calcMaxSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Calculates the maximum size of the set.
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.
calcProfile() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
calcRadiusImage - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Flag to enable calculation and display of radius image (only in non-component mode).
CalcSegmentationStatistics - Class in de.unihalle.informatik.MiToBo.segmentation.basics
Helper class for doing statistical calculations on 2D/3D grayscale 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.
CalcSegmentationStatistics.calcTargets() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics.calcTargets
 
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.
CalcStructureStatistics.StructureCountMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics.StructureCountMode
 
calcThreshold(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Calculate Otsu threshold on given image.
calcThreshold(MTBImageHistogram) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Calculate Otsu threshold on given histogram.
calcTStD(double, double) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Calculates the threshold for the local standard daviation.
calibration - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
calibration object (from ImageJ)
callingOperator - Variable in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
 
callNeuriteScript(String, String) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Call a specified R script for neurite calculations.
callNeuriteSrcipt(Rengine, String, String[]) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Call a specified R script for neurite calculations.
calStDI(MTBImage) - Static method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Calculates the standard deviation of the given image.
candidates - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
cb - Variable in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
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
cellChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Channel for cell boundary detection.
cellContours - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Set of detected cell boundaries.
cellLabelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Label image of cell areas.
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
 
CellTrackerBipartite() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
CellTrackerBipartite(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
centerX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
centerY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
centroid - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
The centroid of the region (not normalised by volume!)
centroids - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
cgal_isClockwiseOriented(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
 
cgal_isConvex(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
 
cgal_isCounterclockwiseOriented(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
 
cgal_isSimple(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Checks if a polygon is simple.
cgal_makePolySimple(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
Simplifies the given polygon.
cgal_orientation(double[], double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
 
cgal_signedArea(double[], double[]) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
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.enhance.GammaCorrection2D
 
channelIdx - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
channelsAreRGB - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
channelsToCopy - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Set of image channels to copy into result stack.
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
checkSelectionConsistency() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
 
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.
cl - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
classify(MTBImage, MTBImage, String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
decide, whether the given entropy image contains an open scratch or not
classify(double[]) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
classLock - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Lock variable to make singleton thread-safe.
classmap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
2D map marking the region enclosed by the snake.
classNameMapping - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Mapping of short names to class objects.
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.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.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.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
close(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
closeButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Close button.
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
 
closingMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
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 de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
codec - Variable in class mtb_io.Save_Image_MTB
codec option if available
codpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
coffset - Variable in class de.unihalle.informatik.MiToBo.drawing.DynamicColorLUT
 
colMarkers - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Array containing column marks.
color - Variable in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing.ColorChooserButton
 
color - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawPolygon2DSet
 
color - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
color2int(Color) - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
color_blue - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
color_graphEdge - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of graph edge points.
color_graphNode - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of graph node points.
color_red - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
color_skelBranch - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of pre-detected branch points.
color_skelSpecial - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of pre-detected special points, for example a 2x2 skeleton region.
color_skelVisitB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of visited graph branch points.
color_skelVisitE - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Color of visited graph edge points.
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.
colorFG - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
colorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
colorPlot() - Method in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Plots the field in colored image.
colors - Variable in class de.unihalle.informatik.MiToBo.drawing.DynamicColorLUT
 
cols - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Number of columns of the table.
com_x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Center of mass in x (just sum, not normalized by area!).
com_y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Center of mass in y (just sum, not normalized by area!).
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
 
compare(TrackEvaluator.TrackObservation, TrackEvaluator.TrackObservation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
compare(TrackEvaluator.TrackSegment, TrackEvaluator.TrackSegment) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
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
 
compareTo(AssociationDistributionNN<S, T>.ObsDistance) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
compareTo(TrackEvaluator.TrackObservation) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
compareTo(TrackEvaluator.TrackSegment) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
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.
ComponentPostprocess.ProcessMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess.ProcessMode
 
comppanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
compression - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
compression - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
compression - Variable in class mtb_io.Save_Image_MTB
compression option if available
compute_pczAhead(MTBTreeNode, Vector<Integer>, Stack<Integer>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Compute probability of all possible associations of neighboring observations including their likelihood
compute_qAhead(int, int, int, int, double, MTBTreeNode) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN
Compute tree of data association prior probabilities depending on previous associations.
computeESS() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Compute effective sample size (ESS).
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
confButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Button to display configuration window.
confEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Config button for energies.
configureSnakes(double, int, double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Configures basic snake parameters.
confObj - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
The object instance.
confWin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
confWin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
confWin - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Collection configuration window.
connectNodesCase1(MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, MTBGraphNode<PartitGraphNodeID>, boolean) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Connect nodes if case 1
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.
containsImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Checks if the box contains an ImagePlus.
containsMTBImage() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Checks if the box contains a MTBImage.
containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Checks if a given point is part of the segment.
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.ContourType - Enum in de.unihalle.informatik.MiToBo.segmentation.contours.extraction
The possible type of contours for segmentation.
ContourOnLabeledComponents.ContourType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents.ContourType
 
contourSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
The set of contours represented as a Vector.
contourSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBContour2DSetROI
Set of 2D contours.
contourType - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Special type of contours to calculate.
contrastEnhancer - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
 
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
convertContourToSnake(MTBContour2D) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Converts a contour into a snake.
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.
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.
correctDirectness(MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Method to correct the direction of every edge inside the skeleton graph from a given root node.
correctGamma(MTBImage, double, int) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Perform gamma correction to the specified channel of the input image, using the given gamma value.
correctGammaAuto(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
Perform gamma correction to the specified channel of the input image.
corrThreshold - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
cost - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphEdge
Cost of the MTBGraphEdge.
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.MTBContour2D
Get the number of inner contours including in the contour object.
countMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Mode for assigning structures to regions.
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
 
cparticles - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
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
 
createColorImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
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.AwtColorDataIOSwing
 
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.MTBDataIOFileSwing
 
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.MTBImageDataIOSwing
 
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.
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
 
createInitBar(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
create rectangular shaped bar as initialization for the scratch
createInitialStates() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
createLabelImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
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
 
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
 
createRectangularElement(int, int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
createRengine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Method to generate a R thread inside the java application.
createRengine() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to generate a R thread inside the java application.
createResultDir(String) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Create directory where all results will be stored.
createVerticalLineElement(int) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
ctrPoints - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
cumulate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
calculate the cumulative histogram
cumulatedObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
cumulated number of previous observations for each time step, required to determine the individual array sizes in the adjacency matrix
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
currentfile - Variable in class mtb_io.Open_Image_MTB
 
currentfileN - Variable in class mtb_io.Open_Image_MTB
 
currentidx - Variable in class mtb_io.Open_Image_MTB
 
currentIndex - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
Index of iterator in set.
currentInput - Static variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get initial directory from environment configuration.
currentInput - Static variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Get initial directory from environment configuration.
currentMax - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
currentSliceOnly - Variable in class mtb_segmentation.Threshold_Image
flag if only current slice is to be thresholded
currentSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Current set of snakes.
currentSnk - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Current snake the energy is based on.
cweights - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
 
cytoDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Cytoplasma detection operator.
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.
CytoplasmAnalyzer2D.DetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D.DetectMode
 

D

data - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
data - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
Data to be displayed.
data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
MTBGraphNode data.
data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
Array holding the histogram data
data - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
The data contained in the table.
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
 
dataObject - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNode
Data object associated with the given node.
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.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.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.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.drawing - package de.unihalle.informatik.MiToBo.drawing
Provides operators to visualize data types.
de.unihalle.informatik.MiToBo.enhance - package de.unihalle.informatik.MiToBo.enhance
Provides classes for image preprocessing and improvement (no filters!).
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.nonlinear - package de.unihalle.informatik.MiToBo.filters.nonlinear
Provides classes implementing nonlinear image filters.
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 arithmetic operations on images.
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.optimization - package de.unihalle.informatik.MiToBo.math.optimization
 
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.nonPDE - package de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
 
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.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.system - package de.unihalle.informatik.MiToBo.tools.system
 
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
 
debug - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
debug - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Debug flag for internal use only.
debug - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
 
debug - Variable in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
Debug flag (not accessible from outside).
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.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
Debugging output
debug - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
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.tools.system.UserTime
For internal use.
decrease - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.stepsize.MTBGammaFixed
Fixed decrease factor for adaptation of all gamma values.
defaultfps - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
degree - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
delimiter - Variable in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Delimiter to be used when exporting the model.
delta - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
X- and Y-coordinate differences of the 8-way neighbors.
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
 
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.MigrationAnalyzer
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
deltaT - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
######################### not required Parameter ###########################
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
deltaY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
denoise - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
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.
depthFirstSearch(Vector<Point2D.Double>, Vector<Integer>, MTBNeuriteSkelGraphNode<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Depth-first-search to collect data from the neurite skeleton graph in a SWC file like format.
destinationImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
detectedNeurites - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Vector of detected neurite sets for each image.
detectedNeuritesSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Final set of detected neurites.
detectedParticles - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
 
detectedRegions - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
detectionMode - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Operator mode to run.
detectionResultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
detectionResultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
detectorMode - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
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.
determineGatingDistance() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
automatic gating distance determination according to:

"Automated and semi-automated cell tracking: addressing portability challenges"
KAN, A. and CHAKRAVORTY, R. and BAILEY, J. and LECKIE, C. and MARKHAM, J. and DOWLING, M.R.
diagonalNeighbors - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Flag for using 8-neighborhood.
diagonalNeighbors - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
dialogItemChanged(GenericDialog, AWTEvent) - Method in class mtb_segmentation.Threshold_Image
 
differencing_X(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in X direction
differencing_XX(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in X direction 2 times
differencing_XY(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in X and Y direction
differencing_XZ(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in X and Y direction
differencing_Y(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in Y direction
differencing_YY(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in Y direction 2 times
differencing_YZ(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in Y and Z direction
differencing_Z(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in Z direction
differencing_ZZ(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
derivative in Z direction 2 times
dilate(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
dilate1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
directed - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
True if MTBGraph is directed.
directed - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
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.
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.
disabledColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
disableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Disable energy calculations completely.
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.
DISAPPEARED - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
discardShortTracks() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
delete trajectories whose length is too short
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
 
dist - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
distance(Point2D.Double, Point2D.Double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
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.
distanceImg - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
The distance field as MTBImage.
distanceMap - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
The distance field as two-dimensional double array.
distanceMetric - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
 
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.DistanceMetric() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.DistanceMetric
 
DistanceTransform.ForegroundColor - Enum in de.unihalle.informatik.MiToBo.morphology
Color of binary image foreground.
DistanceTransform.ForegroundColor() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.DistanceTransform.ForegroundColor
 
distField - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
The calculated 2D vector field from the distance map.
distImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Calculated distance map.
distmet - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Metric for distance map calculation.
distMetric - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
The used distance metric for the distance map calculation.
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Divide the elements of two images (img1/img2)
div(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Divide the elements of two images (img1/img2)
doBatch - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
doErosion - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
doesRequireOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns true, if optimizer requires overlap mask.
DOF - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
doFillHoles - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Flag to enable hole filling.
doGauss - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Preprocess cytoplasm channel by Gaussian smoothing.
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.
doMorphOps - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Flag to enable/disable morphological pre-/postprocessing.
doNormalization - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyNonPDE
do normalization?
doNucleiSeparation - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Flag to enable separation of merged nuclei regions.
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.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.
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.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.drawing
A class to visualize 2D polygons.
DrawPolygon2DSet() - Constructor for class de.unihalle.informatik.MiToBo.drawing.DrawPolygon2DSet
Default constructor.
DrawPolygon2DSet(MTBPolygon2DSet) - Constructor for class de.unihalle.informatik.MiToBo.drawing.DrawPolygon2DSet
Simple constructor.
DrawPolygon2DSet(MTBPolygon2DSet, MTBImageRGB) - Constructor for class de.unihalle.informatik.MiToBo.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.drawing
A class to visualize 2D regions.
DrawRegion2DSet() - Constructor for class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Default constructor where NO parameters are set.
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet) - Constructor for class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Simple constructor to create the most common region image types: see DrawType dtype = COLOR_IMAGE: Mask image with randomly colored regions dtype = MASK_IMAGE: Mask image of type MTB_BYTE, where regions have value 255 dtype = LABEL_IMAGE: Label image of type MTB_INT dtype = ID_IMAGE: ID image of type MTB_INT dtype = TRANSPARENT_IMAGE: Image with transparent randomly colored regions, needs a RGB target image to work
DrawRegion2DSet(DrawRegion2DSet.DrawType, MTBRegion2DSet, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Simple constructor to draw the most common region image types to a given image: dtype = COLOR_IMAGE: Mask image with randomly colored regions dtype = MASK_IMAGE: Mask image of type MTB_BYTE, where regions have value 255 dtype = LABEL_IMAGE: Label image of type MTB_INT dtype = ID_IMAGE: ID image of type MTB_INT dtype = TRANSPARENT_IMAGE: Image with transparent randomly colored regions, needs a RGB target image to work
DrawRegion2DSet.DrawType - Enum in de.unihalle.informatik.MiToBo.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
DrawRegion2DSet.DrawType() - Constructor for enum de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet.DrawType
 
drawRegions(MTBRegion2DSet, int, int, int) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
draw regions to the output image
drawRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
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.drawing.DrawTracks2D
Draw region to an image at time=t and channel=c with specified color.
drawSpots - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
drawSqare(MTBImage, MTBRegion2D, int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.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.drawing
Draw trajectories of tracked observations over time.
DrawTracks2D() - Constructor for class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
Constructor.
drawTrajectories - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
drawTrajectories(Matrix, Matrix, int, int, int, MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
Draw trajectory between two points at the given and all later timepoints until t_last
drawType - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
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
 
duplicateImageJType(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
duplicateNonImageJType(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
DynamicColorLUT - Class in de.unihalle.informatik.MiToBo.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.drawing.DynamicColorLUT
Constructor with a (seeded) random generator and channel offset = 20.
DynamicColorLUT(Random) - Constructor for class de.unihalle.informatik.MiToBo.drawing.DynamicColorLUT
Constructor for a specific random generator and channel offset = 20..
DynamicColorLUT(Random, int) - Constructor for class de.unihalle.informatik.MiToBo.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
 
e_x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
x coordinate of displacement vector defining neighbor hood
e_y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
x coordinate of displacement vector defining neighbor hood
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.
elemCount - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
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
ellipsoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to extract elliptical snake primers.
enableEnergyCalculation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Enable energy calculation in each iteration.
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.
endPointHash - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
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.levelset.nonPDE.MTBEnergySumNonPDE
 
energies - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
energy - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Current energy of the snake.
energy - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
Current energy of the snake.
energyCalculationRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Flag for invoking energy calculations.
energyConfWins - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Mapping of short names to configuration windows.
energyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
energyLabel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Label of available external snake energies, which are usable by the detector.
energyPotential - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
Potential field reconstructed from GVF.
energyRange - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Interval boundaries of adapted energy interval.
energySelection - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Combobox for selecting energies.
EnergySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
###################### required Parameter ######################
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBSet_LevelEnergyDerivable
 
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSet_SnakeEnergyDerivable
 
energySet - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
List of snake energies to be used in segmentation.
energySetFields - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
Fields of a EnergySet we parse
energyTab - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
List of selected energies.
energyTabModel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Model for the energy table.
energyWeights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Individual energy weights.
energyWeightsNormed - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
List of normalized energy weights.
enhanceR - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Niblack factor R.
entireTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The targetIDs of all targets that have ever existed up to current time
entriespanel - Variable in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
panel to hold all the entries
entropyFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
entropyFilterSize - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
entropyImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
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
 
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.IntersectionPoint2D
Checks if two intersection points are equal.
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(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
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
equals(Object) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
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.
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.
erode(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
erode1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
erodeComponent(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
erode one component with given label
erodeSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DException
 
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2DException
 
error - Variable in exception de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2DException
 
error - Variable in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphException
 
error - Variable in exception de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DException
Exception error message.
error_msg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
essPercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
esspercentage - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
estimateMean(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Suche nach bestem Mittelpunkt des Embryos: ueberpruefe kreisfoermige Raster (8 Punkte +Mittelpunkt des Bildes) um Bildmittelpunkt aus Kriterium: max. min.
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
 
euklidDist(double, double, double, double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Hilfsmethode zur Bestimmung der euklidischen Distanz zw. 2 Punkten
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
 
excludeBorderRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
exclude regions that are adjacent to the image borders
excludeMask - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Optional mask to exclude particles in certain regions.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Optional mask to exclude particles in certain regions.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Global exclude mask for image to be segmented.
excludeMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Mask to exclude image pixels from calculations.
excludeParticlesInNuclei - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag to ignore particle in nuclei regions.
excludeSmallRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
exclude regions that are smaller than the predefined (Parameter minArea) minimum
executeOperator(ALDOperatorLocation) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBChooseOpNameFrame
 
existingTargetIDs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The targetIDs of the existing target at the specific time
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.
ext - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
extensions - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
extract(File[], double) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
segment the given images and extract their features for classification
extract(Vector<File>, double) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
segment the given images and extract their features for classification
extractCentroids() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
extract centroids from labeled regions
extractedNeurites - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
extractLocalComponents() - Method in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Extracts list of connected components from Otsu thresholded input image.
extractMolProf(MTBImage, MTBNeurite2DSet, String, String) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Extraction of molecular profiles along the detected neurites.
extractParticles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
extractParticles(MTBImage, MTBNeurite2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Extraction of molecular particles along the detected neurites.
extractPointVectorPolygon(MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Extract the list of polygon points for a polygon.
extractPointVectorSnake(MTBXMLPolygon2DType) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Extract the list of polygon points for a snake.
extractProfiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
extractTrajectoriesWithOffsets() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
extract Hashtables containing the centroid locations of each trajectory
and the offsets for the starting time of each trajectory

F

F - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateLinTransDistributionIndepGaussians
state-transition matrix
factory - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.abstracts.AbstractMultiState
factory that holds information how a target's state is composed
factoryMethod - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
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
falseFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
falseNegativeFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
falsePositiveFileNames - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
featureLines - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Borderlines that separate the neurite from the soma and additionally separate the neurite from its growth cone.
featurePoints - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Vector of detected feature points for each neurite.
featurePoints - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Features of the single neurite branches.
fg_value - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
fgValue - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
field - Variable in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Vector field the potential is reconstructed for.
fieldMap - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
used to work around generics
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, 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.
FieldOperations2D.FieldOperation() - Constructor for enum de.unihalle.informatik.MiToBo.fields.FieldOperations2D.FieldOperation
 
fieldSizeX - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Vector field size in x-direction.
fieldSizeY - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Vector field size in y-direction.
file - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
File name for optionally saving the image.
file_name_noExtension - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Current image name without file extension.
fileName - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
File name of the current multichannel fluorescence image.
fileName - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
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.io.images.ImageWriterMTB
 
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
 
files - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
files - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
List of files (no subdirectories!)
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
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
filterMethod - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
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.
firstOneImageOneConstOrdinal - Variable in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
firstOneImageOnlyOrdinal - Variable in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
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.
FLAG_SOLVER - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
FLAG_SOLVER2 - Static variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
FluorescentCellSegmenter - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
FluorescentCellSegmenter() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
FluorescentCellSegmenter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
fn - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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
 
foreground - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Foreground color of the foreground object.
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.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.MTBWrapperDataIOCmdline
Format the given object value to a string
formatAsString(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.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
 
fp - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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 de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
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
 
frameHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Fixed height of window.
frameWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Fixed width of window.
fromMaxVal - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
fromMinVal - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
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

gamma - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Step-size in iterative snake optimization.
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
gamma - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
gamma - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
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)
GaussFilter.SigmaInterpretation() - Constructor for enum de.unihalle.informatik.MiToBo.filters.linear.GaussFilter.SigmaInterpretation
 
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
 
gaussSigma - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Sigma for Gaussian smoothing.
generateCoarseSoma() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Compute a coarse neuron cell body region (soma).
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
 
generateNeuriteRegions(Vector<Vector<Vector<Line2D.Double>>>, Vector<Vector<Vector<Point2D.Double>>>) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Generate neurite region from calculated features.
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
 
generateSkelGraph() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Compute the skeleton graph for the complete neuron region.
generateStackWithIntermediateResults() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Generates a stack with intermediate results.
generateStructuringElement() - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
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 interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
 
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
get8NeighborsPhase(int, int, byte[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Compute phases of 8 neighbors of (x,y) and store these in the array nb.
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.
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.
getAllPixels(Vector<Point2D.Double>, MTBNeuriteSkelGraphNode<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.
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.
getAreaFracMatrix(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
getAreaFraction(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
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.
getAreaFractions(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
getAreas() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
getArithmeticOperation() - Method in class de.unihalle.informatik.MiToBo.math.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.
getAvgWidths(Hashtable<Integer, Vector<Double>>, Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
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
getBhattacharyyaCoefficient(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Generates binary mask for inside part of the polygon.
getBinaryMask(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Generates binary mask for inside part of the snake.
getBinaryMask(int, int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Generates binary mask for inside part of the snake.
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
 
getBorderLine(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get borderlines between soma/neurite shaft and neurite shaft/growth cone.
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.
getBoundingBox() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
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.
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.
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.
getCentroid(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
auxiliary method to determine the centroid (x,y) and width/heigth of compoment with label in a double array of length 4 (should go in class/record)
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.
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.AwtColorDataIOSwing.ColorChooserButton
 
getCircularities() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
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) - 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, 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.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.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
 
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.
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).
getCorrelationImages() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Compute the correlation images as specified by the parameter object
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.
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.
getCuvature(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
cuvature at point (x,y,z)
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.MTBDataIOFile.MTBDataIOFileButton
 
getData() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
Returns the data read from GUI or file.
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.
getDate() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Get current date for result dirs.
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.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.
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(MTBSegmentationInterface, int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetEnergyDerivable
Get the energy derivative value at 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.
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].
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].
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 and V.
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 U and V.
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.snakes.datatypes.MTBSnake
Returns the dimension of the given membership.
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.
getDirectionalDifferences(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDirectionalities(Hashtable<Integer, Vector<Double>>, Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDirections() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDistance(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
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.
getDistances() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getDistImg() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns calculated distance map.
getDistMatrix(MTBRegion2DSet, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
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.
getDrawType() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Get the kind of region image drawn by the operator
getEccentricities() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
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.
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_ActiveContourEnergyDerivable
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.LevelsetSolveNonPDE
Get value of energy.
getEnergy(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.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
 
getEnergyList() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSet_SnakeEnergyDerivable
 
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
 
getEntropyMeanDifference(MTBImage, MTBImage) - 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
 
getErodeSize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of erodeSize.
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.MTBException
 
getExceptionID() - Method in exception de.unihalle.informatik.MiToBo.core.exceptions.MTBImageException
 
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.
getExtEnergyInit() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Calculate the initial image for the external energy of the snake.
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).
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.
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.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.
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_ActiveContourEnergyDerivable
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.energies.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.
getGraphNode(int, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Get the graph node from partition 'partitionID' in subgraph 'subgraphID'.
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Get the gray value of the regions in a mask image (MASK_IMAGE only).
getGrayValue() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
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.
getHistoryLink(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Gets the port to which the object is currently linked in history.
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.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.
getImageBox(Object) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Gets the image container associated with the given image object.
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.
getImagePlus() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Gets the stored ImagePlus.
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.drawing.DrawRegion2DSet
Get the datatype of the resulting image
getImg() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
one iteration, walk through whole levelset-function and update
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.ImageArithmetics
 
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.tools.image.ImageDimensionReducer
Get value of Input argument inImg.
getInImg1() - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
getInImg2() - Method in class de.unihalle.informatik.MiToBo.math.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.
getInitialSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns initial snake.
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).
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.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.LocallyAdaptiveContrastEnhancement
Returns the input image, null if not set.
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.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.segmentation.levelset.core.LevelsetSolverDerivatives
Get value of inputImg.
getInputImg() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get input image
getInputMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Get MTBImage that has to be stored to disk
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Get the regions that have to be drawn
getInputRegions() - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Get reference to the input regions.
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.imageJ.RoiManagerAdapter
Single access point for singleton functionality.
getInstance() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Single access point for singleton functionality.
getIntensityMeans() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
getIntensityNormalizationMode() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Request mode for normalizing image intensities.
getIntensityStdDevs(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
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.
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.
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing.ColorChooserButton
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
getJComponent() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
 
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.
getKernelImg() - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Get convolution kernel (image).
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.
getKolmogorovSmirnovStatistic(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
getLabel(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
returns the value of labelImg at position (x,y).
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.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
 
getLengths() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
calculates the lengths of the major axes of the best fitting ellipses for each object
assumes the pixels to be square, i.e. deltaX == deltaY
getLevel() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Return the tree level (level identifier).
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!
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.
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.
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.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.
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.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
 
getMeanBackgroundIntensity() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
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.
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
 
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
 
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
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.
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.
getMTBImage() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Gets the stored MTBImage.
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.
getNeighbors() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get all neighbors of the current node.
getNetDirections() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getNetDistances() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
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.
getNeuriteFeatures(Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to calculate the neurite features from the neurite width profile.
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.
getNormal(Point2D.Double, Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get normal vector between two points.
getNormalCentralMoment(int, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Calculate normalized central moment of the region of order p,q.
getNormalizationFactor(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
getNormalizationFactor(SnakeOptimizerSingle) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
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.
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.
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.
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 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.snakes.datatypes.MTBSnake
Returns the number of classes represented in the membership.
getNumberOfFrames() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
getNumberOfInEdges() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Get number of incoming edges for MTBGraphNode.
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
 
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.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.
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.
getOpMode() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of opMode.
getOptimalNeighbor(MTBGraphNode<PartitGraphNodeID>, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Get node of partition 'partitionID' which is connected to current node and has optimal weight
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.
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.
getOutputSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
Get cloned snake object.
getOutputType() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Get output image type
getOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Returns current overlap mask.
getOverlaps() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
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.
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
 
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(Vector<Point2D.Double>, MTBNeuriteSkelGraphNode<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Internal method to traverse the path and return the pixel list.
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.
getPerimeters() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
calculates perimeters of the objects
assumes the pixels to be square, i.e. deltaX == deltaY
getPersistences(Hashtable<Integer, Vector<Double>>, Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
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.nonPDE.LevelsetSolveNonPDE
Get value of phi.
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.MTBContour2D
Get a specific 2D point belonging to the contour 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.MTBContour2D
Get the number of points of the contour 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.MTBContour2D
Get all points belonging to the contour 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.
getPolySet() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Get the polygon set.
getPortHashAccessObject() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Returns access object for port hash.
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.
getPotentialNewPhases2D(boolean, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
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
 
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.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
getRandom() - Method in class de.unihalle.informatik.MiToBo.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.
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 region average intensity array indexed with class labels.
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.
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.
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 region intensity variance array indexed with class labels.
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.
getRepositoryTag(String) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Returns the tag/release of the current jar.
getRepositoryTag() - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Returns the tag/release of the current checkout, as specified in a given info file.
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.
getResultAreas() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Returns separated regions sorted according to original regions.
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.
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.
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.
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.drawing.DrawPolygon2DSet
Get the resulting region image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Get the resulting region 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.LocallyAdaptiveContrastEnhancement
Returns result image.
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.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.ContourOnLabeledComponents
Get reference to the binary image with the calculated contours.
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.regions.filling.FillHoles2D
Get the resulting image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Returns the generated image.
getResultImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Returns image with plotted snakes.
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
 
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.
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.nonlinear.RankOperator
Get value of Output argument resultImg.
getResultImg() - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
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.snakes.datatypes.SnakeHelperOperators.MaskMaker
Returns generated mask.
getResultMTBImage() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
Get resulting image that was read from disk.
getResults() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
Get resulting regions (each detetection corresponds to a region)
getResultSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Returns resulting snake object.
getResultSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Returns resulting snake object.
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.datatypes.SnakeHelperOperators.RegionImageConverter
Returns resulting snake objects.
getResultSnakes() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns the set of result snakes.
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.
getResultVec() - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
 
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.
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
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
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
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.
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(int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
getSize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
 
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
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
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 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.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 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.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 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.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.
getSnakeControlPoints(MTBContour2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Method to get each 7th point of the initial contour as snake control point.
getSnakeIterCount() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get 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.
getSnakeRegion(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Get the region which is included in the snake contour.
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.
getSpacingIntermediate() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Get value of spacingIntermediate.
getSpeeds(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
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.
getStartPoints() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Get the skeleton start points of every single neurite from the inside of the coarse cell body region.
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
getStdDevBackgroundIntensity(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
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
 
getT() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
getTargetImage() - Method in class de.unihalle.informatik.MiToBo.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.
getThreshold() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Get threshold.
getThresTH() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Get value of thresTH.
getTicks() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Declaration of native method for getting ticks.
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.
getTotalDistances(Hashtable<Integer, Vector<Double>>) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
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.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.
getUniqueName(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Generates a unique name for a new roi in the manager.
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].
getUserTime() - Method in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Declaration of native method for user time measurement.
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, 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..
getVersion() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
 
getVersionProvider() - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Returns version provider object.
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_ActiveContourEnergyDerivable
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 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.snakes.datatypes.MTBSnake
 
getWeight(int, int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
getWeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSet_SnakeEnergyDerivable
Returns element i of the weight list.
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_ActiveContourEnergyDerivable
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.energies.MTBSet_SnakeEnergyDerivable
Returns the list of weights.
getWeightsSum() - Method in class de.unihalle.informatik.MiToBo.math.distributions.impl.ParticleDistribution
Get sum 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.
getWindowPosition() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow
Get the current window position
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.
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
 
getXMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal x coordinate represented in class/visibility maps.
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
 
getXMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal x coordinate represented in class/visibility maps.
getXML() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Get the XML file description string if one was available.
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.
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
 
getYMaxCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns maximal y coordinate represented in class/visibility maps.
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
 
getYMinCoordinate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Returns minimal y coordinate represented in class/visibility maps.
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.
getZmax() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
getZmin() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
 
gif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
gradField - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
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.
GradientFieldCalculator2D.GradientMode() - Constructor for enum de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D.GradientMode
 
gradientMode - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The used gradient mode for field calculation.
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 java.lang.Comparable<?> & java.util.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
gratwanderung(int, int, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to travers ridges.
grayValue - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
grayValue - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
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
 
growthCones - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite corresponding growth cone regions as MTBRegion2D objects.
gvf - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
The resulting gradient vector flow field.
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.morphology.HDomeTransform3D
 
h - Variable in class de.unihalle.informatik.MiToBo.tools.HSIConverter
Hue of HIS space.
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.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
 
handleValueChangeEvent(ALDSwingValueChangeEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
 
hasForeign4Neighbor(byte, byte[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Check whether there is a different/foreign phase (then phase) in the 4-neighborhood as represented in the 8 neighborhood nbPhases.
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.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
hasNext() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
haveJNI - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Were we able to load the JNI library?
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.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Image size in y-direction, given in pixel.
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Height of the binary neuron image.
height - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
height - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Height of the processed image.
height - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Skeleton image size in y-direction.
height - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Height of the image where the vector field comes from.
height - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Height of the image.
height - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Size of the image and the calculated gvf field in y-direction.
height - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
height - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Width and height of the given image.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Image height.
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
height - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Height of the given image for the energy.
highBound - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
upper boundary of the last bin
HSIConverter - Class in de.unihalle.informatik.MiToBo.tools
Class to convert values from HSI color space into other color spaces like RGB or so.
HSIConverter() - Constructor for class de.unihalle.informatik.MiToBo.tools.HSIConverter
Standard constructor.
HSIConverter(double, double, double) - Constructor for class de.unihalle.informatik.MiToBo.tools.HSIConverter
Constructor to create a HSIconverter object
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
 

I

i - Variable in class de.unihalle.informatik.MiToBo.tools.HSIConverter
Intensity of HIS space.
i - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.IntObject
 
iconData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
iconLabel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
iconNoData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
icov - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
inverse covariance matrix
id - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Id of the region (uniqueness is not guaranteed nor checked!).
id - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
ID of the region (uniqueness is not guaranteed nor checked!)
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.
iDepth - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Depth of working image.
idxUntitled - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Index to number untitled images popped-up.
ignoreBorder - Variable in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder.PotentialFinderOptFunction
Flag to indicate how the border should be handled.
ignoreInvalidStackSpec - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
ignoreStructsAtBorder - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Flag to ignore structures along border.
ignoreStructsInNuclei - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
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.basics.CalcSegmentationStatistics
Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Height of the image to be generated.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
Height of working image.
iHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Image height.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Input image.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
 
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
The given input image to calculate the external energy from it.
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
image - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
The given input image to calculate the external energy from it.
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
Image arithmetics class for MTBImage objects.
ImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Create empty ImageArithmetics object.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Constructor for arithmetic operations considering two images.
ImageArithmetics(ImageArithmetics.ArithOp, MTBImage, double) - Constructor for class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Constructor for arithmetic operations considering one image and a constant.
ImageArithmetics.ArithOp - Enum in de.unihalle.informatik.MiToBo.math
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
ImageArithmetics.ArithOp() - Constructor for enum de.unihalle.informatik.MiToBo.math.ImageArithmetics.ArithOp
 
imageClosed(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
imageClosed(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
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.IntObject - Class in de.unihalle.informatik.MiToBo.tools.image
 
ImageDimensionReducer.IntObject() - Constructor for class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.IntObject
 
ImageDimensionReducer.ReducerMethod - Enum in de.unihalle.informatik.MiToBo.tools.image
Methods for dimension reduction.
ImageDimensionReducer.ReducerMethod() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer.ReducerMethod
 
imageFiles - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Vector with all image files included in the experiment folder for detection.
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
 
imageNormalized - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
Normalized version of input image used in calculations.
imageNormalized - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
Normalized version of input image used in calculations.
imageOpened(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
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
ImageReaderMTB.OutImageType() - Constructor for enum de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB.OutImageType
 
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
ImageReaderOptionsPane.FileOptionsRefresher - Class in de.unihalle.informatik.MiToBo.gui
 
ImageReaderOptionsPane.FileOptionsRefresher(ImageReaderOptionsPane, File[]) - Constructor for class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
images - Variable in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
images - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
images - Variable in class de.unihalle.informatik.MiToBo.gui.SynchronizedImageWindows
 
imagesAsMasks - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
If flag is true, only masks are copied to result stack.
imageType - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
imageUpdated(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
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.
ImageValueTools.ImageValueModification() - Constructor for enum de.unihalle.informatik.MiToBo.tools.image.ImageValueTools.ImageValueModification
 
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 de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
Image to be segmented
img - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
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.
imgPlusRef - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
ImagePlus object in container.
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_CVRegionFit
Operator to calculate energy parameters, i.e., some statistical numbers on the regions of the segmentation.
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 class.
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
Niblack binarization.
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
Default destructor.
ImgThreshNiblack.Mode - Enum in de.unihalle.informatik.MiToBo.segmentation.thresholds
Niblack processing mode.
ImgThreshNiblack.Mode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack.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.
ImgTophat.tophatMode() - Constructor for enum de.unihalle.informatik.MiToBo.morphology.ImgTophat.tophatMode
 
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
 
imType - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Type of the image to be generated.
include - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
IncludeMask(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
inConst - Variable in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
inContour - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Input contour.
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.
inf - Static variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
inFile - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Input file name.
info - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Information about this region set
inHisto - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Input image.
inImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Optional input image to be used for drawing.
inImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Multi-channel input image.
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.nuclei2D.NucleusDetector2D
Reference to original image, for internal use only
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Binary input image to be analyzed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Multi-channel input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
inImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
inImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
inImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Input image to be processed.
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
inImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Binary input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
 
inImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
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.regions.filling.FillHoles2D
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Input image.
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.CalcGlobalThreshOtsu
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Input image.
inImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
inImg1 - Variable in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
inImg2 - Variable in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
inImgOrig - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Input image to process.
inImgOriginal - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Copy of input image The input image is normalized to intensities in range [0,1], this image is a backup of the original one.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Initialize detector.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Initialization method.
init() - Method in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Initialization method.
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 interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetEnergyDerivable
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
initEnergy(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
initEnergy(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
initEnergy(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
initEnergy(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Distance
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Gradient
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_Intensity
 
initEnergy(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
initEnergy(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
initEnergy(SnakeOptimizerSingleGreedy) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyComputable
Init routine which is called once before the energy is actually used.
initEnergy(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Init routine which is called once before the energy is actually used.
initFromDirectory() - Method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Builds the directory tree by initiating the recursive parse procedure
initFromLabels(MTBImage, MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Helper for constructors from a label image.
initialGammas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Initial step size in snake optimization.
initialize() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
initialize histogram, i.e. determine smallest non empty bin, largest non
empty bin, number of histogram entries and sum of the histogram
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.
initLevelset(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Helper to initialize a two phase level set function of size as given by invalidImg with a circle/sphere of radius 0.5*(sizeX+sizeY+sizeZ)/3.
initLevelset(MTBImage, int, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
Initialize a two phase level set function by thresholding an image.
initNewTab(mxGraph) - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbench
 
initNodeNames() - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
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
 
initWorkbench() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaFrame
 
inModes - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
inner - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
Set of inner contours if available.
innerContourLengthMin - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Minimum number of pixels a inner contour must have (length of the contour).
inputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
inputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Define detector parameters.
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Multichannel fluorescence image of the labeled neuron.
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawPolygon2DSet
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The input image to get the gradient values and differences.
inputImage - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The input image as base for the GVF field calculation.
inputImage - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
The binary input image where the contours should be calculated from.
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
inputImage - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
inputImagePlus - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Input image to be processed.
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.GaussFilter
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
 
inputImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
inputMTBImage - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
inputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator
 
inputPolys - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawPolygon2DSet
 
inputRegions - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Optional set of pre-segmented input regions.
inputRegions - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
inputRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
The input regions where the contours should be calculated from.
inputSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
 
inRange - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.energies.MTBActiveContourEnergy_MeanSep
Dynamic range of image intensities.
inRegion - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Input region.
inRegs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
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
 
inSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Input snake.
inSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Input snake.
int2Color(int) - Method in class de.unihalle.informatik.MiToBo.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
 
intensityImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
intermediateLS - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
intermediateResults - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Set of intermediate segmentation results, required for stack generation.
intImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
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.ImageArithmetics
Inverts the image.
inv(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.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
invalidColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
invalidImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
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.
invokeLaterRepaint(ImageReaderOptionsPane) - Method in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
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
isCellEditable(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
 
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.
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)
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
isHorizontal - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
isImg(Class<?>) - Method in class de.unihalle.informatik.MiToBo.core.gui.MTBOperatorParameterPanel
Checks if image is of correct type.
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.
isRegistered(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Checks if an object is registered in the database.
isRegisteredImageBox(Object) - Static method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Checks if the given image object is already registered.
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
Deprecated. 
isSortedCounterClockwise() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Deprecated. 
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) - 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.snakes.datatypes.MTBSnake
 
isVisible(int, int) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
 
itCounter - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Iteration counter.
itemStateChanged(ItemEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData
 
iterator() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
 
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.basics.CalcSegmentationStatistics
Width of working image.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Width of the image to be generated.
iWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
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
 
Jmax - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
Jmax - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
Jmin - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
jni_containsPoint(double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Determines if a point lies inside a polygon or on its boundary.
jni_isClockwiseOriented() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
JNI method for checking clockwise ordering.
jni_isConvex() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
JNI method for checking if polygon is convex.
jni_isCounterClockwiseOriented() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
JNI method for checking counter-clockwise ordering.
jni_isSimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
JNI method for checking if polygon is simple.
jni_makePolySimple() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
JNI method for eliminating loops in polygons.
jni_makePolySimple() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
JNI method for eliminating loops in polygons.
jni_orientation(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
JNI method for calculating orientation of point w.r.t. to polygon.
join(MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Join a region with this region.
jpeg - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
jpg - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
junitTest - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Internal flag for interrupting recursive calls in unit testing.

K

k - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
keepLargestCC(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
remove all but the largest connected component with label
kernelImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
kernelNormalization - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
kernelOrigin - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
kernels - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
kernelTrunctation - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
keyPressed(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
keyPressed(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
keyReleased(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
keyTyped(KeyEvent) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
 
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.
kurtosis(Vector<Double>, double, double) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
kurtosisFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 

L

L - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GaussianDistribution
 
label(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
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.regions.labeling.LabelComponentsSequential
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Binary nuclei image to be processed.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DAlgos
Input image to process.
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
labelImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
labelInside - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Marker for label of enclosed area.
labelResult - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
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 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
array to hold lambdas of phases, starting with MTBLevelsetMembership.BG_PHASE
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.
lambdaBg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Lambda for background
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
 
lambdaFg - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
Lambda for foreground
largestNonEmptyBin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
largest intensity value contained in the input image
lastDir - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
For convenience: always open last directory for saving.
lastDirectory - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
Last directory selected by user.
lastFile - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
Last file selected by user.
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
leaveOneOutCrossValidation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
leave-one-out cross validation, i.e. iteratively one sample is taken as test
sample whereas all others are used for training
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.
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
LevelsetSolveNonPDE.CoordInt3D - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Just to hold 3D coordinate and nothing else
LevelsetSolveNonPDE.CoordInt3D(int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
LevelsetSolveNonPDE.LevelsetIterator - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Abstract class for iterators of pixels/voxels of the level set function.
LevelsetSolveNonPDE.LevelsetIterator() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIterator
 
LevelsetSolveNonPDE.LevelsetIteratorContourPoints - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Iterator for all contour pixels/voxels of the level set function excluding invalid pixels/voxels.
LevelsetSolveNonPDE.LevelsetIteratorContourPoints() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
LevelsetSolveNonPDE.LevelsetIteratorScan - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE
Iterator for all pixels/voxels of the level set function in scanline fashion excluding invalid pixels/voxels.
LevelsetSolveNonPDE.LevelsetIteratorScan() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
LevelsetSolver - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Superclass for all levelset solvers ever implemented.
LevelsetSolver() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolver
Default constructor.
LevelsetSolverDerivatives - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
A class to solve a LevelSet problem in two dimensions with partial differential equations
LevelsetSolverDerivatives() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
Just initialize the MTBOpBase
lif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
limit - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
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.
localVersion - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBVersionProviderReleaseFile
Local version information.
LOG - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.GenericDiscreteDistribution
Tells if the distribution is internally represented by the natural logarithm of the probability values
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 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
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.math.LogFaculty
array to store log(0!)
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_Ccond - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The probability of the association set of any time step represented by this sample conditional on all previous associations in this sample and all observations up to the specific time step: P(C^t | C^{1:t-1}, Z^{1,t}) for all t
logP_Cjoint - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
The joint probability of the association sets of all time steps represented by this sample conditional on all observations: P(C^{1-t} | Z^{1,t})
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.
lowBound - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
lower boundary of the first bin.
lowerBound - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 

M

M - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
number of observations
m - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
m - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
m1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
m2 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
m_bg - Variable in class mtb_segmentation.Threshold_Image
background pixel value
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, this has nothing to do with the ij.ImageStack's 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.MTBImageByte
reference to the ImagePlus pixel data
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.MTBImageFloat
reference to the ImagePlus pixel data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageInt
image data
m_data - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageShort
reference to the ImagePlus pixel 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_fg - Variable in class mtb_segmentation.Threshold_Image
foreground pixel value
m_height - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
m_idx - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
index of the minimum, median or maximum element in the sorted array
m_img - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
the underlying ImagePlus object
m_img - Variable in class mtb_segmentation.Threshold_Image
image to threshold
m_imgB - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the red channel MTBImage
m_imgG - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the red channel MTBImage
m_imgPlus - Variable in class mtb_segmentation.Threshold_Image
original ImagePlus
m_imgR - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageRGB
reference to the red channel MTBImage
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_labelImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
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_rC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_reg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
2D region object.
m_rT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_rX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_rY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_rZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Radius of the median in the corresponding dimension.
m_sigmaScales - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
noise sigma scale factors for different wavelet scales
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_sizeC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
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_sizeT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
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_sizeX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
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_sizeY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
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_sizeZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Size of the dimensions, size of the real stack.
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 StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
vector of installed StatusListeners
m_statusListeners - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
vector of installed StatusListeners
m_thresh - Variable in class mtb_segmentation.Threshold_Image
threshold
m_threshImg - Variable in class mtb_segmentation.Threshold_Image
thresholded image
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
m_width - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
mad - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
mad - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Maximal allowed discrepancy.
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
 
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
Main panel containing all graphical components.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
Main panel.
mainPanel - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Main panel of main frame.
mainpath - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Root directory of the tree.
makeline(int, int, int, int, Vector<Point2D.Double>) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Draws a line between two points.
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
 
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Create the result table and include the specific table header.
makeTable(Vector<String>, Vector<Double>, Vector<Double>, double, Vector<Integer>, Vector<Long>) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
create results table
makeTable() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
mapHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Height of class/visibility maps.
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/visibility maps.
mapMaxY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Maximal y coordinate of class/visibility maps.
mapMinX - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal x coordinate of class/visibility maps.
mapMinY - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Minimal y coordinate of class/visibility maps.
mapWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Width of class/visibility maps.
markBranchPoints(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Mark branch/special points as first step before building up the whole skeleton graph.
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).
mask - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
mask - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
mask - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Optional mask for excluding image regions from processing.
maskCenterX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskCenterY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskHeight - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Height of the mask to be generated.
maskImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
maskRadiusC - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusT - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusX - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusY - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskRadiusZ - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
maskSize - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
maskSize - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
 
masksize - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
maskSizeX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskSizeY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
maskWidth - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Width of the mask to be generated.
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.
MatchingBipartite_HungarianAlgorithm.ScoreInterpretation() - Constructor for enum de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm.ScoreInterpretation
 
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.ImageArithmetics
Pixelwise maximum
max(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.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_d2c - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Maximum peak distance factor.
maxAlpha - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Maximal possible value of alpha as can be provided by parameter updated.
maxAreaChange - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
maxAreaChange - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
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
maxBeta - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Maximal possible value of beta.
maxCompDist - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Maximal distance of adjacent components.
maxCompSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Minimal size of components in mode ERASE_SMALL_COMPS.
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
maxDist - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
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.
maxFragmentDistance - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
maxFragmentDistance - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Maximum distance to connect a fragment to a detected neuron, given in pixel.
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
maxIter - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
maxIterations - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
maxIterations - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Number of snake iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiff
Maximum number of iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMaxIterations
Maximum number of iterations.
maxIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Maximum number of iterations.
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
maxradius - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Maximal radius of region to be considered for intensity normalization.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Maximum length to define a branch of a neurite as spine (filopodia-like protrusion) in pixel.
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
 
maxSpineLength - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Given maximum lengths for definition of spines.
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
maxVoronoiExpDist - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Voronoi expansion distance.
maxWeight - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
maxWeights - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
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.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
mean - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.MultiStateDistributionIndepGaussians
 
meanAndVariance(int[]) - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
 
meanAreas - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
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
 
measure() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
measures the scratch area, i.e. number of pixels that don't have value 0
measureUnits - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Units to be used for measurements.
measureUnits - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Units for measurements.
medianRadius - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.FluorescentCellSegmenter
 
medianRadius - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
memA - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
Optimization matrix with values of last calculations.
method - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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.
Mica2DTableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2DTableModel
Default constructor.
MigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
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.ImageArithmetics
Pixelwise minimum
min(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Pixelwise minimum
minArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
minArea - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
minAreaGrowth - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Lower threshold for region growth.
minCompSize - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Minimal size of components in mode ERASE_SMALL_COMPS.
minIntensityVariance - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Minimum admissible variance in new snake interior fractions..
minmax_img - Variable in class mtb_segmentation.Threshold_Image
min and max gray value of the current image
minMN - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistribution
Minimum of number of observations and number of targets
minNucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Minimal size of valid nuclei regions.
minRegionSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
minSeedSize - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
minSeedSize - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
minSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
minSize - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
minSizeFraction - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
MinSnakePointNum - Static variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Minimum number of points acceptable for snakes.
minStructureSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Minimal size of structure regions to be considered.
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
minTrackLength - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
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.morphology.BasicMorphology
 
model - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
modelFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
modelTransition - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
modeSelection - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
modeSelection - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
modificationMode - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
moleculeChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
moleculeChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
moleculeImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
molecules - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
morphGradient(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
morphMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Mask size to be used in morphological pre-/postprocessing.
motionFraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
motionFraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Minimum fraction of points which should have stooped to move until the snake optimization stops.
motionFraction - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermMotionDiff
Motion fraction factor.
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.
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_CVRegionFit - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.energies
Active contour energy based on Chan-Vese region fitting for single contour.
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.
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.
MTBActiveContourException.ExceptionType() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.activecontours.exceptions.MTBActiveContourException.ExceptionType
 
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
 
MTBAwtPoint2DDataIOSwing.PointConfigPanel - Class in de.unihalle.informatik.MiToBo.core.dataio
Panel to display and read 2D points.
MTBAwtPoint2DDataIOSwing.PointConfigPanel(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Default constructor.
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
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.MTBDataIOFile
 
MTBDataIOFile.MTBDataIOFileButton - Class in de.unihalle.informatik.MiToBo.core.dataio
 
MTBDataIOFile.MTBDataIOFileButton(Class<?>, Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
MTBDataIOFileSwing - Class in de.unihalle.informatik.MiToBo.core.dataio
Data I/O provider for GUI-OpRunner supporting MiToBo container classes Provides Data I/O for the following classes:
MTBRegion2DSetBag
MTBRegion2DSet
MTBRegion3DSet
MTBPolygon2DSet
MTBContour2DSet
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.MTBDataIOFileSwing
 
MTBDataIOFileSwing.InputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio
Input mode for data.
MTBDataIOFileSwing.InputMode() - Constructor for enum de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.InputMode
 
MTBDataIOFileSwing.MTBDataIOFileInPanel - Class in de.unihalle.informatik.MiToBo.core.dataio
Panel for handling GUI I/O of MiToBo container classes.
MTBDataIOFileSwing.MTBDataIOFileInPanel(Field, Class<?>, Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
Default constructor.
MTBDataIOFileSwing.MTBDataIOFileOutPanel - Class in de.unihalle.informatik.MiToBo.core.dataio
Panel for displaying and saving MiToBo container classes.
MTBDataIOFileSwing.MTBDataIOFileOutPanel(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
Default constructor.
MTBDataIOFileSwing.OutputMode - Enum in de.unihalle.informatik.MiToBo.core.dataio
Output mode for data.
MTBDataIOFileSwing.OutputMode() - Constructor for enum de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.OutputMode
 
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, mxGraph) - 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.
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.FactoryMethod() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.FactoryMethod
 
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
MTBImage.MTBImageType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageType
 
MTBImageArithmetics - Class in de.unihalle.informatik.MiToBo.math
This class that provides convenience functions for the ImageArithmetics class.
MTBImageArithmetics() - Constructor for class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Constructor.
MTBImageArithmetics(MTBOperator) - Constructor for class de.unihalle.informatik.MiToBo.math.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
MTBImageDataIO - Class in de.unihalle.informatik.MiToBo.core.dataio
Implementation of ALDDataIOCmdline interface for MitoBo images.
MTBImageDataIO() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.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.JComboBoxImage - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
Class for handling images opened in GUI.
MTBImageDataIOSwing.JComboBoxImage(String) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Default constructor.
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 MTBImages
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, 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
 
mtbImageRef - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
MTBImage object in container.
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
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
MTBImageWindow.BoundaryPadding() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageWindow.BoundaryPadding
 
mtbImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
MTB input image to work on.
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.MTBBatchInputImageDataIterator - Class in de.unihalle.informatik.MiToBo.core.batch.provider.input.swing
Polygon set iterator class.
MTBIteratorImageData.MTBBatchInputImageDataIterator(String) - Constructor for class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
Default 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
MTBLevelsetEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Interface defining levelset energies to be used with PDE techniques.
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 - Interface in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Created with IntelliJ IDEA.
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 from 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
MTBNeuriteSkelGraphNode.MTBSkeletonNodeType() - Constructor for enum de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
 
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.
MTBOperatorConfigTools - Class in de.unihalle.informatik.MiToBo.core.operator
Helper class for global `MiToBo` operator configuration.
MTBOperatorConfigTools() - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Hidden constructor, never used outside of the class.
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.
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.IntersectionPoint2D - Class in de.unihalle.informatik.MiToBo.core.datatypes
Helper class for function simplify().
MTBPolygon2D.IntersectionPoint2D(double, double) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D.IntersectionPoint2D
Default constructor.
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.
MTBPortHashAccess.MTBHistoryImageBox - Class in de.unihalle.informatik.MiToBo.core.operator
Database object boxing ImagePlus and MTBImage.
MTBPortHashAccess.MTBHistoryImageBox(MTBImage, ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Default constructor for an image pair.
MTBPortHashAccess.MTBHistoryImageBox(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Default constructor for an MTBImage without associated ImagePlus.
MTBPortHashAccess.MTBHistoryImageBox(ImagePlus) - Constructor for class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Default constructor for an ImagePlus without linked MTBImage.
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.
MTBRegion2D(MTBXMLRegion2DType) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct a new MTBRegion2D from a region object that was constructed from a xml-representation.
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(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.
MTBRegion2DSet.RegionSelector - Class in de.unihalle.informatik.MiToBo.core.datatypes
 
MTBRegion2DSet.RegionSelector() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
MTBRegion2DSet.RegionSelector(MTBRegion2DSet, int) - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
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.
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(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.
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.
MTBSegmentationInterface.SegmentationDimension() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.basics.MTBSegmentationInterface.SegmentationDimension
 
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_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
GUI element for configuring collections.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton(Field, Class<?>, Object) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Constructor.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Collection configuration window.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow(Field, Class<?>, Object) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Default constructor.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel - Class in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Internal PDE snake energy GUI table model.
MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel(int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
Default constructor.
MTBSet_ActiveContourEnergyDerivable - Interface in de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes
Common interface for sets of derivable active contour energies.
MTBSet_LevelEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.levelset.core
Container data type for snake energies in PDE approaches.
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_SnakeEnergyDerivable - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.energies
Container data type for snake energies in PDE approaches.
MTBSet_SnakeEnergyDerivable() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSet_SnakeEnergyDerivable
Default contructor for empty set.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSet_SnakeEnergyDerivable
Constructor for a given vector of energies.
MTBSet_SnakeEnergyDerivable(Vector<MTBSnakeEnergyDerivable>, Vector<Double>) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.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.
MTBSnake.SnakeCloner - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to construct new snake object from a given one.
MTBSnake.SnakeCloner(MTBSnake) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
Default constructor.
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
Snake energy to avoid overlap 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
Class for external energy from the gradient image.
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
Class for external energy from the intensity image.
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 pure 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.
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
 
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
 
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
 
MTBTableModelDataIOSwing.TableModelShowButton - Class in de.unihalle.informatik.MiToBo.core.dataio.provider.swing
GUI element for displaying table model data.
MTBTableModelDataIOSwing.TableModelShowButton(Object) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
Constructor.
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.
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
Class for loading/saving primitive datatypes in Alida.
MTBWrapperDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.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
 
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.ImageArithmetics
Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Multiply the elements of two images
mult(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Multiply each image value by a constant
mult(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.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.
MultiChannelParticleAnalyzer2D.ResultImageMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D.ResultImageMode
 
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.
MultiState(MultiStateFactory<T>) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
 
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
 
myClass - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
myData - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
myField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
myobject - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Default object.
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.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
N - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.abstracts.AbstractAssociationDistribution
number of targets
name - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
name - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBGenericEnergyNonPDE
Name of the energy.
naString - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
nbPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
nbPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Phases of the 8-neighbors of the current pixel.
nbPhasesNonredundant - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Non redudant phases in the neighborhood of the current pixel.
negDir - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
neurite - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
 
neuriteColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
neuriteColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Region color of detected neurites to view the neurites in the result image.
neuriteDetection(MTBContour2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Main method for 2D neurite detection.
neuriteDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Define analyzer parameters.
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.
NeuriteDetector2D.NeuriteDetector2DMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D.NeuriteDetector2DMode
 
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.
NeuriteDetector2DAlgos.DetectorExternalEnergy() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos.DetectorExternalEnergy
 
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.
NeuriteExtractor2D.NeuronColor() - Constructor for enum de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D.NeuronColor
 
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
 
neuriteGraph - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite skeleton Graph (NSG) of the current neurite.
neuriteGraphs - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Vector of neurite graphs, one for each localized neurite.
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Mask size of average neurite with in pixel.
neuriteMaskSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
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.
neuriteProfiles - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfileSet
The current list of the neurite profiles.
neuriteRegion - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite corresponding region as MTBRegion2D object.
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Set of neurite regions for detecting particle only inside these regions, an be null for detection all particles in the complete image
neuriteSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DSet
The current set of neurites.
neuriteShaft - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Neurite corresponding neurite shaft region as MTBRegion2D object.
neuriteShaftLengths - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Array of detected lengths of the neurite shafts, without growth cone regions.
neuriteShaftLengths - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Lengths of the single branches of a neurite shaft.
neuriteWidths - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2D
Average widths of the whole neurite, the neurite shaft and the growth cone.
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.
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
 
neuronChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
neuronChannels - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Channel numbers, including the neuron stains for detection of the neurons in the current multichannel fluorescence image.
neuronCoarseSoma - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
2D region of the coarse cell body region (soma).
neuronColor - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
neuronImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Define extractor parameters.
neuronMIP - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Maximum intensity projection (MIP) image of the neuron.
neuronSkelGraph - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
NSG of the whole neuron.
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.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
next() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorContourPoints
 
next() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
nf - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
niblackConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
niblackConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Application based constant for Niblack thresholding.
niblackOperator - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Niblack operator, required if mode is 'NIBLACK'.
nInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
noCheck - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
noCheck - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
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
 
nodeNames - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
nodes - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraph
Vector of included graph nodes.
nodes - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
nodeType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraphNode
MTBSkeletonNodeType of the MTBSkeletonGraphNode.
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.MTBSnakeEnergyCD_KassCurvature
Normalization factor for scaling matrix entries.
normalizationFactor - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Normalization factor for scaling matrix entries.
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.
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.
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.
normalizePotentialToMin(double[], boolean) - Method in class de.unihalle.informatik.MiToBo.fields.VectorField2DPotentialFinder
Function to normalize a potential to the minimum value of 0.
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.MTBSnakeEnergyCD_KassCurvature
Mode of normalization.
normMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
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.GaussFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
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.filling.FillHoles2D
 
notifyListeners(StatusEvent) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
nrs - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
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
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Nuclei channel.
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
nucleiChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Channel number, including the nuclei, in the current multichannel fluorescence image.
nucleiContours - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
(Optional) initial snake contours for nuclei.
nucleiDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Operator for nucleus detection/separation.
nucleiMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Nuclei mask.
nucleiRegions - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Set of detected regions.
nucleus - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Fluorescence labeled nuclei image from the multichannel microscope image.
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.
NucleusDetector2D.NuclDetectMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D.NuclDetectMode
 
nucleusRatio - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
nucleusRatio - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Ratio of nucleus pixels which should be included in a intact neuron region to specify the neuron region as active and use for detection.
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.
NucleusSeparator2D.ResultImageMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D.ResultImageMode
 
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.
NucleusSeparator2DBeamCut.NuclSeparateMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut.NuclSeparateMode
 
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.
nucleusSepOp - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Operator to be applied for nuclei separation.
nucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
nucleusSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Minimum size of nucleus region to set region as intact nucleus.
nucSepOp - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Operation mode of the operator.
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
 
numBlockChange(byte[], int) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Return number of connected components of different/foreign phase then r in the 8 neighborhood nbPhases, which are 4 connected to the current pixel.
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
 
numEntries - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
number of histogram entries
numInitialTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Number of iterations for calculating the GVF field.
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
numIterations - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDIB_GVF2D
 
numNewbornTargets - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator.GeneratorInfo
 
numObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.ObservationAdjacency
 
numOfConnectedNodes(PartitGraphNodeID, int) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
Get number of nodes from partition 'partitionID' connected to current node
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
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBCVFittingEnergyNonPDE
number of phases including background
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
numPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
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

obj - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.ImageShowButton
Image object associated with the button.
objectLabels - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
objects8Connected - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
objects8Connected - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
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.drawing.DrawTracks2D
 
observations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
observations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
 
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
obsIdx - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ObsDistance
 
offsets - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
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
 
onValue - Static variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBStructuringElement
 
opane - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
open(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
open1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
Open_Image_MTB - Class in mtb_io
Plugin for image open dialog
Open_Image_MTB() - Constructor for class mtb_io.Open_Image_MTB
 
openRoiManager() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Gets an instance of the current ROI manager of ImageJ.
openRoiManagerFile(String) - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
 
openWindow() - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Displays configuration window.
openWindows - Static variable in class cmdTools.visualization.DisplayImage
 
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.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.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.singleCellTracking2D.SingleCellMigrationAnalyzer
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
operate() - Method in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
 
operate() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawPolygon2DSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
operate() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
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.LocallyAdaptiveContrastEnhancement
This method does the actual work.
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.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.nonlinear.RankOperator
 
operate() - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
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.ImageArithmetics
 
operate() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
 
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.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.LevelsetSolveNonPDE
This function does the actual work, i.e. optimization of the energy.
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.snakes.datatypes.MTBSnake.SnakeCloner
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
 
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.ImgThresh
 
operate() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
 
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.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
 
operationType - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
The operation which should be applied to the input vector field.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Detection mode.
opMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Operation mode of this separator.
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.
optimizeSnakes(MTBPolygon2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Optimization of the snakes (main snake and inner snakes) with its specified parameters and energies.
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Bitwise OR of the elements of two images
or(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.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.
orientation - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
orientation - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
ostream - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetRBMCDA
 
outdata - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
outEdges - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBGraphNode
Vector of outgoing edges of the MTBGraphNode.
outFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
outImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Output image.
outImageType - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
outImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Binary result image.
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.
outMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Generated mask.
outModes - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
outpath - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
Directory of output results.
outputData - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatools.DataConverter
 
outputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Directory of output results.
outputDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
 
outputObservations - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
outputSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake.SnakeCloner
 
outputType - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
outRegs - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet.RegionSelector
 
outSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Result snake.
outSnake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Resulting snake.
outSnakes - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Result snakes.
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.
overlapMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Mask to indicate overlap regions between snakes.
overlapMaskRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Flag to indicate whether an energy requested the overlap mask.
overlapMaskRequested - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Flag to indicate whether an energy requested overlap mask.
overwrite - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
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_obs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
 
paintFilledRegion(MTBRegion2D, MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Draw a region to an image.
paintZeroWeightEdges - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
param - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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.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.MTBWrapperDataIOCmdline
Method to parse MTB wrapper data from a string.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOCmdline
Convert a string to a Random generator.
parse(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOCmdline
 
particleChannel - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
Define extractor parameters.
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Particle detector.
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteParticleDetector2D
 
particleDetector - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
 
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
 
particleDetector_1 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_2 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_3 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_4 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
particleDetector_5 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
 
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
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
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
partitions - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
path - Variable in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTreeNodeData
Absolute directory path associated with this node.
pathfield - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
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
 
peakdistance - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
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).
pgm - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
 
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
phi - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
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
plotImageToBackground() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
Copies the input image as background into the output frame.
plotSnakesToImage() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns overlay of output snakes onto current input image.
plotSnakesToImage(MTBPolygon2DSet, MTBImage, int[]) - Static method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Returns overlay of given snakes onto given image.
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
png - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
pobs - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiTargetIMMFilter
observation distribution: independent Gaussian mixtures for each target
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.MTBContour2D
The number of contour points.
points - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2D
The contour pixels.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
List of polygon points.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Pixels belonging to region.
points - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
Points belonging to the region
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 - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
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)
Polygon2D_Cgal - Class in de.unihalle.informatik.MiToBo.core.datatypes
Java Native Interface wrapper class for 2D polygons to include CGAL library methods.
Polygon2D_Cgal() - Constructor for class de.unihalle.informatik.MiToBo.core.datatypes.Polygon2D_Cgal
 
polygonSet - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
The set of polygons represented as a Vector.
polygonSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBPolygon2DSetROI
Set of 2D polygons.
polyHelper - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Helper object interfacing CGAL by native methods.
polys - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Result polygon set.
popUpImage(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing
Shows an image to the user.
portHashAccess - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Access object for port hash.
posDir - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
potential - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Potential of the vector field.
potentialNewPhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
Phases the current pixel is (topologically) allowed to change to.
potFinder - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Helper object for reconstructing potential from vector field.
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Raise image values to the power of 'constant'
pow(MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Raise image values to the power of 'exponent'
ppm - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
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
prepareFinalResultStack - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag for preparing final result image(s) stack.
prepareMatching() - Method in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite_HungarianAlgorithm
Preprocess the matrix.
prepareResultImage(MTBImageShort) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Prepare visualization of result.
prepareResultImage() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Prepare visualization of result data by overlay on input image.
prepareResultImageStack() - Method in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Initialize result image stack.
prepareResultImageStack(Vector<MTBImage>) - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Initialize result image stack.
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.
preserveTopology - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
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
 
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
 
printData() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.distributions.impl.AssociationDistributionNN.ProbTreeData
 
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.tracking.multitarget.EvalTracks
 
printHelp() - Static method in class cmdTools.tracking.multitarget.ObservationSeriesGenerator
 
printHelp() - Static method in class cmdTools.tracking.multitarget.ObservationsInfo
 
printHelp() - Static method in class cmdTools.tracking.multitarget.RBMCDATracker
 
printHelp() - Static method in class cmdTools.visualization.DisplayImage
 
printNbPhases(byte[]) - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
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.
printTree() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Prints tree data.
prob - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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, which are processed before: regions smaller than minRegionSize are rejected.
processMask(MTBImage, boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
processMode - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Processing mode.
processMode - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
processMode - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Process mode.
profile - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Profile data along longest skeleton path.
profilePoints - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Points of the profile (neurite region) belonging to the longest path.
profileVector - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
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.dataio.AwtColorDataIOCmdline
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing
 
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.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.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.MTBWrapperDataIOSwing
Interface method to announce class for which IO is provided for.
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.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.MTBTableModelDataIOSwing
Interface method to announce class for which IO is provided for.
providedClasses() - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOCmdline
 
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.
providerClass - Variable in class de.unihalle.informatik.MiToBo.core.operator.MTBOperatorConfigTools
Version provider class to be used in the current session.
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
pUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
Parameter update strategy.
pUpdater - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
Parameter update strategy.
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 de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
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
radiusImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Optional radius image.
rand - Variable in class de.unihalle.informatik.MiToBo.drawing.DynamicColorLUT
 
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
 
random - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
randomColor(Random) - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
RandomGeneratorDataIOCmdline - Class in de.unihalle.informatik.MiToBo.core.dataio
Data I/O provider for ALDOpRunner (commandline) for java.util.Random objects.
RandomGeneratorDataIOCmdline() - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.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
 
RandomGeneratorDataIOSwing.RandomGeneratorChooser - Class in de.unihalle.informatik.MiToBo.core.dataio
 
RandomGeneratorDataIOSwing.RandomGeneratorChooser(Random) - Constructor for class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
randomSeed - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
rankedValueAt(int, int, int, int, int, MTBImage, double[]) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
Compute rank operator value for coordinate (x,y,z,t,c) Treatment at boundaries: Image values are mirrored at the border element to determine values under the mask that are outside the image.
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
RankOperator.RankOpMode() - Constructor for enum de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator.RankOpMode
 
rankOpMode - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
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(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.
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.AwtColorDataIOSwing
 
readData() - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Gets the current coordinates.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing
 
readData(Field, Class<?>, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBImageDataIO
 
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.MTBTableModelDataIO
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Function to get selected image from GUI.
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.MTBTableModelDataIOSwing
 
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing
 
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Gets the data from the configuration window.
readData(Field, Class<?>) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Extracts current collection data.
readData(Field, Class<?>, ALDSwingComponent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
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.
readImage(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
readImage(String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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.GaussFilter
 
readResolve() - Method in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
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.
reduce() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
Method which implements the reduction
reduceC - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
reducerMethod - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
reduceT - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
reduceX - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
reduceY - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
reduceZ - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
regionID - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Region ID of the corresponding neurite region to this neurite skeleton graph.
regionMeans - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of calculated region average values.
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.core.datatypes.MTBRegion3DSet
The set of regions represented as a Vector.
regionSet - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.MTBRegion2DSetROI
Set of 2D regions.
regionsets - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSetBag
the container of the region sets
regionSetVisibility - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
 
regionSizes - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of calculated region sizes.
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.
regionVars - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of calculated region variance values.
regionVoronoize() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to perform Voronoi tesselation.
register(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Registers the object to the database.
registerImageBox(Object) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
Registers the given (image) object.
relabel(byte[][], int, int, MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
find and assign object labels to segmented objects in two frames
remove() - Method in class de.unihalle.informatik.MiToBo.core.batch.provider.input.swing.MTBIteratorImageData.MTBBatchInputImageDataIterator
 
remove(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImageSet
 
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.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIterator
 
removeBorderObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
removeBorderObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
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.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.
removeEnergyButton - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Remove button for energies.
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.GaussFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
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.filling.FillHoles2D
 
removeStatusListener(StatusListener) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
JRI R engine to run R as a single thread.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
R engine to start R thread.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
R engine to call R scripts.
rEngine - Variable in class de.unihalle.informatik.MiToBo.apps.neurons2D.NeuronAnalyzer2D
JRI R engine to run R as a single thread.
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
 
requireCounterClockwiseSnakePointOrder() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
Request snakes ordered counter-clockwise.
requireOverlapMask() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Intended for energies to request overlap mask.
res_x - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
res_y - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
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.
resampleConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
resampleConstant - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Constant for resampling the snake control points.
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
 
resetLabel(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
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.
restoreConfigWins() - Method in class de.unihalle.informatik.MiToBo.core.grappa.MTBGrappaWorkbenchTab
 
result_energy - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for snake energy results.
result_extraction - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for neurite extraction results.
result_presegmentation - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for pre-segmentation.
result_snakes - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result directory for snake results.
resultAreas - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
resultCellImg - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Cytoplasm
Input image with snake contours overlayed (optional).
resultCenters - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Set of detected nuclei centers.
resultContours - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
* The calculated contours, every contour can include several inner contours.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Result data object.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Result data object.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusDetector2D
Result data object containing quantitative data and label images.
resultData - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Vector of result data objects.
resultDataAreaFractions - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: area fractions.
resultDataAvgSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: average size.
resultDataCells - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Local container for cell cytoplasm segmentation result.
resultDataCellSizes - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: cell sizes.
resultDataCounts - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: counts.
resultDataTotalSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Result data: total structure size per cell.
resultDir - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Main directory for result output.
resultDisplayMode - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2D
Mode of how to display result image.
resultDisplayMode - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Mode of how to display result image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Result segmentation image.
resultImage - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawPolygon2DSet
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
Several result formats.
resultImage - Variable in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
* The binary image with the calculated contours and the contours as possible outputs from the operator.
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
resultImage - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
resultImagePlus - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
resultImages - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Local container for set of segmentation result and channel copy images.
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.NucleusSeparator2D
Result label image of separated nuclei.
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.particles2D.MultiChannelParticleAnalyzer2D
Stack with result overlays corresponding to channels.
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Enhanced or segmented result image, either of type double or binary.
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.RankOperator
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Binary result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgClose
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgDilate
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgErode
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.filling.FillHoles2D
Result image.
resultImg - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Result image displaying the snakes as overlay.
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
resultImg - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageDimensionReducer
 
resultingRegions - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
resultingRegions - Variable in class de.unihalle.informatik.MiToBo.segmentation.regions.labeling.LabelComponentsSequential
 
resultingRegionsets - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.HyperStackParticleDetectorUWT2D
 
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
 
resultRegCenters - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Nuclei centers sorted according to former regions.
resultRGBimage - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
RGB image overlay with result nuclei contours.
resultSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
resultsTable - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
resultStats - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Result data object.
resultTable - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Result table showing the the detection and morphology measurements.
resultVector - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_ParticlesMultiChannel
Name of the analyzed image.
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.
rgbValue - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
rho - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
Weighting factor and overlap penalty, respectively.
roiAdapt - Static variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
The object instance.
roiManager - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Reference to the current ImageJ roi manager.
RoiManagerAdapter - Class in de.unihalle.informatik.MiToBo.core.imageJ
Convenience functions for interaction with ImageJ's ROI manager.
RoiManagerAdapter() - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter
Hidden constructor, never called from outside.
RoiManagerAdapter.RoiReader - Class in de.unihalle.informatik.MiToBo.core.imageJ
Class for parsing ImageJ roi files and zip archives.
RoiManagerAdapter.RoiReader(String, boolean) - Constructor for class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Default constructor.
roiManagerAdd - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
roiManagerChecker - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
 
roisAdded - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileOutPanel
 
roitable - Variable in class de.unihalle.informatik.MiToBo.core.imageJ.RoiManagerAdapter.RoiReader
Helper hash table.
root - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTree
Root node of the tree.
roundnessThreshold - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Roundness threshold for components.
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.gui.ImageReaderOptionsPane.FileOptionsRefresher
 
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
 
runIterativeMode() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Cell tissue segmentation in an iterative fashion.
runMeanVarMode() - Method in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Deprecated. 
runOperation(MTBOperator, ImageArithmetics.ArithOp, MTBImage, double) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Run an operation with one input image and one input constant
runOperation(MTBOperator, ImageArithmetics.ArithOp, MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Run an operation with two input images
runtime - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
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

s - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBStringData
The string data to store.
s - Variable in class de.unihalle.informatik.MiToBo.tools.HSIConverter
Saturation of HIS space.
sampleEnergyData - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer
 
sampleInfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
sampleinfo - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASample
Properties represented by this sample.
sampleJointProb - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
SamplingDistribution<T> - Interface in de.unihalle.informatik.MiToBo.math.distributions.interfaces
Interface for densities from which samples can be drawn.
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.
saveIntermediateResultPath - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Path where to save intermediate results.
saveIntermediateResults - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag for saving intermediate results to a specified directory.
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.
saveNeuriteWidthList(Vector<Double[]>, String) - Static method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Method to save the neurites width profile in a file.
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.
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
saveSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleVarCalc
 
saveSnakeLoc - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Path where to save intermediate results.
saveSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Flag to enable/disable saving of intermediate snake results.
saveSVM() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
save resulting svm model file
saveTable(File) - Method in class de.unihalle.informatik.MiToBo.gui.MTBTableModel
Saves the contents of the table to given file, TSV format.
saveToBinFile(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Saves the vector field to a file in binary format.
scaleDown - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
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.datatypes.MTBSnake
Scale factor of the snake for normalization.
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.
scaleIntervalSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
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].
scaleValues - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
scalingK - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Niblack scaling parameter k.
scalprod(MTBLineSegment2D) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBLineSegment2D
Calculates the scalar product of the given segment to this one.
schwelle - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Threshold to suppress peak analysis close to scraggy contours.
scoreMatrix - Variable in class de.unihalle.informatik.MiToBo.math.optimization.MatchingBipartite
Matrix containing pairwise scores of bipartite sets.
scratchArea - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
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, boolean, boolean, boolean, int) - Constructor for class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
ScratchAssayAnalyzer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssayAnalyzer.ScratchOrientation() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer.ScratchOrientation
 
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.KERNEL_TYPE() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.KERNEL_TYPE
 
ScratchAssaySVMTrainer.ScratchOrientation - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssaySVMTrainer.ScratchOrientation() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ScratchOrientation
 
ScratchAssaySVMTrainer.ValidationMethod - Enum in de.unihalle.informatik.MiToBo.apps.scratchAssay
 
ScratchAssaySVMTrainer.ValidationMethod() - Constructor for enum de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer.ValidationMethod
 
scratchFeatures - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
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
 
seen - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
 
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
 
segmentation - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
Segmentation object.
segmentationResult - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
segmentationUpToDate - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Flag indicating if the classmap fits the current snake.
segmentlength - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Snake segment length.
segMode - Variable in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete
Mode how the channel of the image was treated during segmentation.
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_Complete.SegmentationMode() - Constructor for enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Complete.SegmentationMode
 
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.
SegResultEnums.MeasureUnit() - Constructor for enum de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResultEnums.MeasureUnit
 
selectBox - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Combobox to select images.
selectButton - Variable in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing.ColorChooserButton
Button to open selection window.
selectedEnergies - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
List of currently selected energies.
selectedImage - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Recently selected image.
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
 
separate(int, int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
try to separate component with label 2.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing.ColorChooserButton
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile.MTBDataIOFileButton
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.CheckBoxPanel
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.RadioButtonPanel
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.gui.TwoColumnPanel
 
serialVersionUID - Static variable in exception de.unihalle.informatik.MiToBo.io.images.OverwriteException
 
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
Default serial number.
serialVersionUID - Static variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnakePoint2D
 
serialVersionUID - Static variable in class mtb_io.Save_Image_MTB
 
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
 
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
setArithmeticOperation(ImageArithmetics.ArithOp) - Method in class de.unihalle.informatik.MiToBo.math.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.
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
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.
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.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.AwtColorDataIOSwing.ColorChooserButton
 
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, 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.
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.drawing.DrawPolygon2DSet
Specify color in which to draw the snakes.
setColor(Color) - Method in class de.unihalle.informatik.MiToBo.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.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.
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
 
setContourType(ContourOnLabeledComponents.ContourType) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the contour type.
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
 
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.
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.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.
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.
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.drawing.DrawRegion2DSet
Set the kind of region image to be drawn
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.
setEnergyList(Vector<MTBActiveContourEnergyDerivable>) - Method in interface de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDerivable
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<MTBActiveContourEnergyDerivable>) - 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<MTBActiveContourEnergyDerivable>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.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.
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).
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.
setFactoryMethod(MTBImage.FactoryMethod) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
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
 
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).
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.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
 
setH(double) - Method in class de.unihalle.informatik.MiToBo.morphology.HDomeTransform3D
Set current h-parameter (max height of the h-domes).
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.morphology.DistanceTransform
Set image height.
setHeight(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set image height.
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.
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.
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
setImagePlus(ImagePlus) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Stores given image to the container.
setImageType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.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.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(MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Set the 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.ImageArithmetics
 
setInImg2(MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
 
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.
setInner(Vector<MTBContour2D>) - 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).
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(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.LocallyAdaptiveContrastEnhancement
Specify the 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.morphology.HDomeTransform3D
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.snakes.optimize.SnakeOptimizer
Specify an input image for the segmentation.
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.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.
setInputMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
Set MTBImage to store to disk
setInputObservations(Vector<MultiState<MotionModelID>>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Set the input regions to be drawn
setInputRegions(MTBRegion2DSet) - Method in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Set reference to the the input regions.
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
 
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.
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
 
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.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.
setKernels(MTBImage[]) - Method in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
Set smoothing kernels
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.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
 
setLevel(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBTreeNodeRegion2D
Set the tree level (level identifier).
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.
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(BasicMorphology.maskShape, int) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
setMask(MTBStructuringElement) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
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.
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.
setMaximalVoronoiExpansionDistance(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set radius of dilation mask in Voronoi expansion.
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
 
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
 
setMinimalComponentSize(int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set minimal component size for erasing small components.
setMinimalRegionSize(int) - Method in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Specify minimal size of regions considered.
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
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
 
setMTBImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess.MTBHistoryImageBox
Stores given image to the container.
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
 
setNucleiAvgSize(double) - Method in class de.unihalle.informatik.MiToBo.apps.datatypes.cellImages.SegResult_Nuclei
Specify average size of nuclei.
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).
setNumIterations(int) - Method in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Set number of iterations for the GVF field.
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).
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.
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.
setOutputType(MTBImage.MTBImageType) - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
Set output image type
setOverlapMask(int[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Specify new overlap mask.
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.
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.
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
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.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
setRandom(Random) - Method in class de.unihalle.informatik.MiToBo.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.
setRegionID(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Set the region id.
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.
setResultDirs() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Create all output directories for the single detection steps.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
Set the resulting image.
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.ImgClose
Set 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.ImgErode
Set result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgOpen
Set result image.
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.regions.filling.FillHoles2D
Set the result image.
setResultImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set result 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.
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.linear.GaussFilter
Set resulting image.
setResultImg(MTBImage) - Method in class de.unihalle.informatik.MiToBo.filters.linear.LinearFilter
Set resulting image.
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.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
setRoundnessThreshold(double) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Set roundness threshold for eliminating round components.
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
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
setSeedPointImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
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.
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.GaussFilter
Set standard deviation (sigma) in x-dimension.
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
 
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
 
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
 
setSizeY(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
setSizeZ(int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
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.
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.
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
 
setTargetImage(MTBImage) - Method in class de.unihalle.informatik.MiToBo.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.
setThreshold(double) - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
Set threshold
setThresTH(double) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
Set value of thresTH.
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
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.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
 
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.
setValidmask(boolean[][]) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Set the valid mask from external mask data.
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.AwtColorDataIOSwing
 
setValue(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Displays specified coordinates.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing.MTBDataIOFileInPanel
Sets panel to given object value.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing
 
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBWrapperDataIOSwing
 
setValue(Object) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Selects the given image object in combobox.
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.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<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigButton
Updates GUI component with given value.
setValue(Field, Class<?>, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Extracts current collection data.
setValue(Field, Class<?>, ALDSwingComponent, Object) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing
 
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.
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(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 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.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_ActiveContourEnergyDerivable
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.energies.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(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.
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.
setXML(String) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
Set the XML file description string if one was available
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.
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.
shape - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
ShapeAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
ShapeAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
constructor
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.
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 - Variable in class de.unihalle.informatik.MiToBo.apps.cells2D.Mica2D
Flag for showing intermediate results.
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.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 - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showOverlayImage(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showOverlayImage - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
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.
showSnake() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingleGreedy
 
showSnakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Flag to enable/disable display of snake results.
showTrajectoryMap - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showTrajectoryMap(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
showTrajectoryMap - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
sigma - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
sigmaC - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaInterpretation - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaT - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaX - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaY - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
sigmaZ - Variable in class de.unihalle.informatik.MiToBo.filters.linear.GaussFilter
 
silent - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
simplify() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Deprecated. 
SingleCellMigrationAnalyzer - Class in de.unihalle.informatik.MiToBo.apps.singleCellTracking2D
 
SingleCellMigrationAnalyzer() - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
SingleCellMigrationAnalyzer(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
size() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Get the number of contours of this contour set
size - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
number of bins
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.neurites2D.NeuriteMolProfExtractor2D
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeC - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeDilation - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
sizeOpening - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
sizePhases - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeT - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
sizeTH - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizeX - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.IntensityAnalyzer
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ShapeAnalyzer
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizeY - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmentationPostprocessing
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellSegmenter
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
sizeZ - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
skeleton_color - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
The color of the skeleton in the binary image.
skelImage - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Binary skeleton image of the whole neuron.
smallestNonEmptyBin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
smallest intensity value contained in the input image
snake - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
The snake on which the algorithm works.
snakeArea - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
SnakeHelperOperators - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Helper class with internal operators for snakes.
SnakeHelperOperators() - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators
 
SnakeHelperOperators.ContourConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to convert a contour into a snake.
SnakeHelperOperators.ContourConverter(MTBContour2D) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ContourConverter
Default constructor.
SnakeHelperOperators.ImageMaker - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to draw snake to an image.
SnakeHelperOperators.ImageMaker(MTBSnake, int, int, int, String, MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.ImageMaker
Default constructor.
SnakeHelperOperators.MaskMaker - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to generate 2D array mask for snake interior.
SnakeHelperOperators.MaskMaker(MTBSnake, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Default constructor with zero offsets.
SnakeHelperOperators.MaskMaker(MTBSnake, int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
Constructor with non-zero offsets.
SnakeHelperOperators.RegionConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to convert a region into a snake.
SnakeHelperOperators.RegionConverter(MTBRegion2D) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionConverter
Default constructor.
SnakeHelperOperators.RegionImageConverter - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes
Operator class to extract snakes from a region image.
SnakeHelperOperators.RegionImageConverter(MTBImage) - Constructor for class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.RegionImageConverter
Default constructor with parameters.
snakeIterations - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Maximal number of snake iterations in iterative optimization.
snakeIterCount - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Number of snake iterations used in current optimization process.
snakeNum - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
Number of snakes.
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.
SnakeOptimizer.Snake_status() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizer.Snake_status
 
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.EnergyNormalizationMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.EnergyNormalizationMode
 
SnakeOptimizerSingle.IntensityNormalizationMode - Enum in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image intensity normalization mode.
SnakeOptimizerSingle.IntensityNormalizationMode() - Constructor for enum de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle.IntensityNormalizationMode
 
SnakeOptimizerSingleGreedy - Class in de.unihalle.informatik.MiToBo.segmentation.snakes.optimize
Image contour segmentation using parametric snakes.
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.
snakePrimerEllipse - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Set of elliptical snake polygons.
snakePrimerVoronoi - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Set of snake polygons based on Voronoi tesselation.
snakes - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
Set of resulting contours.
solve() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.core.LevelsetSolverDerivatives
solve this levelsetproblem
solve() - Method in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
spacingIntermediate - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
spbox - Variable in class de.unihalle.informatik.MiToBo.gui.ImageReaderOptionsPane
 
splitFilename(String) - Static method in class cmdTools.mtb_imagetools.ImageConvert
 
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2D2PNonPDE
 
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW2DMPNonPDE
 
SQRT_2 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
 
SQRT_3 - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyFW3D2PNonPDE
 
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.
stackSize - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Number of channels in image.
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.apps.neurites2D.NeuriteExtractor2D
Get unit vector.
standardization(Point2D.Double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
 
start - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Variable to save start value.
startDetectionMode() - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
Method to start neurite detection mode with presegmentation, active contours and wavelet based neuron component detection.
startFrame - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.Trajectory2D
 
startReal - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Variable to save real start value.
stateConflict(Matrix, MultiState<MotionModelID>) - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationGenerator
 
statesCont - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
vector of the target states (continuous variables)
statesDiscr - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.MultiState
vector of the target states (discrete variables)
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
StatisticsFilter.FilterMethod() - Constructor for enum de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter.FilterMethod
 
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.GaussFilter
vector of installed StatusListeners
statusListeners - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageReaderMTB
 
statusListeners - Variable in class de.unihalle.informatik.MiToBo.io.images.ImageWriterMTB
 
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
 
stdDeviationFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
stdDevRatio - Variable in class de.unihalle.informatik.MiToBo.enhance.LocallyAdaptiveContrastEnhancement
Ratio of image standard deviation used as threshold for radius calculation.
stepSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2D
 
stepSize - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Step size value for a snake step (gamma) during optimization.
stratifiedCrossValidation() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
stratified k-fold cross validation, i.e. training and test tests contain approximately the same proportions of positive and negative samples in every iteration
stringToType(String) - Static method in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage
For a given String, return the corresponding MTBImageType.
structureMask - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
Structure mask.
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.ImageArithmetics
Subtract the elements of two images (img1 - img2)
sub(MTBImage, MTBImage) - Method in class de.unihalle.informatik.MiToBo.math.MTBImageArithmetics
Subtract the elements two images (img1 - img2)
subgraphEdges - Variable in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
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 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.GreedyGourmetPartitioning
 
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
 
sum - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBImageHistogram
sum of all histogram entries
sumSizeObject - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLevelsetMembership
 
suppressor - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch
 
svmFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
svmFile - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
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

t - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
t - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
t1 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
t2 - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow.MTBSet_SnkEnergyPDEGUITableModel
 
tableChanged(TableModelEvent) - Method in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
 
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).
tabwin - Variable in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBTableModelDataIOSwing.TableModelShowButton
Associated window.
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.drawing.DrawRegion2DSet
 
targetImageType - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
targetList - Variable in class de.unihalle.informatik.MiToBo.segmentation.basics.CalcSegmentationStatistics
List of targets to calculate.
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.
test(Vector<File>, int) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
testRegions(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Test whether the number of pixels from a neuron region contains more than 90% of the pixels from a nucleus region.
testRegions2(MTBRegion2D, MTBRegion2D) - Method in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Test whether a single pixel from a neuron region contains a pixel from a nucleus region.
tf - Variable in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
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
 
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
 
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
Result threshold.
threshold - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThresh
 
threshold(MTBImage, 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, 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
 
thresholdSetupDialog() - Method in class mtb_segmentation.Threshold_Image
Dialog for choosing thresholding parameters
thresTH - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
ticks - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Variable to remember ticks.
tif - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
tiff - Variable in class de.unihalle.informatik.MiToBo.io.tools.ImageFilter
 
time - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.TargetID
A variable to store time information
timeLib - Static variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Basename of the JNI library.
timeOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
timer - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerSingle
Timer object for time measurements.
tmpImg - Variable in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
temp. binary image
tn - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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.
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.MTBContour2D
Method to save a contour with all inner contours in a given MTBImage 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.MTBContour2D
Method to save a contour with all inner contours on a binary image with specific width and height.
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.
topHat1D(double[], int) - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DBeamCut
 
tophat_concave(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Apply a top hat operator to the image for concavity detection.
tophat_convex(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ImgTophat
Apply a top hat operator to the image for convexity detection.
toRGB() - Method in class de.unihalle.informatik.MiToBo.tools.HSIConverter
Method to convert a single color from HSI 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.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.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.energies.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
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
toString() - Method in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
toSWC(String, MTBImageByte) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Method to save neurite skeleton graph as SWC file.
totalNumberOfObjects - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
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.MTBPoint3D
Generate xml-representation of this 3D-point.
toXMLType() - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2D
Construct an object that represents this region by xml.
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.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.
tp - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
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.
track() - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
the actual tracking method
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.drawing.DrawTracks2D
 
trackcolors - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.algo.MultiObservationTrackerRBMCDAIMM
 
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
 
TrackEvaluator.TrackObservation - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluator.TrackObservation(int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackObservation
 
TrackEvaluator.TrackSegment - Class in de.unihalle.informatik.MiToBo.tracking.multitarget.eval
 
TrackEvaluator.TrackSegment(int, int, int, int) - Constructor for class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackSegment
 
trackgraphs - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
trackImage - Variable in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
trackingtime - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.eval.TrackEvaluator.TrackEvaluatorResult
time that elapsed for tracking
tracks - Variable in class de.unihalle.informatik.MiToBo.tracking.multitarget.datatypes.impl.RBMCDASampleInfo
HashMap of the tracks represented by the sample.
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
 
train() - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
the actual svm training
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackAnalyzer
 
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrackVisualizer
 
trajectories - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.TrajectoryExtraction2D
 
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
transform - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 
translate(double, double, double) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Translate current coordinates of the 3D point object.
traversePolygonPointList(Vector<Point2D.Double>, int) - Method in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2D
Helper function for simplify().
traverseSubdir(String, String) - Static method in class de.unihalle.informatik.MiToBo.io.dirs.DirectoryTree
Recursive traversal of subdirectories.
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 class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
type - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Type of the input image and later the type of the calculated 2D vector field.
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

U - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Vector U including the x-values of the vector field.
U - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
U-component-vector of the vector field.
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
 
UndecimatedWaveletTransform.TransformationMode() - Constructor for enum de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform.TransformationMode
 
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.cells2D.Mica2D
Units used in measurements, default is pixels.
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.MigrationAnalyzer
 
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
unitT - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.MigrationAnalyzer
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.ReportGenerator
 
unitXY - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
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
updateButtonColor(Color) - Method in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing.ColorChooserButton
 
updateIDs(Vector<MTBSnakePoint2D>) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Update method for snake point ID's after make snake simple.
updateImageList(String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.provider.swing.MTBImageDataIOSwing.JComboBoxImage
Updates image list and GUI.
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
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.
updateSnakeSegmentation() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Convenience function for updating the segmentation.
updateStatus(MTBLevelsetFunctionDerivable) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetEnergyDerivable
 
updateStatus(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
updateStatus(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_CVRegionFit
 
updateStatus(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
updateStatus(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassCurvature
 
updateStatus(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
updateStatus(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_KassLength
 
updateStatus(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
updateStatus(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCD_OverlapPenalty
 
updateStatus(SnakeOptimizerSingleVarCalc) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
updateStatus(SnakeOptimizerSingleGreedy) - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
 
updateStatus(SnakeOptimizerSingleGreedy) - 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(SnakeOptimizerSingleVarCalc) - Method in interface de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyDerivable
Update internal state of energy object prior to usaging it.
upperBound - Variable in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
useAutoDistance - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
useAutoDistance - Variable in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.SingleCellMigrationAnalyzer
 
useAutoDistanceDetermination(boolean) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
 
useExternalSVM - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
 
useExternalSVM - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySegmenter
 
useJNI - Variable in class de.unihalle.informatik.MiToBo.tools.system.UserTime
Does this instance use JNI and thus user time?
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.
uwtImages - Variable in class de.unihalle.informatik.MiToBo.transforms.UndecimatedWaveletTransform
 

V

V - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Vector V including the y-values of the vector field.
V - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
V-component-vector of the vector field.
valid(int, int, int) - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetFunctionDerivable
should point (x,y,z) be included in calculations
validate() - Method in interface de.unihalle.informatik.MiToBo.segmentation.levelset.core.MTBLevelsetEnergyDerivable
 
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.particles2D.HyperStackParticleDetectorUWT2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.apps.particles2D.ParticleDetectorUWT2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.drawing.DrawTracks2D
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.enhance.GammaCorrection2D
 
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.nonlinear.RankOperator
 
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.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.snakes.optimize.SnakeOptimizer
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.SnakeOptimizerCoupled
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.segmentation.thresholds.CalcGlobalThreshOtsu
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageConverter
 
validateCustom() - Method in class de.unihalle.informatik.MiToBo.tools.image.ImageValueTools
 
validateSeedTextField() - Method in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
validColor - Variable in class de.unihalle.informatik.MiToBo.core.dataio.RandomGeneratorDataIOSwing.RandomGeneratorChooser
 
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.core.datatypes.wrapper.MTBDoubleData
Double value for these object.
value - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.wrapper.MTBIntegerData
 
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.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.core.dataio.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.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.MTBNeuriteSkelGraphNode.MTBSkeletonNodeType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum de.unihalle.informatik.MiToBo.drawing.DrawRegion2DSet.DrawType
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.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.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.ImageArithmetics.ArithOp
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.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.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.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.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.
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.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.core.dataio.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.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.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.drawing.DrawRegion2DSet.DrawType
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.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.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.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.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.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.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.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.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.
var - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBMeijeringFittingEnergyNonPDE
 
varCheckNB - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Size of neighborhood for local variance checks.
varCheckThresh - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Threshold for variance check.
variance(Vector<Double>, double) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
varianceFiltering(MTBImage, int) - Method in class de.unihalle.informatik.MiToBo.filters.nonlinear.StatisticsFilter
 
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.FieldOperations2D
The 2D vector field for several operations.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The resulting 2D vector field.
vectorField - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
The calculated GVF vector field.
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.
vectorFieldImage - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
The resulting 2D vector field stored to an image.
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.apps.neurites2D.NeuriteDetector2DAlgos
Verbose flag for standard console outputs.
verbose - Static variable in class de.unihalle.informatik.MiToBo.core.operator.MTBPortHashAccess
If true, verbose outputs are written to standard output.
verbose - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE
 
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
verbosePrintln(String) - Method in class de.unihalle.informatik.MiToBo.apps.singleCellTracking2D.CellTrackerBipartite
prints the given text if the verbose flag is set
vidpanel - Variable in class de.unihalle.informatik.MiToBo.gui.ImageWriterOptionsPane
 
visiblemap - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.MTBSnake
Visibility map for hiding individual pixels.
vol - Variable in class de.unihalle.informatik.MiToBo.math.distributions.impl.UniformDistribution
 
volume - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3D
The volume of the region (number of points included).
voronoidSnakePrimer() - Method in class de.unihalle.informatik.MiToBo.apps.nuclei2D.NucleusSeparator2DPeakSearch_RegionSeparator
Function to extract Voronoi primers.
VoronoiExpandComponents(MTBImageByte, int) - Method in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
Dilate components, but avoid merges.
voronoiImg - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.neurites.MTBNeurite2DProfile
Image filled with voronoi tesselation data during profile calculation if non-null.
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
 
vx - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 
vy - Variable in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssaySVMTrainer
 

W

w - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.MTBLengthEnergyKB2D2PNonPDE
weight for neighbors
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
 
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.MTBSet_ActiveContourEnergyDataIOCmdline
Used as a substitute for the same field in MTBSet_???
weights - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSetWeightedEnergy
List of energy weights.
white - Variable in class mtb_segmentation.Threshold_Image
white value for current image
whiteTophat(MTBImage) - Method in class de.unihalle.informatik.MiToBo.morphology.BasicMorphology
calculates the white tophat transform, i.e. difference of image and the opening of the image
(also called opening tophat)
width - Variable in class de.unihalle.informatik.MiToBo.apps.cytoplasm2D.CytoplasmAnalyzer2D
 
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteDetector2DAlgos
Image size in x-direction, given in pixel.
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteExtractor2D
Width of the binary neuron image.
width - Variable in class de.unihalle.informatik.MiToBo.apps.neurites2D.NeuriteMolProfExtractor2D
 
width - Variable in class de.unihalle.informatik.MiToBo.apps.particles2D.MultiChannelParticleAnalyzer2D
Width of the processed image.
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBNeuriteSkelGraph
Skeleton image size in x-direction.
width - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBVectorField2D
Width of the image where the vector field comes from.
width - Variable in class de.unihalle.informatik.MiToBo.fields.GradientFieldCalculator2D
Width of the image.
width - Variable in class de.unihalle.informatik.MiToBo.fields.GVFFieldCalculator2D
Size of the image and the calculated gvf field in x-direction.
width - Variable in class de.unihalle.informatik.MiToBo.morphology.ComponentPostprocess
 
width - Variable in class de.unihalle.informatik.MiToBo.morphology.DistanceTransform
Width and height of the given image.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.contours.extraction.ContourOnLabeledComponents
Image width.
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.evaluation.CalcStructureStatistics
 
width - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.energies.MTBSnakeEnergyCDImageBased
Width of the given image for the energy.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.activecontours.datatypes.MTBSet_ActiveContourEnergyDataIOSwing.MTBSet_ActiveContourEnergyConfigWindow
Main frame.
window - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.optimize.termination.MTBTermAreaDiffSlidingOffset
 
winSize - Variable in class de.unihalle.informatik.MiToBo.segmentation.thresholds.ImgThreshNiblack
Size of local sliding window.
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(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.AwtColorDataIOSwing
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing
 
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFile
 
writeData(Object, ALDParameterDescriptor) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBDataIOFileSwing
 
writeData(Object, String) - Method in class de.unihalle.informatik.MiToBo.core.dataio.MTBImageDataIO
 
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.MTBTableModelDataIO
 
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.MTBTableModelDataIOSwing
 
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
 
writeGlobalAttributes(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
writeGraph(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
writeImage(MTBImage, String) - Method in class de.unihalle.informatik.MiToBo.apps.scratchAssay.ScratchAssayAnalyzer
writes the given image to a file with the specified path
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.
writeNodeLabels(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
writePartitions(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 
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)
writeSubgraphs(BufferedWriter) - Method in class de.unihalle.informatik.MiToBo.io.files.GraphvizWriter
 

X

x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
x - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at x-dimension.
x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
x - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
xField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Field for x-coordinate.
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.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Maximal x coordinate of the domain of this contour set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Maximal x coordinate of the domain of this polygon set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Maximal x coordinate of the domain of this region set.
xMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Maximal x coordinate of the domain of this region 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.MTBContour2DSet
Minimal x coordinate of the domain of this contour set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Minimal x coordinate of the domain of this polygon set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Minimal x coordinate of the domain of this region set.
xMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Minimal x coordinate of the domain of this region 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
 
xOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
x-offset of the mask coordinate system.

Y

y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
y - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at y-dimension.
y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
y - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
yField - Variable in class de.unihalle.informatik.MiToBo.core.dataio.MTBAwtPoint2DDataIOSwing.PointConfigPanel
Field for y-coordinate.
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.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBContour2DSet
Maximal y coordinate of the domain of this contour set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Maximal y coordinate of the domain of this polygon set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Maximal y coordinate of the domain of this region set.
yMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Maximal y coordinate of the domain of this region 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.MTBContour2DSet
Minimal y coordinate of the domain of this contour set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPolygon2DSet
Minimal y coordinate of the domain of this polygon set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion2DSet
Minimal y coordinate of the domain of this region set.
yMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Minimal y coordinate of the domain of this region 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
 
yOffset - Variable in class de.unihalle.informatik.MiToBo.segmentation.snakes.datatypes.SnakeHelperOperators.MaskMaker
y-offset of the mask coordinate system.

Z

z - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.images.MTBImage.MTBImageFactory
 
z - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBPoint3D
Point coordinate at z-dimension.
z - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.CoordInt3D
 
z - Variable in class de.unihalle.informatik.MiToBo.segmentation.levelset.nonPDE.LevelsetSolveNonPDE.LevelsetIteratorScan
 
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
zMax - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Maximal y coordinate of the domain of this region set.
zMin - Variable in class de.unihalle.informatik.MiToBo.core.datatypes.MTBRegion3DSet
Minimal z coordinate of the domain of this region set.

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