Index (TrakEM2 2.0.0 API)

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 ini.trakem2.display.Tree.Pair: Two nodes of a tree; there is a unique path that goes from a to b.
a - Variable in class mpicbg.trakem2.transform.ExportUnsignedShort.PatchIntensityRange
abort() - Method in class ini.trakem2.display.FreeHandProfile: for abort (ESC pressed for instance)
ABS_PATH - Static variable in class ini.trakem2.persistence.FSLoader
AbstractAffineTile2D<A extends Model<A> & Affine2D<A>> - Class in mpicbg.trakem2.align: TODO
AbstractAffineTile2D(A, Patch) - Constructor for class mpicbg.trakem2.align.AbstractAffineTile2D
AbstractLayerAlignmentParam - Class in mpicbg.trakem2.align
AbstractLayerAlignmentParam() - Constructor for class mpicbg.trakem2.align.AbstractLayerAlignmentParam
AbstractLayerAlignmentParam(int, int, float, int, int, int, boolean, int, float, int, int, float, float, int, int, int, int, int, float, int, boolean, boolean, boolean, boolean) - Constructor for class mpicbg.trakem2.align.AbstractLayerAlignmentParam
AbstractOffscreenThread - Class in ini.trakem2.display: To be used in combination with the AbstractRepaintThread, as a thread to create graphics offscreen.
AbstractOffscreenThread.RepaintProperties - Interface in ini.trakem2.display
AbstractRepaintThread - Class in ini.trakem2.display
AbstractRepaintThread(Component, String, AbstractOffscreenThread) - Constructor for class ini.trakem2.display.AbstractRepaintThread
AbstractTreeTransferHandler - Class in ini.trakem2.tree: Adapted from freely available code by DeuDeu.
AbstractTreeTransferHandler(DNDTree, int, boolean) - Constructor for class ini.trakem2.tree.AbstractTreeTransferHandler
accept(Node) - Method in class ini.trakem2.display.Node.BranchAndEndNodeIterator
accept(Node) - Method in class ini.trakem2.display.Node.BranchNodeIterator
accept(Node) - Method in class ini.trakem2.display.Node.EndNodeIterator
accept(Node) - Method in class ini.trakem2.display.Node.FilteredIterator
accept(File, String) - Method in class ini.trakem2.io.ImageFileFilter
accept(File, String) - Method in class ini.trakem2.io.XMLFileFilter
accept(T) - Method in interface ini.trakem2.utils.Filter
accuracy - Variable in class ini.trakem2.imaging.filters.GaussianBlur
actionPerformed(ActionEvent) - Method in class ini.trakem2.display.Display
actionPerformed(ActionEvent) - Method in class ini.trakem2.display.DisplayableChooser
actionPerformed(ActionEvent) - Method in class ini.trakem2.display.YesNoDialog
actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.LayerTree
actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.ProjectTree
actionPerformed(ActionEvent) - Method in class ini.trakem2.tree.TemplateTree
ACTIVE_DISPL_COLOR - Static variable in class ini.trakem2.tree.ProjectTree
add(Project, TemplateTree, ProjectTree, LayerTree) - Static method in class ini.trakem2.ControlWindow: Beware that this method is asynchronous, as it delegates the launching to the SwingUtilities.invokeLater method to avoid havoc with Swing components.
add(long, ShapeRoi) - Method in class ini.trakem2.display.AreaList: Adds the given ROI, which is expected in world/LayerSet coordinates, to the area present at Layer with id layer_id, or set it if none present yet.
add(Area, Layer) - Method in class ini.trakem2.display.AreaWrapper: Add an area in world coordinates.
add(Area, AffineTransform) - Method in class ini.trakem2.display.AreaWrapper: Add an area that needs to be transformed by tmp first to bring it to world coordinates; will MODIFY the to_world AffineTransform object.
add(Layer, Displayable, boolean) - Static method in class ini.trakem2.display.Display: Find the displays that show the given Layer, and add the given Displayable to the GUI and sets it active only in the front Display and only if 'activate' is true.
add(Layer, Displayable) - Static method in class ini.trakem2.display.Display
add(LayerSet, ZDisplayable) - Static method in class ini.trakem2.display.Display: Add the ZDisplayable to all Displays that show a Layer belonging to the given LayerSet.
add(DoStep) - Method in class ini.trakem2.display.Displayable.DoEdit
add(String, Object) - Method in class ini.trakem2.display.Displayable.DoEdit
add(Displayable) - Method in class ini.trakem2.display.Layer: Add a displayable and update all Display instances showing this Layer.
add(Displayable, boolean) - Method in class ini.trakem2.display.Layer
add(Displayable, boolean, boolean) - Method in class ini.trakem2.display.Layer
add(Layer) - Method in class ini.trakem2.display.LayerSet: Add a new Layer, inserted according to its Z.
add(ZDisplayable) - Method in class ini.trakem2.display.LayerSet: Add a Displayable to be painted in all Layers, such as a Pipe.
add(Layer, double, double) - Method in class ini.trakem2.display.ManualAlignMode.Landmarks: Returns the index of the newly added point, or -1 if the layer doesn't match.
add(Node<T>, byte) - Method in class ini.trakem2.display.Node: Returns -1 when not added (e.g.
add(Shape, Color, Stroke) - Method in class ini.trakem2.display.Overlay: Add a new Shape to be painted above all other elements in the canvas.
add(Shape, Color, Stroke, boolean) - Method in class ini.trakem2.display.Overlay
add(Shape, Color, Stroke, boolean, boolean, float) - Method in class ini.trakem2.display.Overlay
add(Displayable) - Method in class ini.trakem2.display.Selection
add(Area, CoordinateTransform) - Method in class ini.trakem2.display.VectorDataTransform: Add a coordinate transform @param ct that applies to the @param roi Area only; ASSUMES all rois added do not overlap.
add(Patch) - Static method in class ini.trakem2.persistence.FilePathRepair
add(History.Step<?>) - Method in class ini.trakem2.utils.History: Append a new step.
add(String) - Method in class ini.trakem2.utils.Montage
add(String) - Method in class ini.trakem2.utils.ReconstructArea: To reconstruct from XML, takes a "M ....
add(Vector3, Vector3) - Method in class ini.trakem2.utils.Vector3
addAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
addAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
addAll(Layer, Collection<? extends Displayable>) - Static method in class ini.trakem2.display.Display
addAll(LayerSet, Collection<? extends ZDisplayable>) - Static method in class ini.trakem2.display.Display
addAll(Collection<? extends ZDisplayable>) - Method in class ini.trakem2.display.LayerSet
addAll(String[]) - Method in class ini.trakem2.utils.Montage
addAlphaMask(Roi, int) - Method in class ini.trakem2.display.Patch: Add the given roi, in world coords, to the alpha mask, using the given fill value.
addAlphaMask(Area, int) - Method in class ini.trakem2.display.Patch: Add the given area, in world coords, to the alpha mask, using the given fill value.
addAlphaMaskLocal(Area, int) - Method in class ini.trakem2.display.Patch: Add the given area, in local coordinates, to the alpha mask, using the given fill value.
addArea(long, Area) - Method in class ini.trakem2.display.AreaList: Add a copy of an Area object to the existing, if any, area object at Layer with layer_id as given, or if not existing, just set the copy as it.
AddARGBComposite - Class in ini.trakem2.display.graphics
addBall(double, double, double, long) - Method in class ini.trakem2.display.Ball: Used to add individual ball objects when parsing.
addChangeTreesStep() - Method in class ini.trakem2.display.LayerSet: Add a step to undo the addition or deletion of one or more objects in this project and LayerSet.
addChangeTreesStep(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet: Add a step to undo the addition or deletion of one or more objects in this project and LayerSet, along with an arbitrary set of steps that may alter, for example the data.
addCheckbox(String, boolean) - Method in class ini.trakem2.utils.OptionPanel
addCheckbox(String, boolean, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
addChild(Thing, DefaultMutableTreeNode) - Method in class ini.trakem2.tree.DNDTree: Appends at the end of the parent_node child list, and waits until the tree's UI is updated.
addChild(Thing) - Method in class ini.trakem2.tree.LayerThing
addChild(Thing) - Method in class ini.trakem2.tree.ProjectThing
addChild(ProjectThing, int) - Method in class ini.trakem2.tree.ProjectThing: In addition, if the child contains an object of class ini.trakem2.display.Profile, reorders all children of the parent Thing by the Z of the layers of the profiles.
addChild(ProjectThing, String, Displayable) - Method in class ini.trakem2.tree.ProjectTree: Attempt to add the d as a ProjectThing child of type childType to the parent ProjectThing parent.
addChild(Thing) - Method in class ini.trakem2.tree.TemplateThing
addChild(Thing) - Method in interface ini.trakem2.tree.Thing
addChoice(String, String[], int) - Method in class ini.trakem2.utils.OptionPanel
addChoice(String, String[], int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
addContent(Collection<Content>) - Method in class ini.trakem2.display.Display3D
addContent(Content) - Method in class ini.trakem2.display.Display3D
addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.DBLoader
addCrossLink(long, long, long) - Method in class ini.trakem2.persistence.Loader
addDataEditStep(Set<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet: A new undo step for the "data" field of all Displayable in the set.
addDependents(Collection<DoStep>) - Method in class ini.trakem2.display.Displayable.DoEdits
addDependents(Set<DoStep>) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.FSLoader: All backslashes are converted to slashes to avoid havoc in MSWindows.
addedPatchFrom(String, Patch) - Method in class ini.trakem2.persistence.Loader: Subclasses can override this method to register the URL of the imported image.
addEnablerListener(Checkbox, Component[], Component[]) - Static method in class ini.trakem2.utils.Utils: A helper for GenericDialog checkboxes to control other the enabled state of other GUI elements in the same dialog.
addFatPoint(String, LayerSet, double, double, double, double, Color) - Static method in class ini.trakem2.display.Display3D: Expects uncalibrated wx,wy,wz, (i.e.
addFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.BasicParam
addFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.PluginParam
addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
addGeometricConsensusFilterFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
addItem(int, int, String) - Method in class ini.trakem2.display.Dissector: For reconstruction purposes from XML.
addJob(Bureaucrat) - Method in class ini.trakem2.persistence.Loader: Adds a new job to monitor.
addLayer(LayerSet, Layer) - Method in class ini.trakem2.tree.LayerTree: Used by the Loader.importStack and the "many new layers" command.
addLayerChoice(String, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
addLayerContentStep(Layer) - Method in class ini.trakem2.display.LayerSet: For the Displayable contained in a Layer: their number, and their stack order.
addLayerEditedStep(Layer) - Method in class ini.trakem2.display.LayerSet: For the Z and thickness of a layer.
addLayerEditedStep(List<Layer>) - Method in class ini.trakem2.display.LayerSet: For the Z and thickness of a list of layers.
addLayerRangeChoices(Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
addLayerRangeChoices(Layer, Layer, GenericDialog) - Static method in class ini.trakem2.utils.Utils
addLeafs(List<? extends Thing>, Runnable) - Method in class ini.trakem2.tree.DNDTree: Will add only those for which a node doesn't exist already.
addMesh(LayerSet, VectorString3D, String, Color) - Static method in class ini.trakem2.display.Display3D: Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
addMesh(LayerSet, VectorString3D, String, Color, double[], float) - Static method in class ini.trakem2.display.Display3D: Creates a mesh from the given VectorString3D, which is unbound to any existing Pipe.
addMessage(String) - Method in class ini.trakem2.utils.OptionPanel
addNewChildType(ProjectThing, String) - Method in class ini.trakem2.tree.TemplateTree: Add a new template thing to an existing ProjectThing, so that new instances of template new_child_type can be added to the ProjectThing pt.
addNewChildType(TemplateThing, String) - Method in class ini.trakem2.tree.TemplateTree: tt_parent is the parent TemplateThing tet_child is the child to add to tt parent, and to insert as child to all nodes that host the tt parent.
addNewImage(ImagePlus) - Method in class ini.trakem2.persistence.Loader
addNewImage(ImagePlus, double, double) - Method in class ini.trakem2.persistence.Loader: Mipmaps for this image are generated asynchronously.
addNode(Node<T>, Node<T>, byte) - Method in class ini.trakem2.display.Tree: Will call calculateBoundingBox and repaint.
addNumericField(String, double, int) - Method in class ini.trakem2.utils.OptionPanel
addNumericField(String, double, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
addNumericField(String, int) - Method in class ini.trakem2.utils.OptionPanel
addNumericField(String, int, OptionPanel.Setter) - Method in class ini.trakem2.utils.OptionPanel
addPlugIns(JPopupMenu, String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils: Returns false if none to add.
addPlugIns(String, Project, Callable<Displayable>) - Static method in class ini.trakem2.utils.Utils: Returns null if none to add.
addPoint(double, double, long, double) - Method in class ini.trakem2.display.Ball: Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPoint(int, int, double, double, long) - Method in class ini.trakem2.display.Pipe: Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPoint(int, int, long, double) - Method in class ini.trakem2.display.Polyline: Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPoint(double, double, double, double) - Method in class ini.trakem2.display.Profile: Add a point either at the end or between two existing points, with accuracy depending on magnification.
addPointsAtBegin(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
addPointsAtEnd(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
addPostTask(Runnable) - Method in class ini.trakem2.utils.Bureaucrat: Add a task to run after the Worker has finished or quit.
addRegularizationFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
addRGBColorSliders(GenericDialog, Color) - Static method in class ini.trakem2.utils.Utils
addSibling(Displayable, Displayable) - Method in class ini.trakem2.tree.ProjectTree: Finds the node for the elder and adds the sibling next to it, under the same parent.
addSIFTFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
addSilently(DBObject) - Method in class ini.trakem2.display.Layer: Used for reconstruction purposes.
addSilently(Layer) - Method in class ini.trakem2.display.LayerSet: Add a new Layer silently, ordering by z as well.
addSilently(ZDisplayable) - Method in class ini.trakem2.display.LayerSet: Used for reconstruction purposes, avoids repainting or updating.
addSlice(String, Object) - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
addSlice(String, ImageProcessor) - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
addSlice(String, ImageProcessor, int) - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
addSlice(String) - Method in class ini.trakem2.imaging.LazyVirtualStack
addSlice(Callable<ImageProcessor>) - Method in class ini.trakem2.imaging.LazyVirtualStack
addTab(String, Component) - Method in class ini.trakem2.display.Display: Returns the tab index in this Display's JTabbedPane.
addTag(Tag) - Method in class ini.trakem2.display.Node
addTag(Tag) - Method in interface ini.trakem2.display.Taggable
addTarget(float, float, long, float) - Method in class ini.trakem2.display.Connector
addTarget(double, double, long, double) - Method in class ini.trakem2.display.Connector
addToDatabase(DBObject) - Method in class ini.trakem2.persistence.DBLoader
addToDatabase() - Method in class ini.trakem2.persistence.DBObject
addToDatabase(DBObject) - Method in class ini.trakem2.persistence.FSLoader
addToDatabase(DBObject) - Method in class ini.trakem2.persistence.Loader
addToDatabase(Project) - Method in class ini.trakem2.tree.TemplateThing: Recursive into children! Will add the attributes as well and grab an id for this instance.
addToLinkLater(Node<T>) - Method in class ini.trakem2.display.Tree
addTransformStep(Layer) - Method in class ini.trakem2.display.LayerSet: Add an undo step for the transformations of all Displayable in the layer.
addTransformStep(List<Layer>) - Method in class ini.trakem2.display.LayerSet
addTransformStep(Collection<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet: Add an undo step for the transformations of all Displayable in hs.
addTransformStep() - Method in class ini.trakem2.display.LayerSet: Add an undo step for the transformations of all Displayable in all layers.
addTransformStepWithData(Collection<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet: Add an undo step for the transformations of all Displayable in col, with data as well (for Patch, data includes the CoordinateTransform).
addTransformStepWithDataForAll(Collection<Layer>) - Method in class ini.trakem2.display.LayerSet: Includes all ZDisplayable that paint at any of the given layers.
addUndoMoveStep(Displayable) - Method in class ini.trakem2.display.LayerSet: To undo moving up/down/top/bottom.
addUndoStep(DoStep) - Method in class ini.trakem2.display.LayerSet
addUniqueType(TemplateThing) - Method in class ini.trakem2.Project: Returns false if the type exists already.
addVirtualMatch(PointMatch) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
addWorldAreaTo(Node<?>, Area) - Method in class ini.trakem2.display.AreaTree: Assumes nd is an AreaNode.
addZDisplayable(ZDisplayable) - Method in class ini.trakem2.display.LayerSet: Useful for typeless scripts so that a ZDisplayable can be added; the overloaded method add(Layer) and add(ZDisplayable) is not distinguishable otherwise.
adjustChannels(Image) - Method in class ini.trakem2.display.Patch: Takes an image and scales its channels according to the values packed in this.channels.
adjustChannels(Patch, int) - Method in class ini.trakem2.persistence.Loader
adjustConfidence(int) - Method in class ini.trakem2.display.Node: Adjust the confidence value of this node with its parent.
adjustDimensions() - Method in class ini.trakem2.display.DisplayCanvas: Adjust srcRect and internal variables to the canvas' bounds.
adjustEdgeConfidence(int, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree: Expects world coordinates.
adjustGroupProperties(Collection<Displayable>) - Method in class ini.trakem2.display.Display: Pops up a dialog to adjust the alpha, visible, color, locked and compositeMode of all Displayables in col.
adjustMeasurementOptions() - Method in class ini.trakem2.display.Display
adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.Displayable.SliderListener
adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.RollingPanel: Adjust the sublist of displayed DisplayablePanel.
adjustMinAndMaxGUI() - Method in class ini.trakem2.display.Display
adjustNodeColors(Node<T>) - Method in class ini.trakem2.display.Tree
adjustNodeRadius(float, float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Treeline
adjustProperties() - Method in class ini.trakem2.display.AreaList
adjustProperties() - Method in class ini.trakem2.display.Ball
adjustProperties() - Method in class ini.trakem2.display.Display
adjustProperties() - Method in class ini.trakem2.display.Displayable: Shows a dialog to adjust properties of this object.
adjustProperties() - Method in class ini.trakem2.display.DLabel
adjustProperties() - Method in class ini.trakem2.Project
adjustSrcRect(int, int) - Method in class ini.trakem2.display.DisplayCanvas: Adjust srcRect to new dimensions.
affine - Variable in class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine
AffineTile2D - Class in mpicbg.trakem2.align
AffineTile2D(AffineModel2D, Patch) - Constructor for class mpicbg.trakem2.align.AffineTile2D
AffineTile2D(Patch) - Constructor for class mpicbg.trakem2.align.AffineTile2D
AffineTransformMode - Class in ini.trakem2.display
AffineTransformMode(Display) - Constructor for class ini.trakem2.display.AffineTransformMode
ai - Variable in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
ai - Variable in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
ai - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
ai - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
Align - Class in mpicbg.trakem2.align: A collection of methods regarding SIFT-based alignment TODO Bring the methods and tasks into a class for each method and clean up this mess.
Align() - Constructor for class mpicbg.trakem2.align.Align
Align.ExtractFeaturesThread - Class in mpicbg.trakem2.align: Extracts SIFT-features from a List of Tiles and saves them to disk.
Align.MatchFeaturesAndFindModelThread - Class in mpicbg.trakem2.align
Align.Param - Class in mpicbg.trakem2.align
Align.ParamOptimize - Class in mpicbg.trakem2.align
alignLayer(Layer, int) - Static method in class mpicbg.trakem2.align.Align: Align all patches in a Layer.
alignLayers(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask
alignLayers(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask
alignLayersLinearly(List<Layer>, int) - Static method in class mpicbg.trakem2.align.Align: Align a range of layers by accumulating pairwise alignments of contiguous layers.
alignLayersLinearly(List<Layer>, int, Filter<Patch>) - Static method in class mpicbg.trakem2.align.Align: Align a range of layers by accumulating pairwise alignments of contiguous layers.
alignLayersLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask
alignLayersNonLinearlyJob(LayerSet, int, int, boolean, Rectangle, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignLayersTask
AlignLayersTask - Class in mpicbg.trakem2.align: Register a range of layers using linear or non-linear transformations.
alignLayersTask(Layer) - Static method in class mpicbg.trakem2.align.AlignLayersTask
alignLayersTask(Layer, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask
AlignmentUtils - Class in mpicbg.trakem2.align
AlignmentUtils.ParamPointMatch - Class in mpicbg.trakem2.align
alignMultiLayerMosaic(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask: Align a multi-layer mosaic.
alignMultiLayerMosaicTask(Layer) - Static method in class mpicbg.trakem2.align.AlignTask
alignMultiLayerMosaicTask(Layer, Patch) - Static method in class mpicbg.trakem2.align.AlignTask
alignMultiLayerMosaicTask(List<Layer>, Patch, Align.Param, Align.ParamOptimize, Align.ParamOptimize, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
alignPatches(List<Patch>, Set<Patch>, int) - Static method in class mpicbg.trakem2.align.AlignTask
alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
alignPatches(Align.ParamOptimize, List<Patch>, Collection<Patch>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
alignPatchesTask(List<Patch>, Set<Patch>) - Static method in class mpicbg.trakem2.align.AlignTask
alignSelectedPatches(Selection, int) - Static method in class mpicbg.trakem2.align.Align: Align a selection of patches in a Layer.
alignSelection(Selection, int) - Static method in class mpicbg.trakem2.align.AlignTask
alignSelectionTask(Selection) - Static method in class mpicbg.trakem2.align.AlignTask
AlignTask - Class in mpicbg.trakem2.align: Methods collection to be called from the GUI for alignment tasks.
AlignTask() - Constructor for class mpicbg.trakem2.align.AlignTask
AlignTask.ReferenceData - Class in mpicbg.trakem2.align
alignTileCollections(Align.Param, Collection<AbstractAffineTile2D<?>>, Collection<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align: Align two collections of tiles
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, int) - Static method in class mpicbg.trakem2.align.Align: Align a set of tiles using the following procedure: Extract SIFT-features from all tiles. Establish point-correspondences from consistent sets of feature matches among tile pairs, optionally inspect only those that are already overlapping. Globally align the tile configuration. Both feature extraction and matching are executed in multiple Threads, with the number of Threads being a parameter of the method.
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, int) - Static method in class mpicbg.trakem2.align.Align: Align a set of overlapping tiles using the following procedure: Extract SIFT-features from all tiles. Establish point-correspondences from consistent sets of feature matches among overlapping tiles. Globally align the tile configuration. Both feature extraction and matching are executed in multiple Threads, with the number of Threads being a parameter of the method.
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
alignTiles(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
alpha - Variable in class ini.trakem2.display.Displayable
AlphaMaskPath() - Constructor for class ini.trakem2.persistence.StaleFiles.AlphaMaskPath
always_interpolate_areas_with_distance_map - Static variable in class ini.trakem2.utils.AreaUtils: Project property key.
ambigous - Static variable in class ini.trakem2.utils.MCCube
AmiraImporter - Class in ini.trakem2.io: Parses an amira labelfield and imports the labels as AreaList instances into the project tree.
AmiraImporter() - Constructor for class ini.trakem2.io.AmiraImporter
ANCHORS - Static variable in class ini.trakem2.display.LayerSet
animateBrowsing(int, int) - Method in class ini.trakem2.display.DisplayCanvas: Smoothly move the canvas from x0,y0,layer0 to x1,y1,layer1
animateBrowsing(Rectangle, Layer) - Method in class ini.trakem2.display.DisplayCanvas: Smoothly move the canvas from its current position until the given rectangle is included within the srcRect.
animateBrowsingTo(Coordinate<?>) - Method in class ini.trakem2.display.Display
annotation - Variable in class ini.trakem2.display.Displayable
ap - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
ap - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
append(Line3D) - Method in class ini.trakem2.analysis.Compare.Chain
append(History.Step<?>) - Method in class ini.trakem2.utils.History: Appends a step at the end of the list, without modifying the current index.
appendCoordinateTransform(CoordinateTransform) - Method in class ini.trakem2.display.Patch: Append a CoordinateTransform to the current CoordinateTransformList.
appendCoordinateTransform(List<Patch>, CoordinateTransform, int) - Static method in class lenscorrection.DistortionCorrectionTask
AppendCoordinateTransformThread(List<Patch>, CoordinateTransform, AtomicInteger) - Constructor for class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
appendFilters(IFilter[]) - Method in class ini.trakem2.display.Patch: Append an array of IFilter to the array of existing IFilter.
appendPoint(int, int, long) - Method in class ini.trakem2.display.Polyline: Append a point at the end.
appendPoints(double[], double[], long[], int) - Method in class ini.trakem2.display.Polyline
appendShortest(float, float, StringBuilder) - Static method in class ini.trakem2.utils.M: Appends to @param sb the shortest possible String representation of a float number, according to the desired decimal @param precision.
applies(Object) - Method in interface ini.trakem2.plugin.TPlugIn: Returns true if this plugin can be applied to an Object like @param ob.
applies(Object) - Method in class org.janelia.intensity.MatchIntensities
apply(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
apply() - Method in class ini.trakem2.display.AffineTransformMode
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.AreaList
apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaList
apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.AreaTree.AreaNode
apply(VectorDataTransform) - Method in class ini.trakem2.display.AreaTree.AreaNode
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Ball
apply(VectorDataTransform) - Method in class ini.trakem2.display.Ball
apply() - Method in class ini.trakem2.display.ContrastAdjustmentMode
apply() - Method in class ini.trakem2.display.DefaultMode
apply(int) - Method in class ini.trakem2.display.Displayable.DoEdit: Set the stored data to the stored Displayable.
apply(int) - Method in class ini.trakem2.display.Displayable.DoEdits
apply(int) - Method in class ini.trakem2.display.Displayable.DoTransforms
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Dissector
apply(VectorDataTransform) - Method in class ini.trakem2.display.Dissector
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.DLabel
apply(VectorDataTransform) - Method in class ini.trakem2.display.DLabel
apply(int) - Method in interface ini.trakem2.display.DoStep: Returns true on success.
apply() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
apply(Class<?>, AffineTransform) - Method in class ini.trakem2.display.Layer: Preconcatenate the given AffineTransform to all Displayable objects of class c, without respecting their links.
apply(int) - Method in class ini.trakem2.display.Layer.DoMoveDisplayable
apply(int) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
apply(int) - Method in class ini.trakem2.display.LayerSet.DoMoveZDisplayable
apply() - Method in class ini.trakem2.display.ManualAlignMode
apply() - Method in interface ini.trakem2.display.Mode
apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Node
apply(VectorDataTransform) - Method in class ini.trakem2.display.Node
apply(Node.Operation<T>, Iterator<Node<T>>) - Method in class ini.trakem2.display.Node
apply(Node) - Method in interface ini.trakem2.display.Node.Operation
apply() - Method in class ini.trakem2.display.NonLinearTransformMode
apply(Set<Layer>) - Method in class ini.trakem2.display.NonLinearTransformMode
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Pipe
apply(VectorDataTransform) - Method in class ini.trakem2.display.Pipe
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Polyline
apply(VectorDataTransform) - Method in class ini.trakem2.display.Polyline
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Profile
apply(VectorDataTransform) - Method in class ini.trakem2.display.Profile
apply(int, double[]) - Method in class ini.trakem2.display.Selection
apply(Layer, Area, CoordinateTransform) - Method in class ini.trakem2.display.Tree
apply(VectorDataTransform) - Method in class ini.trakem2.display.Tree
apply(CoordinateTransform, Area) - Method in class ini.trakem2.display.Treeline.RadiusNode
apply(VectorDataTransform) - Method in class ini.trakem2.display.Treeline.RadiusNode
apply(Layer, Area, CoordinateTransform) - Method in interface ini.trakem2.display.VectorData: Applies the 2D transform @ict (which is expected to operate on the world coordinates version of the data contained here) only to the data that falls within the @param roi (in world coords), and then recomputes the bounding box and affine transform (to a translation or identity).
apply(VectorDataTransform) - Method in interface ini.trakem2.display.VectorData
apply(Collection<Displayable>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
apply(int) - Method in class ini.trakem2.tree.RenameThingStep
apply(CoordinateTransform, Area, Area) - Static method in class ini.trakem2.utils.M: Apply in place the @param ict to the Area @param a, but only for the part that intersects the roi.
apply(VectorDataTransform, Area) - Static method in class ini.trakem2.utils.M
apply(VectorDataTransform, Area, boolean) - Static method in class ini.trakem2.utils.M: Parts of @param a not intersected by any of @param vdt rois will be left untouched if @param remove_outside is false.
apply(CoordinateTransform, double[][], int, double[]) - Static method in class ini.trakem2.utils.M: Reuses the @param fp to apply in place.
apply(O) - Method in interface ini.trakem2.utils.Operation
apply(double[]) - Method in class lenscorrection.PolynomialModel2D
apply_bandpass_filter - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
apply_grey_value_erosion - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
applyAndPropagate(Set<Layer>) - Method in class ini.trakem2.display.AffineTransformMode: Skips current layer, since its done already.
applyCorrection - Variable in class lenscorrection.Distortion_Correction.PluginParam
applyFilters(Image) - Method in class ini.trakem2.display.Display
applyFilters(ImageProcessor) - Method in class ini.trakem2.display.Display
applyFilters(ImagePlus) - Method in class ini.trakem2.display.Display
applyInPlace(double[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
applyInPlace(double[]) - Method in class lenscorrection.PolynomialModel2D
applyLayerTransformToPatch(Patch, CoordinateTransform) - Static method in class mpicbg.trakem2.align.Util
applyLayerWise(Collection<Layer>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
applyPatchTask(List<Patch>, String, Operation<Boolean, Patch>, Filter<Patch>) - Method in class ini.trakem2.display.Display: Meant for tasks that require setting an undo and regenerating mipmaps.
applyToSlab(Node.Operation<T>) - Method in class ini.trakem2.display.Node: Apply @param op to this Node and all its subtree nodes until reaching a branch node or end node, inclusive.
applyToSubtree(Node.Operation<T>) - Method in class ini.trakem2.display.Node: Apply @param op to this Node and all its subtree nodes.
applyTransform() - Method in class ini.trakem2.display.DisplayCanvas
applyTransforms(Map<Displayable, AffineTransform>) - Static method in class ini.trakem2.display.LayerSet
applyTransformToLayer(Layer, CoordinateTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.ElasticLayerAlignment
applyTransformToLayer(Layer, AffineTransform, Filter<Patch>) - Static method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment
approximateTransferPixel(int[]) - Method in class ini.trakem2.display.Patch: Transfer an 8-bit or RGB pixel to this image color space, interpolating; the pvalue is modified in place.
area - Variable in class ini.trakem2.display.Patch.TransformProperties
area_color_cues - Variable in class ini.trakem2.display.LayerSet
AREA_DOWNSAMPLING - Static variable in class ini.trakem2.persistence.Loader
AreaContainer - Interface in ini.trakem2.display
areaInInts(Area) - Static method in class ini.trakem2.utils.M: Converts all points in @param area to ints by casting.
areaInIntsByRounding(Area) - Static method in class ini.trakem2.utils.M: Converts all points in @param area to ints by rounding.
AreaList - Class in ini.trakem2.display: A list of brush painted areas similar to a set of labelfields in Amira.
AreaList(Project, String, double, double) - Constructor for class ini.trakem2.display.AreaList
AreaList(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.AreaList: Reconstruct from XML.
AreaList(Project, long, String, float, float, float, boolean, Color, boolean, ArrayList<Long>, AffineTransform) - Constructor for class ini.trakem2.display.AreaList: Reconstruct from the database.
AreaNode(float, float, Layer) - Constructor for class ini.trakem2.display.AreaTree.AreaNode
AreaNode(HashMap<String, String>) - Constructor for class ini.trakem2.display.AreaTree.AreaNode: To reconstruct from XML, without a layer.
AreaTree - Class in ini.trakem2.display
AreaTree(Project, String) - Constructor for class ini.trakem2.display.AreaTree
AreaTree(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.AreaTree: Reconstruct from XML.
AreaTree(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.AreaTree: For cloning purposes, does not call addToDatabase()
AreaTree.AreaNode - Class in ini.trakem2.display
AreaUtils - Class in ini.trakem2.utils
AreaWrapper - Class in ini.trakem2.display
AreaWrapper(Displayable, Area) - Constructor for class ini.trakem2.display.AreaWrapper
AreaWrapper() - Constructor for class ini.trakem2.display.AreaWrapper
AreaWrapper(Area) - Constructor for class ini.trakem2.display.AreaWrapper
AreaWrapper.PaintParameters - Class in ini.trakem2.display
areThereLayerCrossLinks(Set<Layer>, boolean) - Static method in class ini.trakem2.display.Displayable: Returns true if any Displayable objects of different layers in sublist are linked to each other.
ArrayConverter - Class in mpi.fruitfly.general: Title:
ArrayConverter() - Constructor for class mpi.fruitfly.general.ArrayConverter
ArrayToByteProcessor(ImageProcessor, int[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ArrayToByteProcessor(ImageProcessor, float[][]) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ArrayToFloatProcessor(ImageProcessor, double[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ArrayToFloatProcessor(ImageProcessor, float[], int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ARROW - Static variable in class ini.trakem2.display.DLabel
asBufferedImage(Image) - Static method in class ini.trakem2.io.ImageSaver
asContent(Display3D) - Method in class ini.trakem2.display.Display3D.VectorStringContent
asGrey(BufferedImage) - Static method in class ini.trakem2.io.ImageSaver: If the given BufferedImage is of type TYPE_BYTE_GRAY, it will simply return it.
asHexRGBColor(Color) - Static method in class ini.trakem2.utils.Utils
asHexRGBColor(StringBuilder, Color) - Static method in class ini.trakem2.utils.Utils
askAdjustRadius(Node<Float>) - Method in class ini.trakem2.display.Treeline
askForNewTag(int) - Method in class ini.trakem2.display.LayerSet
askForXMLTemplate(Project) - Method in class ini.trakem2.persistence.Loader: Ask for the user to provide a template XML file to extract a root TemplateThing.
askToRemoveTag(int) - Method in class ini.trakem2.display.LayerSet: Returns false if the dialog was canceled or there wasn't any tag to remove.
asList(long[]) - Static method in class ini.trakem2.utils.Utils
asList(long[], int, int) - Static method in class ini.trakem2.utils.Utils
asOptionPanel() - Method in class ini.trakem2.display.AreaWrapper.PaintParameters
asOptionPanel() - Method in class ini.trakem2.imaging.Segmentation.FastMarchingParam
asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.DefaultGraphicsSource: Returns the list given as argument without any modification.
asPaintable(List<? extends Paintable>) - Method in interface ini.trakem2.display.graphics.GraphicsSource: Takes as list of Paintable and returns the same or another list with perhaps a different number of Paintable objects, or some replaced by new Paintable instances.
asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.graphics.TestGraphicsSource: Replaces all Patch instances by a smiley face.
asPaintable(List<? extends Paintable>) - Method in class ini.trakem2.display.GroupingMode.GroupedGraphicsSource: Returns the list given as argument without any modification.
asPoint() - Method in class ini.trakem2.display.Node
asPoint(Node<T>, boolean) - Method in class ini.trakem2.display.Tree: Return the Node as a point in space.
asRGBABytes(int[], byte[], byte[]) - Static method in class ini.trakem2.imaging.P
asRGBBytes(int[]) - Static method in class ini.trakem2.imaging.P
asSafePath(String) - Static method in class ini.trakem2.persistence.FSLoader: Takes a String and returns a copy with the following conversions: / to -, space to _, and \ to -.
assoc(BufferedImage) - Method in class ini.trakem2.display.DisplayCanvas.Screenshot: Associate @param img to this, with a new sid.
asVectorString2D(Polygon, double) - Static method in class ini.trakem2.utils.M
asVectorString3D() - Method in interface ini.trakem2.display.Line3D
asVectorString3D() - Method in class ini.trakem2.display.Pipe: Returns a non-calibrated VectorString3D.
asVectorString3D() - Method in class ini.trakem2.display.Polyline: Returns a non-calibrated VectorString3D.
asVertices() - Method in class ini.trakem2.display.Tree: Return a representation of this Tree with Vertex instead of Node.
asWorldPoints() - Method in class ini.trakem2.display.Ball: Returns a Point3f for every x,y,z ball, in calibrated world space.
at - Variable in class ini.trakem2.display.Displayable
at - Variable in class ini.trakem2.display.Displayable.DataPackage
at - Variable in class ini.trakem2.display.Patch.TransformProperties
autosaver - Static variable in class ini.trakem2.persistence.FSLoader
autoscale_after_filtering - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
autoscroll(Point) - Method in class ini.trakem2.tree.DNDTree
available - Static variable in class ini.trakem2.imaging.filters.FilterEditor
AVG_PHYS_DIST - Static variable in class ini.trakem2.analysis.Compare

B

b - Variable in class ini.trakem2.display.Tree.Pair: Two nodes of a tree; there is a unique path that goes from a to b.
b - Variable in class ini.trakem2.imaging.filters.LUTCustom
background - Variable in class ini.trakem2.tree.DNDTree
backgroundValue - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
Ball - Class in ini.trakem2.display
Ball(Project, String, double, double) - Constructor for class ini.trakem2.display.Ball
Ball(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Ball: Construct an unloaded Ball from the database.
Ball(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Ball: Construct a Ball from an XML entry.
BasicParam() - Constructor for class lenscorrection.Distortion_Correction.BasicParam
Bbuf - Static variable in class ini.trakem2.io.ImageSaver
bestMipmapLevel(double) - Static method in class org.janelia.intensity.Render
BigBrother - Class in ini.trakem2.utils: Supervise all threads, and report uncaught exceptions.
BigBrother(String) - Constructor for class ini.trakem2.utils.BigBrother
BinaryInterpolation2D - Class in ini.trakem2.imaging: Given two binary images of the same dimensions, generate an interpolated image that sits somewhere in between, as specified by the weight.
BinaryInterpolation2D(Image<BitType>, Image<BitType>, float) - Constructor for class ini.trakem2.imaging.BinaryInterpolation2D
bins - Variable in class ini.trakem2.imaging.filters.CLAHE
blend(List<Layer>, boolean, Filter<Patch>) - Static method in class ini.trakem2.imaging.Blending
blend(Set<Patch>, boolean) - Static method in class ini.trakem2.imaging.Blending: For each file, find the weight for the alpha mask according to wether the pixel overlaps with other images (weighted alpha dependent on the distante to the image border and of that on the other images) or not (full alpha).
blend(byte[], byte[]) - Static method in class ini.trakem2.imaging.P
blend(byte[], byte[], byte[], byte[]) - Static method in class ini.trakem2.imaging.P
blend(byte[], byte[], byte[]) - Static method in class ini.trakem2.imaging.P
Blending - Class in ini.trakem2.imaging: Utility functions for blending images together, to remove contrast seams.
Blending() - Constructor for class ini.trakem2.imaging.Blending
blendLayerWise(List<Layer>, boolean, Filter<Patch>) - Static method in class ini.trakem2.imaging.Blending
blendPatches(Set<Patch>, boolean) - Static method in class ini.trakem2.imaging.Blending
blendPre(byte[], byte[]) - Static method in class ini.trakem2.imaging.P: Puts the pi (the greyscale channel) into the R, G and B components of the returned int[] after having multiplied them by the pm (the alpha channel); the alpha channel gets inserted into the int[] as well.
blendPre(byte[], byte[], byte[], byte[]) - Static method in class ini.trakem2.imaging.P: Pre-multiplies alpha.
BlockMatchPairCallable - Class in mpicbg.trakem2.align.concurrent
BlockMatchPairCallable(Triple<Integer, Integer, AbstractModel<?>>, List<Layer>, boolean, boolean, Filter<Patch>, ElasticLayerAlignment.Param, Collection<? extends Point>, Collection<? extends Point>, Rectangle) - Constructor for class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable
BlockMatchPairCallable.BlockMatchResults - Class in mpicbg.trakem2.align.concurrent
BlockMatchResults(Collection<? extends Point>, Collection<? extends Point>, Collection<PointMatch>, Collection<PointMatch>, boolean, boolean, Triple<Integer, Integer, AbstractModel<?>>) - Constructor for class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
blockRadius - Variable in class ini.trakem2.imaging.filters.CLAHE
blockRadius - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
BlowCommander(AreaWrapper, Layer, Rectangle, int, int, List<Runnable>) - Constructor for class ini.trakem2.imaging.Segmentation.BlowCommander
blowRoi(AreaWrapper, Layer, Rectangle, int, int, Runnable) - Static method in class ini.trakem2.imaging.Segmentation
blowRoi(AreaWrapper, Layer, Rectangle, int, int, List<Runnable>) - Static method in class ini.trakem2.imaging.Segmentation
BlowRunner(AreaWrapper, Layer, Rectangle, int, int) - Constructor for class ini.trakem2.imaging.Segmentation.BlowRunner
BLUE - Static variable in class ini.trakem2.display.Channel
bmBlockRadius - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmLocalModelIndex - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmLocalRegionSigma - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmMaxCurvatureR - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmMaxLocalEpsilon - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmMaxLocalTrust - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmMinR - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmRodR - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmScale - Variable in class mpicbg.trakem2.align.ElasticMontage.Param: Block matching
bmSearchRadius - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
bmUseLocalSmoothnessFilter - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
BooleanSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.BooleanSetter
BooleanSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.BooleanSetter
BOTH - Static variable in class ini.trakem2.io.XMLFileFilter
BOTTOM - Static variable in class ini.trakem2.display.LayerSet
bottomPadding() - Method in class ini.trakem2.utils.OptionPanel
bounds - Variable in class ini.trakem2.display.Patch.TransformProperties
box - Variable in class ini.trakem2.display.Patch.PatchImage: The bounding box of the image relative to the original, with x,y as the displacement relative to the pixels of the original image.
BranchAndEndNodeIterator(Node) - Constructor for class ini.trakem2.display.Node.BranchAndEndNodeIterator
branches - Variable in class ini.trakem2.analysis.Centrality.EtchingStep
BranchNodeIterator(Node) - Constructor for class ini.trakem2.display.Node.BranchNodeIterator
branchWise(Collection<Vertex<T>>, int) - Static method in class ini.trakem2.analysis.Centrality
BreadthFirstSubtreeIterator(Node) - Constructor for class ini.trakem2.display.Node.BreadthFirstSubtreeIterator
BRUSH - Static variable in class ini.trakem2.utils.ProjectToolbar: A tool to align objects from two different layers.
brx - Variable in class ini.trakem2.imaging.filters.NormalizeLocalContrast
brx1 - Variable in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
brx2 - Variable in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
bry - Variable in class ini.trakem2.imaging.filters.NormalizeLocalContrast
bry1 - Variable in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
bry2 - Variable in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
Bucket - Class in ini.trakem2.display: A Bucket is a subarea of the Layer area, which contains either other Buckets or a map of stack_index vs.
Bucket(int, int, int, int, int) - Constructor for class ini.trakem2.display.Bucket
Bucketable - Interface in ini.trakem2.display
BUNWARPJ - Static variable in class mpicbg.trakem2.align.AlignLayersTask
bunwarpj.trakem2.transform - package bunwarpj.trakem2.transform
Bureaucrat - Class in ini.trakem2.utils: Sets a Worker thread to work, and waits until it finishes, blocking all user interface input until then, except for zoom and pan, for all given projects.
ByteSetter(ByteProcessor) - Constructor for class mpicbg.trakem2.util.RobustNormalizeLocalContrast.ByteSetter

C

c - Variable in class ini.trakem2.persistence.ImageBytes
cache() - Method in class ini.trakem2.display.Profile: Cache this Profile if needed.
Cache - Class in ini.trakem2.persistence: Access is not synchronized, that is your duty.
Cache(long) - Constructor for class ini.trakem2.persistence.Cache
cache(Displayable, ImagePlus) - Method in class ini.trakem2.persistence.Loader: Add to the cache, or if already there, make it be the last (to be flushed the last).
cache(Patch, ImagePlus) - Method in class ini.trakem2.persistence.Loader
cacheAWT(long, Image) - Method in class ini.trakem2.persistence.Loader
cacheCurrentPath(String) - Method in class ini.trakem2.display.Patch: Cache a proper, good, known path to the image wrapped by this Patch.
cacheImagePlus(long, ImagePlus) - Method in class ini.trakem2.persistence.Loader: Cache any ImagePlus, as long as a unique id is assigned to it there won't be problems; use getNextId to obtain a unique id.
cacheSubtree(Iterable<Node<T>>) - Method in class ini.trakem2.display.Tree
CachingThread - Class in ini.trakem2.utils
CachingThread() - Constructor for class ini.trakem2.utils.CachingThread
CachingThread(Runnable) - Constructor for class ini.trakem2.utils.CachingThread
CachingThread(String) - Constructor for class ini.trakem2.utils.CachingThread
CachingThread(Runnable, String) - Constructor for class ini.trakem2.utils.CachingThread
CachingThread(ThreadGroup, Runnable) - Constructor for class ini.trakem2.utils.CachingThread
CachingThread(ThreadGroup, String) - Constructor for class ini.trakem2.utils.CachingThread
CachingThread(ThreadGroup, Runnable, String) - Constructor for class ini.trakem2.utils.CachingThread
CachingThread(ThreadGroup, Runnable, String, long) - Constructor for class ini.trakem2.utils.CachingThread
calculateBoundingBox(Layer) - Method in interface ini.trakem2.display.AreaContainer: May have the side effect of updating the buckets of the containing container of this Displayable.
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.AreaList: Calculate box, make this width,height be that of the box, and translate all areas to fit in.
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.AreaTree
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.Ball
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.Dissector
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.Pipe
calculateBoundingBox(boolean, Layer) - Method in class ini.trakem2.display.Pipe
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.Polyline
calculateBoundingBox(boolean, Layer) - Method in class ini.trakem2.display.Polyline
calculateBoundingBox() - Method in class ini.trakem2.display.Profile
calculateBoundingBox(boolean) - Method in class ini.trakem2.display.Profile: Calculate the bounding box of the curve in the shape of a Rectangle defined by x,y,width,height.
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.Stack
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.Tree
calculateBoundingBox(Layer) - Method in class ini.trakem2.display.ZDisplayable
calculateDataBoundingBox() - Method in class ini.trakem2.display.Polyline: Returns min_x, min_y, max_x, max_y.
calibratedData() - Method in class ini.trakem2.display.Tree.MeasurementPair
call() - Method in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable
caller(Object) - Static method in class ini.trakem2.utils.Utils: Returns a String representation of the class of the object one step before in the stack trace.
cancel() - Method in class ini.trakem2.display.AffineTransformMode
cancel() - Method in class ini.trakem2.display.ContrastAdjustmentMode
cancel() - Method in class ini.trakem2.display.DefaultMode
cancel() - Method in class ini.trakem2.display.GroupingMode
cancel() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
cancel() - Method in class ini.trakem2.display.ManualAlignMode
cancel() - Method in interface ini.trakem2.display.Mode
cancel(boolean) - Method in class ini.trakem2.utils.TaskOnEDT: Will only prevent execution, not interrupt it if its happening.
cancelTransform() - Method in class ini.trakem2.display.DisplayCanvas
canChangeLayer() - Method in class ini.trakem2.display.AffineTransformMode
canChangeLayer() - Method in class ini.trakem2.display.DefaultMode
canChangeLayer() - Method in class ini.trakem2.display.GroupingMode
canChangeLayer() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
canChangeLayer() - Method in class ini.trakem2.display.ManualAlignMode
canChangeLayer() - Method in interface ini.trakem2.display.Mode
canHaveAsChild(Thing) - Method in class ini.trakem2.tree.LayerThing
canHaveAsChild(Thing) - Method in class ini.trakem2.tree.ProjectThing
canHaveAsChild(String) - Method in class ini.trakem2.tree.ProjectThing
canHaveAsChild(Thing) - Method in class ini.trakem2.tree.TemplateThing
canHaveAsChild(Thing) - Method in interface ini.trakem2.tree.Thing
canJoin(List<? extends Tree<T>>) - Method in class ini.trakem2.display.Tree: Check if it is possible to join all given Trees into this, by using the first one as the receiver (which should be this), and all the others as the ones to be merged into the receiver.
canPan() - Method in class ini.trakem2.display.AffineTransformMode
canPan() - Method in class ini.trakem2.display.DefaultMode
canPan() - Method in class ini.trakem2.display.GroupingMode
canPan() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
canPan() - Method in class ini.trakem2.display.ManualAlignMode
canPan() - Method in interface ini.trakem2.display.Mode
canPerformAction(DNDTree, DefaultMutableTreeNode, int, Point) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
canPerformAction(DNDTree, DefaultMutableTreeNode, int, Point) - Method in class ini.trakem2.tree.DefaultTreeTransferHandler
canReadAndWriteTo(String) - Static method in class ini.trakem2.persistence.Loader
canRedo() - Method in class ini.trakem2.display.LayerSet
canRedo() - Method in class ini.trakem2.utils.History
canSendTo(Layer) - Method in class ini.trakem2.display.Displayable: Subclasses can specify the behaviour, for the default is true.
canSendTo(Layer) - Method in class ini.trakem2.display.Profile: Returns false if the target_layer contains a profile that is directly linked to this profile.
canUndo() - Method in class ini.trakem2.display.LayerSet
canUndo() - Method in class ini.trakem2.utils.History
canUseAWTImage() - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
canZoom() - Method in class ini.trakem2.display.AffineTransformMode
canZoom() - Method in class ini.trakem2.display.DefaultMode
canZoom() - Method in class ini.trakem2.display.GroupingMode
canZoom() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
canZoom() - Method in class ini.trakem2.display.ManualAlignMode
canZoom() - Method in interface ini.trakem2.display.Mode
castCollection(Collection<A>, Class, boolean) - Static method in class ini.trakem2.utils.Utils
CATAParameters() - Constructor for class ini.trakem2.analysis.Compare.CATAParameters
cc_scale - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
cent - Variable in class ini.trakem2.imaging.filters.NormalizeLocalContrast
center(double, double) - Method in class ini.trakem2.display.Display: Center the view, if possible, on x,y.
center(Coordinate<?>) - Method in class ini.trakem2.display.Display
center(Rectangle, double) - Method in class ini.trakem2.display.DisplayCanvas: Show the given r as the srcRect (or as much of it as possible) at the given magnification.
CENTER - Static variable in class ini.trakem2.display.LayerSet
centerAt(Coordinate) - Static method in class ini.trakem2.display.Display
centerAt(Coordinate<Displayable>, boolean, boolean) - Static method in class ini.trakem2.display.Display
centerFloater() - Method in class ini.trakem2.display.AffineTransformMode
centerIfNotWithinSrcRect(Coordinate<?>) - Method in class ini.trakem2.display.Display
Centrality - Class in ini.trakem2.analysis: Following pseudo-code from: Ulrik Brandes.
Centrality() - Constructor for class ini.trakem2.analysis.Centrality
centrality - Variable in class ini.trakem2.analysis.Vertex
Centrality.EtchingStep<T> - Class in ini.trakem2.analysis: An entry of the number of remaining branch vertices versus the set of branches (each as a List<Vertex<T>>) removed.
Chain(Line3D) - Constructor for class ini.trakem2.analysis.Compare.Chain
chain_branches - Variable in class ini.trakem2.analysis.Compare.CATAParameters
changes - Variable in class ini.trakem2.persistence.Loader: Keep track of whether there are any unsaved changes.
Channel - Class in ini.trakem2.display
characters(char[], int, int) - Method in class ini.trakem2.persistence.TMLHandler
check(String) - Static method in class ini.trakem2.utils.Utils
checkAlphaMaskFile() - Method in class ini.trakem2.display.Patch
checkBuckets() - Method in class ini.trakem2.display.Layer
checkBuckets() - Method in class ini.trakem2.display.LayerSet: Checks only buckets for ZDisplayable, not any related to any layer.
checkCoordinateTransformFile() - Method in class ini.trakem2.display.Patch
checkInput() - Method in class ini.trakem2.imaging.BinaryInterpolation2D
checkMipMapFileExists(Patch, double) - Method in class ini.trakem2.persistence.FSLoader: Checks if the mipmap file for the Patch and closest upper level to the desired magnification exists.
checkMipMapFileExists(Patch, double) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns false unless overriden.
checkPath(String) - Static method in class ini.trakem2.io.ImageSaver: Will create parent directories if they don't exist.
checkYN(String) - Static method in class ini.trakem2.utils.Utils
children - Variable in class ini.trakem2.display.Node
ChoiceIntSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceIntSetter
ChoiceIntSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceIntSetter
ChoiceObjectSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceObjectSetter
ChoiceObjectSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceObjectSetter
ChoiceStringSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceStringSetter
ChoiceStringSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceStringSetter
choose(int, int, int, int, Class<?>) - Method in class ini.trakem2.display.Display
choose(int, int, int, int) - Method in class ini.trakem2.display.Display
choose(int, int, int, int, boolean, Class<?>) - Method in class ini.trakem2.display.Display: Find a Displayable to add to the selection under the given point (which is in offscreen coords); will use a popup menu to give the user a range of Displayable objects to select from.
chooseFile(String, String) - Static method in class ini.trakem2.utils.Utils
chooseFile(String, String, String) - Static method in class ini.trakem2.utils.Utils: Select a file from the file system, for saving purposes.
CircularSequence - Class in ini.trakem2.utils
CircularSequence(int) - Constructor for class ini.trakem2.utils.CircularSequence: A sequence of integers from 0 to size that cycle back to zero when reaching the end; the starting point is the last point in the sequence, so that a call to CircularSequence.next() delivers the first value, 0.
CLAHE - Class in ini.trakem2.imaging.filters
CLAHE() - Constructor for class ini.trakem2.imaging.filters.CLAHE
CLAHE(boolean, int, int, float) - Constructor for class ini.trakem2.imaging.filters.CLAHE
CLAHE(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.CLAHE
cleanString(String) - Static method in class ini.trakem2.utils.Utils: Converts sequences of spaces into single space, and trims the ends.
cleanup() - Method in class ini.trakem2.utils.Worker: When quitted or interrupted, executes this method once.
clear() - Method in class ini.trakem2.display.Overlay
clear() - Method in class ini.trakem2.display.Selection: Remove all Displayables from this selection.
clear() - Method in class ini.trakem2.utils.CachingThread
clear() - Method in class ini.trakem2.utils.FieldMapView
clear() - Method in class ini.trakem2.utils.History: Remove all steps from the list and return them.
clearCache() - Method in class ini.trakem2.display.Tree
clearCache - Variable in class mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch
clearColumnScreenshots(LayerSet) - Static method in class ini.trakem2.display.Display
clearColumnScreenshots() - Method in class ini.trakem2.display.Display
clearIntensityMap() - Method in class ini.trakem2.display.Patch
clearIntensityMap(Patch) - Method in class ini.trakem2.persistence.FSLoader
clearIntensityMap(Patch) - Method in class ini.trakem2.persistence.Loader: Clear the intensity map coefficients for a patch.
clearSelection(Layer) - Static method in class ini.trakem2.display.Display
clearSelection() - Static method in class ini.trakem2.display.Display
clearSelection(Project) - Static method in class ini.trakem2.display.Display
clearState() - Method in class ini.trakem2.display.Tree
clearTransform - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
clearVirtualMatches() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D: Remove all virtual matches.
clip() - Method in class ini.trakem2.utils.History: Cut the list after the index, leaving from 0 to index, inclusive, inside.
clone(Collection<Vertex<T>>) - Static method in class ini.trakem2.analysis.Vertex: Clone a collection of vertices, preserving the neighbors.
clone(Project, boolean) - Method in class ini.trakem2.display.AreaList: Performs a deep copy of this object, without the links.
clone(Project, boolean) - Method in class ini.trakem2.display.AreaTree
clone(Project, boolean) - Method in class ini.trakem2.display.Ball: Performs a deep copy of this object, without the links.
clone(Project, boolean) - Method in class ini.trakem2.display.Connector
clone() - Method in class ini.trakem2.display.Displayable: Performs a deep copy of this object.
clone(Project, boolean) - Method in class ini.trakem2.display.Displayable: Performs a deep copy of this object, obtaining its unique id either from the given project or the exact same as this object's id.
clone(Project) - Method in class ini.trakem2.display.Displayable: Performs a deep copy of this object but assigning to it the given project.
clone(Project, boolean) - Method in class ini.trakem2.display.Dissector: Returns a deep copy.
clone(Project, boolean) - Method in class ini.trakem2.display.DLabel: Performs a deep copy of this object, except for the Layer pointer.
clone(Project, LayerSet, Rectangle, boolean, boolean) - Method in class ini.trakem2.display.Layer: Make a copy of this layer into the given LayerSet, enclosing only Displayable objects within the roi, and translating them for that roi x,y.
clone(Project, boolean) - Method in class ini.trakem2.display.LayerSet
clone(Project, Layer, Layer, Rectangle, boolean, boolean, boolean) - Method in class ini.trakem2.display.LayerSet: Clone the contents of this LayerSet, from first to last given layers, and cropping for the given rectangle; does NOT copy the ZDisplayable, which may be copied using the LayerSet.cloneInto method.
clone(Project) - Method in class ini.trakem2.display.Node: Returns a recursive copy of this Node subtree, where the copy of this Node is the root.
clone(Project, boolean) - Method in class ini.trakem2.display.Patch: Performs a copy of this object, without the links, unlocked and visible, except for the image which is NOT duplicated.
clone(Project, boolean) - Method in class ini.trakem2.display.Pipe: Performs a deep copy of this object, without the links.
clone(Project, boolean) - Method in class ini.trakem2.display.Polyline: Performs a deep copy of this object, without the links.
clone(Project, boolean) - Method in class ini.trakem2.display.Profile: Performs a deep copy of this object, unlocked and visible.
clone(Project, boolean) - Method in class ini.trakem2.display.Stack
clone(Project, boolean) - Method in class ini.trakem2.display.Treeline
clone(Project, boolean) - Method in class ini.trakem2.tree.TemplateThing: Recursive into children: clones the whole tree from this node downward.
clone() - Method in class lenscorrection.Distortion_Correction.BasicParam
clone() - Method in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
clone() - Method in class mpi.fruitfly.math.datastructures.FloatArray
clone() - Method in class mpi.fruitfly.math.datastructures.FloatArray2D
clone() - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
clone() - Method in class mpi.fruitfly.math.datastructures.FloatArray4D
clone() - Method in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
clone() - Method in class mpicbg.trakem2.align.Align.Param
clone() - Method in class mpicbg.trakem2.align.Align.ParamOptimize
clone() - Method in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
clone() - Method in class mpicbg.trakem2.align.ElasticMontage.Param
clone() - Method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param
cloneInto(LayerSet, Layer, Layer, Project, LayerSet, Rectangle, boolean) - Static method in class ini.trakem2.display.LayerSet
close(Project) - Static method in class ini.trakem2.display.Display: Find all Display instances that contain a Layer of the given project and close them without removing the Display entries from the database.
close(Layer) - Static method in class ini.trakem2.display.Display: Find all Display instances that contain the layer and close them and remove the Display from the database.
close() - Method in class ini.trakem2.imaging.PatchStack
closed - Variable in class ini.trakem2.display.Profile: Paint/behave as open or closed curve.
coefficients - Variable in class org.janelia.intensity.LinearIntensityMap
collectAllChildren(ArrayList<TemplateThing>) - Method in class ini.trakem2.tree.TemplateThing: Recursive into children.
collectSimilarThings(TemplateThing, HashSet<ProjectThing>) - Method in class ini.trakem2.tree.ProjectThing: Recursive into children, find those of the given type that have the same parent chain as the given TemplateThing.
collectSimilarThings(TemplateThing, HashSet<TemplateThing>) - Method in class ini.trakem2.tree.TemplateThing: Recursive into children, find those of the given type that have the same immediate parent type as the given TemplateThing.
collectSimilarThings2(TemplateThing, HashSet<TemplateThing>) - Method in class ini.trakem2.tree.TemplateThing: Recursive into children, find those of the same type as the given TemplateThing and whose number of children is the same to those of the given TemplateThing (to exclude nested types).
collectThingsOfEqualType(TemplateThing, HashSet<TemplateThing>) - Method in class ini.trakem2.tree.TemplateThing: Find things of the same type, even if their parents are different, recusively into children.
color - Variable in class ini.trakem2.display.Displayable
color - Variable in class ini.trakem2.display.Node
color_cues - Variable in class ini.trakem2.display.LayerSet
colorizeByBranchBetweennessCentrality(int) - Method in class ini.trakem2.display.Tree
colorizeByNodeBetweennessCentrality() - Method in class ini.trakem2.display.Tree
colors - Variable in class ini.trakem2.display.Tree.MeshData
ColorYCbCrComposite - Class in ini.trakem2.display.graphics
COMBINED - Static variable in class ini.trakem2.analysis.Compare
COMBINED_SCORE_INDICES - Static variable in class ini.trakem2.analysis.Compare
commandExecuting(String) - Method in class ini.trakem2.display.ImageJCommandListener
commitLargeUpdate() - Method in class ini.trakem2.persistence.DBLoader: Used in combination with startLargeUpdate()
commitLargeUpdate() - Method in class ini.trakem2.persistence.Loader
commonDTDChildren() - Static method in class ini.trakem2.display.Displayable
commonPointMatches(Tile<?>, Collection<PointMatch>) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D: Extract the common PointMatches of two tiles.
COMPARATOR - Static variable in class ini.trakem2.display.Layer: Compare layers by Z.
Compare - Class in ini.trakem2.analysis
compare(Project, Project) - Static method in class ini.trakem2.utils.Merger: Take two projects and find out what is different among them, independent of id.
Compare.CATAParameters - Class in ini.trakem2.analysis: Compare all to all parameters.
Compare.Chain - Class in ini.trakem2.analysis: Represents a list of concatenated pipes, where each pipe is parent of the next within the ProjectTree.
compareAllToAll(boolean, String, String[], Project[]) - Static method in class ini.trakem2.analysis.Compare
compareAllToAll(boolean, String, String[], Project[], boolean, boolean, int, String) - Static method in class ini.trakem2.analysis.Compare: Gets pipes for all open projects, and generates a matrix of dissimilarities, which gets passed on to the Worker thread and also to a file, if desired.
compareTags(Node<?>, Node<?>) - Static method in class ini.trakem2.utils.Merger: Returns three lists: the tags in common, the tags in this node but not in the other, and the tags in the other but not in this node.
compareTo(Layer) - Method in class ini.trakem2.display.Layer
compareTo(Tag) - Method in class ini.trakem2.display.Tag
compareTo(TemplateThing) - Method in class ini.trakem2.tree.TemplateThing: Compares the String type, for sorting purposes.
componentHidden(ComponentEvent) - Method in class ini.trakem2.display.RollingPanel
componentMoved(ComponentEvent) - Method in class ini.trakem2.display.RollingPanel
componentResized(ComponentEvent) - Method in class ini.trakem2.display.RollingPanel
componentShown(ComponentEvent) - Method in class ini.trakem2.display.RollingPanel
COMPOSITE_ADD - Static variable in class ini.trakem2.display.Displayable
COMPOSITE_COLOR_YCBCR - Static variable in class ini.trakem2.display.Displayable
COMPOSITE_DIFFERENCE - Static variable in class ini.trakem2.display.Displayable
COMPOSITE_MULTIPLY - Static variable in class ini.trakem2.display.Displayable
COMPOSITE_NORMAL - Static variable in class ini.trakem2.display.Displayable
COMPOSITE_SUBTRACT - Static variable in class ini.trakem2.display.Displayable
compositeModes - Static variable in class ini.trakem2.display.Displayable
compute(Collection<Vertex<T>>) - Static method in class ini.trakem2.analysis.Centrality: Computes betweenness centrality of each vertex in the collection of vertices @param vs where all vertices are part of the same graph.
computeAllDegrees() - Method in class ini.trakem2.display.Node: Return a map of node vs degree of that node, for the entire subtree (including this node).
computeAllDegrees() - Method in class ini.trakem2.display.Tree
computeArea() - Method in class ini.trakem2.display.Profile: Calibrated, in units as specified at getLayerSet().getCalibration().getUnit() -- returns zero if this profile is not closed.
computeBinaryFilter3(FloatArray3D, float) - Static method in class mpi.fruitfly.registration.ImageFilter
computeBinaryPlusSobelFilter3(FloatArray3D, float) - Static method in class mpi.fruitfly.registration.ImageFilter
computeCentrality() - Method in class ini.trakem2.display.Tree: Computes betweenness centrality of each node in the tree, using Ulrik Brandes betweenness centrality algorithm.
computeCorrelationCoefficient(double[], double[]) - Static method in class mpi.fruitfly.math.General
computeCrossCorrelation(double, double, boolean) - Method in class mpi.fruitfly.registration.CrossCorrelation2D: Deprecated.
This method is only single threaded, use computeCrossCorrelationMT instead
computeCrossCorrelationMT(double, double, boolean) - Method in class mpi.fruitfly.registration.CrossCorrelation2D: Computes a translational registration with the help of the cross correlation measure.
computeDegree() - Method in class ini.trakem2.display.Node: Traverse the tree from this node all the way to the root node, and count how many nodes apart this node is from the root node: that is the degree.
computeDesirableMinFreeBytes() - Static method in class ini.trakem2.persistence.Loader: 150 Mb per processor, which is ~2x 67 Mb, the size of a 32-bit 4096x4096 image.
computeGaussian(FloatArray2D, float) - Static method in class mpi.fruitfly.registration.ImageFilter
computeGaussian(FloatArray3D, float) - Static method in class mpi.fruitfly.registration.ImageFilter
computeGaussianFast(FloatArray3D, float) - Static method in class mpi.fruitfly.registration.ImageFilter
computeGaussianFastMirror(FloatArray2D, double) - Static method in class mpi.fruitfly.registration.ImageFilter
computeGaussianFastMirror(FloatArray3D, float) - Static method in class mpi.fruitfly.registration.ImageFilter: This class does the gaussian filtering of an image.
computeIncreasingGaussianX(FloatArray2D, float, float) - Static method in class mpi.fruitfly.registration.ImageFilter
computeLaPlaceFilter3(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
computeLaPlaceFilter5(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
computeLaPlaceFilter5(FloatArray3D) - Static method in class mpi.fruitfly.registration.ImageFilter
computeLength() - Method in class ini.trakem2.display.Profile: Calibrated for pixel width only (that is, it assumes pixel aspect ratio 1:1), in units as specified at getLayerSet().getCalibration().getUnit()
computeMedian(double[]) - Static method in class mpi.fruitfly.math.General
computeMedian(float[]) - Static method in class mpi.fruitfly.math.General
computeSegmentsIntersection(float, float, float, float, float, float, float, float) - Static method in class ini.trakem2.utils.M
computeSigma(int, int) - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
computeSobelFilter(FloatArray3D) - Static method in class mpi.fruitfly.registration.ImageFilter
computeTurkeyBiAverage(double[]) - Static method in class mpi.fruitfly.math.General
computeTurkeyBiAverage(double[], double) - Static method in class mpi.fruitfly.math.General
computeTurkeyBiAverage(double[], double[], double) - Static method in class mpi.fruitfly.math.General
computeTurkeyBiMedian(double[], double) - Static method in class mpi.fruitfly.math.General
computeTurkeyBiMedian(float[], float) - Static method in class mpi.fruitfly.math.General
computeTurkeyBiMedianWeights(double[], double) - Static method in class mpi.fruitfly.math.General
condense(Compare.CATAParameters, VectorString3D[], Worker) - Static method in class ini.trakem2.analysis.Compare: Do an all-to-all distance matrix of the given vs, then do a neighbor joining, do a weighted merge of the two VectorString3D being merged, and then finally output the resulting condensed unique VectorString3D with its source array full with all points that make each point in it.
confidence - Variable in class ini.trakem2.display.Node: The confidence value of the edge towards the parent; in other words, how much this node can be trusted to continue from its parent node.
Connector - Class in ini.trakem2.display: A one-to-many connection, represented by one source point and one or more target points.
Connector(Project, String) - Constructor for class ini.trakem2.display.Connector
Connector(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Connector
Connector(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Connector: Reconstruct from XML.
Connector.ConnectorNode - Class in ini.trakem2.display
ConnectorNode(float, float, Layer) - Constructor for class ini.trakem2.display.Connector.ConnectorNode
ConnectorNode(float, float, Layer, float) - Constructor for class ini.trakem2.display.Connector.ConnectorNode
ConnectorNode(HashMap<String, String>) - Constructor for class ini.trakem2.display.Connector.ConnectorNode: To reconstruct from XML, without a layer.
connectTilePairs(Align.Param, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>, int, boolean) - Static method in class mpicbg.trakem2.align.Align: Connect a List of Tiles by geometrically consistent SIFT-feature correspondences.
connectTilePairs(Align.Param, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>, int) - Static method in class mpicbg.trakem2.align.Align: Connect a List of Tiles by geometrically consistent SIFT-feature correspondences.
consumeLastPopupPoint() - Method in class ini.trakem2.display.DisplayCanvas
contains(Layer, double, double) - Method in class ini.trakem2.display.AreaList: Returns whether the point x,y is contained in this object at the given Layer.
contains(Layer, double, double) - Method in class ini.trakem2.display.Ball: Test whether the Ball contains the given point at the given layer.
contains(LayerSet, String) - Static method in class ini.trakem2.display.Display3D
contains(double, double) - Method in class ini.trakem2.display.Displayable: Test whether the given point falls within the perimeter of this Displayable, considering the position x,y.
contains(Layer, double, double) - Method in class ini.trakem2.display.Displayable: Calls contains(x_p, y_p) unless overriden -- in ZDisplayable objects, it tests whether the given point is contained in the part of the ZDisplayable that shows in the given layer.
contains(Layer, double, double) - Method in class ini.trakem2.display.Dissector
contains(double, double) - Method in class ini.trakem2.display.inspect.ShapeProxy
contains(Point2D) - Method in class ini.trakem2.display.inspect.ShapeProxy
contains(double, double, double, double) - Method in class ini.trakem2.display.inspect.ShapeProxy
contains(Rectangle2D) - Method in class ini.trakem2.display.inspect.ShapeProxy
contains(int, int, int) - Method in class ini.trakem2.display.Layer
contains(Displayable) - Method in class ini.trakem2.display.Layer
contains(Class<?>) - Method in class ini.trakem2.display.Layer: Returns true if any of the Displayable objects are of the given class.
contains(Class<?>, boolean) - Method in class ini.trakem2.display.Layer: Returns true if any of the Displayable objects are of the given class; if visible_only is true, will return true only if at least one of the matched objects is visible.
contains(Layer) - Method in class ini.trakem2.display.LayerSet
contains(Displayable) - Method in class ini.trakem2.display.LayerSet
contains(Class<?>) - Method in class ini.trakem2.display.LayerSet: Returns true if any of the ZDisplayable objects are of the given class.
contains(double, double) - Method in class ini.trakem2.display.Patch: Considers the alpha mask.
contains(Layer, double, double) - Method in class ini.trakem2.display.Pipe: Test whether the Pipe contains the given point at the given layer.
contains(Layer, double, double) - Method in class ini.trakem2.display.Polyline
contains(Displayable) - Method in class ini.trakem2.display.Selection
contains(Class<?>) - Method in class ini.trakem2.display.Selection: Returns true if selection contains any items of the given class.
contains(Layer, double, double) - Method in class ini.trakem2.display.Tree: Returns true if the given point falls within a certain distance of any of the treeline segments, where a segment is defined as the line between a clicked point and the next.
contains(Patch) - Method in class ini.trakem2.imaging.PatchStack
contains(long) - Method in class ini.trakem2.persistence.Cache
contains(long, int) - Method in class ini.trakem2.persistence.Cache
containsAffected(Class<?>) - Method in class ini.trakem2.display.Selection: If any of the selected or linked is of Class c.
containsDisplayable(Class<?>) - Method in class ini.trakem2.display.LayerSet: Check in all layers.
containsKey(String) - Method in class ini.trakem2.display.Displayable.DoEdit
containsKey(Object) - Method in class ini.trakem2.utils.FieldMapView: Linear search.
containsKey(Object) - Method in class ini.trakem2.utils.TypedHashMap
containsLocal(Layer, double, double, double) - Method in class ini.trakem2.display.Polyline
containsPoint(int, int) - Method in class ini.trakem2.display.Profile: Check if the given point (usually from a MOUSE_PRESSED MouseEvent) is contained within the boundaries of this object.
containsValue(Object) - Method in class ini.trakem2.utils.FieldMapView: Linear search.
containsValue(Object) - Method in class ini.trakem2.utils.TypedHashMap
ContrastAdjustmentMode - Class in ini.trakem2.display
ContrastAdjustmentMode(Display, List<Displayable>) - Constructor for class ini.trakem2.display.ContrastAdjustmentMode
ContrastEnhancerWrapper - Class in ini.trakem2.imaging
ContrastEnhancerWrapper() - Constructor for class ini.trakem2.imaging.ContrastEnhancerWrapper
ContrastEnhancerWrapper(Patch) - Constructor for class ini.trakem2.imaging.ContrastEnhancerWrapper
ContrastPlot - Class in ini.trakem2.imaging: Copied and modified from Wayne Rasband's ImageJ ContrastPlot inner class in ij.plugin.frame.ContrastAdjuster class, in ImageJ 1.43h.
ContrastPlot(double, double, double, double) - Constructor for class ini.trakem2.imaging.ContrastPlot
ControlClickBehavior - Class in ini.trakem2.display.d3d: A class to provide the behavior on control-clicking on content in the 3D viewer.
ControlClickBehavior(Image3DUniverse, LayerSet) - Constructor for class ini.trakem2.display.d3d.ControlClickBehavior
ControlWindow - Class in ini.trakem2: Static class that shows one project per tab in a JFrame.
convertTo(ImageProcessor, int, boolean) - Static method in class ini.trakem2.utils.Utils: Converts the ImageProcessor to an ImageProcessor of the given type, or the same if of equal type.
convertToBufferedImage(ByteProcessor) - Static method in class ini.trakem2.utils.Utils
convertToFloat(ShortProcessor) - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
convolveGaussianSigma1(float[], float[], CircularSequence) - Static method in class ini.trakem2.utils.M
convolveSeparable(FloatArray2D, float[], float[]) - Static method in class mpi.fruitfly.registration.ImageFilter: convolve an image with a horizontal and a vertical kernel simple straightforward, not optimized---replace this with a trusted better version soon
Coordinate<T> - Class in ini.trakem2.display
Coordinate(double, double, Layer, T) - Constructor for class ini.trakem2.display.Coordinate
coordinate_transformed - Variable in class ini.trakem2.display.Patch.PatchImage: Whether the image was generated with a CoordinateTransform or not.
CoordinateTransformPath() - Constructor for class ini.trakem2.persistence.StaleFiles.CoordinateTransformPath
CoordinateTransformXML - Class in ini.trakem2.io
CoordinateTransformXML() - Constructor for class ini.trakem2.io.CoordinateTransformXML
coords - Variable in class ini.trakem2.display.Tree.MeasurementPair: The ordered list of calibrated coordinates of all nodes in the path of nodes between a and b, both included.
copy() - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform: Clone method
copy(boolean) - Method in class ini.trakem2.imaging.PatchStack
copy(double[], int) - Static method in class ini.trakem2.utils.Utils: Will make a new double[] array, then fit in it as many points from the given array as possible according to the desired new length.
copy(long[], int) - Static method in class ini.trakem2.utils.Utils
copy(double[], int, int) - Static method in class ini.trakem2.utils.Utils
copy(long[], int, int) - Static method in class ini.trakem2.utils.Utils
copy() - Method in class lenscorrection.NonLinearTransform: TODO Make this more efficient
copy() - Method in class lenscorrection.PolynomialModel2D
copyAs(Tree<?>, Class<A>, Class) - Static method in class ini.trakem2.display.Tree: Can copy a Treeline to an AreaTree and viceversa.
copyProperties(Node<?>) - Method in class ini.trakem2.display.Node
CorrectBackground - Class in ini.trakem2.imaging.filters
CorrectBackground() - Constructor for class ini.trakem2.imaging.filters.CorrectBackground
CorrectBackground(int, float) - Constructor for class ini.trakem2.imaging.filters.CorrectBackground
CorrectBackground(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.CorrectBackground
correctDistortionFromSelection(Selection) - Static method in class lenscorrection.DistortionCorrectionTask
correctDistortionFromSelectionParam - Static variable in class lenscorrection.DistortionCorrectionTask
CorrectDistortionFromSelectionParam() - Constructor for class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
correctDistortionFromSelectionTask(Selection) - Static method in class lenscorrection.DistortionCorrectionTask
correctImages() - Method in class lenscorrection.Distortion_Correction
correlate(Patch, Patch, float, double, int, double, double, double) - Static method in class ini.trakem2.imaging.StitchingTEM
correspondenceWeight - Variable in class mpicbg.trakem2.align.Align.Param
count(Class<?>) - Method in class ini.trakem2.display.Layer: Count instances of the given Class.
CountingTaskFactory<I,O> - Class in ini.trakem2.parallel
CountingTaskFactory() - Constructor for class ini.trakem2.parallel.CountingTaskFactory
countObjects(LayerSet) - Static method in class ini.trakem2.persistence.Loader
create(Project, LayerSet) - Static method in class ini.trakem2.display.Layer: Creates a new Layer asking for z and thickness, and adds it to the parent and returns it.
create(Layer) - Method in class ini.trakem2.display.LayerSet: Create a new LayerSet in the middle of the parent Layer.
create(Tree<?>) - Static method in class ini.trakem2.display.TreeConnectorsView
create(I) - Method in class ini.trakem2.parallel.CountingTaskFactory: Generates a Callable task for an ExecutorService to process @param input.
create(I) - Method in class ini.trakem2.parallel.TaskFactory: Generates a Callable task for an ExecutorService to process @param input.
create(Patch, int, ImageProcessor, ByteProcessor, ByteProcessor, int) - Static method in class ini.trakem2.persistence.DownsamplerMipMaps
create(Patch, int, ImageProcessor, ByteProcessor, ByteProcessor) - Static method in class ini.trakem2.persistence.DownsamplerMipMaps
create(Patch, int, int, ImageProcessor, ByteProcessor, ByteProcessor) - Static method in class ini.trakem2.persistence.DownsamplerMipMaps
create(Patch, ImageProcessor, ByteProcessor, ByteProcessor, int) - Static method in class ini.trakem2.persistence.IntegralImageMipMaps: WARNING modifies the outside array when both alpha and outside are not null, and when ip is a ColorProcessor, will also modify ints int[] pixels if alpha or outside are not null (the alpha channel is or'ed in).
create(Worker, Project) - Static method in class ini.trakem2.utils.Bureaucrat: Creates but does not start the Bureaucrat thread.
create(Worker, Project[]) - Static method in class ini.trakem2.utils.Bureaucrat: Creates but does not start the Bureaucrat thread.
create_gaussian_kernel_2D_offset(float, float, float, boolean) - Static method in class mpi.fruitfly.registration.ImageFilter
createAffine() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
createAndStart(Worker, Project) - Static method in class ini.trakem2.utils.Bureaucrat: Creates and start the Bureaucrat thread.
createAndStart(Worker, Project[]) - Static method in class ini.trakem2.utils.Bureaucrat: Creates and start the Bureaucrat thread.
createARGBImage(int[], int, int) - Static method in class ini.trakem2.io.ImageSaver
createARGBImage(int[], int, int) - Static method in class org.janelia.intensity.Render: Create a BufferedImage from an existing pixel array.
createARGBImagePre(int[], int, int) - Static method in class ini.trakem2.io.ImageSaver: Assumes the pixels have been premultiplied.
createArrowhead(double, double, double, double) - Static method in class ini.trakem2.utils.M: Create an arrowhead at the end of the line segment defined by x1,y1 and x2,y2.
createArrowhead(double, double, double, double, double) - Static method in class ini.trakem2.utils.M
createAWTImage(int, Color) - Method in class mpicbg.trakem2.transform.ExportBestFlatImage: Create a java.awt.Image using the Loader.getFlatAWTImage method, using 'true' for the quality flag, which means than an image 2x larger on each side will be generated and then scaled down by area averaging.
createAWTImage(int) - Method in class mpicbg.trakem2.transform.ExportBestFlatImage: Create a java.awt.Image using the Loader.getFlatAWTImage method, using 'true' for the quality flag, which means than an image 2x larger on each side will be generated and then scaled down by area averaging.
createChild(String) - Method in class ini.trakem2.tree.ProjectThing
createChildren(String, int, boolean) - Method in class ini.trakem2.tree.ProjectThing: Creates one instance of the given type and if recursive, also of all possible children of it, and of them, and so on.
createClonedChild(ProjectThing) - Method in class ini.trakem2.tree.ProjectThing: At the moment only for basic types, which by definition have no children.
createColor256Copy() - Method in class ini.trakem2.imaging.PatchStack: Does not respect local transform of the patches, this is intended for confocal stacks.
createContext(ColorModel, ColorModel, RenderingHints) - Method in class ini.trakem2.display.graphics.AddARGBComposite
createContext(ColorModel, ColorModel, RenderingHints) - Method in class ini.trakem2.display.graphics.ColorYCbCrComposite
createContext(ColorModel, ColorModel, RenderingHints) - Method in class ini.trakem2.display.graphics.DifferenceARGBComposite
createContext(ColorModel, ColorModel, RenderingHints) - Method in class ini.trakem2.display.graphics.MultiplyARGBComposite
createContext(ColorModel, ColorModel, RenderingHints) - Method in class ini.trakem2.display.graphics.SubtractARGBComposite
createContext(ColorModel, Rectangle, Rectangle2D, AffineTransform, RenderingHints) - Method in class ini.trakem2.display.paint.USHORTPaint: Return a new USHORTPaintContext that shares the value and ccm fields with this instance.
createCoordinate(Node<T>) - Method in class ini.trakem2.display.Tree
createCoordinateTransformedImage() - Method in class ini.trakem2.display.Patch
createDisplay(Project, Layer) - Static method in class ini.trakem2.display.Display: Creates a new Display with adjusted magnification to fit in the screen.
createEmptyStack() - Method in class ini.trakem2.imaging.PatchStack
createFatPoint(double, double, double, double, Calibration) - Method in class ini.trakem2.display.Display3D: Creates a calibrated sphere to represent a point at LayerSet pixel coordinates wx, wy, wz, with radius wr.
createFlyThrough(List<? extends Region>, double, int, String) - Method in class ini.trakem2.persistence.Loader: Returns an ImageStack, one slice per region.
createGaussianKernel1D(double, boolean) - Static method in class mpi.fruitfly.registration.ImageFilter: This class creates a gaussian kernel
createGaussianKernel2D(float, boolean) - Static method in class mpi.fruitfly.registration.ImageFilter
createGaussianKernel3D(float, boolean) - Static method in class mpi.fruitfly.registration.ImageFilter
createGradients(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
createGray8Copy() - Method in class ini.trakem2.imaging.PatchStack: Does not respect local transform of the patches, this is intended for confocal stacks.
createGrayImage(byte[], int, int) - Static method in class ini.trakem2.io.ImageSaver
createGroupedGraphicSource() - Method in class ini.trakem2.display.ContrastAdjustmentMode
createGroupedGraphicSource() - Method in class ini.trakem2.display.GroupingMode
createGroupedGraphicSource() - Method in class ini.trakem2.display.NonLinearTransformMode
createIcosahedron(int, float) - Static method in class ini.trakem2.utils.M: Returns a "3D Viewer"-ready list mesh, centered at 0,0,0 and with radius as the radius of the enclosing sphere.
createIdPath(String, String, String) - Static method in class ini.trakem2.persistence.FSLoader: For sid=12345 creates 12/34/5.${filename}.jpg Will be fine with other filename-valid chars in sid.
createImage() - Method in class ini.trakem2.display.DisplayCanvas.Screenshot
createImage(ImagePlus) - Method in class ini.trakem2.display.Patch
createImage() - Method in class ini.trakem2.display.Patch
createImage(double, double) - Method in class ini.trakem2.display.Patch.PatchImage
createImage(int[], int, int, DirectColorModel) - Static method in class ini.trakem2.io.ImageSaver
createInterpolatedPolygon(FloatPolygon, double, boolean) - Static method in class ini.trakem2.utils.M: Copied from ImageJ's ij.gui.PolygonRoi.getInterpolatedPolygon, by Wayne Rasband and collaborators.
createInverseDistortionModel(Collection<Distortion_Correction.PointMatchCollectionAndAffine>, int, double, int, int) - Static method in class lenscorrection.Distortion_Correction: Estimates a polynomial distortion model for a set of corresponding points and returns the inverse of this model which then may be used to undo the distortion.
createJFrame(String) - Static method in class ini.trakem2.ControlWindow: Returns a new JFrame with the proper icon from ImageJ.iconPath set, if any.
createLayerStack(Class<?>, int, int) - Method in class ini.trakem2.display.LayerSet: Create a virtual layer stack that acts as a virtual ij.ImageStack, in RGB and set to a scale of max_dimension / Math.max(layer_width, layer_height).
createLazyFlyThrough(List<? extends Region>, double, int, Displayable) - Method in class ini.trakem2.persistence.Loader: Each slice is generated on demand, one slice per Region instance.
createLut() - Method in class ini.trakem2.imaging.PatchStack
createMany(Project, LayerSet) - Static method in class ini.trakem2.display.Layer: Pops up a dialog to choose the first Z coord, the thickness, the number of layers, and whether to skip the creation of any layers whose Z and thickness match that of existing layers.
createMaskedByteImage() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
createMeasurementPair(Tree<Area>.NodePath) - Method in class ini.trakem2.display.AreaTree
createMeasurementPair(Tree<T>.NodePath) - Method in class ini.trakem2.display.Tree
createMeasurementPair(Tree<Float>.NodePath) - Method in class ini.trakem2.display.Treeline
createMesh(ProjectThing, Displayable, int) - Method in class ini.trakem2.display.Display3D: Returns a function that returns a Content object.
createMesh(double, int) - Method in class ini.trakem2.display.Tree.MeasurementPair
createMipMapRelPath(Patch, String) - Static method in class ini.trakem2.persistence.FSLoader: For Patch id=12345 creates 12/34/5.${filename}.jpg
createMLST(Collection<PointMatch>, double) - Static method in class mpicbg.trakem2.align.Align: Temporary helper method that creates
createModel(int) - Static method in class mpicbg.trakem2.align.Util
createMultiTableView() - Method in class ini.trakem2.display.Tree: Create a GUI to list, in three tabs: starting point, branch points, end points, and all points.
createNewNode(float, float, Layer, Node<?>) - Method in class ini.trakem2.display.Tree: Create a new node, copying some properties from the modelNode such as radius or color.
createNewRoi(int, int) - Method in class ini.trakem2.imaging.PatchStack
createNodeRenderer() - Method in class ini.trakem2.tree.DNDTree: Subclasses should override this method to return a subclass of DNDTree.NodeRenderer
createNodeRenderer() - Method in class ini.trakem2.tree.LayerTree
createNodeRenderer() - Method in class ini.trakem2.tree.ProjectTree
createOrigin(VectorString3D, VectorString3D, VectorString3D, int) - Static method in class ini.trakem2.analysis.Compare: Returns an array of 4 Vector3d: the three unit vectors in the same order as the vector strings, and the origin of coordinates.
createOrigin(VectorString3D, VectorString3D, VectorString3D, int, Vector3d[]) - Static method in class ini.trakem2.analysis.Compare
createPatch(Project, String) - Static method in class ini.trakem2.display.Patch: Create a new Patch and register the associated filepath with the project's loader.
createPipeChains(ProjectThing, LayerSet) - Static method in class ini.trakem2.analysis.Compare: For a given pipe, create a VectorString3D for each possible path, as determined by the Project Tree structure and the parent/child relationships.
createPipeChains(ProjectThing, LayerSet, String) - Static method in class ini.trakem2.analysis.Compare
createProcessor(int, int) - Method in class ini.trakem2.imaging.FloatProcessorT2: Returns a new, blank FloatProcessor with the specified width and height.
createProcessor(int, int, int) - Static method in class ini.trakem2.utils.Utils
createResultsTable(String, String[]) - Static method in class ini.trakem2.utils.Utils: Creates a new ResultsTable with the given window title and column titles, and 2 decimals of precision, or if one exists for the given window title, returns it.
createRetiledSibling(Project, String, int, int, int, boolean, int, boolean) - Static method in class ini.trakem2.persistence.ProjectTiler: Take a Project, a size for the image tiles, and a target directory, and create a new copy of the current project in that folder but with the underlying images converted to tiles with a translation-only transform (saved as zipped TIFFs, with extension ".tif.zip").
createReviewStack(Node<T>, Node<T>, Tag, String, int, int, double, int) - Method in class ini.trakem2.display.Tree: The behavior is undefined if @param last is not a descendant of @param first.
createRGBImage(int[], int, int) - Static method in class ini.trakem2.io.ImageSaver
createScaleLevelTransform(int) - Static method in class org.janelia.intensity.Render: Create an affine transformation that compensates for both scale and pixel shift of a mipmap level that was generated by top-left pixel averaging.
createScreenPathRange(GroupingMode.PatchRange, Rectangle, double) - Method in class ini.trakem2.display.ContrastAdjustmentMode
createScreenPathRange(GroupingMode.PatchRange, Rectangle, double) - Method in class ini.trakem2.display.GroupingMode
createScreenPathRange(GroupingMode.PatchRange, Rectangle, double) - Method in class ini.trakem2.display.NonLinearTransformMode
createStream(String) - Static method in class ini.trakem2.utils.Utils
createSubproject(Rectangle, Layer, Layer, boolean) - Method in class ini.trakem2.Project: Create a new subproject for the given layer range and ROI.
createTransform(Vector3d[]) - Static method in class ini.trakem2.analysis.Compare: Creates a transform with the 4 given vectors: X, Y, Z and translation of origin.
createTransformedImage() - Method in class ini.trakem2.display.Patch: Returns a PatchImage object containing the bottom-of-transformation-stack image and alpha mask, if any (except the AffineTransform, which is used for direct hw-accel screen rendering).
createTransformPropertiesTable(List<Displayable>, List<Displayable>, Set<Long>) - Static method in class mpicbg.trakem2.align.AlignTask: Creates a map only for visible patches that intersect vdata.
createUndoMoveStep(Displayable) - Method in class ini.trakem2.display.LayerSet: To undo moving up/down/top/bottom.
createZippedStream(ImagePlus) - Method in class ini.trakem2.persistence.Loader: Returns the ImagePlus as a zipped InputStream of bytes; the InputStream has to be closed by whoever is calling this method.
crop(List<Layer>) - Method in class ini.trakem2.display.AreaList: Retain the data within the layer range, and through out all the rest.
crop(List<Layer>) - Method in class ini.trakem2.display.Ball: Retain the data within the layer range, and throw out all the rest.
crop(List<Layer>) - Method in class ini.trakem2.display.Connector: If the root node (the origin) does not remain within the range, this Connector is left empty.
crop(List<Layer>) - Method in class ini.trakem2.display.Dissector: Retain the data within the layer range, and through out all the rest.
crop(List<Layer>) - Method in class ini.trakem2.display.Pipe: Retain the data within the layer range, and through out all the rest.
crop(List<Layer>) - Method in class ini.trakem2.display.Polyline: Retain the data within the layer range, and through out all the rest.
crop(List<Layer>) - Method in class ini.trakem2.display.Tree: Retain the data within the layer range, and through out all the rest.
crop(List<Layer>) - Method in class ini.trakem2.display.ZDisplayable: Retain the data within the layer range, and through out all the rest.
CrossCorrelation2D - Class in mpi.fruitfly.registration: CrossCorrelation2D.
CrossCorrelation2D(String, String, boolean) - Constructor for class mpi.fruitfly.registration.CrossCorrelation2D
CrossCorrelation2D(ImageProcessor, ImageProcessor, boolean) - Constructor for class mpi.fruitfly.registration.CrossCorrelation2D
crosslink(Collection<Displayable>, boolean) - Static method in class ini.trakem2.display.Patch
ct - Variable in class ini.trakem2.display.Patch.TransformProperties
ct - Variable in class ini.trakem2.display.VectorDataTransform.ROITransform
CT_APPEND - Static variable in class ini.trakem2.display.Display
CT_PREAPPEND - Static variable in class ini.trakem2.display.Display
CT_REPLACE - Static variable in class ini.trakem2.display.Display: coordinate transform transfer modes
CubicBSplineTransform - Class in bunwarpj.trakem2.transform: Class to implement elastic transforms based on cubic B-splines.
CubicBSplineTransform() - Constructor for class bunwarpj.trakem2.transform.CubicBSplineTransform: Empty constructor
CubicBSplineTransform(int, double[][], double[][], int, int) - Constructor for class bunwarpj.trakem2.transform.CubicBSplineTransform: Cubic B-spline transform constructor
CubicBSplineTransform(int, BSplineModel, BSplineModel, int, int) - Constructor for class bunwarpj.trakem2.transform.CubicBSplineTransform: Cubic B-spline transform constructor
CUM_PHYST_DIST - Static variable in class ini.trakem2.analysis.Compare
cumulative() - Method in class ini.trakem2.utils.StopWatch: Total time transcurred from the start.
cut_uneven_ends - Variable in class ini.trakem2.analysis.Compare.CATAParameters
cutNumber(double, int) - Static method in class ini.trakem2.utils.Utils
cutNumber(double, int, boolean) - Static method in class ini.trakem2.utils.Utils: remove_trailing_zeros will leave at least one zero after the comma if appropriate.
CUTOFF_VALUES - Static variable in class mpi.fruitfly.general.ImageArrayConverter

D

d - Variable in class ini.trakem2.analysis.Vertex: Length of the path.
d2s(double, int) - Static method in class ini.trakem2.utils.Utils
dampSpringMesh - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
dampSpringMesh - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
DASHED_STROKE - Static variable in interface ini.trakem2.display.Taggable
data - Variable in class ini.trakem2.analysis.Vertex: The data associated with this node, if any.
data - Variable in class ini.trakem2.display.Tree.MeasurementPair: The ordered list of calibrated data elements of each node in the path of nodes between a and b, both included.
data - Variable in class mpi.fruitfly.math.datastructures.FloatArray
dataType - Variable in class ini.trakem2.utils.ImgLibVolume
db_lock - Variable in class ini.trakem2.persistence.Loader
db_map - Variable in class ini.trakem2.display.LayerSet.LayerBucket
DBLoader - Class in ini.trakem2.persistence
DBLoader() - Constructor for class ini.trakem2.persistence.DBLoader: Create and connect to the database.
DBObject - Class in ini.trakem2.persistence: Base class of all objects that can be saved in a database or XML file.
DBObject(Project) - Constructor for class ini.trakem2.persistence.DBObject: Create new and later add it to the database.
DBObject(Project, long) - Constructor for class ini.trakem2.persistence.DBObject: Reconstruct from database.
DBObject(Loader) - Constructor for class ini.trakem2.persistence.DBObject: For the Project
DCM - Static variable in class ini.trakem2.display.Patch
debug() - Method in class ini.trakem2.display.AreaTree
debug() - Method in class ini.trakem2.display.Bucket
debug() - Method in class ini.trakem2.display.Patch
debug(String) - Method in class ini.trakem2.display.Selection
debug() - Method in class ini.trakem2.persistence.Cache
debug() - Static method in class ini.trakem2.persistence.Loader
debug(String) - Method in class ini.trakem2.tree.LayerThing
debug(String) - Method in class ini.trakem2.tree.ProjectThing
debug(String) - Method in class ini.trakem2.tree.TemplateThing
debug(String) - Method in interface ini.trakem2.tree.Thing
debug - Variable in class ini.trakem2.utils.Lock
debug() - Method in class ini.trakem2.utils.Lock
debug - Static variable in class ini.trakem2.utils.Utils
debug(String) - Static method in class ini.trakem2.utils.Utils
debug_all - Static variable in class ini.trakem2.utils.Lock
debug_clip - Static variable in class ini.trakem2.utils.Utils
debug_event - Static variable in class ini.trakem2.utils.Utils
debug_mouse - Static variable in class ini.trakem2.utils.Utils
debug_sql - Static variable in class ini.trakem2.utils.Utils
debug_thing - Static variable in class ini.trakem2.utils.Utils
debugAll() - Static method in class ini.trakem2.utils.Lock
debugAlpha() - Static method in class ini.trakem2.io.ImageSaver
debugDialog() - Static method in class ini.trakem2.utils.Utils
debugMinMax(String) - Method in class ini.trakem2.imaging.FloatProcessorT2
debugMouse(String) - Static method in class ini.trakem2.utils.Utils
decache(ImagePlus) - Method in class ini.trakem2.persistence.Loader: Throw away all awts that depend on this image, so that they will be recreated next time they are needed.
decache(Object) - Method in class ini.trakem2.Project
decacheAll() - Method in class ini.trakem2.imaging.PatchStack: Remove all awts and snaps from the loader's cache, and repaint (which will remake as many as needed)
decacheAWT(long) - Method in class ini.trakem2.persistence.Loader: Removes from the cache all awt images bond to the given id.
decacheImagePlus(long) - Method in class ini.trakem2.persistence.Loader
decacheImagePlus(long[]) - Method in class ini.trakem2.persistence.Loader
deepClone(Project, boolean) - Method in class ini.trakem2.tree.ProjectThing: Clone this ProjectThing with its template and all its children and objects cloned, and return it.
DEFAULT_AFFINE - Static variable in class ini.trakem2.display.DisplayCanvas
default_alpha - Variable in class ini.trakem2.display.AreaWrapper.PaintParameters
DEFAULT_MIN_R - Static variable in class ini.trakem2.imaging.StitchingTEM
DEFAULT_MIPMAPS_MODE - Static variable in class ini.trakem2.persistence.Loader: Points to Loader.AREA_DOWNSAMPLING.
DEFAULT_STROKE - Static variable in class ini.trakem2.display.DisplayCanvas: Paints a handle on the offscreen x,y.
DefaultExecutorProvider - Class in ini.trakem2.parallel: Default Executor Provider, which creates ExecutorServices from java.util.concurrent.Executors
DefaultExecutorProvider() - Constructor for class ini.trakem2.parallel.DefaultExecutorProvider
DefaultGraphicsSource - Class in ini.trakem2.display.graphics: Handles default mode, i.e.
DefaultGraphicsSource() - Constructor for class ini.trakem2.display.graphics.DefaultGraphicsSource
DefaultMinAndMax - Class in ini.trakem2.imaging.filters: Sets the minimum to zero and the maximum to the maximum supported, or 255 for FloatProcessor and any other unknown ImageProcessor.
DefaultMinAndMax() - Constructor for class ini.trakem2.imaging.filters.DefaultMinAndMax
DefaultMinAndMax(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.DefaultMinAndMax
DefaultMode - Class in ini.trakem2.display
DefaultMode(Display) - Constructor for class ini.trakem2.display.DefaultMode
DefaultTreeTransferHandler - Class in ini.trakem2.tree: Adapted from freely available code by DeuDeu.
DefaultTreeTransferHandler(Project, DNDTree, int) - Constructor for class ini.trakem2.tree.DefaultTreeTransferHandler
deform - Static variable in class mpicbg.trakem2.align.AlignTask
delete(Project, String, StaleFiles.Path) - Static method in class ini.trakem2.persistence.StaleFiles: Generic method called by other methods of this class.
deleteAll() - Method in class ini.trakem2.display.Selection: Delete all selected objects from their Layer.
deleteAlphaMasks(Project) - Static method in class ini.trakem2.persistence.StaleFiles: Delete all files storing a zipped image representing the alpha mask and which are now stale.
deleteCoordinateTransforms(Project) - Static method in class ini.trakem2.persistence.StaleFiles: Delete all files storing a coordinate transform that are now stale.
deleteDisconnectedTiles - Static variable in class mpicbg.trakem2.align.AlignTask
deleteLastSlice() - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
deleteSlice(int) - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
deleteSlice(int) - Method in class ini.trakem2.imaging.LazyVirtualStack
deleteStaleFiles(boolean, boolean) - Method in class ini.trakem2.persistence.FSLoader: Delete stale files under the FSLoader.unuid folder.
deleteStaleFiles(boolean, boolean) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
delta - Variable in class ini.trakem2.analysis.Compare.CATAParameters
delta_envelope - Variable in class ini.trakem2.analysis.Compare.CATAParameters
depth - Variable in class mpi.fruitfly.math.datastructures.FloatArray3D
deselect() - Method in class ini.trakem2.display.Displayable: Tell this Displayable that is has been deselected from a Display.
deselect() - Method in class ini.trakem2.display.Tree
deserialize(String) - Method in class ini.trakem2.persistence.Loader: Attempts to find a file containing a serialized object.
deserializeFeatures(Align.Param, AbstractAffineTile2D<?>) - Static method in class mpicbg.trakem2.align.Align: Retrieve the features only if saved with the exact same relevant SIFT parameters.
deserializeFeatures(Project, Object, String, long) - Static method in class mpicbg.trakem2.align.Util: Retrieve a Collection of Features from the TrakEM2 project folder.
deserializePointMatches(Align.Param, AbstractAffineTile2D<?>, AbstractAffineTile2D<?>) - Static method in class mpicbg.trakem2.align.Align
deserializePointMatches(Project, Object, String, long, long) - Static method in class mpicbg.trakem2.align.Util
desiredModelIndex - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
desiredModelIndex - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
desiredModelIndex - Variable in class mpicbg.trakem2.align.Align.Param
destroy() - Method in class ini.trakem2.display.Ball: Release all memory resources taken by this object.
destroy() - Method in class ini.trakem2.display.Display: Release all resources held by this Display and close the frame.
destroy() - Static method in class ini.trakem2.display.Display3D
destroy() - Method in class ini.trakem2.display.Displayable: Release resources.
destroy() - Method in class ini.trakem2.display.DisplayCanvas
destroy() - Method in class ini.trakem2.display.DisplayNavigator: Release resources.
destroy() - Method in class ini.trakem2.display.ImageJCommandListener
destroy() - Method in class ini.trakem2.display.Layer
destroy() - Method in class ini.trakem2.display.LayerSet
destroy() - Method in class ini.trakem2.display.Pipe: Release all memory resources taken by this object.
destroy() - Method in class ini.trakem2.display.Polyline: Release all memory resources taken by this object.
destroy() - Method in class ini.trakem2.display.Profile: Release all memory resources taken by this object.
destroy() - Method in class ini.trakem2.display.Tree
destroy() - Method in class ini.trakem2.persistence.DBLoader: Release all memory and unregister itself.
destroy() - Method in class ini.trakem2.persistence.FSLoader
destroy() - Method in class ini.trakem2.persistence.Loader: Release all memory and unregister itself.
destroy() - Method in class ini.trakem2.Project
destroy() - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
destroy() - Method in class ini.trakem2.tree.DefaultTreeTransferHandler
destroy() - Method in class ini.trakem2.tree.DNDTree
destroy() - Method in class ini.trakem2.tree.LayerTree
destroy() - Method in class ini.trakem2.tree.ProjectTree
destroy() - Method in class ini.trakem2.tree.TemplateTree
destroy() - Method in class ini.trakem2.utils.DNDInsertImage
destroy() - Static method in class ini.trakem2.utils.ProjectToolbar
destroy(ControlWindow) - Static method in class ini.trakem2.utils.Utils: Destroy house keeping threads.
destroyPreloader(ControlWindow) - Static method in class ini.trakem2.persistence.Loader
DifferenceARGBComposite - Class in ini.trakem2.display.graphics
dimension - Variable in class lenscorrection.Distortion_Correction.BasicParam: Order of the polynomial kernel
dimensions - Variable in class org.janelia.intensity.LinearIntensityMap
direct - Variable in class ini.trakem2.analysis.Compare.CATAParameters
disconnect() - Method in class ini.trakem2.persistence.DBLoader: Disconnect from the database.
dispatcher - Variable in class ini.trakem2.display.Display: A thread to handle user actions, for example an event sent from a popup menu.
dispatcher - Variable in class ini.trakem2.tree.DNDTree
Dispatcher - Class in ini.trakem2.utils
Dispatcher(String) - Constructor for class ini.trakem2.utils.Dispatcher
Dispatcher() - Constructor for class ini.trakem2.utils.Dispatcher
Dispatcher.DispatcherThreadFactory - Class in ini.trakem2.utils
DispatcherThreadFactory(String) - Constructor for class ini.trakem2.utils.Dispatcher.DispatcherThreadFactory
displacePoints(double[][], double, double) - Static method in class ini.trakem2.display.Displayable
Display - Class in ini.trakem2.display: A Display is a class to show a Layer and enable mouse and keyboard manipulation of all its components.
Display(Project, long, Layer, Object[]) - Constructor for class ini.trakem2.display.Display: For reconstruction purposes.
Display(Project, Layer) - Constructor for class ini.trakem2.display.Display: A new Display from scratch, to show the given Layer.
Display(Project, Layer, Displayable) - Constructor for class ini.trakem2.display.Display: Open a new Display centered around the given Displayable.
Display(Project, long, Layer, HashMap<String, String>) - Constructor for class ini.trakem2.display.Display: Reconstruct a Display from an XML entry, to be opened when everything is ready.
display - Variable in class ini.trakem2.display.GroupingMode
display - Variable in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
Display.GridOverlay - Class in ini.trakem2.display
Display3D - Class in ini.trakem2.display: One Display3D instance for each LayerSet (maximum).
Display3D.VectorStringContent - Class in ini.trakem2.display
Display3DGUI - Class in ini.trakem2.display.d3d
Display3DGUI(Image3DUniverse) - Constructor for class ini.trakem2.display.d3d.Display3DGUI
Displayable - Class in ini.trakem2.display: The class that any element to be drawn on a Display must extend.
Displayable(Project, String, double, double) - Constructor for class ini.trakem2.display.Displayable: The minimal public Displayable constructor.
Displayable(Project, long, String, boolean, AffineTransform, float, float) - Constructor for class ini.trakem2.display.Displayable: Reconstruct a Displayable from the database.
Displayable(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Displayable: Reconstruct a Displayable from an XML entry.
Displayable.DataPackage - Class in ini.trakem2.display
Displayable.DoEdit - Class in ini.trakem2.display: For any Displayable data, including: title, visible, locked, color, alpha, and a 'data' type which includes the actual data (points, areas, etc.) and the links,width,height, and transformation (since all the latter are correlated).
Displayable.DoEdits - Class in ini.trakem2.display
Displayable.DoTransforms - Class in ini.trakem2.display
Displayable.SliderListener - Class in ini.trakem2.display
DisplayableChooser - Class in ini.trakem2.display: A class to be used when a click to select Displayable objects on the Display detects that there are more than one under the mouse cursor.
DisplayableChooser(Collection<Displayable>, Object) - Constructor for class ini.trakem2.display.DisplayableChooser
DisplayablePanel - Class in ini.trakem2.display
DisplayablePanel(Display, Displayable) - Constructor for class ini.trakem2.display.DisplayablePanel
DisplayCanvas - Class in ini.trakem2.display
DisplayCanvas(Display, int, int) - Constructor for class ini.trakem2.display.DisplayCanvas
DisplayCanvas.RepaintProperties - Class in ini.trakem2.display
DisplayCanvas.Screenshot - Class in ini.trakem2.display
DisplayCanvas.ScreenshotProperties - Class in ini.trakem2.display
DisplayNavigator - Class in ini.trakem2.display
dispose(Tree<?>) - Static method in class ini.trakem2.display.TreeConnectorsView
Dissector - Class in ini.trakem2.display: Implements the Double Dissector method with scale-invariant grouped labels.
Dissector(Project, String, double, double) - Constructor for class ini.trakem2.display.Dissector
Dissector(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Dissector
Dissector(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Dissector: Reconstruct from XML.
DISSIMILARITY - Static variable in class ini.trakem2.analysis.Compare
distance(double, double, double, double) - Static method in class ini.trakem2.display.Pipe: Calculate distance from one point to another.
distance(double, double, double, double) - Method in class ini.trakem2.display.Profile: Calculate distance from one point to another.
distance - Variable in class ini.trakem2.display.Tree.MeasurementPair: The calibrated path distance between nodes a and b, measured as the sum of all the distances between all consecutive pairs of nodes between a and b.
distance(Tuple3d, Tuple3d) - Static method in class ini.trakem2.utils.M
distance(double, double, double, double, double, double) - Static method in class ini.trakem2.utils.M
distance(double, double, double, double) - Static method in class ini.trakem2.utils.M
distance_type - Variable in class ini.trakem2.analysis.Compare.CATAParameters
distance_type_2 - Variable in class ini.trakem2.analysis.Compare.CATAParameters
distancePointToLine(double, double, double, double, double, double, double, double, double) - Static method in class ini.trakem2.utils.M: In 3D
distancePointToLine(double, double, double, double, double, double) - Static method in class ini.trakem2.utils.M: For a point px,py return its distance to a line defined by points lx1,ly1 and lx2,ly2.
distancePointToSegment(double, double, double, double, double, double, double, double, double) - Static method in class ini.trakem2.utils.M
distancePointToSegment(Vector3d, Vector3d, Vector3d) - Static method in class ini.trakem2.utils.M: Minimum distance between point v0 and a line segment defined by points v1 and v2.
distancePointToSegment(double, double, double, double, double, double) - Static method in class ini.trakem2.utils.M: For a point px,py return its distance to a line SEGMENT defined by points lx1,ly1 and lx2,ly2.
distancePointToSegmentSq(double, double, double, double, double, double, double, double, double) - Static method in class ini.trakem2.utils.M
distancePointToSegmentSq(Vector3d, Vector3d, Vector3d) - Static method in class ini.trakem2.utils.M
distanceSq(Tuple3d, Tuple3d) - Static method in class ini.trakem2.utils.M
distanceSq(double, double, double, double, double, double) - Static method in class ini.trakem2.utils.M
Distortion_Correction - Class in lenscorrection
Distortion_Correction() - Constructor for class lenscorrection.Distortion_Correction
Distortion_Correction.BasicParam - Class in lenscorrection
Distortion_Correction.PluginParam - Class in lenscorrection
Distortion_Correction.PointMatchCollectionAndAffine - Class in lenscorrection
distortionCorrection(double[][], double[][], double[][], int, double, int, int) - Static method in class lenscorrection.Distortion_Correction
DistortionCorrectionTask - Class in lenscorrection: Methods collection to be called from the GUI for alignment tasks.
DistortionCorrectionTask() - Constructor for class lenscorrection.DistortionCorrectionTask
DistortionCorrectionTask.AppendCoordinateTransformThread - Class in lenscorrection: Appends a CoordinateTransform to a list of patches.
DistortionCorrectionTask.CorrectDistortionFromSelectionParam - Class in lenscorrection
DistortionCorrectionTask.SetCoordinateTransformThread - Class in lenscorrection: Sets a CoordinateTransform to a list of patches.
distortSamplingX(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
distortSamplingY(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
DLabel - Class in ini.trakem2.display: This class is named funny to avoid confusion with java.awt.Label.
DLabel(Project, String, double, double) - Constructor for class ini.trakem2.display.DLabel
DLabel(Project, long, String, float, float, int, String, int, int, boolean, AffineTransform) - Constructor for class ini.trakem2.display.DLabel: For reconstruction purposes.
DLabel(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.DLabel: To reconstruct from an XML entry.
DNDInsertImage - Class in ini.trakem2.utils
DNDInsertImage(Display) - Constructor for class ini.trakem2.utils.DNDInsertImage
DNDTree - Class in ini.trakem2.tree: A JTree which has a built-in drag and drop feature.
DNDTree(Project, DefaultMutableTreeNode, Color) - Constructor for class ini.trakem2.tree.DNDTree
DNDTree.NodeRenderer - Class in ini.trakem2.tree
DoChangeTrees(LayerSet) - Constructor for class ini.trakem2.display.LayerSet.DoChangeTrees
doGUILater(boolean, Runnable) - Method in class ini.trakem2.persistence.Loader: Execute a GUI-related task later, in the event dispatch thread context if @param swing is true.
doLater(Callable<T>) - Method in class ini.trakem2.persistence.Loader
DONE - Static variable in class ini.trakem2.imaging.StitchingTEM
doneWaiting() - Static method in class ini.trakem2.display.Display3D
doPainterUpdate(Rectangle, double) - Method in class ini.trakem2.display.ContrastAdjustmentMode
doPainterUpdate(Rectangle, double) - Method in class ini.trakem2.display.GroupingMode
doPainterUpdate(Rectangle, double) - Method in class ini.trakem2.display.NonLinearTransformMode
doProcess(MouseEvent) - Method in class ini.trakem2.display.d3d.ControlClickBehavior
DoStep - Interface in ini.trakem2.display
DOT - Static variable in class ini.trakem2.display.DLabel
DoTransforms() - Constructor for class ini.trakem2.display.Displayable.DoTransforms
DoubleArrayToStack(double[], int, int, int, String, float, float) - Static method in class mpi.fruitfly.general.ImageArrayConverter
doubleIntegralImage(byte[], int, int) - Static method in class ini.trakem2.imaging.FastIntegralImage: Returns an image of @{param w}+1, @{param y}+1, where the first row and the first column are zeros, and the rest contain the sum of the area from 0,0 to that pixel in b.
doubleIntegralImage(float[], int, int) - Static method in class ini.trakem2.imaging.FastIntegralImage: Returns an image of @{param w}+1, @{param y}+1, where the first row and the first column are zeros, and the rest contain the sum of the area from 0,0 to that pixel in b.
DoubleSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.DoubleSetter
DoubleSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.DoubleSetter
DoubleSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.DoubleSetter
DOWN - Static variable in class ini.trakem2.display.LayerSet
DownsamplerMipMaps - Class in ini.trakem2.persistence
DownsamplerMipMaps() - Constructor for class ini.trakem2.persistence.DownsamplerMipMaps
dragControlPoint(int, int, int, double[][], double[][], boolean) - Method in class ini.trakem2.display.Pipe: Drag a control point and adjust the other, dependent one, in a symmetric way or not.
dragControlPoint(int, double, double, double[][], double[][], boolean) - Method in class ini.trakem2.display.Profile: Drag a control point and adjust the other, dependent one, in a symmetric way or not.
dragDropEnd(DragSourceDropEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragEnter(DragSourceDragEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragEnter(DropTargetDragEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragEnter(DropTargetDragEvent) - Method in class ini.trakem2.utils.DNDInsertImage
dragExit(DragSourceEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragExit(DropTargetEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragExit(DropTargetEvent) - Method in class ini.trakem2.utils.DNDInsertImage
dragGestureRecognized(DragGestureEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragOver(DragSourceDragEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragOver(DropTargetDragEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dragOver(DropTargetDragEvent) - Method in class ini.trakem2.utils.DNDInsertImage
dragPoint(int, int, int) - Method in class ini.trakem2.display.Pipe: Move backbone point by the given deltas.
dragPoint(int, int, int) - Method in class ini.trakem2.display.Polyline: Move backbone point by the given deltas.
dragPoint(int, int, int) - Method in class ini.trakem2.display.Profile: Move backbone point.
draw() - Method in class ini.trakem2.imaging.PatchStack
draw(int, int, int, int) - Method in class ini.trakem2.imaging.PatchStack
drawGrid(GeneralPath, double[][], int, int) - Static method in class lenscorrection.NonLinearTransform
drawHandle(Graphics, int, int, double) - Static method in class ini.trakem2.display.DisplayCanvas: Paints a handle on the screen coords.
drawHandle(Graphics2D, double, double, Rectangle, double) - Static method in class ini.trakem2.display.DisplayCanvas
drawInfo(Graphics) - Method in class ini.trakem2.display.FakeImageWindow
drawPoint(Graphics, int, int) - Static method in class ini.trakem2.utils.Utils
drawQuiverField(GeneralPath, double, double, double, double) - Static method in class lenscorrection.NonLinearTransform
drawScreenHandle(Graphics, int, int) - Static method in class ini.trakem2.display.DisplayCanvas: Paints a handle at x,y screen coords.
drawTranslatedImages(FloatArray2D, FloatArray2D, Point, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
DRAWTYPE_ERRORMAP - Static variable in class mpi.fruitfly.general.ImageArrayConverter
DRAWTYPE_OVERLAP - Static variable in class mpi.fruitfly.general.ImageArrayConverter
drop(DropTargetDropEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
drop(DropTargetDropEvent) - Method in class ini.trakem2.utils.DNDInsertImage
dropActionChanged(DragSourceDragEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dropActionChanged(DropTargetDragEvent) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
dropActionChanged(DropTargetDragEvent) - Method in class ini.trakem2.utils.DNDInsertImage
dropAllTags() - Method in class ini.trakem2.display.Tree: Drop all tags from the nodes of this tree.
DTD - Static variable in class ini.trakem2.io.XMLFileFilter
DTDParser - Class in ini.trakem2.tree: Reads either a DOCTYPE chunk from an xml file or a .dtd file directly.
duplicate() - Method in class ini.trakem2.analysis.Compare.Chain
duplicate(IFilter[]) - Static method in class ini.trakem2.imaging.filters.FilterEditor
duplicate(HashMap<Thing, Boolean>) - Method in class ini.trakem2.tree.DNDTree: Shallow copy of the tree: returns a clone of the root node and cloned children, recursively, with all Thing cloned as well, but the Thing object is the same.
duplicateAs(Collection<Displayable>, Class<A>) - Static method in class ini.trakem2.display.Tree: Takes a collection of Tree instances and creates duplicate siblings of the target class.
duplicateChild(Profile, int, Layer) - Method in class ini.trakem2.tree.ProjectTree: Implements the "Duplicate, link and send to next/previous layer" functionality.
duplicateLinkAndSendTo(Displayable, int, Layer) - Method in class ini.trakem2.display.Display

E

EAST - Static variable in class ini.trakem2.display.LayerSet
edit() - Method in class ini.trakem2.display.DLabel
elapsed(String) - Method in class ini.trakem2.utils.StopWatch: Time elapsed since last call to this method or the start.
ELASTIC - Static variable in class mpicbg.trakem2.align.AlignLayersTask
ELASTIC_BLOCK_CORRESPONDENCES - Static variable in class mpicbg.trakem2.align.AlignTask
ElasticLayerAlignment - Class in mpicbg.trakem2.align
ElasticLayerAlignment() - Constructor for class mpicbg.trakem2.align.ElasticLayerAlignment
ElasticLayerAlignment.Param - Class in mpicbg.trakem2.align
ElasticMontage - Class in mpicbg.trakem2.align
ElasticMontage() - Constructor for class mpicbg.trakem2.align.ElasticMontage
ElasticMontage.Param - Class in mpicbg.trakem2.align
elasticParam - Static variable in class mpicbg.trakem2.align.AlignLayersTask
embedAlpha(int[], byte[]) - Static method in class ini.trakem2.persistence.Loader: Embed the alpha-byte into an int[], changes the int[] in place and returns it
embedAlpha(int[], byte[], byte[]) - Static method in class ini.trakem2.persistence.Loader
embedAlphaPre(int[], byte[], byte[]) - Static method in class ini.trakem2.persistence.Loader: Assumes alpha is never null, but outside may be null.
end_nodes - Variable in class ini.trakem2.display.Tree
endElement(String, String, String) - Method in class ini.trakem2.persistence.TMLHandler
EndNodeIterator(Node) - Constructor for class ini.trakem2.display.Node.EndNodeIterator
endWaitingCursor() - Static method in class ini.trakem2.ControlWindow
enhance(FloatArray2D, float) - Static method in class mpi.fruitfly.registration.ImageFilter: in place enhance all values of a FloatArray to fill the given range
EnhanceContrast - Class in ini.trakem2.imaging.filters: Uses the @{link ContrastEnhancer.stretchHistogram(ImageProcessor, double, ImageStatistics) function.
EnhanceContrast() - Constructor for class ini.trakem2.imaging.filters.EnhanceContrast
EnhanceContrast(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.EnhanceContrast
enhanceContrast(Collection<Layer>) - Method in class ini.trakem2.persistence.Loader: Homogenize contrast layer-wise, for all given layers.
enhanceContrast(Collection<Displayable>, Patch) - Method in class ini.trakem2.persistence.Loader: Homogenize contrast for all patches, optionally using the @param reference Patch (can be null).
enlargeArrays() - Method in class ini.trakem2.display.Polyline: Increase the size of the arrays by 5.
enlargeArrays(int) - Method in class ini.trakem2.display.Polyline
enlargeArrays() - Method in class ini.trakem2.display.Profile: Increase the size of the arrays by 5 points.
enlargeToFit(Collection<? extends Displayable>) - Method in class ini.trakem2.display.LayerSet: Enlarge the 2D universe so that all Displayable in the collection fit in it; that is, that no Displayable has a negative x,y position or lays beyond bounds.
enlargeToFit(Displayable, int) - Method in class ini.trakem2.display.LayerSet: Enlarges the display in the given direction; the anchor is the point to keep still, and can be any of LayerSet.NORTHWEST (top-left), etc.
enoughFreeMemory(long) - Static method in class ini.trakem2.persistence.Loader: Measure whether there are at least 'n_bytes' free.
ensure(String) - Static method in class ini.trakem2.utils.Utils
ensure(File) - Static method in class ini.trakem2.utils.Utils: Ensure the file can be written to.
ensureFree(long) - Method in class ini.trakem2.persistence.Cache: Remove and flush the minimal amount of images to ensure there are at least min_free_bytes free.
entrySet() - Method in class ini.trakem2.utils.FieldMapView
envelope_type - Variable in class ini.trakem2.analysis.Compare.CATAParameters
equalContent(Collection<?>, Collection<?>) - Static method in class ini.trakem2.utils.Utils: If both are null will throw an error.
equalContent(Map<?, ?>, Map<?, ?>) - Static method in class ini.trakem2.utils.Utils: If both are null will throw an error.
EqualizeHistogram - Class in ini.trakem2.imaging.filters
EqualizeHistogram() - Constructor for class ini.trakem2.imaging.filters.EqualizeHistogram
EqualizeHistogram(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.EqualizeHistogram
equals(Object) - Method in class ini.trakem2.display.DisplayCanvas.ScreenshotProperties
equals(Object) - Method in class ini.trakem2.display.Tag
equals(Object) - Method in class ini.trakem2.imaging.filters.CLAHE
equals(Object) - Method in class ini.trakem2.imaging.filters.CorrectBackground
equals(Object) - Method in class ini.trakem2.imaging.filters.DefaultMinAndMax
equals(Object) - Method in class ini.trakem2.imaging.filters.EnhanceContrast
equals(Object) - Method in class ini.trakem2.imaging.filters.EqualizeHistogram
equals(Object) - Method in class ini.trakem2.imaging.filters.GaussianBlur
equals(Object) - Method in class ini.trakem2.imaging.filters.Invert
equals(Object) - Method in class ini.trakem2.imaging.filters.LUTBlue
equals(Object) - Method in class ini.trakem2.imaging.filters.LUTCustom
equals(Object) - Method in class ini.trakem2.imaging.filters.LUTCyan
equals(Object) - Method in class ini.trakem2.imaging.filters.LUTGreen
equals(Object) - Method in class ini.trakem2.imaging.filters.LUTMagenta
equals(Object) - Method in class ini.trakem2.imaging.filters.LUTRed
equals(Object) - Method in class ini.trakem2.imaging.filters.LUTYellow
equals(Object) - Method in class ini.trakem2.imaging.filters.Normalize
equals(Object) - Method in class ini.trakem2.imaging.filters.NormalizeLocalContrast
equals(Object) - Method in class ini.trakem2.imaging.filters.RankFilter
equals(Object) - Method in class ini.trakem2.imaging.filters.ResetMinAndMax
equals(Object) - Method in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
equals(Object) - Method in class ini.trakem2.imaging.filters.SubtractBackground
equals(Object) - Method in class ini.trakem2.imaging.filters.ValueToNoise
equals(double, double) - Static method in class ini.trakem2.utils.M
equals(Align.Param) - Method in class mpicbg.trakem2.align.Align.Param: Check if two parameter sets are equal.
equals(Align.ParamOptimize) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
equals(Object) - Method in class mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch
ERROR - Static variable in class ini.trakem2.imaging.StitchingTEM
ERROR_PATH_NOT_FOUND - Static variable in class ini.trakem2.persistence.Loader
estimateDistortion(double[][], double[][], double[][], double, int, int) - Method in class lenscorrection.NonLinearTransform
estimateImageFileSize() - Method in class ini.trakem2.display.Stack
estimateImageFileSize(Patch, int) - Method in class ini.trakem2.persistence.FSLoader: Compute the number of bytes that the ImagePlus of a Patch will take.
estimateImageFileSize(Patch, int) - Method in class ini.trakem2.persistence.Loader
estimateJPEGFileSize(int, int) - Static method in class ini.trakem2.io.ImageSaver: Based on EM images of neuropils with outside alpha masks.
estimateResamplingFactor(LayerSet, double, double) - Static method in class ini.trakem2.display.Display3D
EtchingStep(int, Set<Collection<Vertex<T>>>) - Constructor for class ini.trakem2.analysis.Centrality.EtchingStep
evaluateCorrection(List<List<PointMatch>>) - Method in class lenscorrection.Distortion_Correction
evaluateCorrectionXcorr(int, String) - Method in class lenscorrection.Distortion_Correction
eventOccurred(int) - Method in class ini.trakem2.display.Display
exec(Runnable) - Method in class ini.trakem2.utils.Dispatcher: Submits the task for execution and returns immediately.
exec(Runnable, boolean) - Method in class ini.trakem2.utils.Dispatcher
exec() - Method in class ini.trakem2.utils.Worker.Task
exec(ElasticLayerAlignment.Param, Project, List<Layer>, Set<Layer>, Set<Layer>, Rectangle, boolean, boolean, Filter<Patch>) - Method in class mpicbg.trakem2.align.ElasticLayerAlignment
exec(Project, List<Layer>, Set<Layer>, boolean, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.ElasticLayerAlignment: Stateful.
exec(LayerSet, int, int, int, boolean, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.ElasticLayerAlignment: Stateful.
exec(LayerSet, int, int, int, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.ElasticLayerAlignment: Stateful.
exec(LayerSet, int, int, int, int, boolean, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.ElasticLayerAlignment: Stateful.
exec(List<Patch>, Set<Patch>) - Method in class mpicbg.trakem2.align.ElasticMontage
exec(ElasticMontage.Param, List<Patch>, Set<Patch>) - Method in class mpicbg.trakem2.align.ElasticMontage
exec(RegularizedAffineLayerAlignment.Param, List<Layer>, Set<Layer>, Set<Layer>, Rectangle, boolean, boolean, Filter<Patch>) - Method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment
exec(List<Layer>, Set<Layer>, boolean, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment: Stateful.
exec(LayerSet, int, int, int, boolean, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment: Stateful.
exec(LayerSet, int, int, int, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment: Stateful.
exec(LayerSet, int, int, int, int, boolean, boolean, Rectangle, Filter<Patch>) - Method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment: Stateful.
execSwing(Runnable) - Method in class ini.trakem2.utils.Dispatcher
executeDrop(DNDTree, DefaultMutableTreeNode, DefaultMutableTreeNode, int) - Method in class ini.trakem2.tree.AbstractTreeTransferHandler
executeDrop(DNDTree, DefaultMutableTreeNode, DefaultMutableTreeNode, int) - Method in class ini.trakem2.tree.DefaultTreeTransferHandler
ExecutorProvider - Class in ini.trakem2.parallel: Allow the source ExecutorServices in TrakEM2 to be configured.
ExecutorProvider() - Constructor for class ini.trakem2.parallel.ExecutorProvider
Exp10(double) - Static method in class mpi.fruitfly.math.General
expandAllNodes(JTree, TreePath) - Static method in class ini.trakem2.tree.DNDTree
expandAllNodes(DNDTree, DefaultMutableTreeNode) - Static method in class ini.trakem2.tree.DNDTree: Convenient method.
expanded_states - Variable in class ini.trakem2.persistence.XMLOptions: Is filled up when reading the expanded states of the ProjectTree nodes.
expandNode(DNDTree, DefaultMutableTreeNode) - Static method in class ini.trakem2.tree.DNDTree
expectedModelIndex - Variable in class lenscorrection.Distortion_Correction.BasicParam
expectedModelIndex - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
expectedModelIndex - Variable in class mpicbg.trakem2.align.Align.Param
exponentialWindow(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
exponentialWindow(FloatArray3D) - Static method in class mpi.fruitfly.registration.ImageFilter
export(Project, File, XMLOptions) - Method in class ini.trakem2.persistence.Loader: Exports the project and its images (optional); if export_images is true, it will be asked for confirmation anyway -beware: for FSLoader, images are not exported since it doesn't own them; only their path.
export_images - Variable in class ini.trakem2.persistence.XMLOptions: Specifies whether images must be saved.
ExportARGB - Class in mpicbg.trakem2.transform
ExportARGB() - Constructor for class mpicbg.trakem2.transform.ExportARGB
exportAsLabels(List<Displayable>, Roi, float, int, int, boolean, boolean, boolean) - Static method in class ini.trakem2.display.AreaList: Export all given AreaLists as one per pixel value, what is called a "labels" file; a file dialog is offered to save the image as a tiff stack.
ExportBestFlatImage - Class in mpicbg.trakem2.transform
ExportBestFlatImage(List<Patch>, Rectangle, int, double) - Constructor for class mpicbg.trakem2.transform.ExportBestFlatImage: Class to manage the creation of an ImageProcessor containing a flat 8-bit or RGB image for use in e.g.
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.AreaList
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.AreaTree
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Ball
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Connector
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Display: Export the DTD that defines this object.
exportDTD(String, StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Displayable: Adds simply DTD !ATTRIBUTE tags.
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Displayable
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Dissector
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.DLabel
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Layer: Includes all Displayable objects in the list of possible children.
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.LayerSet: Includes the !ELEMENT
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Patch
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Pipe
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Polyline: Exports to type t2_polyline.
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Profile
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Stack
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Tree: Exports to type t2_treeline.
exportDTD(StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.Treeline
exportDTD(String, StringBuilder, HashSet<String>, String) - Static method in class ini.trakem2.display.ZDisplayable
exportDTD(StringBuilder, HashSet<String>, String) - Method in class ini.trakem2.Project: Export a complete DTD listing to export the project as XML.
exportDTD(StringBuilder, HashSet<String>, String) - Method in class ini.trakem2.tree.TemplateThing: Only the header !ELEMENT and !ATTLIST.
exportFromMipMaps(TreeMap<Integer, Layer>, int, String, Saver, Rectangle, int, int, Class<?>, int, int, boolean, boolean, int) - Static method in class ini.trakem2.persistence.ExportMultilevelTiles
exportFromMipMapsLayerWise(TreeMap<Integer, Layer>, int, String, Saver, Rectangle, int, int, Class<?>, int, int, boolean, boolean, int) - Static method in class ini.trakem2.persistence.ExportMultilevelTiles: When I/O limited, optimize parallel mipmap loading (so that no Thread is waiting on any other Thread to finish loading a mipmap) by generating tiles Patch-wise, processing one Patch at a time, and one Layer per Thread.
exportFromOriginals(TreeMap<Integer, Layer>, int, String, Saver, Rectangle, int, int, Class<?>, int, int, boolean, boolean, int) - Static method in class ini.trakem2.persistence.ExportMultilevelTiles
exportImage(Patch, String, boolean) - Method in class ini.trakem2.persistence.Loader
exportImage(Patch, ImagePlus, String, boolean) - Method in class ini.trakem2.persistence.Loader: Returns the path to the saved image, or null if not saved.
exportLandmarks() - Method in class ini.trakem2.display.ManualAlignMode: Export landmarks into XML file, in patch coordinates.
exportMorphML(Collection<Tree<?>>, Writer) - Static method in class ini.trakem2.io.NeuroML
exportMorphML(Set<Tree<?>>, Writer) - Static method in class ini.trakem2.io.NeuroML
ExportMultilevelTiles - Class in ini.trakem2.persistence
ExportMultilevelTiles() - Constructor for class ini.trakem2.persistence.ExportMultilevelTiles
exportNeuroML(Collection<Tree<?>>, Writer) - Static method in class ini.trakem2.io.NeuroML
exportNeuroML(Set<Tree<?>>, Writer) - Static method in class ini.trakem2.io.NeuroML: Export to NeuroML 1.8.3, with synapses.
exportSVG(StringBuffer, double, String) - Method in class ini.trakem2.display.Ball
exportSVG(StringBuffer, double, String) - Method in class ini.trakem2.display.Displayable: Does nothing unless overriden.
exportSVG(StringBuffer, double, String) - Method in class ini.trakem2.display.Pipe
exportSVG(StringBuffer, double, String) - Method in class ini.trakem2.display.Profile
exportSVG(StringBuffer, double, String) - Method in class ini.trakem2.tree.ProjectThing
exportSVG(ProjectThing, double) - Static method in class ini.trakem2.utils.Render
exportTags() - Method in class ini.trakem2.display.LayerSet
exportTEST(Layer, int, int) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
exportTiles(Layer, int, int, boolean) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort: Create constant size tiles that carpet the areas of the layer where there are images; these tiles are returned in a lazy sequence of Callable objects that create a tripled consisting of the ShortProcessor and the X and Y pixel coordinates of that tile.
ExportUnsignedByte - Class in mpicbg.trakem2.transform
ExportUnsignedByte() - Constructor for class mpicbg.trakem2.transform.ExportUnsignedByte
ExportUnsignedByte.ImageData - Class in mpicbg.trakem2.transform
ExportUnsignedByte.ImageSource - Interface in mpicbg.trakem2.transform
ExportUnsignedByte.MipMapSource - Class in mpicbg.trakem2.transform
ExportUnsignedByte.OriginalSource - Class in mpicbg.trakem2.transform
ExportUnsignedShort - Class in mpicbg.trakem2.transform
ExportUnsignedShort() - Constructor for class mpicbg.trakem2.transform.ExportUnsignedShort
ExportUnsignedShort.PatchIntensityRange - Class in mpicbg.trakem2.transform
ExportUnsignedShort.PatchTransform - Class in mpicbg.trakem2.transform
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.AreaList
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Ball: Similar to exportSVG but the layer_id is saved instead of the z.
exportXML(Project, Writer, String, XMLOptions) - Static method in class ini.trakem2.display.Display: Export all displays of the given project as XML entries.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Displayable: The oid is this objects' id, whereas the 'id' tag will be the id of the wrapper Thing object.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Dissector
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.DLabel
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Layer
exportXML(Writer, String, XMLOptions) - Method in class ini.trakem2.display.LayerSet
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Patch: Opens and closes the tag and exports data.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Pipe: Exports data, the tag is not opened nor closed.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Polyline: Exports data.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Profile
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Stack: Opens and closes the tag and exports data.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Tree
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.ZDisplayable
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.persistence.DBObject: Subclasses can override this method to store the instance as XML.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.Project
exportXML(Writer, String, XMLOptions) - Method in class ini.trakem2.Project: Export the main trakem2 tag wrapping four hierarchies (the project tag, the ProjectTree, and the Top Level LayerSet the latter including all Displayable objects) and a list of displays.
exportXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.tree.ProjectThing: Expects a HashMap<Thing,Boolean> as any.
exportXMLNodeAttributes(StringBuilder, StringBuilder, Node<Area>) - Method in class ini.trakem2.display.AreaTree
exportXMLNodeAttributes(StringBuilder, StringBuilder, Node<T>) - Method in class ini.trakem2.display.Tree
exportXMLNodeAttributes(StringBuilder, StringBuilder, Node<Float>) - Method in class ini.trakem2.display.Treeline: Export the radius only if it is larger than zero.
exportXMLNodeData(StringBuilder, StringBuilder, Node<Area>) - Method in class ini.trakem2.display.AreaTree
exportXMLNodeData(StringBuilder, StringBuilder, Node<T>) - Method in class ini.trakem2.display.Tree
exportXMLNodeData(StringBuilder, StringBuilder, Node<Float>) - Method in class ini.trakem2.display.Treeline
exportXMLTemplate(StringBuffer, StringBuffer, HashSet<String>, String) - Method in class ini.trakem2.tree.TemplateThing
extension() - Method in class ini.trakem2.persistence.StaleFiles.AlphaMaskPath
extension() - Method in class ini.trakem2.persistence.StaleFiles.CoordinateTransformPath
extension() - Method in interface ini.trakem2.persistence.StaleFiles.Path
extractAmiraLabels(ImagePlus, AmiraParameters, Layer, double, double) - Static method in class ini.trakem2.io.AmiraImporter: Returns an ArrayList containing all AreaList objects.
extractAndSaveFeatures(List<AbstractAffineTile2D<?>>, FloatArray2DSIFT.Param, boolean) - Static method in class mpicbg.trakem2.align.ElasticMontage: Extract SIFT features and save them into the project folder.
extractAndSaveLayerFeatures(List<Layer>, Rectangle, double, Filter<Patch>, FloatArray2DSIFT.Param, boolean, int) - Static method in class mpicbg.trakem2.align.AlignmentUtils: Extract SIFT features and save them into the project folder.
extractAndShowGraph(LayerSet, Set<Class<T>>) - Static method in class ini.trakem2.analysis.Graph: Extract the graph based on connectors; leave @param only null to include all types.
extractAndShowGraph(LayerSet) - Static method in class ini.trakem2.analysis.Graph: Shows a dialog to pick which classes is one interested in.
extractAreaLists(ImagePlus, Layer, double, double, float, boolean) - Static method in class ini.trakem2.io.AmiraImporter: Returns a map of label vs AreaList.
extractAreas(ImageProcessor) - Static method in class ini.trakem2.utils.AreaUtils: Extracts all non-background areas.
extractAreas(ImageProcessor, HashMap<Float, Area>, boolean, Rectangle, Thread, boolean) - Static method in class ini.trakem2.utils.AreaUtils: Scan line-wise for all areas, returning a Map of area pixel values in @param ip vs.
extractARGBIntArray(Image) - Static method in class mpicbg.trakem2.transform.ExportARGB
ExtractFeaturesThread(Align.Param, List<AbstractAffineTile2D<?>>, AtomicInteger, AtomicInteger, int) - Constructor for class mpicbg.trakem2.align.Align.ExtractFeaturesThread
extractGraph(LayerSet, Set<Class<T>>) - Static method in class ini.trakem2.analysis.Graph
extractPoints(ProjectThing) - Static method in class ini.trakem2.analysis.Compare: Extracts the list of fiduciary points from the fiducial parent and, if their name is different than "ball", adds their title as key and their first ball as a fiduciary point value of the returned map.
extractSIFTPoints(int, List<Feature>[], List<List<PointMatch>>, List<AbstractAffineModel2D<?>>) - Method in class lenscorrection.Distortion_Correction
extractSIFTPointsThreaded(int, List<Feature>[], List<PointMatch>[], AbstractAffineModel2D<?>[]) - Static method in class lenscorrection.Distortion_Correction
extractTemplate(String) - Static method in class ini.trakem2.tree.DTDParser: Extracts the template by reading the ELEMENT and ATTLIST tags from a .dtd file or the DOCTYPE of an .xml file.

F

FakeImagePlus - Class in ini.trakem2.display: Need a non-null ImagePlus for the ImageCanvas, even if fake.
FakeImagePlus(int, int, Display) - Constructor for class ini.trakem2.display.FakeImagePlus
FakeImageWindow - Class in ini.trakem2.display: A class to prevent ROIs from failing.
FakeImageWindow(ImagePlus, ImageCanvas, Display) - Constructor for class ini.trakem2.display.FakeImageWindow
fast - Variable in class ini.trakem2.imaging.filters.CLAHE
fastConvertToFloat(ByteProcessor) - Static method in class ini.trakem2.utils.Utils: A method that circumvents the findMinAndMax when creating a float processor from an existing processor.
fastConvertToFloat(ShortProcessor) - Static method in class ini.trakem2.utils.Utils: A method that circumvents the findMinAndMax when creating a float processor from an existing processor.
fastConvertToFloat(ImageProcessor, int) - Static method in class ini.trakem2.utils.Utils: A method that circumvents the findMinAndMax when creating a float processor from an existing processor.
fastConvertToFloat(ImageProcessor) - Static method in class ini.trakem2.utils.Utils
FastIntegralImage - Class in ini.trakem2.imaging: Written following the code in ImgLib1's IntegralImage2 and ScaleAreaAveraging2d, authored by Stephan Preibisch and Albert Cardona.
FastIntegralImage() - Constructor for class ini.trakem2.imaging.FastIntegralImage
fastMarching(AreaWrapper, Layer, Rectangle, int, int, Runnable) - Static method in class ini.trakem2.imaging.Segmentation
fastMarching(AreaWrapper, Layer, Rectangle, int, int, List<Runnable>) - Static method in class ini.trakem2.imaging.Segmentation
FastMarchingParam() - Constructor for class ini.trakem2.imaging.Segmentation.FastMarchingParam
fatalError(SAXParseException) - Method in class ini.trakem2.persistence.TMLHandler
fetch(Patch, double) - Method in interface mpicbg.trakem2.transform.ExportUnsignedByte.ImageSource
fetch(Patch, double) - Method in class mpicbg.trakem2.transform.ExportUnsignedByte.MipMapSource
fetch(Patch, double) - Method in class mpicbg.trakem2.transform.ExportUnsignedByte.OriginalSource
fetchArea(long, long) - Method in class ini.trakem2.persistence.DBLoader
fetchArea(long, long) - Method in class ini.trakem2.persistence.FSLoader: Loaded in full from XML file
fetchArea(long, long) - Method in class ini.trakem2.persistence.Loader
fetchAWTImage(Patch, int, int) - Method in class ini.trakem2.persistence.Loader
fetchBallPoints(long) - Method in class ini.trakem2.persistence.DBLoader
fetchBallPoints(long) - Method in class ini.trakem2.persistence.FSLoader: Loaded in full from XML file
fetchBallPoints(long) - Method in class ini.trakem2.persistence.Loader
fetchBezierArrays(long) - Method in class ini.trakem2.persistence.DBLoader: Get the bezier points from the database for the given profile but as a triple array of points, that is, three arrays with 2 arrays (x and y) each.
fetchBezierArrays(long) - Method in class ini.trakem2.persistence.FSLoader: Loaded in full from XML file
fetchBezierArrays(long) - Method in class ini.trakem2.persistence.Loader
fetchCoordinateTransform() - Method in class ini.trakem2.display.Patch: Read in the CoordinateTransform from a file whose name is crafted from the Patch.ct_id and this Patch's DBObject.id.
fetchDataImage(Patch, double) - Method in class ini.trakem2.persistence.FSLoader: Waits until a proper image of the desired size or larger can be returned, which is never the Loader.REGENERATING image.
fetchDataImage(Patch, double) - Method in class ini.trakem2.persistence.Loader: Calls fetchImage(p, mag) unless overriden.
fetchFeatures(Align.Param, AbstractAffineTile2D<?>) - Static method in class mpicbg.trakem2.align.Align
fetchImage(Patch, int) - Method in class ini.trakem2.persistence.FSLoader: So far accepts Layer.IMAGEPLUS and Layer.IMAGEPROCESSOR as format.
fetchImage(Patch) - Method in class ini.trakem2.persistence.Loader
fetchImage(Patch, double) - Method in class ini.trakem2.persistence.Loader: Fetch a suitable awt.Image for the given magnification.
fetchImageMask(Patch) - Method in class ini.trakem2.persistence.FSLoader: Returns the alpha mask image from a file, or null if none stored.
fetchImageMask(Patch) - Method in class ini.trakem2.persistence.Loader: Deprecated.
fetchImagePlus(Patch) - Method in class ini.trakem2.persistence.DBLoader
fetchImagePlus(Patch) - Method in class ini.trakem2.persistence.FSLoader
fetchImagePlus(Stack) - Method in class ini.trakem2.persistence.FSLoader
fetchImagePlus(Patch) - Method in class ini.trakem2.persistence.Loader
fetchImagePlus(Stack) - Method in class ini.trakem2.persistence.Loader
fetchImageProcessor(Patch) - Method in class ini.trakem2.persistence.FSLoader: Fetch the ImageProcessor in a synchronized manner, so that there are no conflicts in retrieving the ImageProcessor for a specific stack slice, for example.
fetchImageProcessor(Patch) - Method in class ini.trakem2.persistence.Loader: Returns null unless overriden.
fetchLabel(DLabel) - Method in class ini.trakem2.persistence.DBLoader
fetchLabel(DLabel) - Method in class ini.trakem2.persistence.FSLoader: Loaded in full from XML file
fetchLabel(DLabel) - Method in class ini.trakem2.persistence.Loader
fetchMipMap(Patch, int, long) - Method in class ini.trakem2.persistence.FSLoader: Does the actual fetching of the file.
fetchMipMapAWT(Patch, int, long) - Method in class ini.trakem2.persistence.FSLoader: Loads the file containing the scaled image corresponding to the given level (or the maximum possible level, if too large) and returns it as an awt.Image, or null if not found.
fetchMipMapAWT(Patch, int, long) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns null unless overriden.
fetchOriginal(Patch) - Method in class ini.trakem2.persistence.DBLoader
fetchOriginal(Patch) - Method in class ini.trakem2.persistence.FSLoader: Loads and returns the original image, which is not cached, or returns null if it's not different than the working image.
fetchOriginal(Patch) - Method in class ini.trakem2.persistence.Loader: Used for the revert command.
fetchPipePoints(long) - Method in class ini.trakem2.persistence.DBLoader
fetchPipePoints(long) - Method in class ini.trakem2.persistence.FSLoader: Loaded in full from XML file
fetchPipePoints(long) - Method in class ini.trakem2.persistence.Loader
fetchPointMatches(Align.Param, AbstractAffineTile2D<?>, AbstractAffineTile2D<?>) - Static method in class mpicbg.trakem2.align.Align: Fetch a Collection of corresponding SIFT-features.
field - Variable in class ini.trakem2.utils.OptionPanel.Setter
FieldMapView - Class in ini.trakem2.utils: Classes extending this class acquire a read-only Map interface to access its declared fields via the reflection API provided by Class.getDeclaredFields() and Field.
FieldMapView() - Constructor for class ini.trakem2.utils.FieldMapView
FilePathRepair - Class in ini.trakem2.persistence: A class to manage "file not found" problems.
fillHoles(Layer) - Method in class ini.trakem2.display.AreaList
fillHoles() - Method in class ini.trakem2.display.AreaWrapper
Filter<T> - Interface in ini.trakem2.utils
filter(List<PointMatch>, Collection<PointMatch>) - Method in interface org.janelia.intensity.PointMatchFilter
filter(List<PointMatch>, Collection<PointMatch>) - Method in class org.janelia.intensity.RansacRegressionFilter
filter(List<PointMatch>, Collection<PointMatch>) - Method in class org.janelia.intensity.RansacRegressionReduceFilter
FilteredIterator(Node) - Constructor for class ini.trakem2.display.Node.FilteredIterator
FilterEditor - Class in ini.trakem2.imaging.filters
FilterEditor() - Constructor for class ini.trakem2.imaging.filters.FilterEditor
filterKaiserBessel(FloatArray2D, boolean) - Static method in class mpi.fruitfly.registration.ImageFilter: Does Kaiser-Bessel-Windowing to prevent the fourier spectra from getting infinite numbers, the border will be faded to black.
filterOutliers - Variable in class mpicbg.trakem2.align.Align.ParamOptimize: Filter outliers
filterPatches(Layer, Filter<Patch>) - Static method in class mpicbg.trakem2.align.AlignmentUtils
finalBox - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
find() - Method in class ini.trakem2.display.Display: Open a GenericDialog to ask for parameters to find all Displayable that abide to them.
find(String, boolean, Class<T>, int, int) - Method in class ini.trakem2.display.Display
find(String, boolean, Class<T>, List<Layer>) - Static method in class ini.trakem2.display.Display
find(double, double) - Method in class ini.trakem2.display.Layer
find(double, double, boolean) - Method in class ini.trakem2.display.Layer: Find the Displayable objects that contain the point.
find(Class<?>, double, double) - Method in class ini.trakem2.display.Layer
find(Class<?>, double, double, boolean) - Method in class ini.trakem2.display.Layer: Find the Displayable objects of Class c that contain the point, with class equality.
find(Class<?>, double, double, boolean, boolean) - Method in class ini.trakem2.display.Layer: Find the Displayable objects of Class c that contain the point, with instanceof if instance_of is true.
find(Rectangle) - Method in class ini.trakem2.display.Layer
find(Rectangle, boolean) - Method in class ini.trakem2.display.Layer: Find the Displayable objects whose bounding box intersects with the given rectangle.
find(Class<?>, Rectangle, boolean) - Method in class ini.trakem2.display.Layer
find(Class<?>, Rectangle, boolean, boolean) - Method in class ini.trakem2.display.Layer: Find the Displayable objects whose bounding box intersects with the given rectangle.
find(Layer, Layer, Area) - Method in class ini.trakem2.display.LayerSet: Find the ZDisplayable objects that intersect with the 3D roi defined by the first and last layers, and the area -all in world coordinates.
find(Class<?>, Layer, Area, boolean) - Method in class ini.trakem2.display.LayerSet: Find any Displayable or ZDisplayable objects of class C which intersect with the Area @param aroi.
find(Class<?>, Layer, Area, boolean, boolean) - Method in class ini.trakem2.display.LayerSet: Find any Displayable or ZDisplayable objects of class C which intersect with the Area @param aroi.
find(Class<?>, Layer, int, int, boolean) - Method in class ini.trakem2.display.LayerSet
find(double, double, double) - Method in class ini.trakem2.display.ManualAlignMode.Landmarks: Returns the index of the closest point, with accuracy depending on magnification.
find(long) - Method in class ini.trakem2.Project: Find the ProjectThing instance with the given id.
findAllOpenImages() - Static method in class ini.trakem2.utils.Utils: Scan the WindowManager for all open images, including stacks.
findAreas(Layer, Rectangle, boolean) - Method in class ini.trakem2.display.LayerSet: Find all java.awt.geom.Area in layer that intersect with box, if visible.
findBasicTypeChildren() - Method in class ini.trakem2.tree.ProjectThing: Recursive into children.
findBasicTypeChildren(HashSet<ProjectThing>, HashSet<ProjectThing>) - Method in class ini.trakem2.tree.ProjectThing: Recursive into children, and adds this instance as well if it's a basic type.
findBestMatch(VectorString3D, VectorString3D, double, boolean, int, float) - Static method in class ini.trakem2.analysis.Compare
findBestMatch(VectorString3D, VectorString3D, double, boolean, int, float, int, boolean, boolean) - Static method in class ini.trakem2.analysis.Compare: Since comparing two sequences starting from one end or starting from the other is not the same at all, this method performs the match starting first from one end and then from the other.
findBestMatch(VectorString3D, VectorString3D, double, boolean, int, float, int, boolean, boolean, double, double, double) - Static method in class ini.trakem2.analysis.Compare
findById(long) - Method in class ini.trakem2.display.Displayable
findById(long) - Method in class ini.trakem2.display.Layer
findById(long) - Method in class ini.trakem2.display.LayerSet: Searches in all ZDisplayables and in all layers, recursively into nested LayerSets.
findById(long) - Method in class ini.trakem2.Project
findChild(Object) - Method in class ini.trakem2.tree.LayerThing: Recursive search for the thing that contains the given object.
findChild(Object) - Method in class ini.trakem2.tree.ProjectThing: Recursive search for the thing that contains the given object.
findChild(long) - Method in class ini.trakem2.tree.ProjectThing: Recursive search for the thing of the given id.
findChild(Object) - Method in class ini.trakem2.tree.TemplateThing: Ah, we love interfaces don't we.
findChild(Object) - Method in interface ini.trakem2.tree.Thing
findChildren(String, String, boolean) - Method in class ini.trakem2.tree.ProjectThing: Recursive into children, searches for the things whose object.toString() matches the given regex, case insensitive.
findChildren(ArrayList<ProjectThing>, Pattern, Pattern, boolean) - Method in class ini.trakem2.tree.ProjectThing: Recursive into children, searches for things whose object.toString() matches the given regex pattern, and stores the found ProjectThing in the given ArrayList.
findChildrenOfType(String) - Method in class ini.trakem2.tree.ProjectThing: Check if this Thing directly contains any child of the given type, and return them all.
findChildrenOfType(Class<T>) - Method in class ini.trakem2.tree.ProjectThing: Check if this Thing directly contains any child of the given object class (including interfaces), and return them all.
findChildrenOfTypeR(String) - Method in class ini.trakem2.tree.ProjectThing: Recursive into children.
findChildrenOfTypeR(HashSet<ProjectThing>, String) - Method in class ini.trakem2.tree.ProjectThing: Recursive into children.
findChildrenOfTypeR(Class<?>) - Method in class ini.trakem2.tree.ProjectThing: Finds them in order.
findChildrenOfTypeR(List<ProjectThing>, Class<?>) - Method in class ini.trakem2.tree.ProjectThing: Finds them in order.
findClosestNode(Collection<Node<T>>, float, float, double) - Method in class ini.trakem2.display.Tree: Expects local coords; with precision depending on magnification.
findClosestNodeW(float, float, Layer, double) - Method in class ini.trakem2.display.Tree: Expects world coords; with precision depending on magnification.
findClosestNodeW(Collection<Node<T>>, float, float, double) - Method in class ini.trakem2.display.Tree: Expects world coords; with precision depending on magnification.
findClosestPoint(int, int, double, double) - Method in class ini.trakem2.display.Pipe: Find the closest point to an interpolated point with precision depending upon magnification.
findClosestPoint(double, double, double, double) - Method in class ini.trakem2.display.Profile: Find the closest point to an interpolated point with precision depending upon magnification.
findClosestSegment(int, int, long, double) - Method in class ini.trakem2.display.Polyline: Returns the index of the first point in the segment made of any two consecutive points.
findConnectors() - Method in class ini.trakem2.display.Tree: Returns an array of two Collection of connectors: the first one has the outgoing connectors, and the second one has the incoming connectors.
findDisplayable(long) - Method in class ini.trakem2.display.LayerSet: Searches in all layers.
findFirstIntersectingNode(Set<Node<T>>, Area) - Method in class ini.trakem2.display.Tree: Expects an Area in local coordinates.
findIntersecting(Class<?>) - Method in class ini.trakem2.display.Tree
findLayerThing(Object) - Method in class ini.trakem2.Project: Find a LayerThing that contains the given object.
findLinkTargets(AffineTransform) - Method in class ini.trakem2.display.AreaTree.AreaNode
findLinkTargets(AffineTransform) - Method in class ini.trakem2.display.Node: Returns a list of Patch to link, which lay under the node.
findMinAndMax() - Method in class ini.trakem2.imaging.FloatProcessorT2
findModel(Model<?>, List<PointMatch>, Collection<PointMatch>, float, float, int, boolean, float, boolean) - Static method in class mpicbg.trakem2.align.Align
findModel(Model<?>, List<PointMatch>, Collection<PointMatch>, float, float, int, boolean, float) - Static method in class mpicbg.trakem2.align.Align
findNearAndGetNext(float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree
findNearAndGetPrevious(float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree
findNearestEdge(float, float, Layer, double) - Method in class ini.trakem2.display.Tree: Considering only the set of consecutive layers currently painted, find a point near an edge with accuracy depending upon magnification.
findNearestEndNode(float, float, Layer) - Method in class ini.trakem2.display.Tree: Find the spatially closest node, in calibrated coords.
findNearestNode(float, float, Layer) - Method in class ini.trakem2.display.Tree: Find the spatially closest node, in calibrated coords; expects local coords.
findNearestPoint(double[][], int, double, double) - Static method in class ini.trakem2.display.Displayable: Fine nearest point in array a, from 0 up to n_points, to point x_p,y_p.
findNearestPoint(double[][], long[], int, double, double, long) - Static method in class ini.trakem2.display.Displayable
findNearestPoint(int, int, long) - Method in class ini.trakem2.display.Polyline: Find closest point within the current layer.
findNextBranchOrEndPoint() - Method in class ini.trakem2.display.Node: Assumes there aren't any cycles.
findNextBranchOrEndPoint(float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree: If the node found near x,y,layer is a branch point, returns it; otherwise the next down the chain; on reaching an end point, returns it.
findNode(float, float, Layer, double) - Method in class ini.trakem2.display.Tree: Find a node in @param layer near the local coords lx,ly, with precision depending on magnification.
findNode(Object, JTree) - Static method in class ini.trakem2.tree.DNDTree: Find the node in the tree that contains the given Thing.
findNode2(Object, JTree) - Static method in class ini.trakem2.tree.DNDTree: Find the node in the tree that contains a Thing which contains the given project_ob.
findNodeNear(float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree
findNodeNear(float, float, Layer, DisplayCanvas, boolean) - Method in class ini.trakem2.display.Tree: Expects world coordinates.
findObject(long) - Method in class ini.trakem2.tree.ProjectThing: Recursive search for the object with the given id.
findObjects(Class<T>) - Method in class ini.trakem2.tree.ProjectThing: Find objects of the given class, as determined by c.isInstance(this.object).
findOpenImages() - Static method in class ini.trakem2.utils.Utils: Scan the WindowManager for non-stack images
findOpenStacks() - Static method in class ini.trakem2.utils.Utils: Scan the WindowManager for open stacks.
findPath(Node, Node) - Static method in class ini.trakem2.display.Node: Obtain the (only) list from node a to node b, including both a (the first element) and b (the last element).
findPath(Area, int, int) - Static method in class ini.trakem2.utils.M: Detect if a point is not in the area, but lays inside one of its path, which is returned as a Polygon.
findPoint(double[][], int, int, double, long) - Method in class ini.trakem2.display.Ball: Find a point in an array, with a precision dependent on the magnification.
findPoint(double[][], long[], int, int, long, double) - Method in class ini.trakem2.display.Pipe: Find a point in an array, with a precision dependent on the magnification.
findPoint(int, int, long, double) - Method in class ini.trakem2.display.Polyline: Find a point in an array, with a precision dependent on the magnification.
findPoint(double[][], double, double, double) - Method in class ini.trakem2.display.Profile: Find a point in an array 'a', with a precision dependent on the magnification.
findPreviousBranchOrRootPoint() - Method in class ini.trakem2.display.Node
findPreviousBranchOrRootPoint(float, float, Layer, DisplayCanvas) - Method in class ini.trakem2.display.Tree
findProject(Loader) - Static method in class ini.trakem2.Project
findProjectThing(Object) - Method in class ini.trakem2.Project: Find a ProjectThing that contains the given object.
findTaggedPairs(Tag, Tag) - Method in class ini.trakem2.display.Tree
findTags() - Method in class ini.trakem2.display.Tree: Search all nodes for unique tags and returns them.
findZDisplayables(Layer, int, int, boolean) - Method in class ini.trakem2.display.LayerSet: Find ZDisplayable objects that contain the point x,y in the given layer.
findZDisplayables(Class<?>, Layer, int, int, boolean) - Method in class ini.trakem2.display.LayerSet: Find ZDisplayable objects of Class c that contain the point x,y in the given layer.
findZDisplayables(Class<?>, Layer, int, int, boolean, boolean) - Method in class ini.trakem2.display.LayerSet: Find ZDisplayable objects of Class c that contain the point x,y in the given layer.
findZDisplayables(Class<?>, Layer, Rectangle, boolean) - Method in class ini.trakem2.display.LayerSet
findZDisplayables(Class<?>, Layer, Rectangle, boolean, boolean) - Method in class ini.trakem2.display.LayerSet: Find ZDisplayable objects of the given class that intersect the given rectangle in the given layer.
findZDisplayables(Class<?>, Layer, Area, boolean, boolean) - Method in class ini.trakem2.display.LayerSet: Find ZDisplayable objects of the given class that intersect the given area in the given layer.
findZDisplayables(Layer, Rectangle, boolean) - Method in class ini.trakem2.display.LayerSet: Find ZDisplayable objects that intersect the given rectangle in the given layer.
finish(AreaContainer, AffineTransform) - Method in class ini.trakem2.imaging.Segmentation.BlowRunner
finishedWorking() - Method in class ini.trakem2.utils.Worker
fireLUT() - Static method in class ini.trakem2.utils.Utils: Returns a byte[3][256] containing the colors of the fire LUT.
fireNodeRemoved(Node<T>) - Method in class ini.trakem2.display.Tree
firstImageIndex - Variable in class lenscorrection.Distortion_Correction.PluginParam
firstIntersectingNode(Layer, Area) - Method in class ini.trakem2.display.Tree: Expects Area in world coords.
firstLayerIndex - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
fit(Collection) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
fit(double[][], double[][], double) - Method in class lenscorrection.NonLinearTransform
fit(Collection) - Method in class lenscorrection.PolynomialModel2D
fix(Point3f, boolean, float[]) - Method in class ini.trakem2.display.Tree: Expects a non-null float[] for reuse, and modifies @param p in place.
fixDir(String) - Static method in class ini.trakem2.utils.Utils: Convert a D:\\this\that\there to D://this/that/there/ Notice it adds an ending backslash.
fixStorageFolders() - Method in class ini.trakem2.persistence.FSLoader: Convert old-style storage folders to new style.
fixZOrdering() - Method in class ini.trakem2.tree.ProjectThing: If this is of type profile_list, order all children Profile by their layer's Z coordinate, ascending.
FL_ERROR - Static variable in class ini.trakem2.utils.Utils: The error to use in floating-point or double floating point literal comparisons.
FLIP_HORIZONTAL - Static variable in class ini.trakem2.display.LayerSet
FLIP_VERTICAL - Static variable in class ini.trakem2.display.LayerSet
flipInRange(int, int) - Static method in class mpi.fruitfly.math.General: return a integer that is flipped in the range [0 ...
FloatArray - Class in mpi.fruitfly.math.datastructures: Title:
FloatArray(float[]) - Constructor for class mpi.fruitfly.math.datastructures.FloatArray
FloatArray2D - Class in mpi.fruitfly.math.datastructures: PhaseCorrelation2D.
FloatArray2D(int, int) - Constructor for class mpi.fruitfly.math.datastructures.FloatArray2D
FloatArray2D(float[], int, int) - Constructor for class mpi.fruitfly.math.datastructures.FloatArray2D
FloatArray3D - Class in mpi.fruitfly.math.datastructures: FloatArray3D.
FloatArray3D(float[], int, int, int) - Constructor for class mpi.fruitfly.math.datastructures.FloatArray3D
FloatArray3D(int, int, int) - Constructor for class mpi.fruitfly.math.datastructures.FloatArray3D
FloatArray4D - Class in mpi.fruitfly.math.datastructures: Title:
FloatArray4D(int, int, int, int) - Constructor for class mpi.fruitfly.math.datastructures.FloatArray4D
FloatArrayToFloatProcessor(ImageProcessor, FloatArray2D) - Static method in class mpi.fruitfly.general.ImageArrayConverter
FloatArrayToImagePlus(FloatArray2D, String, float, float) - Static method in class mpi.fruitfly.general.ImageArrayConverter
FloatArrayToStack(FloatArray3D, String, float, float) - Static method in class mpi.fruitfly.general.ImageArrayConverter
FloatProcessorT2 - Class in ini.trakem2.imaging
FloatProcessorT2(int, int, float[], ColorModel) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatProcessorT2(int, int, float[], ColorModel, double, double) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatProcessorT2(int, int, double, double) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatProcessorT2(int, int) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatProcessorT2(int, int, byte[], double, double) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatProcessorT2(ColorProcessor, int) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatProcessorT2(FloatProcessor) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatProcessorT2(ByteProcessor) - Constructor for class ini.trakem2.imaging.FloatProcessorT2
FloatSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.FloatSetter
FloatSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.FloatSetter
FloatSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.FloatSetter
FloatSetter(ImageProcessor) - Constructor for class mpicbg.trakem2.util.RobustNormalizeLocalContrast.FloatSetter
flush() - Method in class ini.trakem2.display.Ball: Release memory resources used by this object: namely the arrays of points, which can be reloaded with a call to setupForDisplay()
flush(Displayable) - Static method in class ini.trakem2.display.Display: Cleanup internal lists that may contain the given Displayable.
flush() - Method in class ini.trakem2.display.DisplayCanvas: Release offscreen images and stop threads.
flush() - Method in class ini.trakem2.display.DisplayCanvas.Screenshot
flush() - Method in class ini.trakem2.display.DLabel
flush() - Method in class ini.trakem2.display.FakeImagePlus
flush() - Method in class ini.trakem2.display.GroupingMode.ScreenPatchRange
flush() - Method in class ini.trakem2.display.Pipe: Release memory resources used by this object: namely the arrays of points, which can be reloaded with a call to setupForDisplay()
flush() - Method in class ini.trakem2.display.Polyline: Release memory resources used by this object: namely the arrays of points, which can be reloaded with a call to setupForDisplay()
flush() - Method in class ini.trakem2.display.Profile: Release memory resources used by this object: namely the arrays of points, which can be reloaded with a call to setupForDisplay()
flush() - Method in class ini.trakem2.imaging.PatchStack
flush(ImagePlus) - Static method in class ini.trakem2.persistence.Loader: Workaround for ImageJ's ImagePlus.flush() method which calls the System.gc() unnecessarily.
flushAll() - Static method in class ini.trakem2.display.Display: Release memory captured by the offscreen images
flushMipMaps(boolean) - Method in class ini.trakem2.persistence.FSLoader: Remove all mipmap images from the cache, and optionally set the dir_mipmaps to null.
flushMipMaps(long) - Method in class ini.trakem2.persistence.FSLoader: Remove from the cache all images of level larger than zero corresponding to the given patch id.
flushMipMaps(boolean) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
flushMipMaps(long) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
flushTraceCache(Project) - Static method in class ini.trakem2.display.Polyline
flyThrough(Node<T>, Node<T>, int, int, double, int, String) - Method in class ini.trakem2.display.Tree: Fly-through image stack from first to last node.
flyThroughMarked(int, int, double, int, String) - Method in class ini.trakem2.display.Tree: Fly-through image stack from source node to mark node.
fm_dist - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
fm_grey - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
fmp - Static variable in class ini.trakem2.imaging.Segmentation
format - Variable in class ini.trakem2.analysis.Compare.CATAParameters
formats - Variable in class ini.trakem2.analysis.Compare.CATAParameters
formats() - Static method in class ini.trakem2.utils.Saver: Returns the supported formats.
fr - Variable in class ini.trakem2.io.ImageFileHeader
FreeHandProfile - Class in ini.trakem2.display
FreeHandProfile(Profile) - Constructor for class ini.trakem2.display.FreeHandProfile
FSLoader - Class in ini.trakem2.persistence: A class to rely on memory only; except images which are rolled from a folder or their original location and flushed when memory is needed for more.
FSLoader() - Constructor for class ini.trakem2.persistence.FSLoader: Used to open a project from an existing XML file.
FSLoader(String) - Constructor for class ini.trakem2.persistence.FSLoader: Used to create a new project, NOT from an XML file.

G

g - Variable in class ini.trakem2.imaging.filters.LUTCustom
gatherChains(Project[], Compare.CATAParameters) - Static method in class ini.trakem2.analysis.Compare
gatherChains(Project[], Compare.CATAParameters, String[]) - Static method in class ini.trakem2.analysis.Compare: Gather chains for all projects considering the cp.regex, and transforms all relative to the reference Project p[0].
GAUSSIAN - Static variable in class ini.trakem2.persistence.Loader
GaussianBlur - Class in ini.trakem2.imaging.filters: Smooth with a Gaussian.
GaussianBlur() - Constructor for class ini.trakem2.imaging.filters.GaussianBlur
GaussianBlur(double, double, double) - Constructor for class ini.trakem2.imaging.filters.GaussianBlur
GaussianBlur(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.GaussianBlur
gaussianDownsampled(FloatProcessor) - Method in class mpicbg.trakem2.transform.ExportBestFlatImage: Gaussian-downsample to the target dimensions
General - Class in mpi.fruitfly.math
General() - Constructor for class mpi.fruitfly.math.General
generateAllReviewStacks() - Method in class ini.trakem2.display.Tree
generateCoefficientsTiles(Collection<Patch>, T, int) - Static method in class org.janelia.intensity.MatchIntensities
generateGlobe(int, int) - Static method in class ini.trakem2.display.Ball: Generate a globe of radius 1.0 that can be used for any Ball.
generateInterpolatedPoints(double) - Method in class ini.trakem2.display.Pipe
generateInterpolatedPoints(double) - Method in class ini.trakem2.display.Profile
generateLayerMipMaps(Layer[], int) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
generateMesh(double, int) - Method in class ini.trakem2.display.AreaTree
generateMesh(double) - Method in class ini.trakem2.display.Pipe
generateMesh(double, int) - Method in class ini.trakem2.display.Treeline: Returns a list of two lists: the List<Point3f> and the corresponding List<Color3f>.
generateMipMaps(Patch) - Method in class ini.trakem2.persistence.FSLoader: Given an image and its source file name (without directory prepended), generate a pyramid of images until reaching an image not smaller than 32x32 pixels.
generateMipMaps(Collection<Displayable>, boolean) - Method in class ini.trakem2.persistence.FSLoader: Generate image pyramids and store them into files under the dir_mipmaps for each Patch object in the Project.
generateMipMaps(Patch) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns false unless overriden.
generateMipMaps(ArrayList<Displayable>) - Method in class ini.trakem2.persistence.Loader: Returns generateMipMaps(al, false).
generateMipMaps(ArrayList<Displayable>, boolean) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns null unless overriden.
generateRegions(Node<T>, Node<T>, int, int, double) - Method in class ini.trakem2.display.Tree
generateReviewStackForSlab(float, float, Layer, double) - Method in class ini.trakem2.display.Tree
generateReviewStackForSlab(Node<T>) - Method in class ini.trakem2.display.Tree: Generate a review stack from the previous branch node or root, to the next branch node or end node.
generateSkeleton(double, int, int) - Method in class ini.trakem2.display.Tree
generateSubtreeReviewStacks(Node<T>) - Method in class ini.trakem2.display.Tree
generateSubtreeReviewStacks(int, int, Layer, double) - Method in class ini.trakem2.display.Tree
generateTriangles(double, int) - Method in class ini.trakem2.display.AreaList
generateTriangles(double, double[][][]) - Method in class ini.trakem2.display.Ball: Put all balls as a single 'mesh'; the returned list contains all faces as three consecutive Point3f.
generateTriangles(double, int, int) - Method in interface ini.trakem2.display.Line3D
generateTriangles(double, int, int) - Method in class ini.trakem2.display.Pipe: Calibrated.
generateTriangles(double[][][], double) - Static method in class ini.trakem2.display.Pipe: Accepts an arrays as that returned from methods generateJoints and makeTube: first dimension is the list of points, second dimension is the number of vertices defining the circular cross section of the tube, and third dimension is the x,y,z of each vertex.
generateTriangles(double, int, int) - Method in class ini.trakem2.display.Polyline: Calibrated.
generateTriangles(double, int, int, Calibration) - Method in class ini.trakem2.display.Polyline: Returns a list of Point3f that define a polyline in 3D, for usage with an ij3d CustomLineMesh CONTINUOUS.
generateTriangles(ProjectThing, double) - Static method in class ini.trakem2.display.Profile: Takes a profile_list, scans for its Profile children, makes sublists of continuous profiles (if they happen to be branched), and then creates triangles for them using weighted vector strings.
generateTriangles(double, int, int) - Method in class ini.trakem2.display.Tree: Deprecated.
generateTriangles(Displayable, double, int, Map<Layer, Area>) - Static method in class ini.trakem2.utils.AreaUtils: Expects areas in local coordinates to the Displayable @param d.
GenericAffineTile2D<A extends Model<A> & Affine2D<A>> - Class in mpicbg.trakem2.align
GenericAffineTile2D(A, Patch) - Constructor for class mpicbg.trakem2.align.GenericAffineTile2D
get(LayerSet) - Static method in class ini.trakem2.display.Display3D: Get an existing Display3D for the given LayerSet, or create a new one for it (and cache it).
get(long) - Method in class ini.trakem2.display.Layer
get(Class<?>) - Method in class ini.trakem2.display.LayerSet: Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c.
get(ArrayList<Displayable>, Class<?>) - Method in class ini.trakem2.display.LayerSet: Find, in this LayerSet and contained layers and their nested LayerSets if any, all Displayable instances of Class c, which are stored in the given ArrayList; returns the same ArrayList, or a new one if its null.
get(Class<T>) - Method in class ini.trakem2.display.Selection: Returns a list of selected Displayable of class c only.
get(long, int) - Method in class ini.trakem2.persistence.Cache
get(String) - Method in class ini.trakem2.persistence.Cache
get(long) - Method in class ini.trakem2.persistence.Cache
get(Patch) - Method in class ini.trakem2.persistence.StaleFiles.AlphaMaskPath
get(Patch) - Method in class ini.trakem2.persistence.StaleFiles.CoordinateTransformPath
get(Patch) - Method in interface ini.trakem2.persistence.StaleFiles.Path
get(Object) - Method in class ini.trakem2.utils.FieldMapView: Linear search.
get(int) - Method in class ini.trakem2.utils.History
get() - Method in class ini.trakem2.utils.TaskOnEDT
get(long, TimeUnit) - Method in class ini.trakem2.utils.TaskOnEDT
get(Object) - Method in class ini.trakem2.utils.TypedHashMap
get(int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray2D
get(int, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
get(int, int, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray4D
get2DBounds() - Method in class ini.trakem2.display.LayerSet: Returns a new Rectangle of 0, 0, layer_width, layer_height.
get4Ints(int) - Static method in class ini.trakem2.utils.Utils
getAbsolutePath(Patch) - Method in class ini.trakem2.persistence.FSLoader: With slice info appended at the end; only if it exists, otherwise null.
getAbsolutePath(String) - Method in class ini.trakem2.persistence.FSLoader: Return an absolute path made from path: if it's already absolute, retursn itself; otherwise, the parent folder of all relative paths of this Loader is prepended.
getAbsolutePath(Patch) - Method in class ini.trakem2.persistence.Loader: Returns null unless overriden.
getActive() - Static method in class ini.trakem2.ControlWindow
getActive() - Method in class ini.trakem2.display.Display
getActive() - Method in class ini.trakem2.display.Selection
getActive() - Method in class ini.trakem2.display.Tree: The node currently being dragged or edited in some way.
getAffected() - Method in class ini.trakem2.display.Selection: Returns the set of all Displayable objects affected by this selection, that is, the selected ones and their linked ones.
getAffected(Class<?>) - Method in class ini.trakem2.display.Selection: Returns the set of all Displayable objects of the given class affected by this selection, that is, among the selected ones and their linked ones.
getAffine() - Method in class lenscorrection.PolynomialModel2D
getAffineTransform() - Method in class ini.trakem2.display.Displayable
getAffineTransformCopy() - Method in class ini.trakem2.display.Displayable
getAll(Class<T>) - Method in class ini.trakem2.display.Layer: Returns a list of Displayable of class c only.
getAll(Class<T>) - Method in class ini.trakem2.display.LayerSet: Get all Displayable or ZDisplayable of the given class.
getAll(long) - Method in class ini.trakem2.persistence.Cache
getAll() - Method in class ini.trakem2.utils.History: Returns a list with all undo steps.
getAllPaths() - Method in class ini.trakem2.display.AreaList: Returns a table of Long layer ids versus the ArrayList that getPaths(long) returns for it.
getAlpha() - Method in class ini.trakem2.display.Channel
getAlpha() - Method in class ini.trakem2.display.Displayable
getAlpha() - Method in class ini.trakem2.display.LayerPanel
getAlphaMask() - Method in class ini.trakem2.display.Patch: Return a new ByteProcessor representing the alpha mask, if any, over the pixel data.
getAlphaMaskFilePath() - Method in class ini.trakem2.display.Patch
getAlphaMaskId() - Method in class ini.trakem2.display.Patch
getAngle(double, double) - Static method in class ini.trakem2.utils.M: Returns the angle in radians of the given polar coordinates, correcting the Math.atan2 output.
getAnnotation() - Method in class ini.trakem2.display.Displayable: Returns null if none.
getArea(Layer) - Method in class ini.trakem2.display.AreaList
getArea(long) - Method in class ini.trakem2.display.AreaList
getArea() - Method in class ini.trakem2.display.AreaTree.AreaNode: Return Area in local coords.
getArea() - Method in class ini.trakem2.display.AreaWrapper
getArea() - Method in class ini.trakem2.display.Connector.ConnectorNode
getArea() - Method in class ini.trakem2.display.Displayable
getArea() - Method in class ini.trakem2.display.Node: Returns area in local coords.
getArea() - Method in class ini.trakem2.display.Patch: Returns an Area in world coords representing the inside of this Patch.
getArea(Roi) - Static method in class ini.trakem2.utils.M
getArea(ShapeRoi) - Static method in class ini.trakem2.utils.M
getArea() - Method in class ini.trakem2.utils.ReconstructArea
getAreaAt(Layer) - Method in class ini.trakem2.display.AreaList: In world coordinates, a copy of the area at layer.
getAreaAt(Layer) - Method in class ini.trakem2.display.Ball
getAreaAt(Layer) - Method in class ini.trakem2.display.Displayable: This area is meant to represent the entire area where a Displayable paints to in the @param layer.
getAreaAt(Layer) - Method in class ini.trakem2.display.Dissector
getAreaAt(Layer) - Method in class ini.trakem2.display.Pipe
getAreaAt(Layer) - Method in class ini.trakem2.display.Polyline: A little square for each pixel in @param layer.
getAreaAt(Layer) - Method in class ini.trakem2.display.Tree: In world coordinates.
getAreaForBucket(Layer) - Method in class ini.trakem2.display.Displayable: Should call getAreaAt(layer), or methods that are similar but faster.
getAreaForBucket(Layer) - Method in class ini.trakem2.display.Patch: Use this instead of getAreaAt which calls getArea which is ...
getAreas(Layer, Rectangle) - Method in interface ini.trakem2.display.AreaContainer
getAreas(Layer, Rectangle) - Method in class ini.trakem2.display.AreaList
getAreas(Layer, Rectangle) - Method in class ini.trakem2.display.AreaTree: Return the list of areas, in world coordinates, at the given layer, that intersect the given bounding box.
getARGBPixels(byte[]) - Method in class ini.trakem2.imaging.FloatProcessorT2: Return the float array of pixels as a byte array, cropping (no scaling).
getARGBPixels(byte[], byte[]) - Method in class ini.trakem2.imaging.FloatProcessorT2: Return the float array of pixels as a byte array, cropping (no scaling).
getARGBPixels(float[]) - Method in class ini.trakem2.imaging.FloatProcessorT2: Return the float array of pixels as a byte array, with scaling.
getARGBPixels(float[], float[]) - Method in class ini.trakem2.imaging.FloatProcessorT2: Return the float array of pixels as a byte array, cropping (no scaling).
getAutoscrollInsets() - Method in class ini.trakem2.tree.DNDTree
getBackbone() - Method in class ini.trakem2.display.Pipe: Returns a [p_i[0].length][4] array, with x,y,z,radius on the second part.
getBalls() - Method in class ini.trakem2.display.Ball: Returns a [n_points][4] array, with x,y,z,radius on the second part; not transformed, but local! To obtain balls in world coordinates, calibrated, use getWorldBalls().
getBezierArrays() - Method in class ini.trakem2.display.Profile: Returns a triple array, each containing a [2][n_points] array specifiying the x,y of each left control point, backbone point and right control point respectively.
getBitDepth() - Method in class ini.trakem2.imaging.PatchStack
getBooleanProperty(String) - Method in class ini.trakem2.Project
getBoundingBox() - Method in class ini.trakem2.display.Displayable: Bounding box of the transformed data.
getBoundingBox(Rectangle) - Method in class ini.trakem2.display.Displayable: Bounding box of the transformed data.
getBoundingBox(Collection<? extends Displayable>, Rectangle) - Static method in class ini.trakem2.display.Displayable: Bounding box of a collection of transformed Displayables.
getBoundingBox(Rectangle) - Method in class ini.trakem2.display.DLabel: Saves one allocation, returns the same Rectangle, modified (or a new one if null).
getBounds(Rectangle, Layer) - Method in class ini.trakem2.display.AreaList: Returns the bounds of this object as it shows in the given layer.
getBounds(Collection<? extends Node<Area>>) - Method in class ini.trakem2.display.AreaTree
getBounds(Collection<? extends Node<Float>>) - Method in class ini.trakem2.display.Connector
getBounds() - Method in class ini.trakem2.display.Display
getBounds(Rectangle, Layer) - Method in class ini.trakem2.display.Displayable: Will fill bounding box values into given rectangle -- only that part of this object showing in the given layer will be included in the box.
getBounds(Rectangle) - Method in class ini.trakem2.display.Displayable: Bounding box of the transformed data (or 0,0,0,0 when no data).
getBounds() - Method in class ini.trakem2.display.inspect.ShapeProxy
getBounds(Rectangle, Layer) - Method in class ini.trakem2.display.Pipe: Returns the bounds of this object as it shows in the given layer, set into @param r.
getBounds(Rectangle) - Method in class ini.trakem2.display.Stack
getBounds(Rectangle, Layer) - Method in class ini.trakem2.display.Tree
getBounds(Collection<? extends Node<T>>) - Method in class ini.trakem2.display.Tree
getBounds(Collection<? extends Node<Float>>) - Method in class ini.trakem2.display.Treeline
getBounds() - Method in class ini.trakem2.imaging.PatchStack: Assumes all patches are of the same dimensions.
getBounds(int, int) - Method in class ini.trakem2.imaging.Segmentation.FastMarchingParam: Return bounds relative to the given mouse position.
getBounds2D() - Method in class ini.trakem2.display.inspect.ShapeProxy
getBox() - Method in class ini.trakem2.display.Selection: Returns a copy of the box enclosing all selected ob, or null if none.
getBranch(Vertex<T>) - Method in class ini.trakem2.analysis.Vertex: From this vertex to the next branch vertex or end vertex, both inclusive.
getBranchAndEndNodes() - Method in class ini.trakem2.display.Node: Returns a lazy read-only Collection of all branch and end nodes under this node.
getBranchAndEndNodes() - Method in class ini.trakem2.display.Tree
getBranchNodes() - Method in class ini.trakem2.display.Node: Returns a lazy read-only Collection of all branch nodes under this node.
getBranchNodes() - Method in class ini.trakem2.display.Tree
getBranchNodesInPath() - Method in class ini.trakem2.display.Tree.MeasurePathDistance
getBrushSize() - Static method in class ini.trakem2.utils.ProjectToolbar: Hacks on the ij.gui.Toolbar to get the proper value, and defaults to 15 if the value is absurd.
getBucketable() - Method in class ini.trakem2.display.Displayable
getBucketable() - Method in class ini.trakem2.display.ZDisplayable
getBucketMap(Layer) - Method in interface ini.trakem2.display.Bucketable
getBucketMap(Layer) - Method in class ini.trakem2.display.Layer
getBucketMap(Layer) - Method in class ini.trakem2.display.LayerSet
getBucketSide(Bucketable, Layer) - Static method in class ini.trakem2.display.Bucket
getBytePixels() - Method in class ini.trakem2.imaging.FloatProcessorT2: Return the float array of pixels as a byte array, cropping (no scaling).
getBytes() - Method in class ini.trakem2.persistence.Cache: Current estimated space occupied by the images in this cache.
getByType() - Method in class ini.trakem2.tree.ProjectThing: Recursively browse all children to classify all nodes by type.
getCached(long, int) - Method in class ini.trakem2.persistence.Loader
getCachedAWT(long, int) - Method in class ini.trakem2.persistence.Loader
getCachedClosestAboveImage(Patch, double) - Method in class ini.trakem2.persistence.Loader: Above or equal in size.
getCachedClosestBelowImage(Patch, double) - Method in class ini.trakem2.persistence.Loader: Below, not equal.
getCachedImagePlus(long) - Method in class ini.trakem2.persistence.Loader: Simply reads from the cache, does no reloading at all.
getCalibratedThickness() - Method in class ini.trakem2.display.Layer
getCalibratedZ() - Method in class ini.trakem2.display.Layer
getCalibration() - Method in class ini.trakem2.display.FakeImagePlus
getCalibration() - Method in class ini.trakem2.display.LayerSet
getCalibration() - Method in class ini.trakem2.imaging.PatchStack
getCalibrationCopy() - Method in class ini.trakem2.display.LayerSet
getCanvas() - Method in class ini.trakem2.display.Display
getCellTitle() - Method in class ini.trakem2.analysis.Compare.Chain
getChannelAlphas() - Method in class ini.trakem2.display.Display
getChannelAlphas() - Method in class ini.trakem2.display.Patch
getChannelAlphasState() - Method in class ini.trakem2.display.Display
getCharacter(int) - Static method in class ini.trakem2.utils.Utils: 1 A, 2 B, 3 C --- 26 - z, 27 AA, 28 AB, 29 AC --- 26*27 AAA
getCheckbox(int) - Method in class ini.trakem2.utils.OptionPanel: May throw IllegalArgumentException
getCheckBoxes() - Method in class ini.trakem2.utils.OptionPanel
getChildren() - Method in class ini.trakem2.display.Node
getChildren() - Method in class ini.trakem2.tree.LayerThing
getChildren() - Method in class ini.trakem2.tree.ProjectThing
getChildren() - Method in class ini.trakem2.tree.TemplateThing
getChildren() - Method in interface ini.trakem2.tree.Thing
getChildrenCount() - Method in class ini.trakem2.display.Node
getChildrenNodes() - Method in class ini.trakem2.display.Node
getChildTemplate(String) - Method in class ini.trakem2.tree.LayerThing
getChildTemplate(String) - Method in class ini.trakem2.tree.ProjectThing
getChildTemplate(String) - Method in class ini.trakem2.tree.TemplateThing
getChoiceIndex(int) - Method in class ini.trakem2.utils.OptionPanel
getChoiceObject(int) - Method in class ini.trakem2.utils.OptionPanel
getChoices() - Method in class ini.trakem2.utils.OptionPanel
getChoiceString(int) - Method in class ini.trakem2.utils.OptionPanel
getChosen() - Method in class ini.trakem2.display.DisplayableChooser
getClassesToMultiPaint() - Method in class ini.trakem2.display.Display: Only Patch, Stack; AreaList, Profile; and DLabel are considered.
getClosestAbove(long, int) - Method in class ini.trakem2.persistence.Cache
getClosestBelow(long, int) - Method in class ini.trakem2.persistence.Cache
getClosestMipMapLevel(Patch, int, int) - Method in class ini.trakem2.persistence.FSLoader: Return the closest level to level that exists as a file.
getClosestMipMapLevel(Patch, int, int) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns zero unless overriden.
getCoefficients() - Method in class lenscorrection.NonLinearTransform
getColor() - Method in class ini.trakem2.analysis.Compare.Chain: Returns the color of the root pipe.
getColor() - Method in class ini.trakem2.display.Displayable
getColor() - Method in class ini.trakem2.display.LayerPanel
getColor() - Method in interface ini.trakem2.display.Line3D
getColor() - Method in class ini.trakem2.display.Node
getColorCueLayerRange(Layer) - Method in class ini.trakem2.display.LayerSet: Returns the list of layers to paint by considering the range of n_layers_color_cue around the active layer index.
getCols() - Method in class ini.trakem2.utils.Montage: Returns an ArrayList of String[], which can be of unequal length, and each contain the file names of a column.
getComponentColorModel() - Method in class ini.trakem2.display.paint.USHORTPaint
getComposite(byte) - Method in class ini.trakem2.display.Displayable
getComposite(byte, float) - Static method in class ini.trakem2.display.Displayable
getCompositeMode() - Method in class ini.trakem2.display.Displayable
getConfidence() - Method in class ini.trakem2.display.Node
getControlModifier() - Static method in class ini.trakem2.utils.Utils: The CTRL key functionality is passed over to the COMMAND key (aka META key) in a MacOSX.
getCoordinate(int) - Method in class ini.trakem2.display.Connector: Get a coordinate for target i.
getCoordinateAtOrigin() - Method in class ini.trakem2.display.Connector
getCoordinateTransform() - Method in class ini.trakem2.display.Patch: Obtain a copy of the CoordinateTransform that transfers image data to mipmap image data.
getCoordinateTransformBoundingBox() - Method in class ini.trakem2.display.Patch: Get the bounding rectangle of the transformed image relative to the original image.
getCoordinateTransformBoundingBox(Patch, CoordinateTransform) - Static method in class ini.trakem2.display.Patch: Allow reusing a CoordinateTransform that was already loaded from a file.
getCoordinateTransformFilePath() - Method in class ini.trakem2.display.Patch
getCoordinateTransformId() - Method in class ini.trakem2.display.Patch: A value of 0 indicates that there isn't one.
getCoordinateTransformsFolder() - Method in class ini.trakem2.persistence.FSLoader
getCoordinateTransformsFolder() - Method in class ini.trakem2.persistence.Loader: Returns null unless overriden.
getCos(double, double, double, double) - Static method in class ini.trakem2.utils.Utils: The cosinus between two vectors (in polar coordinates), by means of the dot product.
getCount() - Method in class ini.trakem2.display.Ball: Return the number of balls.
getCurrent() - Method in class ini.trakem2.utils.History
getCurrentMemory() - Static method in class ini.trakem2.persistence.Loader
getCurrentPatch() - Method in class ini.trakem2.imaging.PatchStack: Returns the Patch corresponding to the current slice.
getCurrentPath() - Method in class ini.trakem2.display.Patch: Returns the value of the field current_path, which may be null.
getCurrentSlice() - Method in class ini.trakem2.imaging.PatchStack
getD() - Method in class ini.trakem2.display.Displayable.DoEdit
getD() - Method in class ini.trakem2.display.Displayable.DoEdits
getD() - Method in class ini.trakem2.display.Displayable.DoTransforms
getD() - Method in interface ini.trakem2.display.DoStep: May return null.
getD() - Method in class ini.trakem2.display.Layer.DoMoveDisplayable
getD() - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
getD() - Method in class ini.trakem2.display.LayerSet.DoMoveZDisplayable
getD() - Method in class ini.trakem2.tree.RenameThingStep
getData() - Method in class ini.trakem2.display.AreaTree.AreaNode
getData() - Method in class ini.trakem2.display.Node
getData() - Method in class ini.trakem2.display.Tree.MeasurementPair
getData() - Method in class ini.trakem2.display.Tree.Pair: The list of data elements associated with each node in the path, ordered from a to b (both included).
getData() - Method in class ini.trakem2.display.Treeline.RadiusNode
getDataCopy() - Method in class ini.trakem2.display.AreaTree.AreaNode
getDataCopy() - Method in class ini.trakem2.display.Node
getDataCopy() - Method in class ini.trakem2.display.Treeline.RadiusNode
getDataType() - Method in class ini.trakem2.utils.ImgLibVolume
getDepth() - Method in class ini.trakem2.display.LayerSet: Returns the distance from the first layer's Z to the last layer's Z.
getDescriptionString(ImagePlus, FileInfo) - Static method in class ini.trakem2.io.ImageSaver: Returns a string containing information about the specified image.
getDimension() - Method in class lenscorrection.NonLinearTransform
getDimensions() - Method in class ini.trakem2.imaging.PatchStack: Override to return width, height, 1, patch.length, 1
getDimensions(String) - Static method in class ini.trakem2.persistence.Loader: Read out the width,height of an image using LOCI BioFormats.
getDimensions(Patch) - Method in class ini.trakem2.persistence.Loader
getDimensions(String, Font) - Static method in class ini.trakem2.utils.Utils: Get the width and height of single-line text.
getDisplay(LayerSet) - Static method in class ini.trakem2.display.Display3D: Get the Display3D instance that exists for the given LayerSet, if any.
getDisplay() - Method in class ini.trakem2.display.DisplayCanvas
getDisplay() - Method in class ini.trakem2.display.FakeImagePlus
getDisplayableList() - Method in interface ini.trakem2.display.Bucketable
getDisplayableList() - Method in class ini.trakem2.display.Layer: Returns the real list of displayables, not a copy.
getDisplayableList() - Method in class ini.trakem2.display.LayerSet: Returns the real list of displayables, not a copy.
getDisplayables() - Method in class ini.trakem2.display.Layer: Returns a copy of the list of Displayable objects.
getDisplayables(Class<?>) - Method in class ini.trakem2.display.Layer: Returns a list of Displayable of class c only.
getDisplayables(Class<?>, boolean, boolean) - Method in class ini.trakem2.display.Layer
getDisplayables(Class<?>, Rectangle) - Method in class ini.trakem2.display.Layer: Returns a list of all Displayable of class c that intersect the given rectangle.
getDisplayables(Class<?>, Area, boolean) - Method in class ini.trakem2.display.Layer: Returns a list of all Displayable of class c that intersect the given area.
getDisplayables(Class<?>, Area, boolean, boolean) - Method in class ini.trakem2.display.Layer: Check class identity by instanceof instead of equality.
getDisplayables(Class<?>, boolean) - Method in class ini.trakem2.display.Layer: Check class identity with equality, so no superclasses or interfaces are possible.
getDisplayables() - Method in class ini.trakem2.display.LayerSet: Return all the Displayable objects from all the layers of this LayerSet.
getDisplayables(Class<?>) - Method in class ini.trakem2.display.LayerSet: Return all the Displayable objects from all the layers of this LayerSet of the given class.
getDisplayables(Class<?>, Area, boolean) - Method in class ini.trakem2.display.LayerSet: Return all the Displayable objects from all the layers of this LayerSet of the given class that intersect the given area.
getDisplayablesUnderMouse() - Method in class ini.trakem2.display.DisplayCanvas: See DisplayCanvas.getDisplayablesUnderMouse(MouseEvent).
getDisplayablesUnderMouse(MouseEvent) - Method in class ini.trakem2.display.DisplayCanvas: Return the list of Displayable objects under the mouse, sorted by proper stack order.
getDisplayChannelAlphas() - Method in class ini.trakem2.display.Display
getDisplayCount() - Static method in class ini.trakem2.display.Display
getDisplays() - Static method in class ini.trakem2.display.Display
getDistance() - Method in class ini.trakem2.display.Tree.MeasurePathDistance
getDocType() - Method in class ini.trakem2.Project: Returns the String to be used as Document Type of the XML file, generated from the name of the root template thing.
getEdgeConfidence() - Method in class ini.trakem2.display.Node
getEdgeConfidence(Node<T>) - Method in class ini.trakem2.display.Node
getEndNodes() - Method in class ini.trakem2.display.Node: Returns a lazy read-only Collection of all end nodes under this node.
getEndNodes() - Method in class ini.trakem2.display.Tree
getErrorMessage() - Method in class ini.trakem2.imaging.BinaryInterpolation2D
getExecutorService(int) - Static method in class ini.trakem2.parallel.ExecutorProvider: Returns an ExecutorService for Callables that use nThreads number of threads.
getExecutorService(float) - Static method in class ini.trakem2.parallel.ExecutorProvider: Returns an ExecutorService for Callables that use a given fraction of computer resources.
getExpandedStates() - Method in class ini.trakem2.tree.DNDTree: Get the map of Thing vs.
getExpandedStates(HashMap<Thing, Boolean>) - Method in class ini.trakem2.tree.DNDTree: Get the map of Thing vs.
getExtension() - Method in class ini.trakem2.utils.Saver
getFakeImagePlus() - Method in class ini.trakem2.display.DisplayCanvas: CAREFUL: the ImageProcessor of the returned ImagePlus is fake, that is, a 4x4 byte array; but the dimensions that it returns are those of the host LayerSet.
getField(Object, String) - Static method in class ini.trakem2.utils.Utils
getField(Object, Class<?>, String) - Static method in class ini.trakem2.utils.Utils: Get by reflection a private or protected field in the given object.
getFileInfo() - Method in class ini.trakem2.imaging.PatchStack
getFileName(Patch) - Method in class ini.trakem2.persistence.Loader: Equivalent to File.getName(), but subtracts the slice info from it if any.
getFilePath() - Method in class ini.trakem2.display.Patch: If this patch is part of a stack, the file path will contain the slice number attached to it, in the form -----#slice=10 for slice number 10.
getFilePath() - Method in class ini.trakem2.display.Stack
getFilters() - Method in class ini.trakem2.display.Patch
getFirstLayer() - Method in class ini.trakem2.display.AreaList: Returns the layer of lowest Z coordinate Layer where this ZDisplayable has a point in.
getFirstLayer() - Method in class ini.trakem2.display.Ball: Returns the layer of lowest Z coordinate where this ZDisplayable has a point in, or the creation layer if no points yet.
getFirstLayer() - Method in class ini.trakem2.display.Dissector
getFirstLayer() - Method in class ini.trakem2.display.Pipe: Returns the layer of lowest Z coordinate where this ZDisplayable has a point in, or the creation layer if no points yet.
getFirstLayer() - Method in class ini.trakem2.display.Polyline: Returns the layer of lowest Z coordinate where this ZDisplayable has a point in, or the creation layer if no points yet.
getFirstLayer() - Method in class ini.trakem2.display.Stack
getFirstLayer() - Method in class ini.trakem2.display.Tree
getFirstLayer() - Method in class ini.trakem2.display.ZDisplayable: Returns the layer of lowest Z coordinate where this ZDisplayable has a point in.
getFirstMipMapLevelSaved() - Method in class ini.trakem2.Project: Get the mipmap level at which to start saving images.
getFirstNodeCoordinates() - Method in class ini.trakem2.display.Tree.MeasurePathDistance
getFirstPoint() - Method in class ini.trakem2.display.Profile
getFlatAWTImage(Layer, Rectangle, double, int, int, Class<?>, List<? extends Displayable>, boolean, Color) - Method in class ini.trakem2.persistence.Loader
getFlatAWTImage(Layer, Rectangle, double, int, int, Class<?>, List<? extends Displayable>, boolean, Color, Displayable) - Method in class ini.trakem2.persistence.Loader
getFlatImage(Layer, Rectangle, double, int, int, Class<?>, boolean) - Method in class ini.trakem2.persistence.Loader
getFlatImage(Layer, Rectangle, double, int, int, Class<?>, List<? extends Displayable>) - Method in class ini.trakem2.persistence.Loader
getFlatImage(Layer, Rectangle, double, int, int, Class<?>, List<? extends Displayable>, boolean) - Method in class ini.trakem2.persistence.Loader
getFlatImage(Selection, double, int, int, boolean, Color) - Method in class ini.trakem2.persistence.Loader
getFlatImage(Layer, Rectangle, double, int, int, Class<?>, List<? extends Displayable>, boolean, Color) - Method in class ini.trakem2.persistence.Loader: Returns a screenshot of the given layer for the given magnification and srcRect.
getFlatImage(Layer, Rectangle, double, int, int, Class<?>, List<? extends Displayable>, boolean, Color, Displayable) - Method in class ini.trakem2.persistence.Loader
getFloaterX() - Method in class ini.trakem2.display.AffineTransformMode
getFloaterY() - Method in class ini.trakem2.display.AffineTransformMode
getFloatPixels() - Method in class ini.trakem2.imaging.FloatProcessorT2
getFont() - Method in class ini.trakem2.display.DLabel
getForegroundColorValue() - Static method in class ini.trakem2.utils.ProjectToolbar: The luminance of the foreground color.
getFrame() - Method in class ini.trakem2.display.Display
getFront(Project) - Static method in class ini.trakem2.display.Display: Get a pointer to a Display for @param project, or null if none.
getFront() - Static method in class ini.trakem2.display.Display: Can be null.
getFrontLayer() - Static method in class ini.trakem2.display.Display: Get the layer of the front Display, or null if none.
getFrontLayer(Project) - Static method in class ini.trakem2.display.Display: Get the layer of an open Display of the given Project, or null if none.
getFullCoordinateTransform() - Method in class ini.trakem2.display.Patch: Create a CoordinateTransform that incorporates both the CoordinateTransform of this Patch (if present) and its AffineTransform.
getGeneralPath() - Method in class ini.trakem2.utils.ReconstructArea
getGraphicsSource() - Method in class ini.trakem2.display.AffineTransformMode
getGraphicsSource() - Method in class ini.trakem2.display.DefaultMode
getGraphicsSource() - Method in class ini.trakem2.display.GroupingMode
getGraphicsSource() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
getGraphicsSource() - Method in class ini.trakem2.display.ManualAlignMode
getGraphicsSource() - Method in interface ini.trakem2.display.Mode
getHeight() - Method in class ini.trakem2.display.Displayable: Returns the height of the data.
getHeight() - Method in class ini.trakem2.display.FakeImagePlus
getHeight() - Method in class lenscorrection.NonLinearTransform
getHeight() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
getHexRGBColor(Color) - Static method in class ini.trakem2.utils.Utils
getHigherZoomLevel2(double) - Method in class ini.trakem2.display.DisplayCanvas
getHighestMipMapLevel(Patch) - Static method in class ini.trakem2.persistence.Loader: Returns the highest mipmap level for which a mipmap image may have been generated given the dimensions of the Patch.
getHighestMipMapLevel(double) - Static method in class ini.trakem2.persistence.Loader
getId() - Method in interface ini.trakem2.display.Line3D
getId() - Method in class ini.trakem2.persistence.DBObject
getImage() - Method in class ini.trakem2.imaging.PatchStack
getImage() - Method in class ini.trakem2.utils.ImgLibVolume
getImageArray() - Method in class ini.trakem2.imaging.LayerStack: Returns a linear array for each slice, real (not virtual)!
getImageFilePath() - Method in class ini.trakem2.display.Patch: Returns the absolute path to the image file, as read by the OS.
getImageFilePath(Patch) - Method in class ini.trakem2.persistence.FSLoader
getImageFilePath(Patch) - Method in class ini.trakem2.persistence.Loader: Returns null unless overriden.
getImagePlus() - Method in class ini.trakem2.display.FakeImageWindow: Returns the display's FakeImagePlus.
getImagePlus() - Method in class ini.trakem2.display.Patch: Fetches the ImagePlus from the cache; be warned: the returned ImagePlus may have been flushed, removed and then recreated if the program had memory needs that required flushing part of the cache; use @getImageProcessor to get the pixels guaranteed not to be ever null.
getImagePlus() - Method in class ini.trakem2.imaging.LayerStack
getImageProcessor() - Method in class ini.trakem2.display.Patch: Fetches the ImageProcessor from the cache, which will never be flushed or its pixels set to null.
getImageStack() - Method in class ini.trakem2.imaging.PatchStack
getImageStorageFolder() - Method in class ini.trakem2.persistence.FSLoader: Returns a folder proven to be writable for images can be stored into.
getImageStorageFolder() - Method in class ini.trakem2.persistence.Loader
getInfo() - Method in class ini.trakem2.display.AreaList: Measure the volume (in voxels) of this AreaList, and the surface area, the latter estimated as the number of voxels that make the outline.
getInfo() - Method in class ini.trakem2.display.Ball: Returns information on the number of ball objects per layer.
getInfo() - Method in class ini.trakem2.display.Connector
getInfo() - Method in class ini.trakem2.display.Dissector: Returns: - first line: the title of this dissector - second line: the number of items included in this dissector and then a list of 5 tab-separated columns: item tag, radius, x, y, z
getInfo() - Method in class ini.trakem2.display.Pipe
getInfo() - Method in class ini.trakem2.display.Polyline
getInfo(long[]) - Method in class ini.trakem2.io.LoggingInputStream: Returns info as [0] = current time in ms [1] = elapsed time in ms since last call to getInfo(long[]) [2] = n_bytes_read since last call to getInfo(long[]) [3] = accumulated time in ms since last call to resetInfo() [4] = accumulated bytes since last call to resetInfo() So current speed = info[2]/info[1] Kb/s
getInfo() - Method in class ini.trakem2.persistence.DBObject: Returns id and project name; this method is meant to be overriden by any of the subclasses.
getInfo() - Method in class ini.trakem2.Project
getInfo() - Method in class ini.trakem2.tree.DNDTree
getInfo() - Method in class ini.trakem2.tree.LayerThing: Return information on this node and its object.
getInfo() - Method in class ini.trakem2.tree.ProjectThing: Return information on this node and its object, and also on all the children, recursively.
getInfo() - Method in class ini.trakem2.tree.TemplateThing: Return information on this node and its object.
getInfo() - Method in interface ini.trakem2.tree.Thing
getInstance(float) - Static method in class ini.trakem2.display.graphics.AddARGBComposite
getInstance(float) - Static method in class ini.trakem2.display.graphics.ColorYCbCrComposite
getInstance(float) - Static method in class ini.trakem2.display.graphics.DifferenceARGBComposite
getInstance(float) - Static method in class ini.trakem2.display.graphics.MultiplyARGBComposite
getInstance(float) - Static method in class ini.trakem2.display.graphics.SubtractARGBComposite
getInternalFileName(Patch) - Method in class ini.trakem2.persistence.Loader: Equivalent to File.getName(), does not subtract the slice info from it.
getIntersecting(Displayable, Class<T>) - Method in class ini.trakem2.display.Layer: Find the Displayable objects of class 'target' whose perimeter (not just the bounding box) intersect the given Displayable (which is itself included if present in this very Layer).
getIntersection(Displayable) - Method in class ini.trakem2.display.Displayable: Returns the intersection of this Displayable's area with the given one.
getInvertibleCoordinateTransform() - Method in class ini.trakem2.display.Stack
getJobsPopup(Display) - Method in class ini.trakem2.persistence.Loader
getKey() - Method in class ini.trakem2.analysis.Centrality.EtchingStep
getKeyCode() - Method in class ini.trakem2.display.Tag
getLambda() - Method in class lenscorrection.PolynomialModel2D
getLastAdded() - Method in class ini.trakem2.display.Tree
getLastEdited() - Method in class ini.trakem2.display.Tree
getLastLayer() - Method in class ini.trakem2.display.AreaList: Returns the layer of highest Z coordinate Layer where this ZDisplayable has a point in.
getLastNodeCoordinates() - Method in class ini.trakem2.display.Tree.MeasurePathDistance
getLastPoint() - Method in class ini.trakem2.display.Profile
getLastVisited() - Method in class ini.trakem2.display.Tree
getLayer() - Method in class ini.trakem2.display.Display
getLayer() - Method in class ini.trakem2.display.Displayable
getLayer(int) - Method in class ini.trakem2.display.LayerSet: Find a layer by index, or null if none.
getLayer(long) - Method in class ini.trakem2.display.LayerSet: Find a layer with the given id, or null if none.
getLayer(Long) - Method in class ini.trakem2.display.LayerSet: Same as getLayer(long) but without box/unbox.
getLayer(double) - Method in class ini.trakem2.display.LayerSet: Returns the first layer found with the given Z coordinate, rounded to seventh decimal precision, or null if none found.
getLayer(double, double, boolean) - Method in class ini.trakem2.display.LayerSet: Returns null if none has the given z and thickness.
getLayer() - Method in class ini.trakem2.display.Node
getLayer() - Method in class ini.trakem2.display.Selection: Returns the Layer of the Display, or if the latter is null, that of the first selected Displayable.
getLayerCompositeMode(Layer) - Method in class ini.trakem2.display.Display
getLayerHeight() - Method in interface ini.trakem2.display.Bucketable
getLayerHeight() - Method in class ini.trakem2.display.Layer
getLayerHeight() - Method in class ini.trakem2.display.LayerSet
getLayerIds() - Method in class ini.trakem2.display.AreaList
getLayerIds() - Method in class ini.trakem2.display.Ball
getLayerIds() - Method in class ini.trakem2.display.Displayable
getLayerIds() - Method in class ini.trakem2.display.Dissector
getLayerIds() - Method in class ini.trakem2.display.Pipe
getLayerIds() - Method in class ini.trakem2.display.Polyline
getLayerIds() - Method in class ini.trakem2.display.Tree
getLayerIds() - Method in class ini.trakem2.display.ZDisplayable: Get the list of Layer ids on which this ZDisplayable has data on.
getLayerIndex(long) - Method in class ini.trakem2.display.LayerSet
getLayerRange() - Method in class ini.trakem2.display.AreaList: Get the range of layers between the first and last layers in which this AreaList paints to.
getLayers() - Method in class ini.trakem2.display.LayerSet: Returns a copy of the layer list.
getLayers(int, int) - Method in class ini.trakem2.display.LayerSet: Returns a sublist of layers from first to last, both inclusive.
getLayers(Layer, Layer) - Method in class ini.trakem2.display.LayerSet: Returns the layer range from first to last, both included.
getLayerSet() - Method in class ini.trakem2.display.Display
getLayerSet() - Method in class ini.trakem2.display.Displayable
getLayerSet() - Method in interface ini.trakem2.display.Line3D
getLayerSet() - Method in class ini.trakem2.display.ZDisplayable
getLayersWithData() - Method in class ini.trakem2.display.Displayable: Override it to provide Layer pointers directly.
getLayersWithData() - Method in class ini.trakem2.display.Tree
getLayerThingTitle() - Method in class ini.trakem2.display.Layer
getLayerTree() - Method in class ini.trakem2.Project
getLayerWidth() - Method in interface ini.trakem2.display.Bucketable
getLayerWidth() - Method in class ini.trakem2.display.Layer
getLayerWidth() - Method in class ini.trakem2.display.LayerSet
getLinked() - Method in class ini.trakem2.display.Displayable: Return the HashSet of directly linked Displayable objects.
getLinked(Class<?>) - Method in class ini.trakem2.display.Displayable: Return those of Class c from among the directly linked.
getLinkedBox(boolean) - Method in class ini.trakem2.display.Displayable: Returns the sum of bounding boxes of all linked Displayables.
getLinkedBox() - Method in class ini.trakem2.display.Selection: Returns the total box enclosing all selected objects and their linked objects within the current layer, or null if none are selected.
getLinkedGroup(HashSet<Displayable>) - Method in class ini.trakem2.display.Displayable: Return the HashSet of all directly and indirectly linked objects.
getLinkedProperties(Displayable) - Method in class ini.trakem2.display.Displayable: Returns a copy of this object's linked properties table for the given Displayable, which may be empty.
getLinkedProperties() - Method in class ini.trakem2.display.Displayable: Returns a copy of this object's linked properties, which may be empty.
getLinkedProperty(Displayable, String) - Method in class ini.trakem2.display.Displayable: If the key is null or not found, or the aren't any properties linked to the target, returns null; otherwise returns the stored value for key and target.
getLinkedProperty(Displayable, String, String) - Method in class ini.trakem2.display.Displayable: If the key is null or not found, or the aren't any properties linked to the target, returns default_value; otherwise returns the stored value for key and target.
getLoader() - Method in class ini.trakem2.Project
getLocalAffine(double, double) - Method in class ini.trakem2.display.Patch: Return the local affine transformation for a passed location in world coordinates.
getLocalCalibration() - Method in class ini.trakem2.imaging.PatchStack
getLocalScale(double, double) - Method in class ini.trakem2.display.Patch
getLocation() - Method in class ini.trakem2.display.Display
getLogStream() - Static method in class ini.trakem2.utils.Utils
getLowerZoomLevel2(double) - Method in class ini.trakem2.display.DisplayCanvas: Enable zooming out up to the point where the display becomes 10 pixels in width or height.
getMarked() - Method in class ini.trakem2.display.Tree
getMask() - Method in class ini.trakem2.display.Patch.PatchImage: Get the mask.
getMask() - Method in class ini.trakem2.imaging.PatchStack
getMasksFolder() - Method in class ini.trakem2.persistence.FSLoader
getMasksFolder() - Method in class ini.trakem2.persistence.Loader: Returns null unless override.
getMasterTable() - Static method in class ini.trakem2.display.Display3D: The sky will fall on your head if you modify any of the objects contained in this table -- which is a copy of the original, but the objects are the originals.
getMax() - Method in class ini.trakem2.display.Patch
getMaxBytes() - Method in class ini.trakem2.persistence.Cache: Maximum desired space for this cache.
getMeaningfulTitle(Displayable) - Method in class ini.trakem2.Project: Searches upstream in the Project tree for things that have a user-defined name, stops at the first and returns it along with all the intermediate ones that only have a type and not a title, appended.
getMeaningfulTitle2(Displayable) - Method in class ini.trakem2.Project
getMeshResolution() - Method in class ini.trakem2.display.Patch
getMin() - Method in class ini.trakem2.display.Patch
getMinimalBoundingBox(Displayable[]) - Static method in class ini.trakem2.display.Displayable
getMinimalBoundingBox(Class<?>) - Method in class ini.trakem2.display.Layer: Returns null if no Displayable objects of class c exist.
getMinimalBoundingBox(Class<?>, boolean) - Method in class ini.trakem2.display.Layer: Returns null if no Displayable objects of class c exist (or are visible if visible_only is true).
getMinimalBoundingBox(Class<?>) - Method in class ini.trakem2.display.LayerSet: Returns the minimal 2D bounding box for Displayables of class @param c in all layers.
getMinNumMatches() - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
getMinNumMatches() - Method in class lenscorrection.NonLinearTransform
getMinNumMatches() - Method in class lenscorrection.PolynomialModel2D
getMipMapFormat() - Method in class ini.trakem2.persistence.FSLoader: Any of: FSLoader.MIPMAP_JPEG, FSLoader.MIPMAP_PNG, FSLoader.MIPMAP_TIFF, FSLoader.MIPMAP_RAW, FSLoader.MIPMAP_RAG.
getMipMapFormat() - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
getMipMapLevel(double, double) - Static method in class ini.trakem2.persistence.Loader: Transform mag to nearest scale level that delivers an equally sized or larger image.
getMipMapModeIndex(String) - Static method in class ini.trakem2.persistence.Loader: Returns the default (Loader.DEFAULT_MIPMAPS_MODE) if the mode is not recognized.
getMipMapModeName(int) - Static method in class ini.trakem2.persistence.Loader: Returns the default if mode is not recognized.
getMipMapsFolder() - Method in class ini.trakem2.persistence.FSLoader: Returns the path to the directory hosting the file image pyramids.
getMipMapsFolder() - Method in class ini.trakem2.persistence.Loader: Returns null unless overriden.
getMipMapsMode() - Method in class ini.trakem2.Project: The mode (aka algorithmic approach) used to generate mipmaps, which defaults to Loader.DEFAULT_MIPMAPS_MODE.
getMipMapsRegenerationEnabled() - Method in class ini.trakem2.persistence.Loader: Returns the value of mipmaps_regen; to query whether this loader is using mipmaps or not, call instead Loader.isMipMapsRegenerationEnabled().
getMirror(int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray2D
getMirror(int, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
getMode() - Method in class ini.trakem2.display.Display
getMouseX() - Method in class ini.trakem2.display.FreeHandProfile
getMouseY() - Method in class ini.trakem2.display.FreeHandProfile
getName(Class<?>) - Static method in class ini.trakem2.Project: Returns a user-understandable name for the given class.
getNameId() - Method in class ini.trakem2.display.Displayable: If the title is purely numeric, returns it as a double; otherwise returns 0.
getNAreas() - Method in class ini.trakem2.display.AreaList: How many layers does this object paint to.
getNavigator() - Method in class ini.trakem2.display.Display
getNChannels() - Method in class ini.trakem2.imaging.PatchStack: Override to return 1.
getNDisplayables() - Method in class ini.trakem2.display.Layer
getNearestLayer(double) - Method in class ini.trakem2.display.LayerSet
getNearestPointIndex(double, double) - Method in class ini.trakem2.display.Profile
getNeighborCount() - Method in class ini.trakem2.analysis.Vertex
getNeighborLayers(Layer, int) - Method in class ini.trakem2.display.LayerSet: Get up to 'n' layers before and after the given layers.
getNextBlobId() - Method in class ini.trakem2.persistence.FSLoader: Get the next unique id to be used for the Patch's CoordinateTransform or alpha mask.
getNextBlobId() - Method in class ini.trakem2.persistence.Loader: Returns 0 unless overriden.
getNextId() - Method in class ini.trakem2.persistence.DBLoader: Retrieve next id from a sequence for a new DBObject to be added.
getNextId() - Method in class ini.trakem2.persistence.FSLoader: Get the next unique id, not shared by any other object within the same project.
getNextId() - Method in class ini.trakem2.persistence.Loader: Retrieve next id from a sequence for a new DBObject to be added.
getNextTempId() - Method in class ini.trakem2.persistence.Loader: Retrieve next id from a sequence for a temporary Object to be added.
getNFrames() - Method in class ini.trakem2.imaging.PatchStack: Override to return 1.
getNLinked() - Method in class ini.trakem2.display.Selection
getNodeInfo() - Method in class ini.trakem2.tree.ProjectThing: Return information on this node and its object.
getNodesAt(Layer) - Method in class ini.trakem2.display.Tree: Get a copy of the Set of Node that exist at layer; the Node instances are the originals.
getNodesToPaint(Layer) - Method in class ini.trakem2.display.Tree
getNodesToPaint(Layer, List<Layer>) - Method in class ini.trakem2.display.Tree
getNSelected() - Method in class ini.trakem2.display.Selection
getNSlices() - Method in class ini.trakem2.imaging.PatchStack
getNumber(int) - Method in class ini.trakem2.utils.OptionPanel: May throw IllegalArgumentException or NumberFormatException
getNumericFields() - Method in class ini.trakem2.utils.OptionPanel
getObject() - Method in class ini.trakem2.tree.LayerThing
getObject() - Method in class ini.trakem2.tree.ProjectThing
getObject() - Method in class ini.trakem2.tree.TemplateThing: Returns null always, for TemplateThings don't hold any real object.
getObject() - Method in interface ini.trakem2.tree.Thing
getOHeight() - Method in class ini.trakem2.display.Patch: The original height of the pixels in the source image file.
getOpenProject(String) - Static method in class ini.trakem2.persistence.FSLoader
getOrCreateByteArray(int, int) - Static method in class ini.trakem2.utils.CachingThread
getOrCreateByteArray(int) - Static method in class ini.trakem2.utils.CachingThread
getOrCreateFront(Project) - Static method in class ini.trakem2.display.Display
getOrCreateIntArray(int) - Static method in class ini.trakem2.utils.CachingThread
getOrder() - Method in class lenscorrection.PolynomialModel2D
getOriginalPath() - Method in class ini.trakem2.display.Patch: Returns the value of the field original_path, which may be null.
getOriginPoint(boolean) - Method in class ini.trakem2.display.Tree
getOrigins(Class<?>) - Method in class ini.trakem2.display.Connector: Returns the set of Displayable objects under the origin point, or an empty set if none.
getOrigins(Class<?>, boolean) - Method in class ini.trakem2.display.Connector
getOrigins() - Method in class ini.trakem2.display.Connector: Returns the set of Displayable objects under the origin point, or an empty set if none.
getOrMakeImageLoadingLock(long, int) - Method in class ini.trakem2.persistence.Loader
getOrMakeImageLoadingLock(String) - Method in class ini.trakem2.persistence.Loader
getOverlay() - Method in class ini.trakem2.display.Layer: Return the current Overlay or a new one if none yet.
getOverlay() - Method in class ini.trakem2.display.LayerSet: Return the current Overlay or a new one if none yet.
getOWidth() - Method in class ini.trakem2.display.Patch: The original width of the pixels in the source image file.
getPaintingBounds() - Method in class ini.trakem2.display.Tree
getPaintMode(HashMap<Color, Layer>, ArrayList<LayerPanel>) - Method in class ini.trakem2.display.Display: Sets the values atomically, returns the painting mode.
getParent() - Method in class ini.trakem2.display.Layer
getParent() - Method in class ini.trakem2.display.LayerSet
getParent() - Method in class ini.trakem2.display.Node
getParent() - Method in class ini.trakem2.tree.LayerThing
getParent() - Method in class ini.trakem2.tree.ProjectThing
getParent() - Method in class ini.trakem2.tree.TemplateThing
getParent() - Method in interface ini.trakem2.tree.Thing
getParentFolder() - Method in class ini.trakem2.persistence.FSLoader: Return the path to the folder containing the project XML file.
getParentFolder() - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
getParentTitle(Displayable) - Method in class ini.trakem2.Project: Returns the title of the enclosing abstract node in the ProjectTree.
getPatch(Layer, Patch) - Method in class ini.trakem2.imaging.PatchStack: If the 'p' is contained in this PatchStack, get the first Patch found to be contained here and in the given 'layer'
getPatch(int) - Method in class ini.trakem2.imaging.PatchStack: From 0 to getNSlices() -1, otherwise null.
getPatch() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
getPatchArea(boolean) - Method in class ini.trakem2.display.Layer: Returns an Area in world coordinates that represents the inside of all Patches.
getPatches(boolean) - Method in class ini.trakem2.display.Layer
getPath() - Method in class ini.trakem2.display.Tree.MeasurePathDistance
getPath() - Method in class ini.trakem2.display.Tree.NodePath
getPath(ImagePlus) - Static method in class ini.trakem2.persistence.Cache: Returns null if the ImagePlus was preprocessed or doesn't have an original FileInfo (which means the image does not come from a file).
getPath(Patch) - Method in class ini.trakem2.persistence.FSLoader: Returns the stored path for the given Patch image, which may be relative and may contain slice information appended.
getPath(Patch) - Method in class ini.trakem2.persistence.Loader: Returns null unless overriden.
getPathIterator(AffineTransform) - Method in class ini.trakem2.display.inspect.ShapeProxy
getPathIterator(AffineTransform, double) - Method in class ini.trakem2.display.inspect.ShapeProxy
getPaths(long) - Method in class ini.trakem2.display.AreaList: Returns an ArrayList of ArrayList of Point as value with all paths for the Area of the given layer_id.
getPathsCopy() - Method in class ini.trakem2.persistence.FSLoader
getPathsCopy() - Method in class ini.trakem2.persistence.Loader
getPeak() - Method in class ini.trakem2.imaging.PhaseCorrelationCalculator
getPerimeter() - Method in class ini.trakem2.display.Ball: The exact perimeter of this Ball, in integer precision.
getPerimeter() - Method in class ini.trakem2.display.Displayable: Subclasses can override this method to provide the exact contour, otherwise it returns the transformed bounding box of the data.
getPerimeter(int, int, int, int) - Method in class ini.trakem2.display.Displayable: Returns the perimeter enlarged in all West, North, East and South directions, in pixels.
getPerimeter() - Method in class ini.trakem2.display.DLabel
getPerimeter(int, int, int, int) - Method in class ini.trakem2.display.DLabel: Returns the perimeter enlarged in all West, North, East and South directions, in pixels.
getPerimeter() - Method in class ini.trakem2.display.Pipe: The exact perimeter of this pipe, in integer precision.
getPerimeter() - Method in class ini.trakem2.display.Polyline: The exact perimeter of this polyline, in integer precision.
getPerimeter() - Method in class ini.trakem2.display.Profile: The perimeter of this profile, in integer precision.
getPerimeter() - Method in class ini.trakem2.display.Stack: For now, just returns the bounding box---we can refine this later
getPerimeter2D() - Method in class ini.trakem2.display.Profile: Returns the interpolated points as a VectorString2D, calibrated.
getPixel(int, int) - Method in class ini.trakem2.display.FakeImagePlus
getPixel(int, int, double) - Method in class ini.trakem2.display.Layer: Don't use this for fast pixel grabbing; this is intended for the dropper tool and status bar reporting by mouse motion.
getPixel(double, int, int) - Method in class ini.trakem2.display.Patch: Magnification-dependent counterpart to ImageProcessor.getPixel(x, y).
getPixel(double, int, int, int[]) - Method in class ini.trakem2.display.Patch: Magnification-dependent counterpart to ImageProcessor.getPixel(x, y, iArray).
getPixel(int, int, double) - Method in class ini.trakem2.display.Patch: Expects x,y in world coordinates.
getPixel(int, int) - Method in class ini.trakem2.imaging.PatchStack
getPixels(int) - Method in class ini.trakem2.imaging.LayerStack: Returns the pixel array for the specified slice, where 1<=n<=nslices.
getPixelsMaxDimension() - Method in class ini.trakem2.display.LayerSet
getPlugins(String) - Method in class ini.trakem2.Project
getPointCount() - Method in class ini.trakem2.display.Profile: Returns the number of backbone points.
getPointsForSQL() - Method in class ini.trakem2.display.Ball: Return the list of query statements needed to insert all the points in the database.
getPointsForSQL() - Method in class ini.trakem2.display.Pipe: Return the list of query statements needed to insert all the points in the database.
getPolygons(Area) - Static method in class ini.trakem2.utils.M
getPopupItems(ActionListener) - Method in class ini.trakem2.tree.LayerThing
getPopupItems(ActionListener) - Method in class ini.trakem2.tree.ProjectThing
getPopupMenu() - Method in class ini.trakem2.display.Display: Return a context-sensitive popup menu.
getPos(int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray2D
getPos(int, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
getPos(int, int, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray4D
getPreferredSize() - Method in class ini.trakem2.imaging.ContrastPlot: Overrides Component getPreferredSize().
getPreprocessorScriptPath() - Method in class ini.trakem2.display.Patch
getPreprocessorScriptPath(Patch) - Method in class ini.trakem2.persistence.Loader
getPrintableTitle() - Method in class ini.trakem2.display.Layer: Returns a title such as 018__4-K4_2__z1.67 , which is [layer_set index]__[title]__[z coord] .
getProcessor() - Method in class ini.trakem2.display.FakeImagePlus: Returns the super, which is a dummy 4x4
getProcessor(int) - Method in class ini.trakem2.imaging.LayerStack: Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.
getProcessor(int) - Method in class ini.trakem2.imaging.LazyVirtualStack
getProcessor() - Method in class ini.trakem2.imaging.PatchStack
getProfileContent(Displayable) - Static method in class ini.trakem2.display.Display3D: Checks if the given Displayable is a Profile, and tries to find a possible Content object in the Image3DUniverse of its LayerSet according to the title as created from its profile_list ProjectThing.
getProject() - Method in interface ini.trakem2.display.Bucketable
getProject() - Method in interface ini.trakem2.display.Line3D
getProject() - Method in class ini.trakem2.display.Selection: Returns the Project of the Display, or if the latter is null, that of the first selected Displayable.
getProject() - Method in class ini.trakem2.persistence.DBObject
getProject(String) - Static method in class ini.trakem2.Project
getProjectData(boolean) - Method in class ini.trakem2.persistence.TMLHandler: returns 4 objects packed in an array:
getProjects() - Static method in class ini.trakem2.ControlWindow: Returns null if there are no projects
getProjects() - Method in class ini.trakem2.persistence.DBLoader: Fetch all existing projects from the database.
getProjects() - Static method in class ini.trakem2.Project: Return a copy of the list of all open projects.
getProjectTree() - Method in class ini.trakem2.Project
getProjectXMLPath() - Method in class ini.trakem2.persistence.FSLoader
getProperties() - Method in class ini.trakem2.display.Displayable: Returns a copy of this object's properties, or null if none.
getProperties() - Method in class ini.trakem2.imaging.PatchStack
getPropertiesCopy() - Method in class ini.trakem2.Project
getProperty(String) - Method in class ini.trakem2.display.Displayable: If key is null or not found, returns null; otherwise returns the stored value for key.
getProperty(String, String) - Method in class ini.trakem2.display.Displayable: If key is null or not found, returns default_value; otherwise returns the stored value for key.
getProperty(String) - Method in class ini.trakem2.imaging.PatchStack
getProperty(String) - Method in class ini.trakem2.Project: Returns null if not defined.
getProperty(String, float) - Method in class ini.trakem2.Project: Returns the default value if not defined, or if not a number or not parsable as a number.
getProperty(String, int) - Method in class ini.trakem2.Project
getProperty(Object) - Method in class ini.trakem2.utils.Worker
getProvider() - Static method in class ini.trakem2.parallel.ExecutorProvider
getQuicksortValue() - Method in interface mpi.fruitfly.math.Quicksortable
getRawBalls() - Method in class ini.trakem2.display.Ball: Returns the raw data for the balls, sorted by Layer ID versus double[]{z,y,r} .
getRepaintBounds() - Method in class ini.trakem2.display.AffineTransformMode
getRepaintBounds() - Method in class ini.trakem2.display.DefaultMode
getRepaintBounds() - Method in class ini.trakem2.display.GroupingMode
getRepaintBounds() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
getRepaintBounds() - Method in class ini.trakem2.display.ManualAlignMode
getRepaintBounds() - Method in interface ini.trakem2.display.Mode
getResult() - Method in class ini.trakem2.imaging.BinaryInterpolation2D
getResult() - Method in class ini.trakem2.utils.Worker: Returns data generated by the worker, or null if none was set.
getResultsTableTitle() - Method in class ini.trakem2.display.Tree.MeasurementPair
getRGBColorFromHex(String) - Static method in class ini.trakem2.utils.Utils
getRGBPixels() - Method in class ini.trakem2.imaging.FloatProcessorT2: Return the float array of pixels as a byte array, cropping (no scaling).
getRoi() - Method in class ini.trakem2.display.Display: Get the current Roi, if any.
getRoi() - Method in class ini.trakem2.imaging.PatchStack
getRoot() - Method in class ini.trakem2.analysis.Compare.Chain
getRoot() - Method in class ini.trakem2.display.Tree
getRoot() - Method in class ini.trakem2.tree.DNDTree
getRootLayerSet() - Method in class ini.trakem2.Project
getRootLayerThing(Project, ProjectThing, TemplateThing, TemplateThing) - Method in class ini.trakem2.persistence.DBLoader: Fetches the root LayerSet, fills it with children (recursively) and uses the profiles, pipes, etc., from the project_thing.
getRootLayerThing() - Method in class ini.trakem2.Project
getRootNode() - Method in class ini.trakem2.tree.DNDTree
getRootParent() - Method in class ini.trakem2.tree.ProjectThing: Crawl up until finding a parent that has no parent: the root.
getRootProjectThing(Project, TemplateThing, TemplateThing, HashMap<Long, Displayable>) - Method in class ini.trakem2.persistence.DBLoader: Get all the Thing objects, recursively, for the root, and their corresponding encapsulated objects.
getRootProjectThing() - Method in class ini.trakem2.Project
getRootTemplateThing() - Method in class ini.trakem2.Project
getRootThing() - Method in class ini.trakem2.tree.DNDTree
getRootThing() - Method in class ini.trakem2.tree.LayerTree
getRootThing() - Method in class ini.trakem2.tree.ProjectTree
getRootThing() - Method in class ini.trakem2.tree.TemplateTree
getRotX() - Method in class ini.trakem2.display.LayerSet
getRotY() - Method in class ini.trakem2.display.LayerSet
getRotZ() - Method in class ini.trakem2.display.LayerSet
getScaledBytePixels() - Method in class ini.trakem2.imaging.FloatProcessorT2
getScrollStep() - Method in class ini.trakem2.display.Display: The number of layers to scroll through with the wheel; 1 by default.
getSelected() - Static method in class ini.trakem2.display.Display: Return the list of selected Displayable objects of the front Display, or an emtpy list if no Display or none selected.
getSelected(Class<? extends Displayable>) - Static method in class ini.trakem2.display.Display: Return the list of selected Displayable objects of class @param c of the front Display, or an emtpy list if no Display or none selected.
getSelected() - Method in class ini.trakem2.display.Selection: Returns a copy of the list of all selected Displayables (and not their linked ones).
getSelected(Class<?>) - Method in class ini.trakem2.display.Selection: Returns a copy of the list of all selected Displayables (and not their linked ones) of the given class.
getSelectedSorted(Class<? extends Displayable>) - Method in class ini.trakem2.display.Selection: Returns the subset of selected objects of Class c, in the proper order according to the Layer.indexOf or the LayerSet.indexOf.
getSelection() - Method in class ini.trakem2.display.Display
getService(int) - Method in class ini.trakem2.parallel.DefaultExecutorProvider
getService(float) - Method in class ini.trakem2.parallel.DefaultExecutorProvider
getService(int) - Method in class ini.trakem2.parallel.ExecutorProvider
getService(float) - Method in class ini.trakem2.parallel.ExecutorProvider
getShortCellTitle() - Method in class ini.trakem2.analysis.Compare.Chain: Returns max 10 chars, solely the name of the parent's parent node of the root pipe (aka the [lineage] containing the [branch]) or the id if too long.
getShortMeaningfulTitle(Displayable) - Method in class ini.trakem2.Project: Returns the first upstream user-defined name and type, and the id of the displayable tagged at the end.
getShortMeaningfulTitle(ProjectThing, Displayable) - Method in class ini.trakem2.Project
getShortTitle() - Method in class ini.trakem2.display.Displayable
getShortTitle() - Method in class ini.trakem2.display.DLabel
getShortTitle() - Method in class ini.trakem2.display.Tree
getShortTitle() - Method in class ini.trakem2.persistence.DBObject: Sublcasses can override this method to provide a proper String, otherwise calls getTitle()
getSize() - Method in class ini.trakem2.imaging.LayerStack: Returns the number of slices in this stack.
getSize() - Method in class ini.trakem2.imaging.LazyVirtualStack
getSlabNodes() - Method in class ini.trakem2.display.Node: Returns a lazy read-only Collection of the nodes from this node up to the next branch node or end node, inclusive.
getSliceLabel(int) - Method in class ini.trakem2.imaging.LayerStack: Returns the file name of the Nth image.
getSnapshotsMode() - Method in class ini.trakem2.display.LayerSet
getSource() - Method in class ini.trakem2.display.AreaWrapper
getStack(int, double) - Method in class ini.trakem2.display.AreaList: Returns a stack of images representing the pixel data of this LayerSet inside this AreaList.
getStack() - Method in class ini.trakem2.display.FakeImagePlus: Returns a virtual stack made of boxes with the dimension of the ROI or the whole layer, so that pixels are retrieved on the fly.
getStack() - Method in class ini.trakem2.imaging.PatchStack
getStackCount() - Method in class ini.trakem2.display.FakeImagePlus: Returns 1.
getStackIndex(int, int, int) - Method in class ini.trakem2.imaging.PatchStack
getStackPatches() - Method in class ini.trakem2.display.Patch
getStackSize() - Method in class ini.trakem2.imaging.PatchStack
getStatistics(int, int, double, double) - Method in class ini.trakem2.display.FakeImagePlus
getStatistics(int, int, double, double) - Method in class ini.trakem2.imaging.PatchStack
getStorageFolder() - Method in class ini.trakem2.persistence.FSLoader: Return the folder selected by a user to store files into; it's also the parent folder of the UNUId folder, and the recommended folder to store the XML file into.
getStorageFolder() - Method in class ini.trakem2.persistence.Loader: Returns the user's home folder unless overriden.
getSubtreeNodes() - Method in class ini.trakem2.display.Node: Returns a lazy read-only Collection of the nodes belonging to the subtree of this node, including the node itself as the root.
getTabbedPane() - Method in class ini.trakem2.display.Display: Feel free to add more tabs.
getTabIndex(Project) - Static method in class ini.trakem2.ControlWindow: Returns -1 if not found.
getTags(int) - Method in class ini.trakem2.display.LayerSet: If there aren't any tags for keyCode, returns an empty TreeSet.
getTags() - Method in class ini.trakem2.display.Node
getTags() - Method in interface ini.trakem2.display.Taggable
getTargetCount() - Method in class ini.trakem2.display.Connector
getTargetPoints(boolean) - Method in class ini.trakem2.display.Connector
getTargets(Class<?>, boolean) - Method in class ini.trakem2.display.Connector
getTargets(Class<?>) - Method in class ini.trakem2.display.Connector: Returns the list of sets of visible Displayable objects under each target, or an empty list if none.
getTargets() - Method in class ini.trakem2.display.Connector: Returns the list of sets of visible Displayable objects under each target, or an empty list if none.
getTaskName() - Method in class ini.trakem2.utils.Bureaucrat: Returns the task the worker is currently executing, which may change over time.
getTaskName() - Method in class ini.trakem2.utils.Worker
getTemplate() - Method in class ini.trakem2.tree.ProjectThing
getTemplatePathTo(String) - Method in class ini.trakem2.tree.ProjectThing: Returns a list of parent types (String), in order, for the given Thing if it exists as a child in the traversed trees.
getTemplatePathTo(String, ArrayList<TemplateThing>) - Method in class ini.trakem2.tree.TemplateThing: Returns the list of parents to reach a particular child, starting at this, and including the child.
getTemplateRoot(Project) - Method in class ini.trakem2.persistence.DBLoader: Fetch the root of the TemplateThing tree from the database-stored hierarchy of TemplateThing objects defined in the original XML file .
getTemplateRoot() - Method in class ini.trakem2.tree.TrakEM2MLParser: Get the root node of the parsed XML template tree.
getTemplateThing(String) - Method in class ini.trakem2.Project: Returns the proper TemplateThing for the given type, complete with children and attributes if any.
getTemplateTree() - Method in class ini.trakem2.Project
getText() - Method in class ini.trakem2.utils.IntegerField
getThickness() - Method in class ini.trakem2.display.Layer
getThreadName() - Method in class ini.trakem2.utils.Worker
getTitle() - Method in class ini.trakem2.analysis.Compare.Chain
getTitle() - Method in class ini.trakem2.display.Displayable
getTitle() - Method in class ini.trakem2.display.Layer
getTitle() - Method in class ini.trakem2.imaging.PatchStack
getTitle() - Method in class ini.trakem2.persistence.DBObject: Sublcasses can override this method to provide a proper String, otherwise calls toString()
getTitle() - Method in class ini.trakem2.Project
getTitle() - Method in class ini.trakem2.tree.LayerThing: May be null or empty; call toString() to get a textual representation.
getTitle() - Method in class ini.trakem2.tree.ProjectThing
getTitle() - Method in interface ini.trakem2.tree.Thing
getToolId() - Static method in class ini.trakem2.utils.ProjectToolbar
getTransferData(DataFlavor) - Method in class ini.trakem2.tree.TransferableNode
getTransferDataFlavors() - Method in class ini.trakem2.tree.TransferableNode
getTransform(double[][], double[][], double[][]) - Method in class lenscorrection.Distortion_Correction
getTransformPropertiesCopy() - Method in class ini.trakem2.display.Patch
getTransparency() - Method in class ini.trakem2.display.paint.USHORTPaint
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class ini.trakem2.tree.DNDTree.NodeRenderer
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class ini.trakem2.tree.LayerTree.LayerThingNodeRender
getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class ini.trakem2.tree.ProjectTree.ProjectThingNodeRenderer
getTriangles(Volume, int) - Static method in class ini.trakem2.utils.MCCube: Create a list of triangles from the specified image data and the given isovalue.
getTriangles(ImagePlus, int, boolean[], int) - Method in class ini.trakem2.utils.MCTriangulator
getTriangles(Image<T>, int, float[]) - Method in class ini.trakem2.utils.MCTriangulator
getType() - Method in class ini.trakem2.display.DLabel
getType() - Method in class ini.trakem2.display.FakeImagePlus
getType() - Method in class ini.trakem2.display.Patch: Returns the ImagePlus type of this Patch.
getType() - Method in class ini.trakem2.imaging.LayerStack
getType() - Method in class ini.trakem2.imaging.PatchStack
getType(Class<?>) - Static method in class ini.trakem2.Project
getType() - Method in class ini.trakem2.tree.LayerThing
getType() - Method in class ini.trakem2.tree.ProjectThing
getType() - Method in class ini.trakem2.tree.TemplateThing
getType() - Method in interface ini.trakem2.tree.Thing
getUniqueIdentifier() - Method in class ini.trakem2.persistence.DBObject: Create a unique String identifier for this object instance.
getUniqueTypes() - Method in class ini.trakem2.Project: Returns a list of existing unique types in the template tree (thus the 'project' type is not included, nor the label).
getUniqueTypes(HashMap<String, TemplateThing>) - Method in class ini.trakem2.tree.TemplateThing: Recursive into children.
getUniverse() - Method in class ini.trakem2.display.d3d.Display3DGUI
getUniverse() - Method in class ini.trakem2.display.Display3D
getUNUId() - Method in class ini.trakem2.persistence.FSLoader
getUNUId() - Method in class ini.trakem2.persistence.Loader: Get the Universal Near-Unique Id for the project hosted by this loader.
getUNUId() - Method in class ini.trakem2.Project: Return the Universal Near-Unique Id of this project, which may be null for non-FSLoader projects.
getUNUIdFolder() - Method in class ini.trakem2.persistence.FSLoader: Returns the near-unique folder for the project hosted by this FSLoader.
getUNUIdFolder() - Method in class ini.trakem2.persistence.Loader
getUpdatePointForSQL(int) - Method in class ini.trakem2.display.Pipe
getValue() - Method in class ini.trakem2.analysis.Centrality.EtchingStep
getValue() - Method in class ini.trakem2.tree.TemplateThing
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.BooleanSetter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.ChoiceIntSetter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.ChoiceObjectSetter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.ChoiceStringSetter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.DoubleSetter
getValue(Component, int) - Method in class ini.trakem2.utils.OptionPanel.DoubleSetter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.FloatSetter
getValue(Component, int) - Method in class ini.trakem2.utils.OptionPanel.FloatSetter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.IntSetter
getValue(Component, int) - Method in class ini.trakem2.utils.OptionPanel.IntSetter
getValue(Component, int) - Method in class ini.trakem2.utils.OptionPanel.NumericalSetter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.Setter
getValue(Component) - Method in class ini.trakem2.utils.OptionPanel.StringSetter
getValue(K) - Method in class ini.trakem2.utils.TypedHashMap: Typed version of HashMap.get(Object).
getVirtualizationScale() - Method in class ini.trakem2.display.LayerSet: From 0.000...
getVirtualMatches() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
getWidth() - Method in class ini.trakem2.display.Displayable: Returns the width of the data.
getWidth() - Method in class ini.trakem2.display.FakeImagePlus
getWidth() - Method in class lenscorrection.NonLinearTransform
getWidth() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
getWorker() - Method in class ini.trakem2.utils.Bureaucrat
getWorldBalls() - Method in class ini.trakem2.display.Ball: Returns a [n_points][4] array, with x,y,z,radius on the second part, in world coordinates (that is, transformed with this AffineTransform and calibrated with the containing LayerSet's calibration).
getX() - Method in class ini.trakem2.display.Displayable: Returns the x of the bounding box.
getX() - Method in class ini.trakem2.display.Node
getXMLSafeValue(Map.Entry<String, String>, String) - Static method in class ini.trakem2.display.Displayable: Make sure the value is valid for an XML attribute content inside double quotes.
getXMLSafeValue(String) - Static method in class ini.trakem2.display.Displayable
getXPlane(int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
getXPlane_float(int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
getY() - Method in class ini.trakem2.display.Displayable: Returns the y of the bounding box.
getY() - Method in class ini.trakem2.display.Node
getYPlane(int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
getYPlane_float(int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
getZ() - Method in class ini.trakem2.display.Layer
getZDisplayables() - Method in class ini.trakem2.display.LayerSet: Returns a copy of the list of ZDisplayable objects.
getZDisplayables(Class<?>) - Method in class ini.trakem2.display.LayerSet
getZDisplayables(Class<?>, boolean) - Method in class ini.trakem2.display.LayerSet: Returns a list of ZDisplayable of class c only.
getZDisplayables(Class<?>, Layer, Area, boolean) - Method in class ini.trakem2.display.LayerSet: Deprecated.
getZDisplayables(Class<?>, Layer, Area, boolean, boolean) - Method in class ini.trakem2.display.LayerSet: Deprecated.
getZero(int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray2D
getZPlane(int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
getZPlane_float(int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
gLog(double, double) - Static method in class mpi.fruitfly.math.General
gLogInv(double, double) - Static method in class mpi.fruitfly.math.General
goHaveBreakfast() - Method in class ini.trakem2.utils.Bureaucrat: Starts the Bureaucrat thread: sets the worker to work and monitors it until it finishes.
grab(Rectangle, double, Class<?>, int, int, int) - Method in class ini.trakem2.display.Layer: Returns the region defined by the rectangle as an image in the type and format specified.
grab(int, int, Rectangle, double, Class<?>, int, int, int) - Method in class ini.trakem2.display.LayerSet: Returns the region defined by the rectangle as an image in the type and format specified.
grabPixels(BufferedImage) - Static method in class ini.trakem2.persistence.FSLoader: Returns the array of pixels, whose type depends on the bi.getType(); for example, for a BufferedImage.TYPE_BYTE_INDEXED, returns a byte[].
Graph - Class in ini.trakem2.analysis
Graph() - Constructor for class ini.trakem2.analysis.Graph
GraphicsSource - Interface in ini.trakem2.display.graphics
GRAY_LUT - Static variable in class ini.trakem2.persistence.Loader: Whether incremental garbage collection is enabled.
GREEN - Static variable in class ini.trakem2.display.Channel
GREY - Static variable in class ini.trakem2.display.SnapshotPanel
GREY - Static variable in class ini.trakem2.io.RagMipMaps: These are both the 4 supported types and the number of channels that each type has.
GREY - Static variable in class ini.trakem2.io.RawMipMaps: These are both the 4 supported types and the number of channels that each type has.
GREY_ALPHA - Static variable in class ini.trakem2.io.RagMipMaps: These are both the 4 supported types and the number of channels that each type has.
GREY_ALPHA - Static variable in class ini.trakem2.io.RawMipMaps: These are both the 4 supported types and the number of channels that each type has.
gridoverlay - Variable in class ini.trakem2.display.Display
GridOverlay() - Constructor for class ini.trakem2.display.Display.GridOverlay
GroupedGraphicsSource() - Constructor for class ini.trakem2.display.GroupingMode.GroupedGraphicsSource
GroupingMode - Class in ini.trakem2.display
GroupingMode(Display, List<Displayable>) - Constructor for class ini.trakem2.display.GroupingMode
GroupingMode.GroupedGraphicsSource - Class in ini.trakem2.display
GroupingMode.Painter - Class in ini.trakem2.display
GroupingMode.PatchRange - Class in ini.trakem2.display
GroupingMode.ScreenPatchRange<T> - Class in ini.trakem2.display
GroupingMode.SimpleThread - Class in ini.trakem2.display
gs - Variable in class ini.trakem2.display.GroupingMode
GUI(Collection<Patch>, Patch) - Static method in class ini.trakem2.imaging.filters.FilterEditor

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halfSizeInPlace() - Method in class ini.trakem2.imaging.FloatProcessorT2: Resizes this FloatProcessorT2 instance by a factor of two by picking simply all pixels at even coordinates.
handleCacheError(Throwable) - Method in class ini.trakem2.persistence.Loader: Must be called within the context of the db_lock.
handlePathlessImage(ImagePlus) - Method in class ini.trakem2.persistence.FSLoader: Returns the path where the imp is saved to: the storage folder plus a name.
handlePathlessImage(ImagePlus) - Method in class ini.trakem2.persistence.Loader
handlePopupMenu() - Method in class ini.trakem2.display.DisplayCanvas: Overriding to disable it.
handleUpdateGraphics(Component, Rectangle) - Method in class ini.trakem2.display.AbstractRepaintThread: Child classes need to extend this method for handling the need of recreating offscreen images.
hasAlphaChannel() - Method in class ini.trakem2.display.Patch: Whether there is an alpha mask or there is an outside mask caused by a CoordinateTransform.
hasAlphaMask() - Method in class ini.trakem2.display.Patch: Whether there is an alpha mask for the pixel data.
hasChanges() - Method in class ini.trakem2.persistence.DBLoader: Always returns false.
hasChanges() - Method in class ini.trakem2.persistence.Loader: Whether any changes need to be saved.
hasChildren() - Method in class ini.trakem2.display.Node
hasChildren() - Method in class ini.trakem2.tree.LayerThing
hasChildren() - Method in class ini.trakem2.tree.ProjectThing
hasChildren() - Method in class ini.trakem2.tree.TemplateThing
hasChildren() - Method in interface ini.trakem2.tree.Thing
hasCoordinateTransform() - Method in class ini.trakem2.display.Patch
hashCode() - Method in class ini.trakem2.display.DisplayCanvas.ScreenshotProperties
hasKey(K) - Method in class ini.trakem2.utils.TypedHashMap: Typed version of HashMap.containsKey(Object).
hasLinkedGroupWithinLayer(Layer) - Method in class ini.trakem2.display.Displayable
hasNext() - Method in class ini.trakem2.display.Node.FilteredIterator
hasNext() - Method in class ini.trakem2.display.Node.NodeIterator
hasNext() - Method in class ini.trakem2.display.Node.SubtreeIterator
hasParent(String) - Method in class ini.trakem2.tree.ProjectThing: Check if this or any of its parents are of the given type.
hasPoints() - Method in class ini.trakem2.display.Profile
hasProperties() - Method in class ini.trakem2.display.Displayable
hasQuitted() - Method in class ini.trakem2.utils.Worker
hasSameTags(Node<?>) - Method in class ini.trakem2.display.Node
hasStarted() - Method in class ini.trakem2.utils.Worker
hasTag(Tag) - Method in class ini.trakem2.display.Node
hasValue(V) - Method in class ini.trakem2.utils.TypedHashMap: Typed version of HashMap.containsValue(Object).
HEADER_SIZE - Static variable in class ini.trakem2.io.RagMipMaps: Two 4-byte ints, for width and height, and one byte for the type.
HEADER_SIZE - Static variable in class ini.trakem2.io.RawMipMaps: Two 4-byte ints, for width and height, and one byte for the type.
HEIGHT - Static variable in class ini.trakem2.display.Channel
height - Variable in class ini.trakem2.display.Displayable.DataPackage
height - Variable in class ini.trakem2.display.Displayable: Width and height of the data, not the bounding box.
HEIGHT - Static variable in class ini.trakem2.display.DisplayablePanel
height - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam: In pixels, of the the underlying image to copy around the mouse.
height - Variable in class ini.trakem2.io.ImageFileHeader
height - Variable in class ini.trakem2.persistence.ImageBytes
height - Variable in class mpi.fruitfly.math.datastructures.FloatArray2D
height - Variable in class mpi.fruitfly.math.datastructures.FloatArray3D
hide() - Method in class ini.trakem2.imaging.PatchStack
hide_disconnected - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
hideDeselected(boolean) - Method in class ini.trakem2.display.Display
hideDisconnectedTiles - Static variable in class mpicbg.trakem2.align.AlignTask
hideExcept(ArrayList<Class<?>>, boolean) - Method in class ini.trakem2.display.Layer: Hide all except those whose type is in 'type' list, whose visibility flag is left unchanged.
hideExcept(ArrayList<Class<?>>, boolean) - Method in class ini.trakem2.display.LayerSet: Hide all except those whose type is in 'type' list, whose visibility flag is left unchanged.
high_frequency_threshold - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
History - Class in ini.trakem2.utils: A class to represent a generic undo/redo history.
History() - Constructor for class ini.trakem2.utils.History: New unlimited history list.
History(int) - Constructor for class ini.trakem2.utils.History
History.Step<T> - Interface in ini.trakem2.utils
hs_linked - Variable in class ini.trakem2.display.Displayable: The Displayable objects this one is linked to.
hs_unloadable - Variable in class ini.trakem2.persistence.Loader

I

id - Variable in class ini.trakem2.persistence.DBObject
identityConnect(Tile<?>, Tile<?>, double) - Static method in class org.janelia.intensity.MatchIntensities
identityTolerance - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
identityTolerance - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
identityTolerance - Variable in class mpicbg.trakem2.align.Align.Param
IFilter - Interface in ini.trakem2.imaging.filters
IJError - Class in ini.trakem2.utils: A class to easily show the stack trace of an error in different operating systems.
IJError() - Constructor for class ini.trakem2.utils.IJError
IMAGE - Static variable in class ini.trakem2.display.Layer
image - Variable in class ini.trakem2.display.MipMapImage
ImageArrayConverter - Class in mpi.fruitfly.general
ImageArrayConverter() - Constructor for class mpi.fruitfly.general.ImageArrayConverter
ImageBytes - Class in ini.trakem2.persistence: Represent an image with byte arrays: 1 channel: grey 2 channels: grey + alpha 3 channels: RGB 4 channels: RGBA
ImageBytes(byte[][], int, int) - Constructor for class ini.trakem2.persistence.ImageBytes
imageClosed(ImagePlus) - Method in class ini.trakem2.display.Display
ImageData - Interface in ini.trakem2.display: An interface to label Displayable objects as containing images.
ImageData(ByteProcessor, ByteProcessor, double, double) - Constructor for class mpicbg.trakem2.transform.ExportUnsignedByte.ImageData
ImageFileFilter - Class in ini.trakem2.io: Filters out non-accepted image formats.
ImageFileFilter() - Constructor for class ini.trakem2.io.ImageFileFilter
ImageFileFilter(String, String) - Constructor for class ini.trakem2.io.ImageFileFilter
ImageFileHeader - Class in ini.trakem2.io
ImageFileHeader(String) - Constructor for class ini.trakem2.io.ImageFileHeader: Reads the header of the image file at filepath using an IFormatReader from the bio-formats library, and then extracts the {link #width}, ImageFileHeader.height and ImageFileHeader.type of the image.
ImageFilter - Class in mpi.fruitfly.registration: Title: ImageFilter.
ImageFilter() - Constructor for class mpi.fruitfly.registration.ImageFilter
ImageJCommandListener - Class in ini.trakem2.display: Intercept ImageJ menu commands if the current active image is a FakeImagePlus (from a ini.trakem2.display.Display.)
ImageJCommandListener() - Constructor for class ini.trakem2.display.ImageJCommandListener
imageOpened(ImagePlus) - Method in class ini.trakem2.display.Display
IMAGEPLUS - Static variable in class ini.trakem2.display.Layer
ImagePreprocessor - Interface in ini.trakem2.imaging: Any class implementing this interface is suitable as an image preprocessor for a TrakEM2 project.
IMAGEPROCESSOR - Static variable in class ini.trakem2.display.Layer
ImageSaver - Class in ini.trakem2.io: Provides the necessary thread-safe image file saver utilities.
ImageToDoubleArray1D(ImageProcessor) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ImageToDoubleArray1DZeroPadding(ImageProcessor, int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
imageToFloatAndMask(Image, FloatProcessor, FloatProcessor) - Static method in class mpicbg.trakem2.align.Util: Transfer and ARGB AWT image into a FloatProcessor with its grey values and a FloatProcessor with its alpha values as [0...1].
ImageToFloatArray2D(ImageProcessor) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ImageToFloatArray2DDeprecated(ImageProcessor) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ImageToFloatArray2DZeroPadding(ImageProcessor, int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
ImageToIntArray(ImageProcessor) - Static method in class mpi.fruitfly.general.ImageArrayConverter
img1 - Variable in class mpi.fruitfly.registration.CrossCorrelation2D
img2 - Variable in class mpi.fruitfly.registration.CrossCorrelation2D
ImgLibVolume<T extends RealType<T>> - Class in ini.trakem2.utils: This class encapsulates an mpicbg.imglib.Image object, for use in Marching Cubes.
ImgLibVolume(Image<T>, float[]) - Constructor for class ini.trakem2.utils.ImgLibVolume
importAmiraLabels(Layer, double, double, String) - Static method in class ini.trakem2.io.AmiraImporter: Returns the array of AreaList or null if the file dialog is canceled.
importGrid(Layer) - Method in class ini.trakem2.persistence.Loader
importGrid(Layer, String) - Method in class ini.trakem2.persistence.Loader: Import a grid of images and put them in the layer.
importImage() - Method in class ini.trakem2.display.Display
importImage(Layer, double, double, String, boolean) - Method in class ini.trakem2.persistence.Loader: Import an image into the given layer, in a separate task thread.
importImage(Project, double, double) - Method in class ini.trakem2.persistence.Loader
importImage(Project, double, double, String, boolean) - Method in class ini.trakem2.persistence.Loader: Import a new image at the given coordinates; does not puts it into any layer, unless it's a stack -in which case importStack is called with the current front layer of the given project as target.
importImages(Layer) - Method in class ini.trakem2.persistence.Loader
importImages(Layer, String, String, double, double, boolean, float, int) - Method in class ini.trakem2.persistence.Loader: Import images from the given text file, which is expected to contain 4 columns or optionally 9 columns:
importLabelsAsAreaLists(Layer) - Method in class ini.trakem2.persistence.Loader
importLabelsAsAreaLists(Layer, String, double, double, float, boolean) - Method in class ini.trakem2.persistence.Loader: If base_x or base_y are Double.MAX_VALUE, then those values are asked for in a GenericDialog.
importLandmarks() - Method in class ini.trakem2.display.ManualAlignMode: Import landmarks from XML file.
importNextImage() - Method in class ini.trakem2.display.Display
importNextImage(Project, double, double) - Method in class ini.trakem2.persistence.Loader
importSequenceAsGrid(Layer) - Method in class ini.trakem2.persistence.Loader
importSequenceAsGrid(Layer, String) - Method in class ini.trakem2.persistence.Loader
importSequenceAsGrid(Layer, String, String[]) - Method in class ini.trakem2.persistence.Loader: Import a sequence of images as a grid, and put them in the layer.
importStack(Layer, ImagePlus, boolean) - Method in class ini.trakem2.persistence.Loader
importStack(Layer, ImagePlus, boolean, String) - Method in class ini.trakem2.persistence.Loader
importStack(Layer, double, double, ImagePlus, boolean, String, boolean) - Method in class ini.trakem2.persistence.Loader: Imports an image stack from a multitiff file and places each slice in the proper layer, creating new layers as it goes.
importStackAsPatches(Project, Layer, double, double, ImagePlus, boolean, String) - Method in class ini.trakem2.persistence.DBLoader: Returns the last Patch.
importStackAsPatches(Project, Layer, double, double, ImagePlus, boolean, String) - Method in class ini.trakem2.persistence.FSLoader: Returns the last Patch.
importStackAsPatches(Project, Layer, ImagePlus, boolean, String) - Method in class ini.trakem2.persistence.Loader
importStackAsPatches(Project, Layer, double, double, ImagePlus, boolean, String) - Method in class ini.trakem2.persistence.Loader
importTags(String, boolean) - Method in class ini.trakem2.display.LayerSet
include_coordinate_transform - Variable in class ini.trakem2.persistence.XMLOptions: If true, then Patch.exportXML(StringBuilder, String, XMLOptions) will write the @{link CoordinateTransform} XML into the XML file.
index - Static variable in class ini.trakem2.display.Polyline: Helper vars for mouse events.
index() - Method in class ini.trakem2.utils.History
indexAtEnd() - Method in class ini.trakem2.utils.History
indexAtStart() - Method in class ini.trakem2.utils.History
indexOf(Displayable) - Method in class ini.trakem2.display.Layer: Returns -1 if not found.
indexOf(Layer) - Method in class ini.trakem2.display.LayerSet: From zero to size-1.
indexOf(ZDisplayable) - Method in class ini.trakem2.display.LayerSet: Returns the reverse index of ZDisplayable zd, which is the actual index as seen in the screen.
indexOf(LayerThing) - Method in class ini.trakem2.tree.LayerThing
indexOf(Object, Object[]) - Static method in class ini.trakem2.utils.Utils
infiniteArea() - Static method in class ini.trakem2.utils.AreaUtils
ini.trakem2 - package ini.trakem2
ini.trakem2.analysis - package ini.trakem2.analysis
ini.trakem2.display - package ini.trakem2.display
ini.trakem2.display.d3d - package ini.trakem2.display.d3d
ini.trakem2.display.graphics - package ini.trakem2.display.graphics
ini.trakem2.display.inspect - package ini.trakem2.display.inspect
ini.trakem2.display.paint - package ini.trakem2.display.paint
ini.trakem2.imaging - package ini.trakem2.imaging
ini.trakem2.imaging.filters - package ini.trakem2.imaging.filters
ini.trakem2.io - package ini.trakem2.io
ini.trakem2.parallel - package ini.trakem2.parallel
ini.trakem2.persistence - package ini.trakem2.persistence
ini.trakem2.plugin - package ini.trakem2.plugin
ini.trakem2.scripting - package ini.trakem2.scripting
ini.trakem2.tree - package ini.trakem2.tree
ini.trakem2.utils - package ini.trakem2.utils
init(String) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform: Initialize cubic B-spline transform from the parameters of a string
init() - Method in class ini.trakem2.display.d3d.Display3DGUI
init() - Static method in class ini.trakem2.display.Display3D
init(String[]) - Method in class ini.trakem2.display.Displayable.DoEdits
init() - Method in class ini.trakem2.display.DisplayCanvas.Screenshot
init(int, int, int) - Method in class ini.trakem2.utils.MCCube: initializes a MCCube object _________ 0______x /v0 v1/| /| /________/ | / | |v3 v2| /v5 y/ |z |________|/ v7 v6
initLoader() - Method in class ini.trakem2.utils.ImgLibVolume: Create the image cursor anew.
initModel() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
initModel() - Method in class mpicbg.trakem2.align.AffineTile2D
initModel() - Method in class mpicbg.trakem2.align.GenericAffineTile2D
initModel() - Method in class mpicbg.trakem2.align.RigidTile2D: Initialize the model with the parameters of the AffineTransform of the Patch.
initModel() - Method in class mpicbg.trakem2.align.SimilarityTile2D: Initialize the model with the parameters of the AffineTransform of the Patch.
initModel() - Method in class mpicbg.trakem2.align.TranslationTile2D: Initialize the model with the parameters of the AffineTransform of the Patch.
initThreads() - Method in class ini.trakem2.display.GroupingMode
insertBetween(int, int, double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
insertNode(Node<T>, Node<T>, Node<T>, byte) - Method in class ini.trakem2.display.Tree
insertPoint(int, int, int, long) - Method in class ini.trakem2.display.Polyline
insertSegmentations(Collection<? extends Displayable>) - Method in class ini.trakem2.tree.ProjectTree: Creates a new node of basic type for each AreaList, Ball, Pipe or Polyline present in the ArrayList.
insertXMLOptions(StringBuilder, String) - Method in class ini.trakem2.persistence.FSLoader: Specific options for the Loader which exist as attributes to the Project XML node.
insertXMLOptions(StringBuilder, String) - Method in class ini.trakem2.persistence.Loader
inspector - Variable in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
InspectPatchTrianglesMode - Class in ini.trakem2.display.inspect: A view-only mode that shows, using LayerSet.getOverlay(), the triangle of the transform mesh in the Patch under the cursor.
InspectPatchTrianglesMode(Display) - Constructor for class ini.trakem2.display.inspect.InspectPatchTrianglesMode
InspectPatchTrianglesMode.Inspector - Class in ini.trakem2.display.inspect
IntegerField - Class in ini.trakem2.utils
IntegerField(int, int) - Constructor for class ini.trakem2.utils.IntegerField
IntegralHistogram2d - Class in ini.trakem2.imaging: An integral histogram for 2d images.
IntegralHistogram2d() - Constructor for class ini.trakem2.imaging.IntegralHistogram2d
integralHistogram2d(short[], int, int, int, double, double) - Static method in class ini.trakem2.imaging.IntegralHistogram2d: Returns a byte[] of dimensions (width + 1) * (height + 1) * nBins, representing the integral histogram of the 2d image.
IntegralImageMipMaps - Class in ini.trakem2.persistence
IntegralImageMipMaps() - Constructor for class ini.trakem2.persistence.IntegralImageMipMaps
interpolate(Layer, Layer, boolean) - Method in class ini.trakem2.display.AreaList: Interpolate areas between the given first and last layers, both of which must contain an area.
interpolateAllGaps(boolean, boolean) - Method in class ini.trakem2.display.AreaTree: Processes shorter chains first.
interpolateTowardsParent(Node<Area>, boolean, boolean) - Method in class ini.trakem2.display.AreaTree: Find the nearest parent with a non-null, non-empty Area, and interpolate from nd to it.
interpolatorFactory - Variable in class org.janelia.intensity.LinearIntensityMap
INTERRUPTED - Static variable in class ini.trakem2.imaging.StitchingTEM
intersects(Layer, Rectangle) - Method in class ini.trakem2.display.AreaList
intersects(Layer, Area) - Method in class ini.trakem2.display.AreaList
intersects(Area, double, double) - Method in class ini.trakem2.display.AreaList
intersects(Area) - Method in class ini.trakem2.display.AreaTree.AreaNode: Expects @param a in local coords.
intersects(Area, double, double) - Method in class ini.trakem2.display.Ball
intersects(Area) - Method in class ini.trakem2.display.Connector.ConnectorNode
intersects(Displayable) - Method in class ini.trakem2.display.Displayable: Check if this perimeter's intersects that of the given Displayable.
intersects(Area) - Method in class ini.trakem2.display.Displayable
intersects(Layer, Area) - Method in class ini.trakem2.display.Displayable: Calls intersects(area) unless overriden -- intended for ZDisplayable objects to return whether they intersect the given area at the given layer.
intersects(Layer, Rectangle) - Method in class ini.trakem2.display.Displayable
intersects(Area, double, double) - Method in class ini.trakem2.display.Dissector
intersects(double, double, double, double) - Method in class ini.trakem2.display.inspect.ShapeProxy
intersects(Rectangle2D) - Method in class ini.trakem2.display.inspect.ShapeProxy
intersects(Area) - Method in class ini.trakem2.display.Node: Expects Area in local coords.
intersects(Displayable, boolean) - Method in class ini.trakem2.display.Patch
intersects(Displayable) - Method in class ini.trakem2.display.Patch
intersects(Area, double, double) - Method in class ini.trakem2.display.Pipe
intersects(Layer, Rectangle) - Method in class ini.trakem2.display.Pipe: Expects Rectangle in world coords.
intersects(Layer, Area) - Method in class ini.trakem2.display.Pipe: Expects Area in world coords.
intersects(Area, double, double) - Method in class ini.trakem2.display.Polyline
intersects(Area, double, double) - Method in class ini.trakem2.display.Stack
intersects(Area, double, double) - Method in class ini.trakem2.display.Tree
intersects(Layer, Rectangle) - Method in class ini.trakem2.display.Tree: Expects Rectangle in world coords.
intersects(Layer, Area) - Method in class ini.trakem2.display.Tree: Expects Area in world coords.
intersects(Area) - Method in class ini.trakem2.display.Treeline.RadiusNode: Expects @param a in local coords.
intersects(Area, double, double) - Method in class ini.trakem2.display.ZDisplayable
intersects(Area, Area) - Static method in class ini.trakem2.utils.M: Test whether the areas intersect each other.
intersects(AbstractAffineTile2D<?>, boolean) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
intersects(AbstractAffineTile2D<?>) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
intersectsOrigin(Area, Layer) - Method in class ini.trakem2.display.Connector
intersectsOrigin(double, double, Layer) - Method in class ini.trakem2.display.Connector: Whether the area of the root node intersects the world coordinates wx, wy at Layer la.
IntSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.IntSetter
IntSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.IntSetter
IntSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.IntSetter
invalidateVolatile() - Method in class ini.trakem2.display.DisplayCanvas
invalidateVolatile() - Method in class ini.trakem2.display.DisplayNavigator
inverseTransform(AffineTransform, double, double) - Static method in class ini.trakem2.utils.M
inverseTransform(double[][]) - Method in class lenscorrection.NonLinearTransform
inverseTransformPoint(double, double) - Method in class ini.trakem2.display.Displayable
Invert - Class in ini.trakem2.imaging.filters
Invert() - Constructor for class ini.trakem2.imaging.filters.Invert
Invert(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.Invert
invertLookupTable() - Method in class ini.trakem2.imaging.PatchStack
invoke(Object...) - Method in interface ini.trakem2.plugin.TPlugIn: Run the plugin directly.
invoke(Object...) - Method in class org.janelia.intensity.MatchIntensities
invokeLater(Runnable) - Static method in class ini.trakem2.utils.Utils: Invoke in the context of the event dispatch thread.
ip - Variable in class mpicbg.trakem2.util.RobustNormalizeLocalContrast.ByteSetter
ip - Variable in class mpicbg.trakem2.util.RobustNormalizeLocalContrast.FloatSetter
ip - Variable in class mpicbg.trakem2.util.RobustNormalizeLocalContrast.ShortSetter
isActive() - Method in class ini.trakem2.display.Channel
isActive() - Method in class ini.trakem2.utils.Bureaucrat
isActiveWindow() - Method in class ini.trakem2.display.Display
isAligned - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
isAligned - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
isAnyNear(Collection<Node<Area>>, float, float, float) - Method in class ini.trakem2.display.AreaTree: Returns true if the given point falls within a certain distance of any of the treeline segments, where a segment is defined as the line between a clicked point and the next.
isAnyNear(Collection<Node<T>>, float, float, float) - Method in class ini.trakem2.display.Tree
isApproxEqual(double, double, double) - Static method in class mpi.fruitfly.math.General
isAreaROI(Roi) - Static method in class ini.trakem2.utils.M: Returns true if the roi is of closed shape type like an OvalRoi, ShapeRoi, a Roi rectangle, etc.
isAsynchronous() - Method in class ini.trakem2.persistence.Loader: Test whether this Loader needs recurrent calls to a "save" of some sort, such as for the FSLoader.
isBasicType(String) - Static method in class ini.trakem2.Project: Returns true if the type is 'patch', 'layer', 'layer_set', 'profile', 'profile_list' 'pipe'.
isBeingDestroyed() - Method in class ini.trakem2.Project
isBetter(Rectangle, Bucketable) - Method in class ini.trakem2.display.Bucket: Determine whether the rectangle is smaller than the layer dimensions padded in by one bucket_side -- if not, makes little sense to use buckets, and it's better to do linear search without the TreeMap overhead.
isBottom(Displayable) - Method in class ini.trakem2.display.Layer: Within its own class only.
isBottom(ZDisplayable) - Method in class ini.trakem2.display.LayerSet
isBottom(Displayable) - Method in class ini.trakem2.display.LayerSet: Hub method: ZDisplayable or into the Displayable's Layer.
isBranching() - Method in class ini.trakem2.analysis.Vertex
isCached(Patch, double) - Method in class ini.trakem2.persistence.Loader: Returns true if there is a cached awt image for the given mag and Patch id.
isCalibrated() - Method in class ini.trakem2.display.LayerSet
isCancelled() - Method in class ini.trakem2.utils.TaskOnEDT
isClosed() - Method in class ini.trakem2.display.FakeImageWindow
isClosed() - Method in class ini.trakem2.display.Profile
isConnected() - Method in class ini.trakem2.persistence.DBLoader: Find out whether the connection is up.
isControlDown(InputEvent) - Static method in class ini.trakem2.utils.Utils: The CTRL key functionality is passed over to the COMMAND key (aka META key) in a MacOSX.
isDataEditTool(int) - Static method in class ini.trakem2.utils.ProjectToolbar
isDataFlavorSupported(DataFlavor) - Method in class ini.trakem2.tree.TransferableNode
isDeletable() - Method in class ini.trakem2.display.AreaList
isDeletable() - Method in class ini.trakem2.display.Ball
isDeletable() - Method in class ini.trakem2.display.Displayable
isDeletable() - Method in class ini.trakem2.display.Dissector
isDeletable() - Method in class ini.trakem2.display.DLabel
isDeletable() - Method in class ini.trakem2.display.LayerSet
isDeletable() - Method in class ini.trakem2.display.Patch
isDeletable() - Method in class ini.trakem2.display.Pipe
isDeletable() - Method in class ini.trakem2.display.Polyline
isDeletable() - Method in class ini.trakem2.display.Profile
isDeletable() - Method in class ini.trakem2.display.Stack
isDeletable() - Method in class ini.trakem2.display.Tree
isDisplayed(Displayable) - Static method in class ini.trakem2.display.Display3D: Checks if there is any Display3D instance currently showing the given Displayable.
isDone() - Method in class ini.trakem2.utils.TaskOnEDT
isDragging() - Method in class ini.trakem2.display.AffineTransformMode
isDragging() - Method in class ini.trakem2.display.ContrastAdjustmentMode
isDragging() - Method in class ini.trakem2.display.DefaultMode
isDragging() - Method in class ini.trakem2.display.DisplayCanvas
isDragging() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
isDragging() - Method in class ini.trakem2.display.ManualAlignMode
isDragging() - Method in interface ini.trakem2.display.Mode
isDragging() - Method in class ini.trakem2.display.NonLinearTransformMode
isEmpty() - Method in class ini.trakem2.display.Displayable.DoEdit
isEmpty() - Method in class ini.trakem2.display.Displayable.DoEdits
isEmpty() - Method in class ini.trakem2.display.Displayable.DoTransforms
isEmpty() - Method in interface ini.trakem2.display.DoStep
isEmpty() - Method in class ini.trakem2.display.Layer.DoMoveDisplayable
isEmpty() - Method in class ini.trakem2.display.Layer: Checks if there are any Displayable or if any ZDisplayable paints in this layer.
isEmpty() - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
isEmpty() - Method in class ini.trakem2.display.LayerSet.DoMoveZDisplayable
isEmpty() - Method in class ini.trakem2.display.Node.NodeCollection: Override to avoid calling size().
isEmpty() - Method in class ini.trakem2.display.Selection
isEmpty() - Method in class ini.trakem2.display.TransformationStep
isEmpty() - Method in class ini.trakem2.tree.RenameThingStep
isEmpty() - Method in class ini.trakem2.utils.FieldMapView
isEmpty() - Method in interface ini.trakem2.utils.History.Step
isEmpty(Area) - Static method in class ini.trakem2.utils.M
isEmptyAt(Layer) - Method in class ini.trakem2.display.LayerSet
isEnding() - Method in class ini.trakem2.analysis.Vertex
isExpanded(Thing) - Method in class ini.trakem2.tree.DNDTree: Check if there is a node holding the given Thing, and whether such node is expanded.
isExpanded(DefaultMutableTreeNode) - Method in class ini.trakem2.tree.DNDTree
isExpanded() - Method in class ini.trakem2.tree.LayerThing
isExpanded() - Method in class ini.trakem2.tree.ProjectThing
isExpanded() - Method in class ini.trakem2.tree.TemplateThing
isExpanded() - Method in interface ini.trakem2.tree.Thing
isFillPaint() - Method in class ini.trakem2.display.AreaList
isGUIEnabled() - Static method in class ini.trakem2.ControlWindow
isHSB() - Method in class ini.trakem2.imaging.LayerStack: Override: always false.
isIdentical(History.Step<?>) - Method in class ini.trakem2.display.TransformationStep
isIdentical(History.Step<?>) - Method in interface ini.trakem2.utils.History.Step
isIdenticalProjectSource(Loader) - Method in class ini.trakem2.persistence.DBLoader
isIdenticalTo(Object) - Method in class ini.trakem2.display.Displayable.DoEdit
isIdenticalTo(Object) - Method in class ini.trakem2.display.Displayable.DoEdits
isIdenticalTo(Object) - Method in class ini.trakem2.display.Displayable.DoTransforms
isIdenticalTo(Object) - Method in interface ini.trakem2.display.DoStep
isIdenticalTo(Object) - Method in class ini.trakem2.display.Layer.DoMoveDisplayable
isIdenticalTo(Object) - Method in class ini.trakem2.display.LayerSet.DoChangeTrees
isIdenticalTo(Object) - Method in class ini.trakem2.display.LayerSet.DoMoveZDisplayable
isIdenticalTo(Object) - Method in class ini.trakem2.tree.RenameThingStep
isImagePlusCached(Patch) - Method in class ini.trakem2.persistence.Loader
isInputEnabled() - Method in class ini.trakem2.display.DisplayCanvas
isInputEnabled() - Method in class ini.trakem2.Project
isInvalidTypeName(String) - Method in class ini.trakem2.tree.TemplateTree: Returns true if @param type conforms with ^[a-zA-Z][a-zA-Z0-9_]*$
isInvertedLut() - Method in class ini.trakem2.imaging.PatchStack
isLayerSetType(String) - Static method in class ini.trakem2.Project
isLayerType(String) - Static method in class ini.trakem2.Project
isLinked() - Method in class ini.trakem2.display.Displayable: Check if this object is directly linked to any other Displayable objects.
isLinked(Class<?>) - Method in class ini.trakem2.display.Displayable: Check if this object is directly linked to a Displayable object of the given Class.
isLinked(Displayable) - Method in class ini.trakem2.display.Displayable: Check if thisobject is directly linked to the given Displayable.
isLinked() - Method in class ini.trakem2.display.Profile: Returns true if it's linked to at least one patch in the same Layer.
isLiveFilteringEnabled() - Method in class ini.trakem2.display.Display
isLocked() - Method in class ini.trakem2.display.Displayable: Check if this or any of the Displayables in the linked group is locked.
isLocked() - Method in class ini.trakem2.display.Selection: Test if any of the selection objects is directly or indirectly locked.
isLocked2() - Method in class ini.trakem2.display.Displayable: Return the value of the field 'locked'.
isMipMapsRegenerationEnabled() - Method in class ini.trakem2.persistence.Loader: Whether mipmaps should be generated.
isNested() - Method in class ini.trakem2.tree.TemplateThing: Determine whether this instance is nested inside the tree of an instance of the same type (for example, a neurite_branch inside another neurite_branch)
isOnlyLinkedTo(Class<?>) - Method in class ini.trakem2.display.Displayable: Check if this object is directly linked only to Displayable objects of the given class (returns true) or to none (returns true as well).
isOnlyLinkedTo(Class<?>, Layer) - Method in class ini.trakem2.display.Displayable: Check if this object is directly linked only to Displayable objects of the given class in the same layer (returns true).
isOutOfRepaintingClip(double, Rectangle, Rectangle) - Method in class ini.trakem2.display.Displayable
isOutOfRepaintingClip(Rectangle, double) - Method in class ini.trakem2.display.Displayable: For the DisplayNavigator.
isPainted(Displayable) - Method in class ini.trakem2.display.DisplayNavigator: Returns true if the given Displayable has been painted as an image and false if as a box or not at all.
isPartiallyWithinViewport(Displayable) - Method in class ini.trakem2.display.Display: Check if a panel for the given Displayable is partially visible in the JScrollPane
isPixelsVirtualizationEnabled() - Method in class ini.trakem2.display.LayerSet
isPopupTrigger(MouseEvent) - Static method in class ini.trakem2.utils.Utils: OS-agnostic diagnosis of whether the click was for the contextual popup menu.
isPreprocessed() - Method in class ini.trakem2.display.Patch
isProcessor() - Method in class ini.trakem2.imaging.PatchStack
isProjectType(String) - Static method in class ini.trakem2.Project
isQuit() - Method in class ini.trakem2.utils.Dispatcher
isReadOnly() - Method in class ini.trakem2.display.Display
isReady() - Method in class ini.trakem2.persistence.DBLoader: Check if settings are in.
isRelativePath(String) - Static method in class ini.trakem2.persistence.FSLoader
isRGB() - Method in class ini.trakem2.imaging.LayerStack: Override: always false.
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.AreaList
isRoughlyInside(Rectangle) - Method in class ini.trakem2.display.AreaTree.AreaNode
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.Ball
isRoughlyInside(Rectangle) - Method in class ini.trakem2.display.Connector.ConnectorNode
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.Displayable: If this Displayable intersects with @param r or almost intersects, then returns true.
isRoughlyInside(Rectangle) - Method in class ini.trakem2.display.Node: May return a false positive but never a false negative.
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.Patch
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.Pipe
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.Polyline
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.Profile
isRoughlyInside(Layer, Rectangle) - Method in class ini.trakem2.display.Tree: Fast and dirty, never returns a false negative but may return a false positive.
isRoughlyInside(Rectangle) - Method in class ini.trakem2.display.Treeline.RadiusNode
isSelected() - Method in class ini.trakem2.display.Channel
isSelected(Displayable) - Method in class ini.trakem2.display.Display
isShowing(Layer) - Method in class ini.trakem2.display.Display
isShowing(Displayable) - Method in class ini.trakem2.display.RollingPanel
isSignalImage(Image) - Static method in class ini.trakem2.persistence.Loader: Returns true if the awt is a signaling image like NOT_FOUND or REGENERATING.
isSmallerThan2GB() - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
isSnapPaintable(long) - Method in class ini.trakem2.persistence.Loader: Check if an awt exists to paint as a snap.
isStack() - Method in class ini.trakem2.display.Patch: Returns true if this Patch holds direct links to at least one other image in a different layer.
isSupportedType() - Method in class ini.trakem2.io.ImageFileHeader
isTagging() - Method in class ini.trakem2.display.Tree
isTop(Displayable) - Method in class ini.trakem2.display.Layer: Within its own class only.
isTop(ZDisplayable) - Method in class ini.trakem2.display.LayerSet
isTop(Displayable) - Method in class ini.trakem2.display.LayerSet: Hub method: ZDisplayable or into the Displayable's Layer.
isTrakEM2Subfile(File) - Static method in class ini.trakem2.utils.Utils: Returns true if the file cannonical path contains "/trakem2." (adjusted for Windows as well).
isTrakEM2Subpath(String) - Static method in class ini.trakem2.utils.Utils: Returns true if the path contains "/trakem2." (adjusted for Windows as well).
isTransforming() - Method in class ini.trakem2.display.Display: Find out whether this Display is Transforming its active Displayable.
isTransforming(Displayable) - Static method in class ini.trakem2.display.Display: Find whether any Display is transforming the given Displayable.
isTransforming() - Method in class ini.trakem2.display.DisplayCanvas
isUnloadable(Displayable) - Method in class ini.trakem2.persistence.Loader
isUnreadable() - Method in class ini.trakem2.persistence.TMLHandler
isURL(String) - Static method in class ini.trakem2.persistence.FSLoader
isValidIdentifier(String) - Static method in class ini.trakem2.utils.Utils
isVirtual() - Method in class ini.trakem2.display.FakeImagePlus
isVirtual() - Method in class ini.trakem2.imaging.LayerStack: Always return true.
isVisible() - Method in class ini.trakem2.display.Displayable
isWaiting() - Method in class ini.trakem2.display.DisplayableChooser
isWithinViewport(Displayable) - Method in class ini.trakem2.display.Display: Check if a panel for the given Displayable is completely visible in the JScrollPane
isWorking() - Method in class ini.trakem2.utils.Worker
itemStateChanged(ItemEvent) - Method in class ini.trakem2.display.Channel
iter_inc - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
iterations - Static variable in class org.janelia.intensity.MatchIntensities
iterations - Variable in class org.janelia.intensity.RansacRegressionFilter
iterations - Variable in class org.janelia.intensity.RansacRegressionReduceFilter
iterator() - Method in class ini.trakem2.display.Node.NodeCollection
iterator() - Method in class ini.trakem2.parallel.ParallelMapping

J

java3d - Static variable in class ini.trakem2.utils.Utils
join(List<? extends Tree<T>>) - Method in class ini.trakem2.display.Tree
join() - Method in class ini.trakem2.utils.Worker

K

kernelExpandMatrix(double[][]) - Method in class lenscorrection.NonLinearTransform
kernelExpandMatrixNormalize(double[][]) - Method in class lenscorrection.NonLinearTransform
keyPressed(KeyEvent) - Method in class ini.trakem2.display.AreaList
keyPressed(KeyEvent) - Method in class ini.trakem2.display.AreaTree
keyPressed(KeyEvent, DisplayCanvas, Layer) - Method in class ini.trakem2.display.AreaWrapper
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Ball
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Displayable
keyPressed(KeyEvent) - Method in class ini.trakem2.display.DisplayCanvas
keyPressed(KeyEvent) - Method in class ini.trakem2.display.DLabel
keyPressed(KeyEvent) - Method in class ini.trakem2.display.LayerSet
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Patch
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Pipe
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Polyline
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Profile
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Tree
keyPressed(KeyEvent) - Method in class ini.trakem2.display.Treeline
keyPressed(KeyEvent) - Method in class ini.trakem2.display.YesNoDialog
keyPressed(KeyEvent) - Method in class ini.trakem2.tree.DNDTree
keyPressed(KeyEvent) - Method in class ini.trakem2.tree.ProjectTree
keyPressed(KeyEvent) - Static method in class ini.trakem2.utils.ProjectToolbar
keyReleased(KeyEvent) - Method in class ini.trakem2.display.DisplayCanvas
keyReleased(KeyEvent) - Method in class ini.trakem2.display.YesNoDialog
keyReleased(KeyEvent) - Method in class ini.trakem2.tree.DNDTree
keySet() - Method in class ini.trakem2.utils.FieldMapView
keyTyped(KeyEvent) - Method in class ini.trakem2.display.DisplayCanvas
keyTyped(KeyEvent) - Method in class ini.trakem2.display.YesNoDialog
keyTyped(KeyEvent) - Method in class ini.trakem2.tree.DNDTree
killRoi() - Method in class ini.trakem2.display.FakeImagePlus: Forward kill roi to the last_temp of the associated Display.
killRoi() - Method in class ini.trakem2.imaging.PatchStack

L

la - Variable in class ini.trakem2.display.Node
lambda - Variable in class lenscorrection.Distortion_Correction.BasicParam: Regularization factor
lambda - Variable in class mpicbg.trakem2.align.Align.Param: Regularization weight.
lambda - Variable in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param
lambda1 - Static variable in class org.janelia.intensity.MatchIntensities
lambda2 - Static variable in class org.janelia.intensity.MatchIntensities
lambdaRegularize - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
Landmarks(Layer) - Constructor for class ini.trakem2.display.ManualAlignMode.Landmarks
largest_possibly_needed_area - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
largestGraphOnly - Static variable in class mpicbg.trakem2.align.AlignTask
last_autotrace_start - Variable in class ini.trakem2.display.Polyline
last_color - Static variable in class ini.trakem2.display.Displayable
last_dir - Static variable in class ini.trakem2.utils.Utils: The path of the directory from which images have been recently loaded.
last_file - Static variable in class ini.trakem2.utils.Utils: The path of the last opened file.
last_popup - Variable in class ini.trakem2.display.DisplayCanvas: In world coordinates.
last_radius - Static variable in class ini.trakem2.display.Treeline
lastLayerIndex - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
lateralAreaOfTruncatedCone(double, double, double) - Static method in class ini.trakem2.utils.M
launchTPlugIn(KeyEvent, String, Project, Displayable) - Static method in class ini.trakem2.utils.Utils: Returns null if no plugin was launched.
layer - Variable in class ini.trakem2.display.Coordinate
layer - Variable in class ini.trakem2.display.Displayable
layer - Variable in class ini.trakem2.display.GroupingMode
Layer - Class in ini.trakem2.display
Layer(Project, double, double, LayerSet) - Constructor for class ini.trakem2.display.Layer
Layer(Project, long, double, double) - Constructor for class ini.trakem2.display.Layer: Reconstruct from database
Layer(Project, long, HashMap<String, String>) - Constructor for class ini.trakem2.display.Layer: Reconstruct from XML file.
layer - Variable in class ini.trakem2.display.LayerPanel
layer - Variable in class ini.trakem2.display.Region
layer - Variable in class ini.trakem2.display.VectorDataTransform
Layer.DoMoveDisplayable - Class in ini.trakem2.display
layer1Fixed - Variable in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
layer2Fixed - Variable in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
layer_set - Variable in class ini.trakem2.display.ZDisplayable
layerName(Layer) - Static method in class mpicbg.trakem2.align.AlignmentUtils
LayerPanel - Class in ini.trakem2.display
LayerPanel(Display, Layer) - Constructor for class ini.trakem2.display.LayerPanel
layerRemoved(Layer) - Method in class ini.trakem2.display.AreaList
layerRemoved(Layer) - Method in class ini.trakem2.display.Ball
layerRemoved(Layer) - Method in class ini.trakem2.display.Connector: If the root node is in Layer @param la, then all nodes are removed.
layerRemoved(Layer) - Method in class ini.trakem2.display.Dissector
layerRemoved(Layer) - Method in class ini.trakem2.display.Pipe
layerRemoved(Layer) - Method in class ini.trakem2.display.Polyline
layerRemoved(Layer) - Method in class ini.trakem2.display.Tree
layerRemoved(Layer) - Method in class ini.trakem2.display.ZDisplayable: Update internal datastructures to reflect the fact that @param layer has been removed from the containing LayerSet.
layerScale - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
LayerSet - Class in ini.trakem2.display: A LayerSet is a container for a list of Layer.
LayerSet(Project, long) - Constructor for class ini.trakem2.display.LayerSet: Dummy.
LayerSet(Project, String, double, double, Layer, float, float) - Constructor for class ini.trakem2.display.LayerSet: Create a new LayerSet with a 0,0,0 rotation vector and default 20,20 px Displayable width,height.
LayerSet(Project, long, String, float, float, double, double, double, float, float, boolean, int, AffineTransform) - Constructor for class ini.trakem2.display.LayerSet: Reconstruct from the database.
LayerSet(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.LayerSet: Reconstruct from an XML entry.
layerset - Variable in class org.janelia.intensity.MatchIntensities
LayerSet.DoChangeTrees - Class in ini.trakem2.display: Records the state of the LayerSet.al_layers, each Layer.al_displayables and all the trees and unique types of Project.
LayerSet.DoMoveZDisplayable - Class in ini.trakem2.display
LayerSet.LayerBucket - Class in ini.trakem2.display: A Bucket for the ZDisplayable parts that show in every Layer.
LayerStack - Class in ini.trakem2.imaging: This class represents an entire LayerSet of Patch objects only, as it is presented read-only to ImageJ.
LayerStack(LayerSet, double, int, Class<?>, int, boolean) - Constructor for class ini.trakem2.imaging.LayerStack
LayerStack(List<Layer>, Rectangle, double, int, Class<?>, int, boolean) - Constructor for class ini.trakem2.imaging.LayerStack: If scale <=0 || scale > 1, throws IllegalArgumentException.
LayerStack(LayerSet, double, int, Class<?>, int) - Constructor for class ini.trakem2.imaging.LayerStack
LayerThing - Class in ini.trakem2.tree
LayerThing(TemplateThing, Project, Object) - Constructor for class ini.trakem2.tree.LayerThing
LayerThing(TemplateThing, Project, long, String, Object, ArrayList<LayerThing>) - Constructor for class ini.trakem2.tree.LayerThing: Reconstruct from database, in combination with the setup() method.
LayerThingNodeRender() - Constructor for class ini.trakem2.tree.LayerTree.LayerThingNodeRender
LayerTree - Class in ini.trakem2.tree
LayerTree(Project, LayerThing) - Constructor for class ini.trakem2.tree.LayerTree
LayerTree.LayerThingNodeRender - Class in ini.trakem2.tree
LazyVirtualStack - Class in ini.trakem2.imaging
LazyVirtualStack(int, int, int) - Constructor for class ini.trakem2.imaging.LazyVirtualStack
lbucks - Variable in class ini.trakem2.display.LayerSet: For fast search.
ldu(int) - Static method in class mpi.fruitfly.math.General: fast floor ld of unsigned v
LEFT_RIGHT - Static variable in class ini.trakem2.imaging.StitchingTEM
length() - Method in interface ini.trakem2.display.Line3D
length() - Method in class ini.trakem2.display.Pipe: The number of clicked, backbone points in this pipe.
length() - Method in class ini.trakem2.display.Polyline: The number of points in this pipe.
length() - Method in class ini.trakem2.utils.Vector3
lenscorrection - package lenscorrection
LEVENSHTEIN - Static variable in class ini.trakem2.analysis.Compare
Line3D - Interface in ini.trakem2.display: By definition, only ZDisplayable objects may implement Line3D.
LINEAR - Static variable in class mpicbg.trakem2.align.AlignLayersTask
LINEAR_PHASE_CORRELATION - Static variable in class mpicbg.trakem2.align.AlignTask
LINEAR_SIFT_CORRESPONDENCES - Static variable in class mpicbg.trakem2.align.AlignTask
LinearIntensityMap<T extends RealType<T>> - Class in org.janelia.intensity: Transfer intensities by a linear function y=ax+b with the coefficients a and b being stored as a RealComposite<T> 2d-vector (a, b) in a map.
LinearIntensityMap(RandomAccessibleInterval<T>, InterpolatorFactory<RealComposite<T>, RandomAccessible<RealComposite<T>>>) - Constructor for class org.janelia.intensity.LinearIntensityMap
LinearIntensityMap(RandomAccessibleInterval<T>) - Constructor for class org.janelia.intensity.LinearIntensityMap
LinearIntensityMap(RandomAccessibleInterval<T>, LinearIntensityMap.Interpolation) - Constructor for class org.janelia.intensity.LinearIntensityMap
LinearIntensityMap.Interpolation - Enum in org.janelia.intensity
link(Displayable) - Method in class ini.trakem2.display.Displayable: Link the given Displayable with this Displayable, and then tell the given Displayable to link this.
link(Displayable, boolean) - Method in class ini.trakem2.display.Displayable: Link the given Displayable with this Displayable, and then tell the given Displayable to link this.
LINK_STATE - Static variable in class ini.trakem2.display.DisplayablePanel
linked_props - Variable in class ini.trakem2.display.Displayable: The table of tables of properties: for any target Displayable, there is a set of properties specific of the relationship between this Displayable and the target one.
linked_props_origins - Variable in class ini.trakem2.display.Displayable: The call back hooks to remove any linked properties in other Displayable instances when this Displayable is removed.
linkPatches() - Method in class ini.trakem2.display.AreaList
linkPatches() - Method in class ini.trakem2.display.Ball
linkPatches() - Method in class ini.trakem2.display.Displayable: Link the Patch objects that lay underneath the bounding box of this Displayable, so that they cannot be dragged independently.
linkPatches() - Method in class ini.trakem2.display.Dissector
linkPatches() - Method in class ini.trakem2.display.Patch: Override to cancel.
linkPatches() - Method in class ini.trakem2.display.Pipe: Scan the Display and link Patch objects that lay under this Pipe's bounding box.
linkPatches() - Method in class ini.trakem2.display.Polyline
linkPatches() - Method in class ini.trakem2.display.Stack
linkPatches() - Method in class ini.trakem2.display.Tree
linkPatches() - Method in class ini.trakem2.display.ZDisplayable: Link the Patch objects that lay underneath the part of the bounding box of this profile that shows in the current layer, so that they cannot be dragged independently.
links - Variable in class ini.trakem2.display.Displayable.DataPackage
load(String) - Static method in class ini.trakem2.io.RagMipMaps
load(String) - Static method in class ini.trakem2.io.RawMipMaps
load(String, int) - Static method in class ini.trakem2.io.RawMipMaps
load(int, int, int) - Method in class ini.trakem2.utils.ImgLibVolume: Load the value at the specified position
load(String) - Method in class lenscorrection.NonLinearTransform
Loader - Class in ini.trakem2.persistence: Handle all data-related issues with a virtualization engine, including load/unload and saving, saving as and overwriting.
Loader() - Constructor for class ini.trakem2.persistence.Loader
loader - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
Loader.ImageLoadingLock - Class in ini.trakem2.persistence
localModelIndex - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
localRegionSigma - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
Lock - Class in ini.trakem2.utils: For thread synchronization.
Lock() - Constructor for class ini.trakem2.utils.Lock
lock() - Method in class ini.trakem2.utils.Lock
LOCK_STATE - Static variable in class ini.trakem2.display.DisplayablePanel
locked - Variable in class ini.trakem2.display.Displayable
locked - Variable in class ini.trakem2.utils.Lock
log(String) - Static method in class ini.trakem2.utils.Utils: Intended for the user to see.
log(Object) - Static method in class ini.trakem2.utils.Utils
log(String, Object) - Static method in class ini.trakem2.utils.Utils: Pretty-print the object, for example arrays as [0, 1, 2].
Log10(double) - Static method in class mpi.fruitfly.math.General
log2(String) - Static method in class ini.trakem2.utils.Utils: Intended for developers: prints to terminal.
log2(Object) - Static method in class ini.trakem2.utils.Utils: Pretty-print the object, for example arrays as [0, 1, 2].
log2(String, Object) - Static method in class ini.trakem2.utils.Utils: Pretty-print the object, for example arrays as [0, 1, 2].
log2(String, Object, Object...) - Static method in class ini.trakem2.utils.Utils
log2(Object...) - Static method in class ini.trakem2.utils.Utils
logAll(String) - Static method in class ini.trakem2.utils.Utils: Print in all printable places: log window, System.out.println, and status bar.
LoggingInputStream - Class in ini.trakem2.io: A class to monitor an input stream for speed and total byte download.
LoggingInputStream(InputStream) - Constructor for class ini.trakem2.io.LoggingInputStream
logMany2(Object...) - Static method in class ini.trakem2.utils.Utils
logStamped(String) - Static method in class ini.trakem2.utils.Utils: Intended for the user to see; time-stamps every logging line.
longIntegralImage(byte[], int, int) - Static method in class ini.trakem2.imaging.FastIntegralImage: Returns an image of @{param w}+1, @{param y}+1, where the first row and the first column are zeros, and the rest contain the sum of the area from 0,0 to that pixel in b.
longIntegralImage(short[], int, int) - Static method in class ini.trakem2.imaging.FastIntegralImage: Returns an image of @{param w}+1, @{param y}+1, where the first row and the first column are zeros, and the rest contain the sum of the area from 0,0 to that pixel in b.
low_frequency_threshold - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
ls - Variable in class ini.trakem2.display.d3d.ControlClickBehavior
luminance(Color) - Static method in class ini.trakem2.utils.Utils: 0.3 * R + 0.6 * G + 0.1 * B
LUTBlue - Class in ini.trakem2.imaging.filters
LUTBlue() - Constructor for class ini.trakem2.imaging.filters.LUTBlue
LUTBlue(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTBlue
LUTCustom - Class in ini.trakem2.imaging.filters
LUTCustom() - Constructor for class ini.trakem2.imaging.filters.LUTCustom
LUTCustom(float, float, float) - Constructor for class ini.trakem2.imaging.filters.LUTCustom
LUTCustom(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTCustom
LUTCyan - Class in ini.trakem2.imaging.filters
LUTCyan() - Constructor for class ini.trakem2.imaging.filters.LUTCyan
LUTCyan(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTCyan
LUTGreen - Class in ini.trakem2.imaging.filters
LUTGreen() - Constructor for class ini.trakem2.imaging.filters.LUTGreen
LUTGreen(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTGreen
LUTMagenta - Class in ini.trakem2.imaging.filters
LUTMagenta() - Constructor for class ini.trakem2.imaging.filters.LUTMagenta
LUTMagenta(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTMagenta
LUTOrange - Class in ini.trakem2.imaging.filters
LUTOrange() - Constructor for class ini.trakem2.imaging.filters.LUTOrange
LUTOrange(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTOrange
LUTRed - Class in ini.trakem2.imaging.filters
LUTRed() - Constructor for class ini.trakem2.imaging.filters.LUTRed
LUTRed(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTRed
LUTYellow - Class in ini.trakem2.imaging.filters
LUTYellow() - Constructor for class ini.trakem2.imaging.filters.LUTYellow
LUTYellow(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.LUTYellow

M

M - Class in ini.trakem2.utils: TrakEM2's mathematician.
M() - Constructor for class ini.trakem2.utils.M
M_2PI - Static variable in class mpi.fruitfly.math.General
magicWand(AreaWrapper, Layer, Rectangle, int, int, Runnable, boolean, boolean) - Static method in class ini.trakem2.imaging.Segmentation
magicWand(AreaWrapper, Layer, Rectangle, int, int, List<Runnable>, boolean, boolean) - Static method in class ini.trakem2.imaging.Segmentation
magnification - Variable in class ini.trakem2.display.GroupingMode
magnificationUpdated(Rectangle, double) - Method in class ini.trakem2.display.AffineTransformMode
magnificationUpdated(Rectangle, double) - Method in class ini.trakem2.display.DefaultMode
magnificationUpdated(Rectangle, double) - Method in class ini.trakem2.display.GroupingMode
magnificationUpdated(Rectangle, double) - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
magnificationUpdated(Rectangle, double) - Method in class ini.trakem2.display.ManualAlignMode
magnificationUpdated(Rectangle, double) - Method in interface ini.trakem2.display.Mode
main(String[]) - Static method in class ini.trakem2.imaging.FastIntegralImage: For testing.
main(String[]) - Static method in class ini.trakem2.imaging.IntegralHistogram2d
main(String[]) - Static method in class ini.trakem2.tree.DTDParser
main(String[]) - Static method in class org.janelia.intensity.LinearIntensityMap
main(String...) - Static method in class org.janelia.intensity.MatchIntensities
main(String...) - Static method in class org.janelia.intensity.Render
makeAdjustPropertiesDialog() - Method in class ini.trakem2.display.Displayable
makeAllPathsRelativeTo(String, Project) - Method in class ini.trakem2.persistence.FSLoader: Try to make all paths in ht_paths be relative to the given xml_path.
makeAllPathsRelativeTo(String, Project) - Method in class ini.trakem2.persistence.Loader
makeBrush(int, double) - Static method in class ini.trakem2.display.AreaWrapper: This method could get tones of improvement, which should be pumped upstream into ImageJ's RoiBrush class which is creating it at every while(true) {} iteration!!! The returned area has its coordinates centered around 0,0
makeEnvelope(Compare.CATAParameters, VectorString3D) - Static method in class ini.trakem2.analysis.Compare: From a condensed VectorString3D, create the radius at each point.
makeFlatColorImage() - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
makeFlatFloatGrayImageAndAlpha() - Method in class mpicbg.trakem2.transform.ExportBestFlatImage: While the data is in the 8-bit range, the format is as a FloatProcessor.
makeFlatGrayImage(List<Patch>, Rectangle, int, double) - Static method in class ini.trakem2.display.Patch: Deprecated.
makeFlatGrayImage() - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
makeFlatGrayImageAndAlpha() - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
makeFlatImage(int, Layer, Rectangle, double, Collection<Patch>, Color) - Static method in class ini.trakem2.display.Patch: Defaults to setMinAndMax = true.
makeFlatImage(int, Layer, Rectangle, double, Collection<Patch>, Color, boolean) - Static method in class ini.trakem2.display.Patch: Creates an ImageProcessor of the specified type.
makeFlatImage(Layer[], Rectangle, double, int, int, boolean, boolean) - Method in class ini.trakem2.persistence.Loader
makeFlatImage(Layer[], Rectangle, double, int, int, boolean, boolean, Color) - Method in class ini.trakem2.persistence.Loader
makeFlatImage(Layer[], Rectangle, double, int, int, boolean, String, boolean, Color) - Method in class ini.trakem2.persistence.Loader: If the srcRect is null, makes a flat 8-bit or RGB image of the entire layer.
makeFlatImage(List<Patch>, Rectangle, double, double, ExportUnsignedByte.ImageSource) - Static method in class mpicbg.trakem2.transform.ExportUnsignedByte
makeFlatImage(List<Patch>, Rectangle) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort: Create a flat image into which Patch instances are transferred considering their min and max values.
makeFlatImage(List<Patch>, Rectangle, double) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
makeFlatImage(List<Patch>, Rectangle, double, double) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
makeFlatImage(List<Patch>, Rectangle, double, double, boolean) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
makeFlatImageARGB(List<Patch>, Rectangle, double, double, boolean) - Static method in class mpicbg.trakem2.transform.ExportARGB
makeFlatImageARGBFromMipMaps(List<Patch>, Rectangle, double, double) - Static method in class mpicbg.trakem2.transform.ExportARGB: Returns nonsense or throws an Exception if mipmaps are not available.
makeFlatImageARGBFromOriginals(List<Patch>, Rectangle, double, double) - Static method in class mpicbg.trakem2.transform.ExportARGB: Limited to 2GB arrays for the requested image.
makeFlatImageFromMipMaps(List<Patch>, Rectangle, double, double) - Static method in class mpicbg.trakem2.transform.ExportUnsignedByte: Works only when mipmaps are available, returning nonsense otherwise.
makeFlatImageFromOriginals(List<Patch>, Rectangle, double, double) - Static method in class mpicbg.trakem2.transform.ExportUnsignedByte
makeFlatImageStack(List<Layer>, Rectangle, double) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort: Returns a stack of ShortProcessor, with dimensions as in the roi.
makeGenericDialog(String) - Static method in class ini.trakem2.ControlWindow: For the generic dialogs to be parented properly.
makeGrayLut() - Static method in class ini.trakem2.persistence.Loader
makeImage(ImageProcessor, FloatProcessor) - Method in class ini.trakem2.display.GroupingMode.ScreenPatchRange
makeLocalTo(Displayable) - Method in class ini.trakem2.display.VectorDataTransform: Returns a copy whose roi and ct are local to the affine transform of @param d.
makeMouseBrush(int, double) - Static method in class ini.trakem2.display.AreaWrapper
makeNode(Thing) - Static method in class ini.trakem2.tree.DNDTree
makeNode(Thing, boolean) - Static method in class ini.trakem2.tree.DNDTree: Returns a DefaultMutableTreeNode with all its children.
makeObject(TemplateThing) - Method in class ini.trakem2.Project: Make an object of the type the TemplateThing can hold.
makePatchesDir(File) - Method in class ini.trakem2.persistence.Loader
makePatchStack() - Method in class ini.trakem2.display.Patch: Retuns a virtual ImagePlus with a virtual stack if necessary.
makePlot(Compare.CATAParameters, String, VectorString3D) - Static method in class ini.trakem2.analysis.Compare
makePrescaledTiles(Layer[], Class<?>, Rectangle, int, int, String, int, Saver, int, int, boolean, boolean, int) - Static method in class ini.trakem2.persistence.ExportMultilevelTiles: Generate e.g.
makePrescaledTiles(Layer[], Class<?>, Rectangle, int, int, String, int, Saver, int, int, boolean, boolean, int) - Method in class ini.trakem2.persistence.Loader
makeProjectName() - Method in class ini.trakem2.persistence.FSLoader
makeProjectName() - Method in class ini.trakem2.persistence.Loader
makeRelativePath(String) - Method in class ini.trakem2.persistence.FSLoader: Takes the given path and tries to makes it relative to this instance's project_file_path, if possible.
makeRelativePath(String) - Method in class ini.trakem2.persistence.Loader: Returns @param path unless overriden.
makeStripe(Patch, Roi, double) - Static method in class ini.trakem2.imaging.StitchingTEM
makeStripe(Patch, Roi, double, boolean) - Static method in class ini.trakem2.imaging.StitchingTEM
makeTitle(Displayable) - Static method in class ini.trakem2.display.Display3D
makeTitle(Patch) - Static method in class ini.trakem2.display.Display3D
makeTPS(Set<PointMatch>) - Static method in class mpicbg.trakem2.align.ElasticLayerAlignment
makeTube(double[], double[], double[], double[], int, int, Calibration) - Static method in class ini.trakem2.display.Pipe
makeValidIdentifier(String) - Static method in class ini.trakem2.utils.Utils: user=> (def pat #"\b[a-zA-Z]+[\w]*\b") #'user/pat user=>(re-seq pat "abc def 1a334") ("abc" "def") user=> (re-seq pat "abc def a334") ("abc" "def" "a334")
makeVirtualConnection(AbstractAffineTile2D<?>) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D: Add a virtual connection between two Tiles.
makeYesNoCancelDialog(String, String) - Static method in class ini.trakem2.ControlWindow: For the YesNoCancelDialog dialogs to be parented properly.
makeYesNoDialog(String, String) - Static method in class ini.trakem2.ControlWindow: For the YesNoDialog dialogs to be parented properly.
ManualAlignMode - Class in ini.trakem2.display
ManualAlignMode(Display) - Constructor for class ini.trakem2.display.ManualAlignMode
ManualAlignMode.Landmarks - Class in ini.trakem2.display
manyToManyInterpolation(Area, Area, int) - Static method in class ini.trakem2.utils.AreaUtils
map(ExportUnsignedShort.PatchTransform, double, double, ShortProcessor, ShortProcessor) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
map(ExportUnsignedShort.PatchTransform, double, double, double, ShortProcessor, ShortProcessor) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
map(ExportUnsignedShort.PatchTransform, double, double, double, ShortProcessor, ShortProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
map(IterableInterval<S>, IterableInterval<RealComposite<T>>) - Static method in class org.janelia.intensity.LinearIntensityMap
mapARGB(IterableInterval<ARGBType>, IterableInterval<RealComposite<T>>) - Static method in class org.janelia.intensity.LinearIntensityMap
mapComposite(IterableInterval<RealComposite<S>>, IterableInterval<RealComposite<T>>) - Static method in class org.janelia.intensity.LinearIntensityMap
mapCrop(IterableInterval<S>, IterableInterval<RealComposite<T>>) - Static method in class org.janelia.intensity.LinearIntensityMap
mapIntensities(Patch, ImagePlus) - Method in class ini.trakem2.persistence.FSLoader
mapIntensities(Patch, ImagePlus) - Method in class ini.trakem2.persistence.Loader
mapIntensities(ExportUnsignedShort.PatchIntensityRange, double, double) - Static method in class mpicbg.trakem2.transform.ExportUnsignedShort
markNear(float, float, Layer, double) - Method in class ini.trakem2.display.Tree
markStaleFileForDeletionUponSaving(String) - Method in class ini.trakem2.persistence.Loader: Add a file path for removal when the XML is successfully saved.
mask - Variable in class ini.trakem2.display.Patch.PatchImage: The alpha mask, coordinate-transformed if null != ct.
maskBorder(int) - Method in class ini.trakem2.display.Patch: Make the border have an alpha of zero.
maskBorder(int, int, int, int) - Method in class ini.trakem2.display.Patch: Make the border have an alpha of zero.
maskBorders(Collection<Displayable>, int, int, int, int) - Method in class ini.trakem2.persistence.Loader: Make the border have an alpha of zero.
maskBorders(int, int, int, int, Collection<Displayable>) - Method in class ini.trakem2.persistence.Loader: Make the border have an alpha of zero.
maskBordersLayerWise(Collection<Layer>, int, int, int, int) - Method in class ini.trakem2.persistence.Loader: Make the border have an alpha of zero.
matches(String, String) - Static method in class ini.trakem2.utils.Utils
MatchFeaturesAndFindModelThread(Align.Param, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>, AtomicInteger, AtomicInteger, int, boolean) - Constructor for class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
MatchFeaturesAndFindModelThread(Align.Param, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>, AtomicInteger, AtomicInteger, int) - Constructor for class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
MatchIntensities - Class in org.janelia.intensity
MatchIntensities() - Constructor for class org.janelia.intensity.MatchIntensities
mawts - Variable in class ini.trakem2.persistence.Loader
max - Variable in class ini.trakem2.imaging.filters.ValueToNoise
max - Variable in class ini.trakem2.utils.OptionPanel.NumericalSetter
max(int, int) - Static method in class mpi.fruitfly.math.General
max(float, float) - Static method in class mpi.fruitfly.math.General
max(double, double) - Static method in class mpi.fruitfly.math.General
max - Variable in class mpicbg.trakem2.transform.ExportUnsignedShort.PatchIntensityRange
MAX_EDGE_CONFIDENCE - Static variable in class ini.trakem2.display.Node: Maximum possible confidence in an edge (ranges from 0 to 5, inclusive).
max_iterations - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
max_mut - Variable in class ini.trakem2.analysis.Compare.CATAParameters
max_possible_area - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
MAX_RETRIES - Variable in class ini.trakem2.persistence.Loader
maxCurvatureR - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
maxDim(Displayable) - Static method in class ini.trakem2.persistence.Loader
maxEpsilon - Variable in class lenscorrection.Distortion_Correction.BasicParam: Maximal allowed alignment error in px
maxEpsilon - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam: Maximal accepted alignment error in px
maxEpsilon - Variable in class mpicbg.trakem2.align.Align.Param: Maximal allowed alignment error in px
maxEpsilon - Variable in class org.janelia.intensity.RansacRegressionFilter
maxEpsilon - Variable in class org.janelia.intensity.RansacRegressionReduceFilter
maxIterations - Variable in class mpicbg.trakem2.align.Align.ParamOptimize: Maximal number of iteration allowed for the optimizer.
maxIterationsOptimize - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
maxIterationsOptimize - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
maxIterationsSpringMesh - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
maxIterationsSpringMesh - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
maxLocalEpsilon - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
maxLocalTrust - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
maxNumFailures - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam: Maximal number of consecutive slices for which no model could be found
maxNumNeighbors - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam: Maximal number of consecutive sections to be tested for an alignment model
maxNumThreads - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
maxNumThreads - Variable in class mpicbg.trakem2.align.ElasticMontage.Param: Change this in case you want to limit the number of parallel threads to a specific number.
maxNumThreadsSift - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
maxNumThreadsSift - Variable in class mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch
maxPlateauwidth - Variable in class mpicbg.trakem2.align.Align.ParamOptimize: Maximal number of iterations allowed to not change the parameter to be optimized.
maxPlateauwidthOptimize - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
maxPlateauwidthOptimize - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
maxPlateauwidthSpringMesh - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
maxPlateauwidthSpringMesh - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
maxStretchSpringMesh - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
maxStretchSpringMesh - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
maxTrust - Variable in class org.janelia.intensity.RansacRegressionFilter
maxTrust - Variable in class org.janelia.intensity.RansacRegressionReduceFilter
MCCube - Class in ini.trakem2.utils
MCTriangulator - Class in ini.trakem2.utils
MCTriangulator() - Constructor for class ini.trakem2.utils.MCTriangulator
mean_factor - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
meanFactor - Variable in class mpicbg.trakem2.align.Align.ParamOptimize
measure(ResultsTable) - Method in class ini.trakem2.display.AreaList
measure() - Method in class ini.trakem2.display.AreaList: Returns a double array with 0=volume, 1=lower_bound_surface, 2=upper_bound_surface_smoothed, 3=upper_bound_surface, 4=max_diameter, 5=all_tops_and_bottoms All measures are approximate.
measure(ResultsTable) - Method in class ini.trakem2.display.Ball: Returns a listing of all balls contained here, one per row with index, x, y, z, and radius, all calibrated.
measure(ResultsTable) - Method in class ini.trakem2.display.Connector
measure(ResultsTable) - Method in class ini.trakem2.display.Displayable: Does nothing unless overriden.
measure(ResultsTable) - Method in class ini.trakem2.display.Dissector
measure(ResultsTable) - Method in class ini.trakem2.display.Pipe
measure(ResultsTable) - Method in class ini.trakem2.display.Polyline
measure(ResultsTable) - Method in class ini.trakem2.display.Profile: Measures the calibrated length, the lateral surface as the length times the layer thickness, and the volume (if closed) as the area times the layer thickness.
measure(Profile[], ResultsTable, long) - Static method in class ini.trakem2.display.Profile: Assumes Z-coord sorted list of profiles, as stored in a "profile_list" ProjectThing type.
measure() - Method in class ini.trakem2.display.Selection: Call measure(ResultsTable) on every selected Displayable.
measure(ResultsTable) - Method in class ini.trakem2.display.Tree: Measures number of branch points and end points, and total cable length.
measure(HashMap<Class<?>, ResultsTable>) - Method in class ini.trakem2.tree.ProjectThing: Call on children things, and on itself if it contains a basic data type directly.
measure() - Method in class ini.trakem2.tree.ProjectThing: Measure each node, recursively into children, and at the end display all the result tables, one for each data type.
measureArea(Area, Loader) - Static method in class ini.trakem2.utils.M: Returns the approximated area of the given Area object; Loader can be null; if not, it's used to secure memory space.
measureArea(Point3f, Point3f, Point3f) - Static method in class ini.trakem2.utils.M: Compute the area of the triangle defined by 3 points in 3D space, returning half of the length of the vector resulting from the cross product of vectors p1p2 and p1p3.
measureAreas(ResultsTable) - Method in interface ini.trakem2.display.AreaContainer
measureAreas(ResultsTable) - Method in class ini.trakem2.display.AreaList
measureAreas(ResultsTable) - Method in class ini.trakem2.display.AreaTree
measureDistance() - Method in class ini.trakem2.display.Tree.MeasurementPair
measureDistance() - Method in class ini.trakem2.display.Tree.Pair: The calibrated distance from a to b.
MeasurementPair(Tree<T>.NodePath) - Constructor for class ini.trakem2.display.Tree.MeasurementPair
MeasurementPair(Node<T>, Node<T>, List<Node<T>>) - Constructor for class ini.trakem2.display.Tree.MeasurementPair
measurePathDistance(Node<T>, Node<T>, ResultsTable) - Method in class ini.trakem2.display.Tree: Reuses @param rt unless it is null, in which case it creates a new one.
measurePathDistance(Node<T>, Node<T>) - Method in class ini.trakem2.display.Tree: Measure the distance, in calibrated units, between nodes a and b of this tree.
MeasurePathDistance(Tree, Node, Node) - Constructor for class ini.trakem2.display.Tree.MeasurePathDistance
measureSize(ImagePlus) - Static method in class ini.trakem2.persistence.Loader
measureTaggedPairs(Tag, Tag) - Method in class ini.trakem2.display.Tree
median(int, int, long[], int, double, double, int) - Static method in class ini.trakem2.imaging.IntegralHistogram2d
median(ShortProcessor, int, double, double, int) - Static method in class ini.trakem2.imaging.IntegralHistogram2d
MEDIAN_PHYS_DIST - Static variable in class ini.trakem2.analysis.Compare
medianRadius - Variable in class ini.trakem2.imaging.filters.CorrectBackground: Radius for integral median filter
merge(ArrayList<Displayable>) - Static method in class ini.trakem2.display.AreaList: Merge all arealists contained in the ArrayList to the first one found, and remove the others from the project, and only if they belong to the same LayerSet.
merge(List<Connector>) - Static method in class ini.trakem2.display.Connector: Takes the List of Connector instances and adds the targets of all to the first one.
merge(byte[], byte[]) - Static method in class ini.trakem2.imaging.P: Merges into alpha if outside is null, otherwise returns alpha as is.
Merger - Class in ini.trakem2.utils
Merger() - Constructor for class ini.trakem2.utils.Merger
mergeTargets(Connector) - Method in class ini.trakem2.display.Connector
MeshData(List<Point3f>, List<Color3f>) - Constructor for class ini.trakem2.display.Tree.MeshData
meshResolution - Variable in class ini.trakem2.display.Patch
meshResolution - Variable in class ini.trakem2.display.Patch.TransformProperties
min - Variable in class ini.trakem2.imaging.filters.ValueToNoise
min - Variable in class ini.trakem2.utils.OptionPanel.NumericalSetter
min(int, int) - Static method in class mpi.fruitfly.math.General
min(double, double) - Static method in class mpi.fruitfly.math.General
min(float, float) - Static method in class mpi.fruitfly.math.General
min - Variable in class mpicbg.trakem2.transform.ExportUnsignedShort.PatchIntensityRange
MIN_BUCKET_SIZE - Static variable in class ini.trakem2.display.Bucket
min_chunk - Variable in class ini.trakem2.analysis.Compare.CATAParameters
MIN_FREE_BYTES - Static variable in class ini.trakem2.persistence.Loader: The minimal number of memory bytes that should always be free.
min_matches - Variable in class ini.trakem2.analysis.Compare.CATAParameters
min_R - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
minInlierRatio - Variable in class lenscorrection.Distortion_Correction.BasicParam: Inlier/candidates ratio
minInlierRatio - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam: Inlier/candidates ratio
minInlierRatio - Variable in class mpicbg.trakem2.align.Align.Param: Inlier/candidates ratio
minInlierRatio - Variable in class org.janelia.intensity.RansacRegressionFilter
minInlierRatio - Variable in class org.janelia.intensity.RansacRegressionReduceFilter
minMax(Iterable<PointMatch>) - Static method in class org.janelia.intensity.RansacRegressionReduceFilter
minNumInliers - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam: Minimal absolute number of inliers
minNumInliers - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam: Minimal absolute number of inliers
minNumInliers - Variable in class mpicbg.trakem2.align.Align.Param: Minimal absolute number of inliers
minNumInliers - Variable in class org.janelia.intensity.RansacRegressionFilter
minNumInliers - Variable in class org.janelia.intensity.RansacRegressionReduceFilter
minR - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
MIPMAP_FORMATS - Static variable in class ini.trakem2.persistence.FSLoader
MIPMAP_JPEG - Static variable in class ini.trakem2.persistence.FSLoader
MIPMAP_MODES - Static variable in class ini.trakem2.persistence.Loader
MIPMAP_PNG - Static variable in class ini.trakem2.persistence.FSLoader
MIPMAP_RAG - Static variable in class ini.trakem2.persistence.FSLoader
MIPMAP_RAW - Static variable in class ini.trakem2.persistence.FSLoader
MIPMAP_TIFF - Static variable in class ini.trakem2.persistence.FSLoader
MipMapImage - Class in ini.trakem2.display: A MipMap is a container for an Image and its corresponding inverse x/y scale relative to an original Image it was generated from.
MipMapImage(Image, double, double) - Constructor for class ini.trakem2.display.MipMapImage
mipmaps_regen - Variable in class ini.trakem2.persistence.Loader: If mipmaps regeneration is enabled or not.
MipMapSource() - Constructor for class mpicbg.trakem2.transform.ExportUnsignedByte.MipMapSource
mix(Color, Color) - Static method in class ini.trakem2.utils.Utils: Mix colors visually: red + green = yellow, etc.
Mode - Interface in ini.trakem2.display
mode - Static variable in class mpicbg.trakem2.align.AlignLayersTask
mode - Static variable in class mpicbg.trakem2.align.AlignTask: The mode used for alignment, which defaults to LINEAR_SIFT_CORRESPONDENCES but can take the values ELASTIC_BLOCK_CORRESPONDENCES and LINEAR_PHASE_CORRELATION.
model - Variable in class org.janelia.intensity.RansacRegressionFilter
model - Variable in class org.janelia.intensity.RansacRegressionReduceFilter
modelStrings - Static variable in class lenscorrection.Distortion_Correction.BasicParam: Implemeted transformation models for choice
modelStrings - Static variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam: Transformation models for choice
modelStrings - Static variable in class mpicbg.trakem2.align.Align.Param: Implemeted transformation models for choice
MONO - Static variable in class ini.trakem2.display.Channel
Montage - Class in ini.trakem2.utils
Montage(String, boolean) - Constructor for class ini.trakem2.utils.Montage
montageLayers(Align.ParamOptimize, List<Layer>, boolean, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
montageLayers(Align.ParamOptimize, List<Layer>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
montageLayers(ElasticMontage.Param, List<Layer>) - Static method in class mpicbg.trakem2.align.AlignTask
montageLayersTask(List<Layer>) - Static method in class mpicbg.trakem2.align.AlignTask: Montage each layer independently.
montageWithPhaseCorrelation(Collection<Patch>) - Static method in class ini.trakem2.imaging.StitchingTEM
montageWithPhaseCorrelation(List<Layer>, Worker) - Static method in class ini.trakem2.imaging.StitchingTEM
montageWithPhaseCorrelation(Collection<Patch>, StitchingTEM.PhaseCorrelationParam) - Static method in class ini.trakem2.imaging.StitchingTEM: Perform montage based on phase correlation
montageWithPhaseCorrelationTask(Collection<Patch>) - Static method in class ini.trakem2.imaging.StitchingTEM: For each Patch, find who overlaps with it and perform a phase correlation or cross-correlation with it; then consider all successful correlations as links and run the optimizer on it all.
montageWithPhaseCorrelationTask(List<Layer>) - Static method in class ini.trakem2.imaging.StitchingTEM
mouseClicked(MouseEvent) - Method in class ini.trakem2.display.Channel
mouseClicked(MouseEvent) - Method in class ini.trakem2.display.DisplayablePanel
mouseClicked(MouseEvent) - Method in class ini.trakem2.display.DisplayNavigator
mouseClicked(MouseEvent) - Method in class ini.trakem2.display.LayerPanel
mouseClicked(MouseEvent) - Method in class ini.trakem2.display.SnapshotPanel
mouseClicked(MouseEvent) - Method in class ini.trakem2.tree.LayerTree
mouseClicked(MouseEvent) - Method in class ini.trakem2.tree.ProjectTree
mouseClicked(MouseEvent) - Method in class ini.trakem2.tree.TemplateTree
mouseClicked(MouseEvent) - Method in class ini.trakem2.utils.ProjectToolbar
mouseDragged(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.AffineTransformMode
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.AreaList
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.AreaTree
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.AreaWrapper
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Ball
mouseDragged(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.ContrastAdjustmentMode
mouseDragged(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.DefaultMode
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Displayable
mouseDragged(MouseEvent) - Method in class ini.trakem2.display.DisplayCanvas
mouseDragged(MouseEvent) - Method in class ini.trakem2.display.DisplayNavigator
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Dissector
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.DLabel
mouseDragged(MouseEvent, int, int, double, double) - Method in class ini.trakem2.display.FreeHandProfile
mouseDragged(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
mouseDragged(MouseEvent, int, int, int, int, int, int, Rectangle, double) - Method in class ini.trakem2.display.LayerSet
mouseDragged(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.ManualAlignMode
mouseDragged(MouseEvent, int, int, int, int, int, int) - Method in interface ini.trakem2.display.Mode
mouseDragged(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.NonLinearTransformMode
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Pipe
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Polyline
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Profile: Execute the mouseDragged MouseEvent on this Profile.
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Tree
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Treeline
mouseDragged(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.imaging.Segmentation.BlowCommander
mouseDragged(MouseEvent) - Method in class ini.trakem2.tree.LayerTree
mouseDragged(MouseEvent) - Method in class ini.trakem2.tree.ProjectTree
mouseDragged(MouseEvent) - Method in class ini.trakem2.tree.TemplateTree
mouseEntered(MouseEvent) - Method in class ini.trakem2.display.Channel
mouseEntered(MouseEvent) - Method in class ini.trakem2.display.DisplayablePanel
mouseEntered(MouseEvent) - Method in class ini.trakem2.display.DisplayCanvas
mouseEntered(MouseEvent) - Method in class ini.trakem2.display.DisplayNavigator
mouseEntered(MouseEvent) - Method in class ini.trakem2.display.LayerPanel
mouseEntered(MouseEvent) - Method in class ini.trakem2.display.SnapshotPanel
mouseEntered(MouseEvent) - Method in class ini.trakem2.tree.LayerTree
mouseEntered(MouseEvent) - Method in class ini.trakem2.tree.ProjectTree
mouseEntered(MouseEvent) - Method in class ini.trakem2.tree.TemplateTree
mouseEntered(MouseEvent) - Method in class ini.trakem2.utils.ProjectToolbar
mouseExited(MouseEvent) - Method in class ini.trakem2.display.Channel
mouseExited(MouseEvent) - Method in class ini.trakem2.display.DisplayablePanel
mouseExited(MouseEvent) - Method in class ini.trakem2.display.DisplayCanvas
mouseExited(MouseEvent) - Method in class ini.trakem2.display.DisplayNavigator
mouseExited(MouseEvent) - Method in class ini.trakem2.display.LayerPanel
mouseExited(MouseEvent) - Method in class ini.trakem2.display.SnapshotPanel
mouseExited(MouseEvent) - Method in class ini.trakem2.tree.LayerTree
mouseExited(MouseEvent) - Method in class ini.trakem2.tree.ProjectTree
mouseExited(MouseEvent) - Method in class ini.trakem2.tree.TemplateTree
mouseExited(MouseEvent) - Method in class ini.trakem2.utils.ProjectToolbar
mouseMoved(MouseEvent) - Method in class ini.trakem2.display.DisplayCanvas
mouseMoved(MouseEvent) - Method in class ini.trakem2.display.DisplayNavigator
mouseMoved(int, int) - Method in class ini.trakem2.display.FakeImagePlus
mousePressed(MouseEvent, int, int, double) - Method in class ini.trakem2.display.AffineTransformMode
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.AreaList
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.AreaTree
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.AreaWrapper
mousePressed(MouseEvent, Layer, int, int, double, List<Runnable>) - Method in class ini.trakem2.display.AreaWrapper
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Ball
mousePressed(MouseEvent) - Method in class ini.trakem2.display.Channel
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Connector: Add a root or child nodes to root.
mousePressed(MouseEvent, int, int, double) - Method in class ini.trakem2.display.ContrastAdjustmentMode
mousePressed(MouseEvent, int, int, double) - Method in class ini.trakem2.display.DefaultMode
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Displayable
mousePressed(MouseEvent) - Method in class ini.trakem2.display.DisplayablePanel
mousePressed(MouseEvent) - Method in class ini.trakem2.display.DisplayCanvas
mousePressed(MouseEvent) - Method in class ini.trakem2.display.DisplayNavigator
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Dissector
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.DLabel
mousePressed(int, int) - Method in class ini.trakem2.display.FreeHandProfile
mousePressed(MouseEvent, int, int, double) - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
mousePressed(MouseEvent) - Method in class ini.trakem2.display.LayerPanel
mousePressed(MouseEvent, int, int, Rectangle, double) - Method in class ini.trakem2.display.LayerSet
mousePressed(MouseEvent, int, int, double) - Method in class ini.trakem2.display.ManualAlignMode
mousePressed(MouseEvent, int, int, double) - Method in interface ini.trakem2.display.Mode
mousePressed(MouseEvent, int, int, double) - Method in class ini.trakem2.display.NonLinearTransformMode
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Patch
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Pipe
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Polyline
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Profile: Execute the mousePressed MouseEvent on this Profile.
mousePressed(MouseEvent) - Method in class ini.trakem2.display.SnapshotPanel
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Tree
mousePressed(MouseEvent, Layer, int, int, double) - Method in class ini.trakem2.display.Treeline
mousePressed(MouseEvent) - Method in class ini.trakem2.tree.LayerTree
mousePressed(MouseEvent) - Method in class ini.trakem2.tree.ProjectTree
mousePressed(MouseEvent) - Method in class ini.trakem2.tree.TemplateTree
mousePressed(MouseEvent) - Method in class ini.trakem2.utils.ProjectToolbar
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.AffineTransformMode
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.AreaList
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.AreaTree
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.AreaWrapper
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Ball
mouseReleased(MouseEvent) - Method in class ini.trakem2.display.Channel
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.ContrastAdjustmentMode
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.DefaultMode
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Displayable
mouseReleased(MouseEvent) - Method in class ini.trakem2.display.DisplayablePanel
mouseReleased(MouseEvent) - Method in class ini.trakem2.display.DisplayCanvas
mouseReleased(MouseEvent) - Method in class ini.trakem2.display.DisplayNavigator
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Dissector
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.DLabel
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.FreeHandProfile
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
mouseReleased(MouseEvent) - Method in class ini.trakem2.display.LayerPanel
mouseReleased(MouseEvent, int, int, int, int, int, int, Rectangle, double) - Method in class ini.trakem2.display.LayerSet
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.ManualAlignMode
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in interface ini.trakem2.display.Mode
mouseReleased(MouseEvent, int, int, int, int, int, int) - Method in class ini.trakem2.display.NonLinearTransformMode
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Pipe
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Polyline
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Profile: Execute the mouseReleased MouseEvent on this Profile.
mouseReleased(MouseEvent) - Method in class ini.trakem2.display.SnapshotPanel
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Tree
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.display.Treeline
mouseReleased(MouseEvent, Layer, int, int, int, int, int, int) - Method in class ini.trakem2.imaging.Segmentation.BlowCommander
mouseReleased(MouseEvent) - Method in class ini.trakem2.tree.LayerTree
mouseReleased(MouseEvent) - Method in class ini.trakem2.tree.ProjectTree
mouseReleased(MouseEvent) - Method in class ini.trakem2.tree.TemplateTree
mouseReleased(MouseEvent) - Method in class ini.trakem2.utils.ProjectToolbar
mouseWheelMoved(MouseWheelEvent) - Method in class ini.trakem2.display.Displayable: Does nothing unless overriden.
mouseWheelMoved(MouseWheelEvent) - Method in class ini.trakem2.display.DisplayCanvas: Key/Mouse bindings like: - ij.gui.StackWindow: wheel to scroll slices (in this case Layers) - Inkscape: control+wheel to zoom (apple+wheel in macosx, since control+wheel zooms desktop)
mouseWheelMoved(MouseWheelEvent) - Method in class ini.trakem2.display.RollingPanel
mouseWheelMoved(MouseWheelEvent) - Method in class ini.trakem2.display.Tree
mouseWheelMoved(MouseWheelEvent) - Method in class ini.trakem2.display.Treeline
move(Set<Displayable>, Layer, Layer) - Method in class ini.trakem2.display.LayerSet: Move all Displayable objects in the HashSet to the given target layer.
move(int, Displayable) - Method in class ini.trakem2.display.LayerSet: Change z position in the layered stack, which defines the painting order.
move(int) - Method in class ini.trakem2.tree.ProjectThing: Moves this ProjectThing up and down the parent's children list.
move(int) - Method in class ini.trakem2.utils.CircularSequence: Will wrap around.
moveBlow(int, int) - Method in class ini.trakem2.imaging.Segmentation.BlowRunner
moveBottom(Displayable) - Method in class ini.trakem2.display.Layer: Within its own class only.
moveDown(Displayable) - Method in class ini.trakem2.display.Layer: Within its own class only.
moveDown(Layer, Displayable) - Method in class ini.trakem2.display.LayerSet: Move the given Displayable to the next layer if possible.
moveDown() - Method in class ini.trakem2.display.Selection: Send all selected components to the next layer.
moveTop(Displayable) - Method in class ini.trakem2.display.Layer: Within its own class only.
moveUp(Displayable) - Method in class ini.trakem2.display.Layer: Within its own class only.
moveUp(Layer, Displayable) - Method in class ini.trakem2.display.LayerSet: Move the given Displayable to the previous layer if possible.
moveUp() - Method in class ini.trakem2.display.Selection: Send all selected components to the previous layer.
mpi.fruitfly.general - package mpi.fruitfly.general
mpi.fruitfly.math - package mpi.fruitfly.math
mpi.fruitfly.math.datastructures - package mpi.fruitfly.math.datastructures
mpi.fruitfly.registration - package mpi.fruitfly.registration
mpicbg.trakem2.align - package mpicbg.trakem2.align
mpicbg.trakem2.align.concurrent - package mpicbg.trakem2.align.concurrent
mpicbg.trakem2.transform - package mpicbg.trakem2.transform
mpicbg.trakem2.util - package mpicbg.trakem2.util
multipleHypotheses - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
multipleHypotheses - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
multipleHypotheses - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
MultiplyARGBComposite - Class in ini.trakem2.display.graphics
MultiThreading - Class in mpi.fruitfly.general: MultiThreading.
MultiThreading() - Constructor for class mpi.fruitfly.general.MultiThreading

N

n1 - Variable in class mpi.fruitfly.math.datastructures.FloatArray4D
n2 - Variable in class mpi.fruitfly.math.datastructures.FloatArray4D
n3 - Variable in class mpi.fruitfly.math.datastructures.FloatArray4D
n4 - Variable in class mpi.fruitfly.math.datastructures.FloatArray4D
n_layers_color_cue - Variable in class ini.trakem2.display.LayerSet
n_points - Variable in class ini.trakem2.display.Ball: The number of points.
n_points - Variable in class ini.trakem2.display.Pipe: The number of points.
n_points - Variable in class ini.trakem2.display.Polyline: The number of points.
n_points - Variable in class ini.trakem2.display.Profile: The number of points.
names - Variable in class lenscorrection.Distortion_Correction.PluginParam: Original and calibrated images are supposed to have the same names, but are in different directories
nBins - Variable in class ini.trakem2.imaging.filters.CorrectBackground: Number of histogram bins.
neighbors - Variable in class ini.trakem2.analysis.Vertex
neighborWeight - Static variable in class org.janelia.intensity.MatchIntensities
NeuroML - Class in ini.trakem2.io
NeuroML() - Constructor for class ini.trakem2.io.NeuroML
New_DB_Project - Class in ini.trakem2
New_DB_Project() - Constructor for class ini.trakem2.New_DB_Project
New_Project - Class in ini.trakem2
New_Project() - Constructor for class ini.trakem2.New_Project
newDBProject() - Static method in class ini.trakem2.Project: Create a new PostgreSQL-based TrakEM2 project.
newFixedThreadPool(int) - Static method in class ini.trakem2.utils.Utils: Creates a new fixed thread pool whose threads are in the same ThreadGroup as the Thread that calls this method.
newFixedThreadPool(String) - Static method in class ini.trakem2.utils.Utils: Creates a new fixed thread pool with as many threads as CPUs, and whose threads are in the same ThreadGroup as the Thread that calls this method.
newFixedThreadPool(int, String) - Static method in class ini.trakem2.utils.Utils
newFixedThreadPool(int, String, boolean) - Static method in class ini.trakem2.utils.Utils
newFSProject(String) - Static method in class ini.trakem2.Project: Creates a new project to be based on .xml and image files, not a database.
newFSProject(String, TemplateThing) - Static method in class ini.trakem2.Project
newFSProject(String, TemplateThing, String) - Static method in class ini.trakem2.Project: Creates a new project to be based on .xml and image files, not a database.
newFSProject(String, TemplateThing, String, boolean) - Static method in class ini.trakem2.Project
newInstance(float, float, Layer) - Method in class ini.trakem2.display.AreaTree.AreaNode
newInstance() - Method in class ini.trakem2.display.AreaTree
newInstance(float, float, Layer) - Method in class ini.trakem2.display.Connector.ConnectorNode
newInstance() - Method in class ini.trakem2.display.Connector
newInstance(float, float, Layer) - Method in class ini.trakem2.display.Node
newInstance() - Method in class ini.trakem2.display.Tree: Create a new instance, intialized with same ZDisplayable-level parameters (affine, color, title, etc.).
newInstance() - Method in class ini.trakem2.display.Treeline
newInstance(float, float, Layer) - Method in class ini.trakem2.display.Treeline.RadiusNode
newNode(float, float, Layer, Node<?>) - Method in class ini.trakem2.display.AreaTree
newNode(HashMap<String, String>) - Method in class ini.trakem2.display.AreaTree
newNode(float, float, Layer, Node<?>) - Method in class ini.trakem2.display.Connector
newNode(HashMap<String, String>) - Method in class ini.trakem2.display.Connector
newNode(float, float, Layer, Node<?>) - Method in class ini.trakem2.display.Tree
newNode(HashMap<String, String>) - Method in class ini.trakem2.display.Tree: To reconstruct from XML.
newNode(float, float, Layer, Node<?>) - Method in class ini.trakem2.display.Treeline
newNode(HashMap<String, String>) - Method in class ini.trakem2.display.Treeline
newThread(Runnable) - Method in class ini.trakem2.utils.Dispatcher.DispatcherThreadFactory
newThreads() - Static method in class mpi.fruitfly.general.MultiThreading
newThreads(int) - Static method in class mpi.fruitfly.general.MultiThreading
next(Layer) - Method in class ini.trakem2.display.LayerSet
next() - Method in class ini.trakem2.display.Node.BreadthFirstSubtreeIterator
next() - Method in class ini.trakem2.display.Node.FilteredIterator
next() - Method in class ini.trakem2.display.Node.SlabIterator
next() - Method in class ini.trakem2.utils.CircularSequence
nextLayer(int) - Method in class ini.trakem2.display.Display: If shift is down, scroll to the next non-empty layer; otherwise, if scroll_step is larger than 1, then scroll 'scroll_step' layers ahead; else just the next Layer.
nextNonEmpty(Layer) - Method in class ini.trakem2.display.LayerSet
Node<T> - Class in ini.trakem2.display: Can only have one parent, so there aren't cyclic graphs.
Node(float, float, Layer) - Constructor for class ini.trakem2.display.Node
Node(HashMap<String, String>) - Constructor for class ini.trakem2.display.Node: To reconstruct from XML, without a layer.
Node.BranchAndEndNodeIterator - Class in ini.trakem2.display
Node.BranchNodeIterator - Class in ini.trakem2.display
Node.BreadthFirstSubtreeIterator - Class in ini.trakem2.display: For a given starting node, iterates over the complete set of children nodes, recursively and breadth-first.
Node.EndNodeIterator - Class in ini.trakem2.display
Node.FilteredIterator - Class in ini.trakem2.display
Node.NodeCollection - Class in ini.trakem2.display: Read-only Collection with a very expensive size().
Node.NodeIterator - Class in ini.trakem2.display: Stateful abstract Node iterator.
Node.Operation - Interface in ini.trakem2.display: An operation to be applied to a specific Node.
Node.SlabIterator - Class in ini.trakem2.display: For a given starting node, iterates all the way to the next end node or branch node, inclusive.
Node.SubtreeIterator - Class in ini.trakem2.display
NODE_FLAVOR - Static variable in class ini.trakem2.tree.TransferableNode
node_layer_map - Variable in class ini.trakem2.display.Tree
NodeCollection(Node, Class<?>) - Constructor for class ini.trakem2.display.Node.NodeCollection
NodeIterator(Node) - Constructor for class ini.trakem2.display.Node.NodeIterator
NodePath(Node<T>, Node<T>) - Constructor for class ini.trakem2.display.Tree.NodePath
NodePath(Node<T>, Node<T>, List<Node<T>>) - Constructor for class ini.trakem2.display.Tree.NodePath: Assumes that a is the first element in path, and b the last, and that a has a lower degree than b (that is, a is upstream of b).
NodeRenderer() - Constructor for class ini.trakem2.tree.DNDTree.NodeRenderer
NonLinearTransform - Class in lenscorrection
NonLinearTransform(double[][], double[], double[], int, int, int) - Constructor for class lenscorrection.NonLinearTransform
NonLinearTransform(int, int, int) - Constructor for class lenscorrection.NonLinearTransform
NonLinearTransform() - Constructor for class lenscorrection.NonLinearTransform
NonLinearTransform(String) - Constructor for class lenscorrection.NonLinearTransform
NonLinearTransform(double[][], int, int) - Constructor for class lenscorrection.NonLinearTransform
NonLinearTransformMode - Class in ini.trakem2.display
NonLinearTransformMode(Display, List<Displayable>) - Constructor for class ini.trakem2.display.NonLinearTransformMode
NonLinearTransformMode(Display) - Constructor for class ini.trakem2.display.NonLinearTransformMode
NORM_VALUES - Static variable in class mpi.fruitfly.general.ImageArrayConverter
normalize - Variable in class ini.trakem2.analysis.Compare.CATAParameters
Normalize - Class in ini.trakem2.imaging.filters
Normalize() - Constructor for class ini.trakem2.imaging.filters.Normalize
Normalize(double, double) - Constructor for class ini.trakem2.imaging.filters.Normalize
Normalize(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.Normalize
normalize(Vector3) - Method in class ini.trakem2.utils.Vector3
normalize(FloatArray) - Static method in class mpi.fruitfly.registration.ImageFilter
NormalizeLocalContrast - Class in ini.trakem2.imaging.filters
NormalizeLocalContrast() - Constructor for class ini.trakem2.imaging.filters.NormalizeLocalContrast
NormalizeLocalContrast(int, int, float, boolean, boolean) - Constructor for class ini.trakem2.imaging.filters.NormalizeLocalContrast
NormalizeLocalContrast(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.NormalizeLocalContrast
normFloatArray(FloatArray) - Static method in class mpi.fruitfly.general.ImageArrayConverter
normPixelValuesToByte(int[][], boolean) - Static method in class mpi.fruitfly.general.ImageArrayConverter
normPixelValuesToByte(float[][], boolean) - Static method in class mpi.fruitfly.general.ImageArrayConverter
normPixelValuesToByte(float[][][], boolean) - Static method in class mpi.fruitfly.general.ImageArrayConverter
NORTH - Static variable in class ini.trakem2.display.LayerSet
NORTHEAST - Static variable in class ini.trakem2.display.LayerSet
NORTHWEST - Static variable in class ini.trakem2.display.LayerSet
NOT_FOUND - Static variable in class ini.trakem2.persistence.Loader
notationDeclaration(String, String, String) - Method in class ini.trakem2.persistence.TMLHandler
now() - Static method in class ini.trakem2.utils.Utils: Returns the time as HH:MM:SS
nStaticServiceThreads() - Static method in class ini.trakem2.persistence.FSLoader
NUM_PROCESSORS - Static variable in class ini.trakem2.parallel.Process
numberOfImages - Variable in class lenscorrection.Distortion_Correction.PluginParam
numCoefficients - Static variable in class org.janelia.intensity.MatchIntensities
NumericalSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.NumericalSetter
NumericalSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.NumericalSetter
NumericalSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.NumericalSetter

O

o_height - Variable in class ini.trakem2.display.Patch.TransformProperties
o_width - Variable in class ini.trakem2.display.Patch.TransformProperties
ob - Variable in class ini.trakem2.utils.OptionPanel.Setter
object - Variable in class ini.trakem2.display.Coordinate
object - Variable in class ini.trakem2.display.Region
obtainOrigin(Line3D[], int, Vector3d[]) - Static method in class ini.trakem2.analysis.Compare: Generate calibrated origin of coordinates.
off - Variable in class ini.trakem2.display.AbstractRepaintThread
offsetToPowerOf2(int) - Static method in class mpi.fruitfly.math.General: Berechnet die Differenz(Offset) der ganzzahligen Eingabe zur naechsten Zweierpotenz.
onBackground() - Method in class ini.trakem2.utils.Worker: Whether the work is done on the background, without need to bring ImageJ toolbar to front for instance.
oneDimArrayToTwoDimArray(double[], int, int) - Static method in class mpi.fruitfly.general.ArrayConverter
oneDimArrayToTwoDimArrayInvert(double[], int, int) - Static method in class mpi.fruitfly.general.ArrayConverter
open(String, boolean) - Static method in class ini.trakem2.io.ImageSaver
Open_DB_Project - Class in ini.trakem2
Open_DB_Project() - Constructor for class ini.trakem2.Open_DB_Project
Open_Project - Class in ini.trakem2
Open_Project() - Constructor for class ini.trakem2.Open_Project
openDBProject() - Static method in class ini.trakem2.Project: Open a TrakEM2 project from the database.
opener - Variable in class ini.trakem2.persistence.Loader
openFromStream(InputStream, boolean) - Static method in class ini.trakem2.io.ImageSaver: The stream IS NOT closed by this method.
openFSProject(String, boolean) - Method in class ini.trakem2.persistence.FSLoader: Returns TMLHandler.getProjectData() .
openFSProject(String) - Static method in class ini.trakem2.Project
openFSProject(String, boolean) - Static method in class ini.trakem2.Project: Opens a project from an .xml file.
openGreyImage(String) - Static method in class ini.trakem2.io.ImageSaver
openGreyTIFF(String) - Static method in class ini.trakem2.io.ImageSaver
openImage(String, boolean) - Static method in class ini.trakem2.io.ImageSaver: Open an image file including the alpha channel if it has one; will open JPEG, PNG and BMP.
openImage(String) - Method in class ini.trakem2.persistence.Loader: Fixes paths before presenting them to the file system, in an OS-dependent manner.
openImagePlus(String) - Method in class ini.trakem2.persistence.Loader: Tries up to MAX_RETRIES to open an ImagePlus at path if there is an OutOfMemoryError.
openJpegAlpha(String) - Static method in class ini.trakem2.io.ImageSaver: Open a jpeg file including the alpha channel if it has one.
openLater() - Static method in class ini.trakem2.display.Display: After reloading a project from the database, open the Displays that the project had.
openPNGAlpha(String) - Static method in class ini.trakem2.io.ImageSaver
openStack() - Method in class ini.trakem2.persistence.Loader: A dialog to open a stack, making sure there is enough memory for it.
openTextFile(String) - Static method in class ini.trakem2.utils.Utils
openTextFileChars(String) - Static method in class ini.trakem2.utils.Utils
openTextFileLines(String) - Static method in class ini.trakem2.utils.Utils: Returns the file found at path as an array of lines, or null if not found.
openTIFF(String, boolean) - Static method in class ini.trakem2.io.ImageSaver: Opens RGB or RGB + alpha images stored in TIFF format.
Operation<I,O> - Interface in ini.trakem2.utils
optimizeTileConfiguration(ArrayList<AbstractAffineTile2D<?>>, ArrayList<AbstractAffineTile2D<?>>, StitchingTEM.PhaseCorrelationParam) - Static method in class ini.trakem2.imaging.StitchingTEM: Optimize tile configuration by removing bad matches
optimizeTileConfiguration(Align.ParamOptimize, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align: Align a set of tiles that are interconnected by point-correspondences.
OptionPanel - Class in ini.trakem2.utils
OptionPanel() - Constructor for class ini.trakem2.utils.OptionPanel
OptionPanel.BooleanSetter - Class in ini.trakem2.utils
OptionPanel.ChoiceIntSetter - Class in ini.trakem2.utils
OptionPanel.ChoiceObjectSetter - Class in ini.trakem2.utils
OptionPanel.ChoiceStringSetter - Class in ini.trakem2.utils
OptionPanel.DoubleSetter - Class in ini.trakem2.utils
OptionPanel.FloatSetter - Class in ini.trakem2.utils
OptionPanel.IntSetter - Class in ini.trakem2.utils
OptionPanel.NumericalSetter - Class in ini.trakem2.utils
OptionPanel.Setter - Class in ini.trakem2.utils
OptionPanel.StringSetter - Class in ini.trakem2.utils
org.janelia.intensity - package org.janelia.intensity
originalPatches - Variable in class ini.trakem2.display.GroupingMode
OriginalSource() - Constructor for class mpicbg.trakem2.transform.ExportUnsignedByte.OriginalSource
outside - Variable in class ini.trakem2.display.Patch.PatchImage: The outside mask, coordinate-transformed if null != ct.
overlap - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
Overlay - Class in ini.trakem2.display
Overlay() - Constructor for class ini.trakem2.display.Overlay
overwriteXMLFile - Variable in class ini.trakem2.persistence.XMLOptions: Whether to overwrite the XML file or not.

P

p - Variable in class ini.trakem2.display.Ball: The array of clicked points.
p - Variable in class ini.trakem2.display.Pipe: The array of clicked points.
p - Variable in class ini.trakem2.display.Polyline: The array of clicked x,y points as [2][n].
p - Variable in class ini.trakem2.display.Profile: The array of clicked points.
P - Class in ini.trakem2.imaging
P() - Constructor for class ini.trakem2.imaging.P
p - Static variable in class lenscorrection.Distortion_Correction
p - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
p - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
p_i - Variable in class ini.trakem2.display.Pipe: The array of interpolated points generated from p, p_l and p_r.
p_i - Variable in class ini.trakem2.display.Profile: The array of interpolated points generated from p, p_l and p_r.
p_l - Variable in class ini.trakem2.display.Pipe: The array of left control points, one for each clicked point.
p_l - Variable in class ini.trakem2.display.Profile: The array of left control points, one for each clicked point.
p_layer - Variable in class ini.trakem2.display.Ball: The array of Layers over which each point lives
p_layer - Variable in class ini.trakem2.display.Pipe: The array of Layers over which the points of this pipe live
p_layer - Variable in class ini.trakem2.display.Polyline: The array of Layers over which the points of this pipe live
p_r - Variable in class ini.trakem2.display.Pipe: The array of right control points, one for each clicked point.
p_r - Variable in class ini.trakem2.display.Profile: The array of right control points, one for each clicked point.
p_snap - Static variable in class mpicbg.trakem2.align.AlignTask: The ParamOptimize object containg all feature extraction and registration model parameters for the "snap" function.
p_width - Variable in class ini.trakem2.display.Ball: The width of each point.
p_width - Variable in class ini.trakem2.display.Pipe: The width of each point.
p_width_i - Variable in class ini.trakem2.display.Pipe: The interpolated width for each interpolated point.
pack() - Method in class ini.trakem2.display.Display
pack(LayerSet) - Static method in class ini.trakem2.display.Display
PADDING - Static variable in class ini.trakem2.display.Selection: Outward padding in pixels around the selected Displayables maximum enclosing box that may need repainting when updating the screen.
paint() - Method in class ini.trakem2.display.AbstractOffscreenThread
paint(Rectangle) - Method in class ini.trakem2.display.AbstractRepaintThread: Queue a new request for painting, updating offscreen graphics.
paint(Rectangle, boolean) - Method in class ini.trakem2.display.AbstractRepaintThread: Queue a new request for painting.
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.AreaList
paint(Graphics2D, AffineTransform, boolean, Color) - Method in class ini.trakem2.display.AreaWrapper
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Ball
paint(Graphics2D, Rectangle, double, Color) - Method in class ini.trakem2.display.Bucket
paint(Graphics2D) - Method in class ini.trakem2.display.Display.GridOverlay
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Displayable
paint(Graphics) - Method in class ini.trakem2.display.DisplayablePanel
paint(Graphics) - Method in class ini.trakem2.display.DisplayCanvas
paint(Graphics) - Method in class ini.trakem2.display.DisplayNavigator
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Dissector
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.DLabel
paint(Graphics) - Method in class ini.trakem2.display.FakeImageWindow
paint(Graphics, double, Rectangle, boolean) - Method in class ini.trakem2.display.FreeHandProfile
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.GroupingMode.ScreenPatchRange
paint(Graphics) - Method in class ini.trakem2.display.LayerPanel
paint(Graphics2D, Rectangle, double, boolean, int, Layer) - Method in class ini.trakem2.display.LayerSet
paint(Graphics2D, Rectangle, double) - Method in class ini.trakem2.display.ManualAlignMode.Landmarks
paint(Graphics2D, Rectangle, double) - Method in class ini.trakem2.display.Overlay
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in interface ini.trakem2.display.Paintable
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Patch
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Pipe
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Polyline
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Profile
paint(Graphics) - Method in class ini.trakem2.display.SnapshotPanel: Paint the snapshot image over a black background that represents a scaled Layer.
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Stack: Slow paint: will wait until the image is generated and cached, then paint it.
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Tree
paint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>, boolean, boolean) - Method in class ini.trakem2.display.Tree
paint(Graphics) - Method in class ini.trakem2.display.YesNoDialog
paint(Graphics) - Method in class ini.trakem2.imaging.ContrastPlot
paint(Pipe, Map<Layer, ImageProcessor>, int, float) - Static method in class ini.trakem2.utils.Utils: Paints an approximation of the pipe into the set of slices.
paint_arrows - Variable in class ini.trakem2.display.LayerSet
paint_edge_confidence_boxes - Variable in class ini.trakem2.display.LayerSet
PAINT_ERODE - Static variable in class ini.trakem2.display.AreaWrapper
PAINT_EXCLUDE - Static variable in class ini.trakem2.display.AreaWrapper
paint_mode - Variable in class ini.trakem2.display.AreaWrapper.PaintParameters
PAINT_OVERLAP - Static variable in class ini.trakem2.display.AreaWrapper
paint_tags - Variable in class ini.trakem2.display.LayerSet
Paintable - Interface in ini.trakem2.display
paintAsBox(Graphics2D) - Method in class ini.trakem2.display.Displayable
paintData(Graphics2D, Rectangle, Tree<Area>, AffineTransform, Color, Layer) - Method in class ini.trakem2.display.AreaTree.AreaNode
paintData(Graphics2D, Rectangle, Tree<Float>, AffineTransform, Color, Layer) - Method in class ini.trakem2.display.Connector.ConnectorNode
paintData(Graphics2D, Rectangle, Tree<T>, AffineTransform, Color, Layer) - Method in class ini.trakem2.display.Node
paintData(Graphics2D, Rectangle, Tree<Float>, AffineTransform, Color, Layer) - Method in class ini.trakem2.display.Treeline.RadiusNode
painter - Variable in class ini.trakem2.display.GroupingMode
Painter() - Constructor for class ini.trakem2.display.GroupingMode.Painter
paintHandle(Graphics2D, Rectangle, double, Tree<Area>) - Method in class ini.trakem2.display.AreaTree.AreaNode
paintHandle(Graphics2D, Rectangle, double, Tree<Float>) - Method in class ini.trakem2.display.Connector.ConnectorNode
paintHandle(Graphics2D, Rectangle, double, Tree<T>) - Method in class ini.trakem2.display.Node
paintHandle(Graphics2D, Rectangle, double, Tree<T>, boolean) - Method in class ini.trakem2.display.Node: Paint in the context of offscreen space, without transformations.
paintOffscreen(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Displayable: Paints waiting for data to load, if necessary.
paintOffscreen(Layer, int, int, Rectangle, double, Displayable, int, Rectangle, Loader, HashMap<Color, Layer>, ArrayList<LayerPanel>, int, GraphicsSource, boolean, ArrayList<Displayable>) - Method in class ini.trakem2.display.DisplayCanvas: Deprecated.
paintOffscreen(Layer, List<Layer>, int, int, Rectangle, double, Displayable, int, Rectangle, Loader, HashMap<Color, Layer>, ArrayList<LayerPanel>, int, GraphicsSource, boolean, ArrayList<Displayable>, boolean) - Method in class ini.trakem2.display.DisplayCanvas: This method uses data only from the arguments, and changes none.
paintOffscreen(Layer, List<Layer>, ArrayList<Displayable>, Displayable, int, int, int, Loader, HashMap<Color, Layer>, ArrayList<LayerPanel>, int, GraphicsSource, boolean, int) - Method in class ini.trakem2.display.DisplayCanvas
paintOffscreen(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Patch
paintOnTop(Graphics2D, Display, Rectangle, double) - Method in class ini.trakem2.display.graphics.DefaultGraphicsSource: Paints bounding boxes of selected objects as pink and active object as white.
paintOnTop(Graphics2D, Display, Rectangle, double) - Method in interface ini.trakem2.display.graphics.GraphicsSource: The canvas will call this method after painting everything else.
paintOnTop(Graphics2D, Display, Rectangle, double) - Method in class ini.trakem2.display.graphics.TestGraphicsSource: Does nothing.
PaintParameters() - Constructor for class ini.trakem2.display.AreaWrapper.PaintParameters
paintsAt(Layer) - Method in class ini.trakem2.display.AreaList
paintsAt(Layer) - Method in class ini.trakem2.display.Ball
paintsAt(Layer) - Method in class ini.trakem2.display.Tree
paintsAt(Layer) - Method in class ini.trakem2.display.ZDisplayable: Check if this instance will paint anything at the level of the given Layer.
paintsBelow(Displayable, Displayable) - Method in class ini.trakem2.display.Display: If the other paints under the base.
paintSnapshot(Graphics2D, Layer, List<Layer>, Rectangle, double) - Method in class ini.trakem2.display.Displayable
paintSnapshot(Graphics2D, Layer, List<Layer>, Rectangle, double) - Method in class ini.trakem2.display.Dissector: Always paint as box.
paintSnapshot(Graphics2D, Layer, List<Layer>, Rectangle, double) - Method in class ini.trakem2.display.Patch
paintSnapshot(Graphics2D, Layer, List<Layer>, Rectangle, double) - Method in class ini.trakem2.display.Tree
paintsWithFalseColor() - Method in class ini.trakem2.display.Patch
Pair(Node<T>, Node<T>) - Constructor for class ini.trakem2.display.Tree.Pair
pair - Variable in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
pairOverlappingTiles(List<AAT>, List<AbstractAffineTile2D<?>[]>, boolean) - Static method in class mpicbg.trakem2.align.AbstractAffineTile2D: Search a List of Tiles for overlapping pairs.
pairOverlappingTiles(List<AAT>, List<AbstractAffineTile2D<?>[]>) - Static method in class mpicbg.trakem2.align.AbstractAffineTile2D: Search a List of Tiles for overlapping pairs.
pairOverlappingTiles(List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>, boolean) - Static method in class mpicbg.trakem2.align.AbstractAffineTile2D: Search two Lists of Tiles for overlapping pairs.
pairOverlappingTiles(List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>) - Static method in class mpicbg.trakem2.align.AbstractAffineTile2D: Search two Lists of Tiles for overlapping pairs.
pairTiles(List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>) - Static method in class mpicbg.trakem2.align.AbstractAffineTile2D: Pair all Tiles from a List.
pairTiles(List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>) - Static method in class mpicbg.trakem2.align.AbstractAffineTile2D: Pair all Tiles from two Lists.
pairwiseAlign(AbstractAffineTile2D<?>, Set<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align
pairwiseAlignTileConfiguration(List<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align
ParallelMapping<I,O> - Class in ini.trakem2.parallel: Like clojure's pmap, given a sequence of inputs obtained from an Iterable, this Iterable will apply a function to each input ahead of consumption in a pool of threads managed by an ExecutorService.
ParallelMapping(Iterable, TaskFactory<I, O>) - Constructor for class ini.trakem2.parallel.ParallelMapping
ParallelMapping(Iterator, TaskFactory<I, O>) - Constructor for class ini.trakem2.parallel.ParallelMapping
ParallelMapping(int, Iterable, TaskFactory<I, O>) - Constructor for class ini.trakem2.parallel.ParallelMapping
ParallelMapping(int, Iterator, TaskFactory<I, O>) - Constructor for class ini.trakem2.parallel.ParallelMapping
param - Static variable in class mpicbg.trakem2.align.Align
Param() - Constructor for class mpicbg.trakem2.align.Align.Param
Param() - Constructor for class mpicbg.trakem2.align.ElasticLayerAlignment.Param
Param(int, int, float, int, int, int, boolean, int, float, int, int, float, boolean, float, int, int, int, int, int, float, int, boolean, boolean, boolean, boolean, int, double, double, int, float, float, int, float, float, int, boolean, double, float, int, float, int, double, boolean, boolean) - Constructor for class mpicbg.trakem2.align.ElasticLayerAlignment.Param
Param() - Constructor for class mpicbg.trakem2.align.ElasticMontage.Param
Param() - Constructor for class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param
Param(int, int, float, int, int, int, boolean, int, float, int, int, float, double, float, int, int, int, int, int, float, int, boolean, boolean, boolean, int, boolean, boolean) - Constructor for class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param
paramOptimize - Static variable in class mpicbg.trakem2.align.Align
ParamOptimize() - Constructor for class mpicbg.trakem2.align.Align.ParamOptimize
ParamPointMatch() - Constructor for class mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch
parent - Variable in class ini.trakem2.display.Node
parse(String) - Static method in class ini.trakem2.io.CoordinateTransformXML
parseDTD(StringBuilder) - Static method in class ini.trakem2.tree.DTDParser: Parses a chunk of text into a hierarchy of TemplateThing instances, the roots of which are in the returned array.
parseDTDFile(String) - Static method in class ini.trakem2.tree.DTDParser: Parses the tags of a .dtd file.
parseXMLFile(String) - Static method in class ini.trakem2.tree.DTDParser: Parses a !DOCTYPE chunk from an .xml file, if any.
parseXMLOptions(HashMap<String, String>) - Method in class ini.trakem2.persistence.FSLoader: Specific options for the Loader which exist as attributes to the Project XML node.
parseXMLOptions(HashMap<String, String>) - Method in class ini.trakem2.Project
part(long, ShapeRoi) - Method in class ini.trakem2.display.AreaList: Subtracts the given ROI, and then creates a new AreaList with identical properties and the content of the subtracted part.
paste() - Method in class ini.trakem2.display.FakeImageWindow
paste() - Method in class ini.trakem2.imaging.PatchStack
Patch - Class in ini.trakem2.display
Patch(Project, String, double, double, ImagePlus) - Constructor for class ini.trakem2.display.Patch: Construct a Patch from an image; most likely you will need to add the file path to the imp by calling Loader.addedPatchFrom(String, Patch), as in this example: project.getLoader().addedPatchFrom("/path/to/file.png", thePatch);
Patch(Project, long, String, float, float, int, int, int, boolean, double, double, AffineTransform) - Constructor for class ini.trakem2.display.Patch: Reconstruct a Patch from the database.
Patch(Project, String, float, float, int, int, int, float, Color, boolean, double, double, AffineTransform, String) - Constructor for class ini.trakem2.display.Patch: Create a new Patch defining all necessary parameters; it is the responsibility of the caller to ensure that the parameters are in agreement with the image contained in the file_path.
Patch(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Patch: Reconstruct from an XML entry.
patch - Variable in class mpicbg.trakem2.align.AbstractAffineTile2D
patch - Variable in class mpicbg.trakem2.transform.ExportUnsignedShort.PatchIntensityRange
Patch.PatchImage - Class in ini.trakem2.display
Patch.TransformProperties - Class in ini.trakem2.display
patches - Variable in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
patches - Variable in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
patches - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
patches_dir - Variable in class ini.trakem2.persistence.XMLOptions: Is used if Patch images have to be exported to a new directory.
PatchRange() - Constructor for class ini.trakem2.display.GroupingMode.PatchRange
PatchScript - Class in ini.trakem2.scripting
PatchScript() - Constructor for class ini.trakem2.scripting.PatchScript
PatchStack - Class in ini.trakem2.imaging: Assumed is all Patch instances in the array are of the same size, live in consecutive layers of the same thickness.
PatchStack(Patch[], int) - Constructor for class ini.trakem2.imaging.PatchStack
path - Variable in class ini.trakem2.display.Tree.NodePath: The ordered list of nodes from a to b, both included.
PEN - Static variable in class ini.trakem2.utils.ProjectToolbar: A tool to draw/edit.
PENCIL - Static variable in class ini.trakem2.utils.ProjectToolbar: A tool to draw freehand and then autoconvert to Bezier curves.
PhaseCorrelationCalculator - Class in ini.trakem2.imaging
PhaseCorrelationCalculator(ImagePlus, ImagePlus) - Constructor for class ini.trakem2.imaging.PhaseCorrelationCalculator
PhaseCorrelationParam(double, float, boolean, boolean, double, double) - Constructor for class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
PhaseCorrelationParam() - Constructor for class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam: Empty constructor
Pipe - Class in ini.trakem2.display
Pipe(Project, String, double, double) - Constructor for class ini.trakem2.display.Pipe
Pipe(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Pipe: Construct an unloaded Pipe from the database.
Pipe(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Pipe: Construct a Pipe from an XML entry.
PIXELARRAY - Static variable in class ini.trakem2.display.Layer
plot_height - Variable in class ini.trakem2.analysis.Compare.CATAParameters
plot_max_x - Variable in class ini.trakem2.analysis.Compare.CATAParameters
plot_max_y - Variable in class ini.trakem2.analysis.Compare.CATAParameters
plot_width - Variable in class ini.trakem2.analysis.Compare.CATAParameters
PluginParam() - Constructor for class lenscorrection.Distortion_Correction.PluginParam
pm12 - Variable in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
pm21 - Variable in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
po - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
PointMatchCollectionAndAffine(AffineTransform, Collection<PointMatch>) - Constructor for class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine
pointMatches - Variable in class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine
PointMatchFilter - Interface in org.janelia.intensity
Polyline - Class in ini.trakem2.display: A sequence of points that make multiple chained line segments.
Polyline(Project, String) - Constructor for class ini.trakem2.display.Polyline: New empty Polyline.
Polyline(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Polyline
Polyline(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Polyline: Reconstruct from XML.
PolynomialModel2D - Class in lenscorrection: A wrpper for NonLinearTransform and the AbstractAffineModel2D to which it is regularized.
PolynomialModel2D() - Constructor for class lenscorrection.PolynomialModel2D
popNode(Node<T>) - Method in class ini.trakem2.display.Tree: Remove a node only (not its subtree).
port - Variable in class ini.trakem2.utils.RedPhone: May change up to 31000, searching for a port not in use; the port that will be used is printed.
postGaussian - Variable in class ini.trakem2.imaging.filters.CorrectBackground: Whether to process the approximated median filter with a Gaussian
pow(int, int) - Static method in class mpi.fruitfly.math.General
PP - Static variable in class ini.trakem2.display.AreaWrapper
ppm - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
preAppendCoordinateTransform(CoordinateTransform) - Method in class ini.trakem2.display.Patch: Pre-append a CoordinateTransform to the current CoordinateTransformList.
preConcatenate(AffineTransform, Collection<Displayable>) - Static method in class ini.trakem2.display.Displayable: Preconcatenate the at to every Displayable in ds, without touching their links; then the buckets are updated for all necessary layers.
preload(Collection<Patch>, double, boolean) - Static method in class ini.trakem2.persistence.Loader: Disabled when on low memory condition, or when num_preloader_threads is smaller than 1.
preload(Patch, double, boolean) - Static method in class ini.trakem2.persistence.Loader: Returns null when on low memory condition.
preload_ahead - Variable in class ini.trakem2.display.LayerSet
prePaint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Displayable
prePaint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.GroupingMode.ScreenPatchRange
prepaint - Variable in class ini.trakem2.display.LayerSet
prePaint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in interface ini.trakem2.display.Paintable
prePaint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Patch: Paint first whatever is available, then request that the proper image be loaded and painted.
prePaint(Graphics2D, Rectangle, double, boolean, int, Layer, List<Layer>) - Method in class ini.trakem2.display.Stack: Will not paint but fork a task to create an image to paint later, when not already cached.
preProcess(Patch, ImagePlus, long) - Method in class ini.trakem2.persistence.Loader
PREPROCESSED - Static variable in class ini.trakem2.persistence.Loader
preset - Variable in class ini.trakem2.analysis.Compare.CATAParameters
preset_names - Variable in class ini.trakem2.analysis.Compare.CATAParameters
presets - Variable in class ini.trakem2.analysis.Compare.CATAParameters
preTransform(AffineTransform, boolean) - Method in class ini.trakem2.display.Displayable: preConcatenate the given affine transform to this Displayable's affine.
previous(Layer) - Method in class ini.trakem2.display.LayerSet
previous() - Method in class ini.trakem2.utils.CircularSequence
previousLayer(int) - Method in class ini.trakem2.display.Display: If shift is down, scroll to the previous non-empty layer; otherwise, if scroll_step is larger than 1, then scroll 'scroll_step' layers backward; else just the previous Layer.
previousNonEmpty(Layer) - Method in class ini.trakem2.display.LayerSet
print(Throwable) - Static method in class ini.trakem2.utils.IJError
print(Throwable, boolean) - Static method in class ini.trakem2.utils.IJError
print() - Method in class lenscorrection.NonLinearTransform
printCache() - Method in class ini.trakem2.persistence.Loader
printCaches() - Static method in class ini.trakem2.persistence.Loader
printCacheStatus() - Static method in class ini.trakem2.persistence.Loader
printCaller(Object) - Static method in class ini.trakem2.utils.Utils: Find out which method from which class called the method where the printCaller is used; for debugging purposes.
printCaller(Object, int) - Static method in class ini.trakem2.utils.Utils
printDebugInfo() - Method in class ini.trakem2.display.LayerSet
printInfo() - Method in class mpicbg.trakem2.transform.ExportBestFlatImage
println(String) - Method in class mpicbg.trakem2.align.TileConfiguration
printMemState() - Static method in class ini.trakem2.persistence.Loader
printPoints() - Method in class ini.trakem2.display.Profile
process() - Method in class ini.trakem2.imaging.BinaryInterpolation2D
process(float) - Method in class ini.trakem2.imaging.BinaryInterpolation2D: The first time, it will prepare the distance transform images, which are computed only once.
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.CLAHE
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.CorrectBackground
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.DefaultMinAndMax
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.EnhanceContrast
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.EqualizeHistogram
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.GaussianBlur
process(ImageProcessor) - Method in interface ini.trakem2.imaging.filters.IFilter: Execute the filter, returning possibly a new ImageProcessor, or the same as given.
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.Invert
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.LUTBlue
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.LUTCustom
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.LUTCyan
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.LUTGreen
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.LUTMagenta
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.LUTRed
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.LUTYellow
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.Normalize
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.NormalizeLocalContrast
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.RankFilter
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.ResetMinAndMax
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.SubtractBackground
process(ImageProcessor) - Method in class ini.trakem2.imaging.filters.ValueToNoise
process(I, int) - Method in class ini.trakem2.parallel.CountingTaskFactory: The actual processing on the given @param input; override to define a task to be performed over @param input.
Process - Class in ini.trakem2.parallel: For all methods, if the number of processors given as argument is zero or larger than the maximum available plus 2, the number of processors will be adjusted to fall within the range [1, max+2].
Process() - Constructor for class ini.trakem2.parallel.Process
process(I) - Method in class ini.trakem2.parallel.TaskFactory: The actual processing on the given @param input; override to define a task to be performed over @param input.
processAdjustPropertiesDialog(GenericDialog) - Method in class ini.trakem2.display.Displayable
processKeyBinding(KeyStroke, KeyEvent, int, boolean) - Method in class ini.trakem2.tree.DNDTree: Prevent processing.
processKeyEvent(KeyEvent) - Method in class ini.trakem2.tree.DNDTree: Removing all KeyListener and ActionMap is not enough: one must override this method to stop the JTree from reacting to keys.
processKeyEvent(KeyEvent) - Method in class ini.trakem2.utils.IntegerField
Profile - Class in ini.trakem2.display: A class to be a user-outlined profile over an image, which is painted with a particular color and also holds an associated text label.
Profile(Project, String, double, double) - Constructor for class ini.trakem2.display.Profile: A new user-requested Profile.
Profile(Project, String, double, double, Point2D.Double[]) - Constructor for class ini.trakem2.display.Profile: Construct a Bezier Profile object from a set of points mixed in this pattern: PCCPCCPCCPCCP , so, [PCC]n where P = backbone point and C = control point.
Profile(Project, long, String, float, boolean, Color, double[][][], boolean, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Profile: Construct a Bezier Profile from the database.
Profile(Project, long, String, float, float, float, boolean, Color, boolean, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Profile: Construct a Bezier Profile from the database, but the points will be loaded later, when actually needed, by calling setupForDisplay().
Profile(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Profile: Construct a Bezier Profile from an XML entry.
Profile_List() - Constructor for class ini.trakem2.tree.ProjectThing.Profile_List
progressive(Iterable, TaskFactory<I, O>, Collection<O>) - Static method in class ini.trakem2.parallel.Process: Takes a Collection of inputs, applies a function to each created by the generator, and places their output in outputs in the same order as each input was retrieved from inputs.
progressive(Iterable, TaskFactory<I, O>, Collection<O>, int) - Static method in class ini.trakem2.parallel.Process: Takes a Collection of inputs, applies a function to each created by the generator, and places their output in outputs in the same order as each input was retrieved from inputs.
progressive(Iterable, TaskFactory<I, O>) - Static method in class ini.trakem2.parallel.Process: Takes a Collection of inputs, applies a function to each created by the generator.
progressive(Iterable, TaskFactory<I, O>, int) - Static method in class ini.trakem2.parallel.Process
project - Variable in class ini.trakem2.persistence.DBObject
Project - Class in ini.trakem2: The top-level class in control.
Project(long, String) - Constructor for class ini.trakem2.Project: Constructor used by the Loader to find projects.
project - Variable in class ini.trakem2.tree.DNDTree
ProjectThing - Class in ini.trakem2.tree
ProjectThing(TemplateThing, Project, Object) - Constructor for class ini.trakem2.tree.ProjectThing: Create a new ProjectThing of the given type to contain the given Object.
ProjectThing(TemplateThing, Project, long, Object, ArrayList<ProjectThing>) - Constructor for class ini.trakem2.tree.ProjectThing: Reconstruct a ProjectThing from the database, used in combination with the 'setup' method.
ProjectThing.Profile_List - Class in ini.trakem2.tree
ProjectThingNodeRenderer() - Constructor for class ini.trakem2.tree.ProjectTree.ProjectThingNodeRenderer
ProjectTiler - Class in ini.trakem2.persistence
ProjectTiler() - Constructor for class ini.trakem2.persistence.ProjectTiler
ProjectToolbar - Class in ini.trakem2.utils
ProjectTree - Class in ini.trakem2.tree: A class to hold a tree of Thing nodes
ProjectTree(Project, ProjectThing) - Constructor for class ini.trakem2.tree.ProjectTree
ProjectTree.ProjectThingNodeRenderer - Class in ini.trakem2.tree
propagateTransformAfter - Static variable in class mpicbg.trakem2.align.AlignLayersTask
propagateTransformBefore - Static variable in class mpicbg.trakem2.align.AlignLayersTask
props - Variable in class ini.trakem2.display.Displayable: The table of key/value property pairs of this Displayable.
PROXIMITY - Static variable in class ini.trakem2.analysis.Compare
PROXIMITY_MUT - Static variable in class ini.trakem2.analysis.Compare
proxy - Variable in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
put(long, Image, int) - Method in class ini.trakem2.persistence.Cache
put(long, ImagePlus, int) - Method in class ini.trakem2.persistence.Cache
put(String, String) - Method in class ini.trakem2.utils.FieldMapView
putAll(Map<? extends String, ? extends String>) - Method in class ini.trakem2.utils.FieldMapView
putData(Area) - Method in class ini.trakem2.display.AreaWrapper: Does not set the @param area, but copies its internal data.
putTag(String, int) - Method in class ini.trakem2.display.LayerSet: Returns an existing immutable Tag instance if already there, or stores a new one and returns it.

Q

queueForMipmapRemoval(Patch, boolean) - Method in class ini.trakem2.persistence.FSLoader: Queue/unqueue for mipmap removal on shutdown without saving; the yes, when true, makes the p be queued, and when false, be removed from the queue.
queueForMipmapRemoval(Patch, boolean) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
quicksort(float[], Object[]) - Static method in class ini.trakem2.utils.M
quicksort(float[], Object[], int, int) - Static method in class ini.trakem2.utils.M: Adapted from Stephan Preibisch's mpi.fruitfly.math.General homonimous method.
quicksort(double[], int, int) - Static method in class mpi.fruitfly.math.General
quicksort(float[], int, int) - Static method in class mpi.fruitfly.math.General
quicksort(Quicksortable[], int, int) - Static method in class mpi.fruitfly.math.General
quicksort(Vector, int, int) - Static method in class mpi.fruitfly.math.General
quicksort(float[], Point[], int, int) - Static method in class mpi.fruitfly.math.General
quicksort(double[], int[], int, int) - Static method in class mpi.fruitfly.math.General
Quicksortable - Interface in mpi.fruitfly.math: TODO
quit() - Method in class ini.trakem2.display.AbstractOffscreenThread
quit() - Method in class ini.trakem2.display.AbstractRepaintThread: Will gracefully kill this thread by breaking its infinite wait-for-event loop, and also call cancel on all registered offscreen threads.
quit() - Method in class ini.trakem2.utils.Bureaucrat: Waits until worker finishes before returning.
quit() - Method in class ini.trakem2.utils.Dispatcher
quit() - Method in class ini.trakem2.utils.RedPhone
quit() - Static method in class ini.trakem2.utils.StdOutWindow
quit - Variable in class ini.trakem2.utils.Worker
quit() - Method in class ini.trakem2.utils.Worker: If interrupt_on_quit, then it will call thread.getThreadGroup().interrupt() to set a quit flag to each child thread.
quitJob(String) - Method in class ini.trakem2.persistence.Loader: Names as generated for popup menu items in the getJobsPopup method.
quitThreads() - Method in class ini.trakem2.display.GroupingMode
quitWhenDone() - Method in class ini.trakem2.utils.Dispatcher

R

r - Variable in class ini.trakem2.display.Region
r - Variable in class ini.trakem2.display.Treeline.RadiusNode
r - Variable in class ini.trakem2.imaging.filters.LUTCustom
R270 - Static variable in class ini.trakem2.display.LayerSet
R90 - Static variable in class ini.trakem2.display.LayerSet
radius - Variable in class ini.trakem2.imaging.filters.RankFilter
radius - Variable in class ini.trakem2.imaging.filters.SubtractBackground
radius - Static variable in class org.janelia.intensity.MatchIntensities
RadiusNode(float, float, Layer) - Constructor for class ini.trakem2.display.Treeline.RadiusNode
RadiusNode(float, float, Layer, float) - Constructor for class ini.trakem2.display.Treeline.RadiusNode
RadiusNode(HashMap<String, String>) - Constructor for class ini.trakem2.display.Treeline.RadiusNode: To reconstruct from XML, without a layer.
RagMipMaps - Class in ini.trakem2.io: Like RawMipMaps, but the alpha channel is compressed with GZIP.
RagMipMaps() - Constructor for class ini.trakem2.io.RagMipMaps
randomizeColors(Image3DUniverse) - Static method in class ini.trakem2.display.d3d.Display3DGUI
ranges - Variable in class ini.trakem2.display.GroupingMode
RankFilter - Class in ini.trakem2.imaging.filters
RankFilter() - Constructor for class ini.trakem2.imaging.filters.RankFilter
RankFilter(double, int) - Constructor for class ini.trakem2.imaging.filters.RankFilter
RankFilter(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.RankFilter
RansacRegressionFilter - Class in org.janelia.intensity
RansacRegressionFilter() - Constructor for class org.janelia.intensity.RansacRegressionFilter
RansacRegressionReduceFilter - Class in org.janelia.intensity
RansacRegressionReduceFilter() - Constructor for class org.janelia.intensity.RansacRegressionReduceFilter
ratio_space_color - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
RawMipMaps - Class in ini.trakem2.io
RawMipMaps() - Constructor for class ini.trakem2.io.RawMipMaps
rawSendToSiblingProject(ProjectThing, int, Project, ProjectThing) - Method in class ini.trakem2.tree.ProjectTree: Assumes that both projects have the same TemplateThing structure, and assumes that the parent of the (source_pt and the landing_parent instances are of the same type.
reaction - Variable in class ini.trakem2.utils.OptionPanel.Setter
read() - Method in class ini.trakem2.io.LoggingInputStream
read(byte[]) - Method in class ini.trakem2.io.LoggingInputStream
read(byte[], int, int) - Method in class ini.trakem2.io.LoggingInputStream
read(String) - Static method in class ini.trakem2.io.RagMipMaps
read(String) - Static method in class ini.trakem2.io.RawMipMaps
readAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
readAlignmentFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
readFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.BasicParam
readFields(GenericDialog) - Method in class lenscorrection.Distortion_Correction.PluginParam
readFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
readFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
readGeometricConsensusFilterFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
readLegacyXML(LayerSet, HashMap<String, String>, HashMap<Displayable, String>) - Method in class ini.trakem2.display.Connector
readRegularizationFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
readSIFTFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
readXY(char[], int, float[]) - Static method in class ini.trakem2.utils.ReconstructArea: Assumes all read chars will be digits except for the separator (single white space char), and won't fail (but generate ugly results) when any char is not a digit.
rebuild() - Method in class ini.trakem2.tree.DNDTree: Rebuilds the entire tree, starting at the root Thing object.
rebuild(Thing) - Method in class ini.trakem2.tree.DNDTree: Rebuilds the entire tree, starting at the given Thing object.
rebuild(DefaultMutableTreeNode, boolean) - Method in class ini.trakem2.tree.DNDTree: Rebuilds the entire tree, from the given node downward.
ReconstructArea - Class in ini.trakem2.utils: Reconstruct an Area from a list of XML <t2_path d="M ...
ReconstructArea() - Constructor for class ini.trakem2.utils.ReconstructArea
recoverOOME() - Method in class ini.trakem2.persistence.Loader: Recover from an OutOfMemoryError: release 1/2 of all memory AND execute the garbage collector.
recreateBuckets() - Method in class ini.trakem2.display.Layer
recreateBuckets(boolean) - Method in class ini.trakem2.display.LayerSet: Recreate the ZDisplayable buckets, and also the Layer Displayable buckets if desired.
recreateBuckets(Layer, boolean) - Method in class ini.trakem2.display.LayerSet: Recreate the ZDisplayable buckets for layer, and also the Layer Displayable buckets if desired.
recreateBuckets(Collection<Layer>, boolean) - Method in class ini.trakem2.display.LayerSet: Regenerate the quad-tree bucket system for the ZDisplayable instances that have data at each of the given layers, and optionally regenerate the buckets as well for the 2D Displayable instances of that layer as well.
recreateBuckets(Collection<Layer>) - Method in class ini.trakem2.persistence.Loader
recreateBuckets(Layer[]) - Method in class ini.trakem2.persistence.Loader: Recreate buckets for each Layer, one thread per layer, in as many threads as CPUs.
RED - Static variable in class ini.trakem2.display.Channel
REDO - Static variable in interface ini.trakem2.display.DoStep
redoOneStep() - Method in class ini.trakem2.display.AffineTransformMode
redoOneStep() - Method in class ini.trakem2.display.DefaultMode
redoOneStep() - Method in class ini.trakem2.display.GroupingMode
redoOneStep() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
redoOneStep() - Method in class ini.trakem2.display.LayerSet: Redoes one step of the ongoing transformation history, otherwise of the overall LayerSet history.
redoOneStep() - Method in class ini.trakem2.display.ManualAlignMode
redoOneStep() - Method in interface ini.trakem2.display.Mode
redoOneStep() - Method in class ini.trakem2.utils.History: Returns null if there aren't any more steps to redo.
RedPhone - Class in ini.trakem2.utils: Send any input to port 29391 and TrakEM2 will try to save all FSLoader projects to XML files.
RedPhone() - Constructor for class ini.trakem2.utils.RedPhone
regenerateMipMaps(Collection<? extends Displayable>) - Method in class ini.trakem2.persistence.FSLoader: Order the regeneration of all mipmaps for the Patch instances in patches, setting up a task that blocks input until all completed.
regenerateMipMaps(Patch) - Method in class ini.trakem2.persistence.FSLoader: Queue the regeneration of mipmaps for the Patch; returns immediately, having submitted the job to an executor queue; returns a Future if the task was submitted, null if not.
regenerateMipMaps(Patch) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns null unless overriden.
regenerateMipMaps(Collection<? extends Displayable>) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns null unless overriden.
REGENERATING - Static variable in class ini.trakem2.persistence.Loader
regex - Variable in class ini.trakem2.analysis.Compare.CATAParameters
Region<T> - Class in ini.trakem2.display
Region(Rectangle, Layer, T) - Constructor for class ini.trakem2.display.Region
registerStackSlices(Patch) - Static method in class mpicbg.trakem2.align.AlignTask
regularize - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam: Regularization for approximate alignment
regularize - Variable in class mpicbg.trakem2.align.Align.Param: Use a regularized model instead of a pure one.
regularize - Variable in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param: Regularization
RegularizedAffineLayerAlignment - Class in mpicbg.trakem2.align
RegularizedAffineLayerAlignment() - Constructor for class mpicbg.trakem2.align.RegularizedAffineLayerAlignment
RegularizedAffineLayerAlignment.Param - Class in mpicbg.trakem2.align
regularizerIndex - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
regularizerIndex - Variable in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param
regularizerModelIndex - Variable in class mpicbg.trakem2.align.Align.Param
rejectIdentity - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam: Ignore identity transform up to a given tolerance
rejectIdentity - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam: Ignore identity transform up to a given tolerance
rejectIdentity - Variable in class mpicbg.trakem2.align.Align.Param: Ignore identity transform up to a given tolerance
relativeIndexOf(Displayable) - Method in class ini.trakem2.display.Layer: Get the index of the given Displayable relative to the rest of its class.
releaseAll() - Method in class ini.trakem2.persistence.Loader: Empties the caches.
releaseAll() - Static method in class ini.trakem2.utils.CachingThread: Tell all instances to clear their caches.
releaseAllCaches() - Static method in class ini.trakem2.persistence.Loader
releaseMemory(long) - Method in class ini.trakem2.persistence.Loader: Free up to @param min_free_bytes.
releaseMemory2() - Method in class ini.trakem2.persistence.Loader: Deprecated.
releaseToFit(int, int, int, float) - Method in class ini.trakem2.persistence.Loader: Ensure there is at least width * height * factor * type{8-bit: 1; 16-bit: 3; 32-bit or RGB: 4}
releaseToFit(long) - Method in class ini.trakem2.persistence.Loader: Release enough memory so that as many bytes as passed as argument can be loaded.
reliabilityAnalysis(String[]) - Static method in class ini.trakem2.analysis.Compare: Reliability analysis of pipe comparisons: compares all to all, recording the score position of homonimous pipes in other projects.
reliabilityAnalysis(String[], boolean, boolean, boolean, double, double, double, double) - Static method in class ini.trakem2.analysis.Compare
reliabilityAnalysisSpaceExploration(String[]) - Static method in class ini.trakem2.analysis.Compare
remaining_branch_vertices - Variable in class ini.trakem2.analysis.Centrality.EtchingStep
remove(Project) - Static method in class ini.trakem2.ControlWindow
remove(Layer) - Static method in class ini.trakem2.display.Display: Find all Display instances that are showing the layer and either move to the next or previous layer, or close it if none.
remove(boolean) - Method in class ini.trakem2.display.Display: Close this Display window.
remove(Layer, Displayable) - Static method in class ini.trakem2.display.Display: Find the displays that show the given Layer, and remove the given Displayable from the GUI.
remove(ZDisplayable) - Static method in class ini.trakem2.display.Display
remove(ProjectThing) - Static method in class ini.trakem2.display.Display3D: Considers there is only one Display3D for each LayerSet.
remove(boolean) - Method in class ini.trakem2.display.Displayable: Remove from both the database and any Display that shows the Layer in which this Displayable is shown.
remove(Displayable) - Method in class ini.trakem2.display.Layer: Will recreate the buckets; if you intend to remove many, use "removeAll" instead, so that the expensive operation of recreating the buckets is done only once.
remove(boolean) - Method in class ini.trakem2.display.Layer: Remove this layer and all its contents from the project.
remove(boolean) - Method in class ini.trakem2.display.LayerSet
remove(Layer) - Method in class ini.trakem2.display.LayerSet: Remove a child.
remove(ZDisplayable) - Method in class ini.trakem2.display.LayerSet: Remove a child.
remove(int) - Method in class ini.trakem2.display.ManualAlignMode.Landmarks
remove() - Method in class ini.trakem2.display.Node.NodeIterator
remove(Node<T>) - Method in class ini.trakem2.display.Node
remove(Shape) - Method in class ini.trakem2.display.Overlay
remove(boolean) - Method in class ini.trakem2.display.Patch: Remove only if linked to other Patches or to noone.
remove(Displayable) - Method in class ini.trakem2.display.Selection: Remove the given displayable from this selection.
remove(long) - Method in class ini.trakem2.display.TransformationStep
remove(boolean) - Method in class ini.trakem2.display.ZDisplayable
remove(long, int) - Method in class ini.trakem2.persistence.Cache: Remove one mipmap level, if there.
remove(long) - Method in class ini.trakem2.persistence.Cache
remove(boolean) - Method in class ini.trakem2.persistence.DBObject: Subclasses can override this method to perform other tasks before removing itself from the database.
remove() - Method in class ini.trakem2.Project: Remove the project from the database and release memory.
remove(boolean) - Method in class ini.trakem2.Project: Remove the project from the database and release memory.
remove(Displayable) - Method in class ini.trakem2.Project: Removes an object from this Project.
remove(boolean) - Method in class ini.trakem2.tree.LayerThing: Remove this instance, cascading the remove action to the children and the objects.
remove(Layer, boolean) - Method in class ini.trakem2.tree.LayerTree
remove(boolean, LayerThing, DefaultMutableTreeNode) - Method in class ini.trakem2.tree.LayerTree: If the given node is null, it will be searched for.
remove(boolean) - Method in class ini.trakem2.tree.ProjectThing
remove(boolean, boolean) - Method in class ini.trakem2.tree.ProjectThing
remove(DefaultMutableTreeNode, boolean, boolean, int) - Method in class ini.trakem2.tree.ProjectTree: Remove the node, its Thing and the object hold by the thing from the database.
remove(boolean, ProjectThing, DefaultMutableTreeNode) - Method in class ini.trakem2.tree.ProjectTree: If the given node is null, it will be searched for.
remove(Set<? extends Displayable>, DefaultMutableTreeNode) - Method in class ini.trakem2.tree.ProjectTree: Remove the Thing and DefaultMutableTreeNode that wrap each of the Displayable; calls softRemove on each Displayable, and does NOT call remove on the Displayable.
remove(boolean) - Method in class ini.trakem2.tree.TemplateThing
remove(Object) - Method in class ini.trakem2.utils.FieldMapView
remove(long) - Method in class ini.trakem2.utils.History: Empty all elements from each Step in the list that match the given id, and return them.
remove(long) - Method in interface ini.trakem2.utils.History.Step: Remove objects in this step that have the given id, and return a list of them.
remove(Displayable) - Static method in class ini.trakem2.utils.Search: Remove from the tables if there.
remove(Object) - Method in class ini.trakem2.utils.TypedHashMap
remove2(boolean) - Method in class ini.trakem2.display.Displayable: Remove also from the trees if present; does nothing more than remove(boolean) unless overriden.
remove2(boolean) - Method in class ini.trakem2.display.LayerSet
remove2(boolean) - Method in class ini.trakem2.display.Profile
remove2(boolean) - Method in class ini.trakem2.display.Stack: Avoid calling the trees: the stack exists only in the LayerSet ZDisplayable's list.
remove2(boolean) - Method in class ini.trakem2.display.Tree
remove2(boolean) - Method in class ini.trakem2.display.ZDisplayable
remove_disconnected - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
removeAll(Set<Displayable>) - Method in class ini.trakem2.display.Layer: Remove a set of children.
removeAll(Set<ZDisplayable>) - Method in class ini.trakem2.display.LayerSet: Remove a child.
removeAll(Collection<Displayable>) - Method in class ini.trakem2.display.Selection: Remove all given displayables from this selection.
removeAll(Set<Displayable>) - Method in class ini.trakem2.Project: Calls Project.removeAll(col, null)
removeAll(Set<Displayable>, DefaultMutableTreeNode) - Method in class ini.trakem2.Project: Remove any set of Displayable objects from the Layer, LayerSet and Project Tree as necessary.
removeAllTags() - Method in class ini.trakem2.display.LayerSet
removeAllTags() - Method in class ini.trakem2.display.Node
removeAllTags() - Method in interface ini.trakem2.display.Taggable
removeAlphaMask(Patch) - Method in class ini.trakem2.persistence.Loader: Deprecated.
removeAlphaMasks(Collection<Patch>) - Static method in class ini.trakem2.display.Display
removeAndFlushAll() - Method in class ini.trakem2.persistence.Cache: Flush all mipmaps, and forget all mipmaps and imps.
removeAndFlushPyramid(long) - Method in class ini.trakem2.persistence.Cache: Does not alter the ImagePlus.
removeAndFlushSome(long) - Method in class ini.trakem2.persistence.Cache: Returns the number of released bytes.
removeAndFlushSome(int) - Method in class ini.trakem2.persistence.Cache
removeCached(long, int) - Method in class ini.trakem2.persistence.Loader: Only the indicated level for the given Patch id.
removeCached(long) - Method in class ini.trakem2.persistence.Loader: All levels of the Patch.
removeChild(LayerThing) - Method in class ini.trakem2.tree.LayerThing
removeChild(ProjectThing) - Method in class ini.trakem2.tree.ProjectThing
removeChild(TemplateThing) - Method in class ini.trakem2.tree.TemplateThing
removeCoordinateTransforms(List<Patch>) - Method in class ini.trakem2.display.Display
removeCrossLink(long, long) - Method in class ini.trakem2.persistence.DBLoader: Remove a link between two objects.
removeCrossLink(long, long) - Method in class ini.trakem2.persistence.Loader: Remove a link between two objects.
removeEntry(K) - Method in class ini.trakem2.utils.TypedHashMap: Typed version of HashMap.remove(Object).
removeExtension(String) - Static method in class ini.trakem2.utils.Utils
removeFile(File) - Static method in class ini.trakem2.utils.Utils: Remove the file, or if it's a directory, recursively go down subdirs and remove all contents, but will stop on encountering a non-hidden file that is not an empty dir.
removeFrom3D(ProjectThing) - Static method in class ini.trakem2.display.Display3D: Remove all basic type children contained in pt and its children, recursively.
removeFromDatabase(DBObject) - Method in class ini.trakem2.persistence.DBLoader
removeFromDatabase() - Method in class ini.trakem2.persistence.DBObject
removeFromDatabase(DBObject) - Method in class ini.trakem2.persistence.FSLoader
removeFromDatabase(DBObject) - Method in class ini.trakem2.persistence.Loader
removeFromLinkLater(Node<T>) - Method in class ini.trakem2.display.Tree
removeFromOffscreens(Layer) - Method in class ini.trakem2.display.LayerSet
removeFromPrev(Displayable) - Method in class ini.trakem2.display.Selection: Removes the given Displayable from the selection and previous selection list.
removeFromUnloadable(Displayable) - Method in class ini.trakem2.persistence.Loader
removeImageLoadingLock(Loader.ImageLoadingLock) - Method in class ini.trakem2.persistence.Loader
removeImagePlus(long) - Method in class ini.trakem2.persistence.Cache: Remove only the ImagePlus, if there.
removeJob(Bureaucrat) - Method in class ini.trakem2.persistence.Loader
removeLastUndoStep() - Method in class ini.trakem2.display.LayerSet
removeLinkedProperties(Displayable) - Method in class ini.trakem2.display.Displayable: Removes and returns the table of properties lined to the target Displayable.
removeLinkedPropertiesFromOrigins() - Method in class ini.trakem2.display.Displayable: Tell any other Displayable that has a linked property with this Displayable to remove it.
removeMipMaps(Patch) - Method in class ini.trakem2.persistence.FSLoader: Gets data from the Patch and queues a new task to do the file removal in a separate task manager thread.
removeMipMaps(Patch) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
removeNode(Node<T>) - Method in class ini.trakem2.display.Tree: If the tree is a cyclic graph, it may destroy all.
removeNode(DefaultMutableTreeNode) - Method in class ini.trakem2.tree.DNDTree
removePoint(int) - Method in class ini.trakem2.display.Ball: Remove a point.
removePoint(int) - Method in class ini.trakem2.display.Pipe: Remove a point from the bezier backbone and its two associated control points.
removePoint(int) - Method in class ini.trakem2.display.Polyline: Remove a point from the bezier backbone and its two associated control points.
removePoint(int) - Method in class ini.trakem2.display.Profile: Remove a point from the bezier backbone and its two associated control points.
removePrefixedFiles(File, String, ArrayList<String>) - Static method in class ini.trakem2.utils.Utils: Returns true if all files and their subdirectories, recursively, under parent folder have been removed.
removeProjectThing(Object, boolean) - Method in class ini.trakem2.Project: Remove the ProjectThing that contains the given object, which will remove the object itself as well.
removeProjectThing(Object, boolean, boolean, int) - Method in class ini.trakem2.Project: Remove the ProjectThing that contains the given object, which will remove the object itself as well.
removeProjectThingLadder(ProjectThing, int) - Method in class ini.trakem2.tree.ProjectTree: Recursive as long as levels is above zero.
removeReviews() - Method in class ini.trakem2.display.Tree
removeScalingRotationShear(List<Patch>) - Method in class ini.trakem2.display.Display
removeSerializedFeatures(Patch) - Method in class ini.trakem2.persistence.FSLoader: Remove the file, if it exists, with serialized features for patch.
removeSerializedPointMatches(Patch) - Method in class ini.trakem2.persistence.FSLoader: Remove the file, if it exists, with serialized point matches for patch.
removeTabs(Project) - Static method in class ini.trakem2.utils.Search
removeTag(String, int) - Method in class ini.trakem2.display.LayerSet: Removes the tag from the list of possible tags, and then from wherever it has been assigned.
removeTag(Tag) - Method in class ini.trakem2.display.LayerSet
removeTag(Tag) - Method in class ini.trakem2.display.Node
removeTag(Tag) - Method in interface ini.trakem2.display.Taggable
removeUniqueType(String) - Method in class ini.trakem2.Project: Remove a unique type from the HashMap.
removeVirtualMatch(PointMatch) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
rename(ProjectThing) - Method in class ini.trakem2.tree.ProjectTree
rename(String) - Method in class ini.trakem2.tree.TemplateThing: Change the type to new_name.
RenameThingStep - Class in ini.trakem2.tree
renameType(String, String) - Method in class ini.trakem2.tree.TemplateTree: Rename a TemplateThing type from @param old_name to @param new_name.
Render - Class in ini.trakem2.utils: For now, generates a .shapes file that I can load into Blender with the CurveMorphing CPython module by means of the load_shapes_v1.4.3.py script.
Render(Thing) - Constructor for class ini.trakem2.utils.Render
render(Thing) - Method in class ini.trakem2.utils.Render: Recursive search for profile_list and pipe objects
Render - Class in org.janelia.intensity: Render a patch.
render(Patch, int, int, FloatProcessor, FloatProcessor, ColorProcessor, double, double, double) - Static method in class org.janelia.intensity.Render: Renders a patch, mapping its intensities [min, max] → [0, 1]
repaint(boolean, Layer) - Method in class ini.trakem2.display.Ball: Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Profile.
repaint(Layer, Displayable, int) - Static method in class ini.trakem2.display.Display
repaint(Layer, Displayable, Rectangle, int) - Static method in class ini.trakem2.display.Display
repaint(Layer, Displayable, Rectangle, int, boolean) - Static method in class ini.trakem2.display.Display: Find the displays that show the given Layer, and repaint the given Displayable; does NOT update graphics for the offscreen image.
repaint(Layer, Displayable, Rectangle, int, boolean, boolean) - Static method in class ini.trakem2.display.Display
repaint(Displayable) - Static method in class ini.trakem2.display.Display
repaint(Layer, Rectangle, int) - Static method in class ini.trakem2.display.Display: Repaint the given Rectangle in all Displays showing the layer, updating the offscreen image if any.
repaint(Layer, int, Rectangle, boolean) - Static method in class ini.trakem2.display.Display
repaint(Layer, int, Rectangle, boolean, boolean) - Static method in class ini.trakem2.display.Display
repaint(Layer, Rectangle, int, boolean) - Static method in class ini.trakem2.display.Display: Repaint the given Rectangle in all Displays showing the layer, optionally updating the offscreen image (if any).
repaint(Layer, Displayable) - Static method in class ini.trakem2.display.Display: Repaint the DisplayablePanel (and DisplayNavigator) only for the given Displayable, in all Displays showing the given Layer.
repaint(LayerSet, Displayable, int) - Static method in class ini.trakem2.display.Display
repaint(LayerSet, Displayable, Rectangle, int) - Static method in class ini.trakem2.display.Display
repaint(LayerSet, Displayable, Rectangle, int, boolean) - Static method in class ini.trakem2.display.Display: Repaint the Displayable in every Display that shows a Layer belonging to the given LayerSet.
repaint(LayerSet) - Static method in class ini.trakem2.display.Display: Repaint the entire LayerSet, in all Displays showing a Layer of it.
repaint(LayerSet, Rectangle) - Static method in class ini.trakem2.display.Display: Repaint the given box in the LayerSet, in all Displays showing a Layer of it.
repaint(Layer) - Static method in class ini.trakem2.display.Display: Repaint the entire Layer, in all Displays showing it, including the tabs.
repaint() - Static method in class ini.trakem2.display.Display: Call repaint on all open Displays.
repaint() - Method in class ini.trakem2.display.Displayable: Repaint this Displayable in all Display instances that are showing it.
repaint(Displayable) - Method in class ini.trakem2.display.DisplayCanvas: Repaint as much as the bounding box around the given Displayable.
repaint(Displayable, int) - Method in class ini.trakem2.display.DisplayCanvas: Repaint as much as the bounding box around the given Displayable plus the extra padding.
repaint(Displayable, int, boolean) - Method in class ini.trakem2.display.DisplayCanvas
repaint(HashSet<Displayable>) - Method in class ini.trakem2.display.DisplayCanvas: Repaint the clip corresponding to the sum of all boundingboxes of Displayable objects in the hashset.
repaint(Rectangle, int) - Method in class ini.trakem2.display.DisplayCanvas: Repaint the given offscreen Rectangle after transforming its data on the fly to the srcRect and magnification of this DisplayCanvas.
repaint(Rectangle, int, boolean) - Method in class ini.trakem2.display.DisplayCanvas: Repaint the given Rectangle after transforming its data on the fly to the srcRect and magnification of this DisplayCanvas.
repaint(boolean) - Method in class ini.trakem2.display.DisplayCanvas: Repaint everything, updating offscreen graphics if so specified.
repaint() - Method in class ini.trakem2.display.DisplayCanvas: Overridden to multithread.
repaint(int, int, int, int) - Method in class ini.trakem2.display.DisplayCanvas: Overridden to multithread.
repaint() - Method in class ini.trakem2.display.DisplayNavigator: Multithreaded.
repaint(boolean) - Method in class ini.trakem2.display.DisplayNavigator
repaint(Displayable) - Method in class ini.trakem2.display.DisplayNavigator: Only its bounding box.
repaint(int, int, int, int) - Method in class ini.trakem2.display.DisplayNavigator: Overridden to multithread.
repaint(Rectangle) - Method in class ini.trakem2.display.DisplayNavigator: Box is given in offscreen canvas coords.
repaint(boolean, Layer) - Method in class ini.trakem2.display.Pipe: Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Pipe.
repaint(boolean, Layer) - Method in class ini.trakem2.display.Polyline: Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Pipe.
repaint() - Method in class ini.trakem2.display.Profile
repaint(boolean) - Method in class ini.trakem2.display.Profile: Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Profile.
repaint(boolean, Layer) - Method in class ini.trakem2.display.Tree: Repaints in the given ImageCanvas only the area corresponding to the bounding box of this Pipe.
repaint(Object) - Static method in class ini.trakem2.utils.Search: Repaint (refresh the text in the cells) only if any of the selected tabs in any of the search frames contains the given object in its rows.
REPAINT_MULTI_LAYER - Static variable in class ini.trakem2.display.Display
REPAINT_RGB_LAYER - Static variable in class ini.trakem2.display.Display
REPAINT_SINGLE_LAYER - Static variable in class ini.trakem2.display.Display
repaintAll() - Method in class ini.trakem2.display.Display: Repaint both the canvas and the navigator, updating the graphics, and the title and tabs.
repaintAll2() - Method in class ini.trakem2.display.Display: Repaint the canvas updating graphics, the navigator without updating graphics, and the title.
repaintAll3() - Method in class ini.trakem2.display.Display: Repaint the canvas updating graphics, and the navigator without updating graphics.
repainter - Static variable in class ini.trakem2.persistence.FSLoader
repaintSnapshot(Displayable) - Static method in class ini.trakem2.display.Display: Repaint the snapshot for the given Displayable both at the DisplayNavigator and on its panel,and only if it has not been painted before.
repaintSnapshots(LayerSet) - Static method in class ini.trakem2.display.Display
repaintSnapshots(Layer) - Static method in class ini.trakem2.display.Display
repaintToolbar() - Static method in class ini.trakem2.display.Display
repaintWindow() - Method in class ini.trakem2.imaging.PatchStack
repairGUI() - Method in class ini.trakem2.display.Display: Repair possibly missing panels and other components by simply resetting the same Layer
reposition(Layer) - Method in class ini.trakem2.display.LayerSet: Used by the Layer.setZ method.
requireAltDownToEditRadius() - Method in class ini.trakem2.display.Connector
requireAltDownToEditRadius() - Method in class ini.trakem2.display.Treeline
reRoot(float, float, Layer, double) - Method in class ini.trakem2.display.Tree: Reroots at the point closest to the x,y,layer_id world coordinate.
reRoot(Node<T>) - Method in class ini.trakem2.display.Tree
reset() - Method in class ini.trakem2.analysis.Vertex: All but neighbors.
reset(HashMap<Thing, Boolean>) - Method in class ini.trakem2.tree.DNDTree: Set the root Thing, and the expanded state of all nodes if expanded_state is not null.
resetBox() - Method in class ini.trakem2.display.AffineTransformMode: Recalculate box and reset handles.
resetBox() - Method in class ini.trakem2.display.Selection: Recalculate box and reset handles.
resetControlPoints(int) - Method in class ini.trakem2.display.Pipe: Set the control points to the same value as the backbone point which they control.
resetControlPoints(int) - Method in class ini.trakem2.display.Profile: Set the control points to the same value as the backbone point which they control.
resetInfo() - Method in class ini.trakem2.io.LoggingInputStream: Put the counter to zero.
resetLayerAlphas() - Method in class ini.trakem2.display.Display: Set all layer alphas to zero, and repaint canvas.
resetLayerColors() - Method in class ini.trakem2.display.Display: Remove all red/blue coloring of layers, and repaint canvas.
resetLayerComposites() - Method in class ini.trakem2.display.Display
ResetMinAndMax - Class in ini.trakem2.imaging.filters
ResetMinAndMax() - Constructor for class ini.trakem2.imaging.filters.ResetMinAndMax
ResetMinAndMax(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.ResetMinAndMax
resetNonActive() - Method in class ini.trakem2.imaging.PatchStack: Reset temporary changes such as from dragging B&C sliders and so on, in the current slice (the current Patch).
resetRootLayerThing(LayerThing, HashMap<Thing, Boolean>) - Method in class ini.trakem2.Project: For undo purposes.
resetRootProjectThing(ProjectThing, HashMap<Thing, Boolean>) - Method in class ini.trakem2.Project: For undo purposes.
resetRootTemplateThing(TemplateThing, HashMap<Thing, Boolean>) - Method in class ini.trakem2.Project: For undo purposes.
resetView(LayerSet) - Static method in class ini.trakem2.display.Display3D
resize(int) - Method in class ini.trakem2.utils.History: Resize to maximum the given size, removing from the beginning.
resizeArea(int, double) - Method in class ini.trakem2.imaging.Segmentation.FastMarchingParam
resizeCanvas(Rectangle) - Method in class ini.trakem2.display.Display
resizeCanvas() - Method in class ini.trakem2.display.Display
resizeInPlace(int, int) - Method in class ini.trakem2.imaging.FloatProcessorT2
resolutionSpringMesh - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
restartMipMapThreads(int) - Static method in class ini.trakem2.persistence.FSLoader: Restart the ExecutorService for mipmaps with n_threads.
restore() - Method in class ini.trakem2.display.Selection: Restore the previous selection.
restoreCalibration(HashMap<String, String>) - Method in class ini.trakem2.display.LayerSet: Restore calibration from the given XML attributes table.
restoreMenuBar() - Static method in class ini.trakem2.utils.Utils: Restore ImageJ's MenuBar
restoreNodesExpandedState(Project) - Method in class ini.trakem2.persistence.DBLoader: Affects only those set to true; the rest are left untouched.
restorePaths(Map<Long, String>, String, String) - Method in class ini.trakem2.persistence.FSLoader
restorePaths(Map<Long, String>, String, String) - Method in class ini.trakem2.persistence.Loader
restXML(StringBuilder, String, XMLOptions) - Method in class ini.trakem2.display.Displayable: Add properties, links, etc.
result - Variable in class ini.trakem2.utils.Worker: Extending classes may store a resulting piece of data.
revalidateComponent(Component) - Static method in class ini.trakem2.utils.Utils: Like calling pack() on a Frame but on a Component.
reverse() - Method in class ini.trakem2.display.Pipe: Reverses the order of the points in the arrays.
reverse() - Method in class ini.trakem2.display.Polyline
reverse(double[]) - Static method in class ini.trakem2.utils.Utils: Reverse in place an array of doubles.
reverse(long[]) - Static method in class ini.trakem2.utils.Utils: Reverse in place an array of longs.
revert() - Method in class ini.trakem2.display.Patch: Revert the ImagePlus to the one stored in original_path, if any; will revert all linked patches if this is part of a stack.
revert(Patch) - Method in class ini.trakem2.imaging.PatchStack
revertAll() - Method in class ini.trakem2.imaging.PatchStack
RGB - Static variable in class ini.trakem2.io.RagMipMaps: These are both the 4 supported types and the number of channels that each type has.
RGB - Static variable in class ini.trakem2.io.RawMipMaps: These are both the 4 supported types and the number of channels that each type has.
RGB_COLOR_MODEL - Static variable in class ini.trakem2.io.ImageSaver
RGBA - Static variable in class ini.trakem2.io.RagMipMaps: These are both the 4 supported types and the number of channels that each type has.
RGBA - Static variable in class ini.trakem2.io.RawMipMaps: These are both the 4 supported types and the number of channels that each type has.
RGBA_COLOR_MODEL - Static variable in class ini.trakem2.io.ImageSaver
RGBA_PRE_COLOR_MODEL - Static variable in class ini.trakem2.io.ImageSaver
RigidTile2D - Class in mpicbg.trakem2.align
RigidTile2D(RigidModel2D, Patch) - Constructor for class mpicbg.trakem2.align.RigidTile2D
RigidTile2D(Patch) - Constructor for class mpicbg.trakem2.align.RigidTile2D
RobustNormalizeLocalContrast - Class in ini.trakem2.imaging.filters
RobustNormalizeLocalContrast() - Constructor for class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
RobustNormalizeLocalContrast(int, int, int, float, int, int, float) - Constructor for class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
RobustNormalizeLocalContrast(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
RobustNormalizeLocalContrast - Class in mpicbg.trakem2.util
RobustNormalizeLocalContrast() - Constructor for class mpicbg.trakem2.util.RobustNormalizeLocalContrast
RobustNormalizeLocalContrast.ByteSetter - Class in mpicbg.trakem2.util
RobustNormalizeLocalContrast.FloatSetter - Class in mpicbg.trakem2.util
RobustNormalizeLocalContrast.PixelSetter - Interface in mpicbg.trakem2.util
RobustNormalizeLocalContrast.ShortSetter - Class in mpicbg.trakem2.util
rod - Variable in class lenscorrection.Distortion_Correction.BasicParam: Closest/next closest neighbour distance ratio
rod - Variable in class mpicbg.trakem2.align.Align.Param: Closest/next closest neighbour distance ratio
rod - Variable in class mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch: Closest/next closest neighbor distance ratio
rodR - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
roi - Variable in class ini.trakem2.display.VectorDataTransform.ROITransform
ROITransform(Area, CoordinateTransform) - Constructor for class ini.trakem2.display.VectorDataTransform.ROITransform: A coordinate transform @param ct that applies to the @param roi Area only.
rollback() - Method in class ini.trakem2.persistence.DBLoader: Used when errors ocurr during a large insertion.
rollback() - Method in class ini.trakem2.persistence.Loader
RollingPanel - Class in ini.trakem2.display
RollingPanel(Display, Class<?>) - Constructor for class ini.trakem2.display.RollingPanel
root - Variable in class ini.trakem2.display.LayerSet.LayerBucket
root - Variable in class ini.trakem2.display.Tree
rotate(double, int, int) - Method in class ini.trakem2.display.AffineTransformMode: Rotate the objects in the current selection by the given angle, in degrees, relative to the x_o, y_o origin.
rotate(double, double, double) - Method in class ini.trakem2.display.Displayable: Rotate relative to an anchor point.
rotate(double, double, double, boolean) - Method in class ini.trakem2.display.Displayable: Rotate relative to an anchor point.
rotate(double, double, double) - Method in class ini.trakem2.display.Selection: Rotate the objects in the current selection by the given angle, in degrees, relative to the x_o, y_o origin.
rotate_v_around_axis(Vector3, Vector3, double, double) - Static method in class ini.trakem2.utils.Vector3: From my former program, A_3D_Editing.java and Pipe.java
rotatePoints(double[][], double, double, double) - Static method in class ini.trakem2.display.Displayable: Rotate 2D points relative to the given pivot point by the given rot angle (in radians), in the 2D plane.
ROTATIONS - Static variable in class ini.trakem2.display.LayerSet
roughlyFindZDisplayables(Layer, Rectangle, boolean) - Method in class ini.trakem2.display.LayerSet: Find ZDisplayable objects that intersect the given rectangle in the given layer.
rp - Variable in class ini.trakem2.display.AbstractOffscreenThread
run() - Method in class ini.trakem2.display.AbstractOffscreenThread
run() - Method in class ini.trakem2.display.AbstractRepaintThread
run() - Method in class ini.trakem2.display.GroupingMode.SimpleThread
run() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode.Inspector
run(ImagePlus, String) - Method in interface ini.trakem2.imaging.ImagePreprocessor
run(String) - Method in class ini.trakem2.New_DB_Project
run(String) - Method in class ini.trakem2.New_Project
run(String) - Method in class ini.trakem2.Open_DB_Project
run(String) - Method in class ini.trakem2.Open_Project
run(Patch, ImagePlus, String) - Static method in class ini.trakem2.scripting.PatchScript: Run the script at path on the ImagePlus of patch.
run() - Method in class ini.trakem2.utils.Bureaucrat
run(String) - Method in class ini.trakem2.utils.Utils
run() - Method in class ini.trakem2.utils.Worker.Task
run(String) - Method in class lenscorrection.Distortion_Correction
run() - Method in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
run(DistortionCorrectionTask.CorrectDistortionFromSelectionParam, List<Patch>, Displayable, Layer, Worker) - Static method in class lenscorrection.DistortionCorrectionTask
run(DistortionCorrectionTask.CorrectDistortionFromSelectionParam, List<Patch>, Displayable, Layer) - Static method in class lenscorrection.DistortionCorrectionTask
run() - Method in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
run() - Method in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
run() - Method in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
run(ImageProcessor, int, int, int, float, int, int, float) - Static method in class mpicbg.trakem2.util.RobustNormalizeLocalContrast
run(RandomAccessibleInterval<S>) - Method in class org.janelia.intensity.LinearIntensityMap
run(List<Layer>, int, double, int, double, double, double, Rectangle) - Method in class org.janelia.intensity.MatchIntensities
RUNTIME - Static variable in class ini.trakem2.persistence.Loader

S

s - Variable in class ini.trakem2.imaging.filters.EnhanceContrast: Percent of saturated pixels to leave outside the min, max range.
safeCompute(Collection<Vertex<T>>) - Static method in class ini.trakem2.analysis.Centrality: Like @see compute, but operates on a copy of all Vertex instances, and return a Collection with the same order as @param vs.
safeCopy(String, String) - Static method in class ini.trakem2.utils.Utils
sampleAverageScale(CoordinateTransform, int, int, double) - Static method in class org.janelia.intensity.Render: Sample the average scaling of a given CoordinateTransform by transferring a set of point samples using the CoordinateTransform and then least-squares fitting a SimilarityModel2D to it.
saturate_when_autoscaling - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
save(String, byte[][], int, int) - Static method in class ini.trakem2.io.RagMipMaps
save(String, byte[][], int, int) - Static method in class ini.trakem2.io.RawMipMaps
save(Project, XMLOptions) - Method in class ini.trakem2.persistence.FSLoader: Overwrites the XML file.
save(Project, XMLOptions) - Method in class ini.trakem2.persistence.Loader: Calls saveAs() unless overriden.
save() - Method in class ini.trakem2.Project: Save the project regardless of what getLoader().hasChanges() reports.
save(double) - Method in class ini.trakem2.utils.Render: Popup a dialog to save a .shapes file with all the curves of the objects inside.
save(ImagePlus, String) - Method in class ini.trakem2.utils.Saver
save(String) - Method in class lenscorrection.NonLinearTransform
saveAs(Project, XMLOptions) - Method in class ini.trakem2.persistence.FSLoader: The saveAs called from menus via saveTask.
saveAs(String, XMLOptions) - Method in class ini.trakem2.persistence.FSLoader: Meant for programmatic access, such as calls to project.saveAs(path, overwrite) which call exactly this method.
saveAs(Project, XMLOptions) - Method in class ini.trakem2.persistence.Loader: Save the project under a different name by choosing from a dialog, and exporting all images (will popup a YesNoCancelDialog to confirm exporting images.)
saveAs(Project, String, XMLOptions) - Method in class ini.trakem2.persistence.Loader: Exports to an XML file chosen by the user in a dialog if @param xmlpath is null.
saveAs(String, XMLOptions) - Method in class ini.trakem2.persistence.Loader: Meant to be overriden -- as is, will set options.XMLOptions.export_images to this.getClass() != FSLoader.class.
saveAs(String, boolean) - Method in class ini.trakem2.Project: This is not the saveAs used from the menus; this one is meant for programmatic access.
saveAsARGBJpeg(int[], int, int, String, float) - Static method in class ini.trakem2.io.ImageSaver: Save as ARGB jpeg.
saveAsGreyJpeg(byte[], int, int, String, float) - Static method in class ini.trakem2.io.ImageSaver
saveAsJpeg(ImageProcessor, String, float, boolean) - Static method in class ini.trakem2.io.ImageSaver: Returns true on success.
saveAsJpeg(BufferedImage, String, float, boolean) - Static method in class ini.trakem2.io.ImageSaver: Will not flush the given BufferedImage.
saveAsJpegAlpha(BufferedImage, String, float) - Static method in class ini.trakem2.io.ImageSaver: Save an RGB jpeg including the alpha channel if it has one; can be read only by ImageSaver.openJpegAlpha method; in other software the alpha channel is confused by some other color channel.
saveAsJpegAlpha(Image, String, float) - Static method in class ini.trakem2.io.ImageSaver: Save an RGB jpeg including the alpha channel if it has one; can be read only by ImageSaver.openJpegAlpha method; in other software the alpha channel is confused by some other color channel.
saveAsPNG(ImageProcessor, String) - Static method in class ini.trakem2.io.ImageSaver
saveAsPNG(Image, String) - Static method in class ini.trakem2.io.ImageSaver
saveAsPNG(BufferedImage, String) - Static method in class ini.trakem2.io.ImageSaver: Save a PNG with or without alpha channel with default compression at maximum level (9, expressed as 0 in the ImageWriter compression quality because 0 indicates "maximum compression is important").
saveAsTIFF(ImageProcessor, String, boolean) - Static method in class ini.trakem2.io.ImageSaver: WARNING fails when there is an alpha channel: generates an empty file.
saveAsTIFF(Image, String, boolean) - Static method in class ini.trakem2.io.ImageSaver: Will not flush @param awt.
saveAsTIFF(BufferedImage, String, boolean) - Static method in class ini.trakem2.io.ImageSaver
saveAsZip(ImagePlus, String) - Static method in class ini.trakem2.io.ImageSaver: Returns true on success.
saveFileName - Variable in class lenscorrection.Distortion_Correction.PluginParam
saveImages() - Method in class ini.trakem2.imaging.PatchStack: Store working copies and remake the awts and repaint.
saveOrLoad - Variable in class lenscorrection.Distortion_Correction.PluginParam
Saver - Class in ini.trakem2.utils
Saver(String) - Constructor for class ini.trakem2.utils.Saver
saveRoi() - Method in class ini.trakem2.imaging.PatchStack
saveTask(Project, String) - Method in class ini.trakem2.persistence.Loader: Run save or saveAs in a Bureaucract that blocks user input to the project being saved.
saveTask(String) - Method in class ini.trakem2.Project
saveToFile(File, String) - Static method in class ini.trakem2.utils.Utils
saveToFile(String, String, String) - Static method in class ini.trakem2.utils.Utils
saveWithoutCoordinateTransforms() - Method in class ini.trakem2.Project: Save an XML file that is stripped of coordinate transforms, and merely refers to them by the 'ct_id' attribute of each 't2_patch' element; this method will NOT overwrite the XML file but save into a new one, which is chosen from a file dialog.
scale(double, double) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
scale(double, double) - Method in class ini.trakem2.display.AffineTransformMode: Scale all selected objects and their links by by the given scales, relative to the floater position.
scale(double, double, double, double) - Method in class ini.trakem2.display.Displayable: Scale relative to an anchor point (will translate as necessary).
scale(double, double, double, double, boolean) - Method in class ini.trakem2.display.Displayable: Scale relative to an anchor point (will translate as necessary).
scale(double, double, double, double) - Method in class ini.trakem2.display.Selection: Scale all selected objects and their links by by the given scales, relative to the origin position.
scale(double, Vector3) - Method in class ini.trakem2.utils.Vector3
scale - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
scale - Static variable in class org.janelia.intensity.MatchIntensities
scaleAreaAverage(double[], int, int, int, int) - Static method in class ini.trakem2.imaging.FastIntegralImage
scaleAreaAverage(long[], int, int, int, int) - Static method in class ini.trakem2.imaging.FastIntegralImage
scaleByte(ByteProcessor) - Static method in class mpicbg.trakem2.align.ElasticMontage
scaleImage(ImagePlus, double, boolean) - Static method in class ini.trakem2.persistence.Loader
scaleImage(ImagePlus, int, boolean) - Static method in class ini.trakem2.persistence.Loader
scaleLevel - Variable in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
scalePoints(double[][], double, double, double, double) - Static method in class ini.trakem2.display.Displayable: Scale 2D points relative to the given pivot point xo,yo.
scaleUP - Variable in class mpicbg.trakem2.transform.ExportBestFlatImage
scaleX - Variable in class ini.trakem2.display.MipMapImage
scaleY - Variable in class ini.trakem2.display.MipMapImage
score(double, double, double, double[]) - Static method in class ini.trakem2.analysis.Compare
score_mut_only - Variable in class ini.trakem2.analysis.Compare.CATAParameters
scoreAllToAll(VectorString3D[], int, double, boolean, int, float, boolean, boolean, Worker) - Static method in class ini.trakem2.analysis.Compare: Returns the half matrix of scores, with values copied from one half matrix to the other, and a diagonal of zeros.
screenPatchRanges - Variable in class ini.trakem2.display.GroupingMode
scroll(int, int) - Method in class ini.trakem2.display.DisplayCanvas
scrollToShow(Displayable) - Method in class ini.trakem2.display.RollingPanel
Search - Class in ini.trakem2.utils
searchRadius - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
Segmentation - Class in ini.trakem2.imaging
Segmentation() - Constructor for class ini.trakem2.imaging.Segmentation
Segmentation.BlowCommander - Class in ini.trakem2.imaging
Segmentation.BlowRunner - Class in ini.trakem2.imaging
Segmentation.FastMarchingParam - Class in ini.trakem2.imaging
select(Displayable) - Method in class ini.trakem2.display.Display
select(Displayable, boolean) - Method in class ini.trakem2.display.Display: Select/deselect accordingly to the current state and the shift key.
select(Layer) - Method in class ini.trakem2.Project: Find the node in the layer tree with a Thing that contains the given object, and set it selected/highlighted, deselecting everything else first.
select(Displayable) - Method in class ini.trakem2.Project: Find the node in any tree with a Thing that contains the given Displayable, and set it selected/highlighted, deselecting everything else first.
SELECT - Static variable in class ini.trakem2.utils.ProjectToolbar: A tool to select and move Displayable objects (black arrow).
selectAll() - Method in class ini.trakem2.display.Selection: Select all objects in the Display's current layer, preserving the active one (if any) as active; includes all the ZDisplayables, whether visible in this layer or not.
selectAll(Layer) - Method in class ini.trakem2.display.Selection: Select all objects in the given layer, preserving the active one (if any) as active.
selectAll(Roi, boolean) - Method in class ini.trakem2.display.Selection: Select all objects under the given roi, in the current display's layer.
selectAll(Collection<? extends Displayable>) - Method in class ini.trakem2.display.Selection
selectAllVisible() - Method in class ini.trakem2.display.Selection: Select all isVisible() objects in the Display's current layer, preserving the active one (if any) as active; includes all the ZDisplayables, whether visible in this layer or not, as long as their return true from isVisible().
selectFile(String) - Static method in class ini.trakem2.utils.Utils: Returns null or the selected directory and file.
selectInDisplay(ProjectThing, boolean) - Method in class ini.trakem2.tree.ProjectTree
Selection - Class in ini.trakem2.display: Keeps track of selected objects and mediates their transformation.
Selection(Display) - Constructor for class ini.trakem2.display.Selection: The Display can be null, as long as paint, OvalHandle.contains, setTransforming, and getLinkedBox methods are never called on this object.
selectNode(Object, DNDTree) - Static method in class ini.trakem2.tree.DNDTree: Deselects whatever node is selected in the tree, and tries to select the one that contains the given object.
selectNode(Layer) - Method in class ini.trakem2.tree.LayerTree: Deselects whatever node is selected in the tree, and tries to select the one that contains the given object.
sendToSiblingProject(DefaultMutableTreeNode) - Method in class ini.trakem2.tree.ProjectTree: When two or more people work on the same XML file, images may be the same but segmentations and the transformations of the images may diverge.
sendToSiblingProjectTask(DefaultMutableTreeNode) - Method in class ini.trakem2.tree.ProjectTree
seqFindId(ImagePlus) - Method in class ini.trakem2.persistence.Cache
serialize(Object, String) - Method in class ini.trakem2.persistence.Loader: Serializes the given object into the path.
serializeFeatures(Align.Param, AbstractAffineTile2D<?>, Collection<Feature>) - Static method in class mpicbg.trakem2.align.Align
serializeFeatures(Project, Object, String, long, Collection<Feature>) - Static method in class mpicbg.trakem2.align.Util: Save a Collection of Features to the TrakEM2 project folder.
serializePointMatches(Align.Param, AbstractAffineTile2D<?>, AbstractAffineTile2D<?>, Collection<PointMatch>) - Static method in class mpicbg.trakem2.align.Align: Save a Collection of PointMatches two-sided.
serializePointMatches(Project, Object, String, long, long, Collection<PointMatch>) - Static method in class mpicbg.trakem2.align.Util: Save a Collection of PointMatches two-sided.
set(int, BSplineModel, BSplineModel, int, int) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform: Set cubic B-spline transform values
set(int, double[][], double[][], int, int) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform: Set cubic B-spline transform constructor
set(Param, int, int, int, int) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
set(CubicBSplineTransform) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
set(int, double, double, Layer, double) - Method in class ini.trakem2.display.Ball: Set the x,y,radius raw pixel values for the ball at index i.
set(Displayable) - Method in class ini.trakem2.display.DisplayablePanel: For instance-recycling purposes.
set(Shape) - Method in class ini.trakem2.display.inspect.ShapeProxy: Replace the wrapped Shape with s.
set(int, double, double) - Method in class ini.trakem2.display.ManualAlignMode.Landmarks: Sets the point at @param index to the new location.
set(ImagePlus) - Method in class ini.trakem2.display.Patch: Set a new ImagePlus for this Patch.
set(Displayable) - Method in class ini.trakem2.display.SnapshotPanel
set(double, boolean, boolean, int, boolean, boolean, boolean) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
set(DefaultMutableTreeNode, Thing, HashMap<Thing, Boolean>) - Method in class ini.trakem2.tree.DNDTree: Recursive
set(int, int, int, int) - Method in class ini.trakem2.utils.ImgLibVolume
set(double, double, double) - Method in class ini.trakem2.utils.Vector3
set(NonLinearTransform) - Method in class lenscorrection.NonLinearTransform
set(PolynomialModel2D) - Method in class lenscorrection.PolynomialModel2D
set(float, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray2D
set(float, int, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
set(float, int, int, int, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray4D
setActive(boolean) - Method in class ini.trakem2.display.Channel
setActive(Displayable) - Method in class ini.trakem2.display.Display: Used by the Selection exclusively.
setActive(Object, Displayable) - Static method in class ini.trakem2.display.Display
setActive(Displayable) - Method in class ini.trakem2.display.Selection
setActive(Node<T>) - Method in class ini.trakem2.display.Tree: The node currently being dragged or edited in some way.
setActiveChannel(Channel) - Method in class ini.trakem2.display.Display: Set the channel as active and the others as inactive.
setAffine(AbstractAffineModel2D<?>) - Method in class lenscorrection.PolynomialModel2D
setAffine(Class<? extends AbstractAffineModel2D<?>>) - Method in class lenscorrection.PolynomialModel2D
setAffineTransform(AffineTransform) - Method in class ini.trakem2.display.Displayable: Sets the matrix values of this Displayable's AffineTransform to those of the given AffineTransform.
setAffineTransform(AffineTransform) - Method in class ini.trakem2.display.Stack
setAllVisible(boolean) - Method in class ini.trakem2.display.Layer: Returns the collection of Displayable whose visibility state has changed.
setAllVisible(boolean) - Method in class ini.trakem2.display.LayerSet: Returns the collection of Displayable whose visibility state has changed.
setAlpha(float, boolean) - Method in class ini.trakem2.display.Channel: For reconstructing purposes.
setAlpha(float) - Method in class ini.trakem2.display.Channel
setAlpha(float) - Method in class ini.trakem2.display.Displayable
setAlpha(float, boolean) - Method in class ini.trakem2.display.Displayable
setAlpha(float) - Method in class ini.trakem2.display.LayerPanel
setAlpha(float) - Method in class ini.trakem2.display.LayerSet: Overiding.
setAlpha(float, boolean) - Method in class ini.trakem2.display.Patch
setAlpha(float) - Method in class ini.trakem2.display.Selection
setAlphaMask(ByteProcessor) - Method in class ini.trakem2.display.Patch: Must call updateMipMaps() afterwards.
setAnnotation(String) - Method in class ini.trakem2.display.Displayable
setArea(long, Area) - Method in class ini.trakem2.display.AreaList: Directly place an Area for the specified layer.
setAsBackground(boolean) - Method in class ini.trakem2.utils.Worker
setAverage(boolean) - Method in class ini.trakem2.utils.ImgLibVolume: Does nothing.
setBackground(Color) - Method in class ini.trakem2.display.DisplayablePanel
setBeta(double[][]) - Method in class lenscorrection.NonLinearTransform
setBrushSize(int) - Static method in class ini.trakem2.utils.ProjectToolbar: Change the brush size by the given length increment (in pixel units).
setBucketsEnabled(boolean) - Method in class ini.trakem2.display.Layer
setCalibration(Calibration) - Method in class ini.trakem2.display.FakeImagePlus: Forward to LayerSet.
setCalibration(Calibration) - Method in class ini.trakem2.display.LayerSet: Set the calibration to a clone of the given calibration.
setCalibration(Calibration) - Method in class ini.trakem2.imaging.PatchStack
setCalibrationSuper(Calibration) - Method in class ini.trakem2.display.FakeImagePlus
setChanged(boolean) - Method in class ini.trakem2.persistence.Loader
setChannel(int, float) - Method in class ini.trakem2.display.Display: Make the given channel have the given alpha (transparency).
setClosingTask(Runnable) - Method in class ini.trakem2.display.YesNoDialog
setColor(Displayable, Color) - Static method in class ini.trakem2.display.Display3D
setColor(Color) - Method in class ini.trakem2.display.Displayable
setColor(Color) - Method in class ini.trakem2.display.LayerPanel
setColor(Color) - Method in class ini.trakem2.display.Node
setColor(Color) - Method in class ini.trakem2.display.Profile
setColor(Color) - Method in class ini.trakem2.display.Selection
setColor(Color) - Method in class ini.trakem2.display.ZDisplayable
setColor(Color) - Method in class ini.trakem2.imaging.PatchStack
setColorChannel(Layer, Color) - Method in class ini.trakem2.display.Display: Set a layer to be painted as a specific color channel in the canvas.
setCompositeMode(byte) - Method in class ini.trakem2.display.Displayable: Sets the composite mode, which determines how is this image painted to the screen relative to the other images.
setConfidence(byte) - Method in class ini.trakem2.display.Node: Set the confidence value of this node with its parent.
setCoordinateTransform(List<Patch>, CoordinateTransform, int) - Method in class ini.trakem2.display.Display
setCoordinateTransform(List<Patch>, CoordinateTransform, boolean) - Method in class ini.trakem2.display.Display: Deprecated.
Use Display.setCoordinateTransform(List, CoordinateTransform, int) instead which implements pre-appending as a third mode.
setCoordinateTransform(CoordinateTransform) - Method in class ini.trakem2.display.Patch: Set a CoordinateTransform to this Patch.
setCoordinateTransform(List<Patch>, CoordinateTransform, int) - Static method in class lenscorrection.DistortionCorrectionTask
setCoordinateTransformSilently(CoordinateTransform) - Method in class ini.trakem2.display.Patch: For reconstruction purposes, overwrites the present CoordinateTransform, if any, with the given one.
SetCoordinateTransformThread(List<Patch>, CoordinateTransform, AtomicInteger) - Constructor for class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
setCurrentSlice(Patch) - Method in class ini.trakem2.imaging.PatchStack
setCursor(int, int, int, int) - Method in class ini.trakem2.display.DisplayCanvas: Sets the cursor based on the current tool and cursor location.
setCursorToAll(Cursor) - Static method in class ini.trakem2.display.Display
setData(Area) - Method in class ini.trakem2.display.AreaTree.AreaNode
setData(T) - Method in class ini.trakem2.display.Node
setData(Float) - Method in class ini.trakem2.display.Treeline.RadiusNode: Set the radius to a positive value.
setDebug(boolean) - Static method in class ini.trakem2.utils.Utils
setDebugMouse(boolean) - Static method in class ini.trakem2.utils.Utils
setDebugSQL(boolean) - Static method in class ini.trakem2.utils.Utils
setDefaultMinAndMax(double, double) - Method in class ini.trakem2.imaging.ContrastPlot: Set default min and max (of the image, not of the plot).
setDesirableMinFreeBytes(long) - Static method in class ini.trakem2.persistence.Loader: If the number of minimally free memory bytes (100 Mb times the number of CPU cores) is too low for your (giant) images, set it to a larger value here.
setDimension(int) - Method in class lenscorrection.NonLinearTransform: Deletes all dimension dependent properties
setDimensions(double, double) - Method in class ini.trakem2.display.Displayable: Not accepted if zero or negative.
setDimensions(double, double, boolean) - Method in class ini.trakem2.display.Displayable: Sets the dimensions of the bounding box.
setDimensions(double, double) - Method in class ini.trakem2.display.DisplayCanvas: Does not repaint.
setDimensions(int, int) - Method in class ini.trakem2.display.FakeImagePlus: Used to resize the canvas.
setDimensions(float, float, float, float) - Method in class ini.trakem2.display.LayerSet: May leave objects beyond the visible window.
setDimensions(float, float, int) - Method in class ini.trakem2.display.LayerSet: Returns false if any Displayables are being partially or totally cropped away.
setDimensions(int, int, int) - Method in class ini.trakem2.imaging.PatchStack
setDrawingSize(int, int) - Method in class ini.trakem2.display.DisplayCanvas
setEdgeConfidence(byte) - Method in class ini.trakem2.display.Tree: Find an edge near the world coords x,y,layer with precision depending upon magnification, and adjust its confidence to @param confidence.
setEnabled(Container, boolean) - Static method in class ini.trakem2.utils.Utils: Recursively enable/disable all components of the @param root Container.
setExpandedSilently(Thing, boolean) - Method in class ini.trakem2.tree.DNDTree: Does not incur in firing a TreeExpansion event, and affects the node only, not any of its parents.
setExpandedSilently(DefaultMutableTreeNode, boolean) - Method in class ini.trakem2.tree.DNDTree
setf(int, float) - Method in class mpicbg.trakem2.util.RobustNormalizeLocalContrast.ByteSetter
setf(int, float) - Method in class mpicbg.trakem2.util.RobustNormalizeLocalContrast.FloatSetter
setf(int, float) - Method in interface mpicbg.trakem2.util.RobustNormalizeLocalContrast.PixelSetter
setf(int, float) - Method in class mpicbg.trakem2.util.RobustNormalizeLocalContrast.ShortSetter
setField(Object, Class<?>, String, Object) - Static method in class ini.trakem2.utils.Utils
setFileInfo(FileInfo) - Method in class ini.trakem2.imaging.PatchStack
setFilePath(String) - Method in class ini.trakem2.display.Stack: Will decache the ImagePlus if loaded.
setFilters(IFilter[]) - Method in class ini.trakem2.display.Patch: Set an array of @{link IFilter, which are applied in order to the ImageProcessor after the preprocessor script is applied but before the rest of TrakEM2 sees the image.
setFirstMipMapLevelSaved(double) - Method in class ini.trakem2.Project: Returns the newly set mipmap level (an integer, made by a floor operation on level), or the current one if level is NaN or negative.
setFloater(int, int) - Method in class ini.trakem2.display.AffineTransformMode: No display bounds are checked, the floater can be placed wherever you want.
setFrom(Component, int) - Method in class ini.trakem2.utils.OptionPanel.NumericalSetter
setFrom(Component) - Method in class ini.trakem2.utils.OptionPanel.Setter: Will set the field if no exception is thrown when reading it.
setFront(Layer, Displayable) - Static method in class ini.trakem2.display.Display: Grab the last selected display (or create an new one if none) and show in it the layer,centered on the Displayable object.
setGUIEnabled(boolean) - Static method in class ini.trakem2.ControlWindow: Prevents ControlWindow from displaying projects.
setHeapFraction(float) - Static method in class ini.trakem2.persistence.Loader
setHistogram(ImageStatistics, Color) - Method in class ini.trakem2.imaging.ContrastPlot
setImage(Image) - Method in class ini.trakem2.imaging.PatchStack
setImageFile(Patch, ImagePlus) - Method in class ini.trakem2.persistence.FSLoader: Returns the absolute path to a file that contains the given ImagePlus image - which may be the path as described in the ImagePlus FileInfo object itself, or a totally new file.
setImageFile(Patch, ImagePlus) - Method in class ini.trakem2.persistence.Loader: Does nothing and returns null unless overridden.
setImageJToolbar() - Static method in class ini.trakem2.utils.ProjectToolbar: Restore ImageJ's toolbar.
setInitialMagnification(double) - Method in class ini.trakem2.display.DisplayCanvas: Used to constrain magnification so that only snapshots are used for painting when opening a new, large and filled Display.
setInvertibleCoordinateTransform(InvertibleCoordinateTransform) - Method in class ini.trakem2.display.Stack
setInvertibleCoordinateTransformSilently(InvertibleCoordinateTransform) - Method in class ini.trakem2.display.Stack: For reconstruction purposes, overwrites the present InvertibleCoordinateTransform, if any, with the given one.
setLambda(float) - Method in class lenscorrection.PolynomialModel2D
setLastAdded(Node<T>) - Method in class ini.trakem2.display.Tree
setLastEdited(Node<T>) - Method in class ini.trakem2.display.Tree
setLastMarked(Node<T>) - Method in class ini.trakem2.display.Tree
setLastVisited(Node<T>) - Method in class ini.trakem2.display.Tree: The node that paints in green, which is the receiver of events.
setLayer(Layer) - Method in class ini.trakem2.display.Display
setLayer(Layer, boolean) - Method in class ini.trakem2.display.Displayable
setLayer(Layer) - Method in class ini.trakem2.display.Displayable
setLayer(Layer, boolean) - Method in class ini.trakem2.display.LayerSet: 'update' in database or not.
setLayer(Layer) - Method in class ini.trakem2.display.Node
setLayer(Layer) - Method in class ini.trakem2.display.ZDisplayable
setLayerCompositeMode(Layer, byte) - Method in class ini.trakem2.display.Display
setLayerSet(LayerSet) - Method in class ini.trakem2.display.ZDisplayable
setLayerSet(LayerSet, boolean) - Method in class ini.trakem2.display.ZDisplayable
setLinkedProperties(Displayable, Map<String, String>) - Method in class ini.trakem2.display.Displayable: Add all the properties in map p as properties linked to the target Displayable.
setLinkedProperty(Displayable, String, String) - Method in class ini.trakem2.display.Displayable: Add a property that is specific to the relationship between this Displayable and the target, and will be deleted when the target Displayable is deleted.
setLocation(Point) - Method in class ini.trakem2.display.Display
setLocation(double, double) - Method in class ini.trakem2.display.Displayable: Sets the top left of the bounding box to x,y.
setLocked(boolean) - Method in class ini.trakem2.display.Displayable: Set the locking state of this Displayable, which affects that of its linked Displayable objects.
setLocked(boolean) - Method in class ini.trakem2.display.Selection: Lock / unlock all selected objects.
setLogStream(PrintStream) - Static method in class ini.trakem2.utils.Utils
setLookAndFeel() - Static method in class ini.trakem2.ControlWindow
setLut(ColorModel) - Method in class ini.trakem2.display.Selection: Apply the given LUT to all selected 8-bit, 16-bit, 32-bit images.
setMagnification(double) - Method in class ini.trakem2.display.DisplayCanvas
setMaxBytes(long) - Method in class ini.trakem2.persistence.Cache
setMeshResolution(List<Patch>, int) - Method in class ini.trakem2.display.Display
setMeshResolution(int) - Method in class ini.trakem2.display.Patch: Change the resolution of meshes used to render patches transformed by a CoordinateTransform.
setMinAndMax(double, double) - Method in class ini.trakem2.display.Patch: The min and max values are stored with the Patch, so that the image can be flushed away but the non-destructive contrast settings preserved.
setMinAndMax(Collection<? extends Displayable>, double, double) - Method in class ini.trakem2.persistence.Loader
setMinimumDimensions() - Method in class ini.trakem2.display.LayerSet: Used by the Loader after loading blindly a lot of Patches.
setMinMax(double, double) - Method in class ini.trakem2.imaging.FloatProcessorT2
setMipMapFormat(int) - Method in class ini.trakem2.persistence.FSLoader
setMipMapFormat(int) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
setMipMapsMode(int) - Method in class ini.trakem2.Project
setMipMapsRegeneration(boolean) - Method in class ini.trakem2.persistence.FSLoader
setMipMapsRegeneration(boolean) - Method in class ini.trakem2.persistence.Loader
setMode(Mode) - Method in class ini.trakem2.display.Display
setNewCoordinateTransform(CoordinateTransform) - Method in class ini.trakem2.display.Patch: Writes the CoordinateTransform t to the trakem2.transforms/ directory, using the unique Patch.ct_id and this Patch's DBObject.id to generate a file path for it.
setNoCheck(int, int, int, int) - Method in class ini.trakem2.utils.ImgLibVolume
setObject(Object) - Method in class ini.trakem2.tree.ProjectThing: Used by the TMLHandler; can be used only once.
setOrder(int) - Method in class lenscorrection.PolynomialModel2D
setOverlay(Overlay) - Method in class ini.trakem2.display.Layer: Set to null to remove the Overlay.
setOverlay(Overlay) - Method in class ini.trakem2.display.LayerSet: Set to null to remove the Overlay.
setParent(LayerSet) - Method in class ini.trakem2.display.Layer
setParent(Layer) - Method in class ini.trakem2.display.LayerSet
setParent(Thing) - Method in class ini.trakem2.tree.LayerThing
setParent(Thing) - Method in class ini.trakem2.tree.ProjectThing
setParent(Thing) - Method in class ini.trakem2.tree.TemplateThing
setParent(Thing) - Method in interface ini.trakem2.tree.Thing
setParentSilently(LayerSet) - Method in class ini.trakem2.display.Layer: Used for reconstruction purposes.
setPixels(int, int, float[]) - Method in class ini.trakem2.imaging.FloatProcessorT2: Set pixels and change image dimensions if width and height are different than the current.
setPixels(Object, int) - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
setPixelsMaxDimension(int) - Method in class ini.trakem2.display.LayerSet
setPixelsVirtualizationEnabled(boolean) - Method in class ini.trakem2.display.LayerSet
setPoints(double[][], double[][], double[][]) - Method in class ini.trakem2.display.Profile
setPoints(double[][], double[][], double[][], boolean) - Method in class ini.trakem2.display.Profile
setPosition(float, float) - Method in class ini.trakem2.display.Node
setPosition(float[]) - Method in class ini.trakem2.display.Node: Expects two dimensions.
setPosition(int, int, int) - Method in class ini.trakem2.imaging.PatchStack
setPosition(int) - Method in class ini.trakem2.utils.CircularSequence: Will wrap around if k<0 or k>size.
setPreprocessorScriptPath(String) - Method in class ini.trakem2.display.Patch: After setting a preprocessor script, it is advisable that you call updateMipMaps() immediately.
setPreprocessorScriptPath(Patch, String) - Method in class ini.trakem2.persistence.Loader: Set a preprocessor script that will be executed on the ImagePlus of the Patch when loading it, before TrakEM2 sees it at all.
setPreprocessorScriptPathSilently(Patch, String) - Method in class ini.trakem2.persistence.Loader: Set a preprocessor script that will be executed on the ImagePlus of the Patch when loading it, before TrakEM2 sees it at all.
setPriority(int) - Method in class ini.trakem2.utils.Worker
setProcessor(String, ImageProcessor) - Method in class ini.trakem2.display.FakeImagePlus
setProcessor(String, ImageProcessor) - Method in class ini.trakem2.imaging.PatchStack
setProjectToolbar() - Static method in class ini.trakem2.utils.ProjectToolbar: Set macro buttons for TrakEM2 in ImageJ's toolbar
setProperties(AbstractOffscreenThread.RepaintProperties) - Method in class ini.trakem2.display.AbstractOffscreenThread
setProperty(String, String) - Method in class ini.trakem2.display.Displayable: Set a key/valye property pair; to remove a property, set the value to null.
setProperty(String, Object) - Method in class ini.trakem2.imaging.PatchStack
setProperty(String, String) - Method in class ini.trakem2.Project
setProperty(Object, Object) - Method in class ini.trakem2.utils.Worker
setProvider(ExecutorProvider) - Static method in class ini.trakem2.parallel.ExecutorProvider
setQuality(float) - Method in class ini.trakem2.utils.Saver
setRadius(int, double) - Method in class ini.trakem2.display.Ball: Set the radius (raw pixel value) for the ball at index i.
setReceivesInput(Project, boolean) - Static method in class ini.trakem2.display.Display: Toggle user input; pan and zoom are always enabled though.
setReceivesInput(boolean) - Method in class ini.trakem2.display.DisplayCanvas
setReceivesInput(boolean) - Method in class ini.trakem2.Project: Tells the displays concerning this Project to accept/reject input.
setRepaint(boolean) - Static method in class ini.trakem2.display.Display: Set a flag to enable/disable repainting of all Display instances.
setRoi(Roi) - Method in class ini.trakem2.imaging.PatchStack
setRoi(Rectangle) - Method in class ini.trakem2.imaging.PatchStack
setRoot(Node<T>) - Method in class ini.trakem2.display.Tree: Used when reconstructing from XML.
setRotVector(double, double, double) - Method in class ini.trakem2.display.LayerSet
setScrollStep(int) - Method in class ini.trakem2.display.Display
setSelected(boolean) - Method in class ini.trakem2.display.Channel
setSlice(int) - Method in class ini.trakem2.display.FakeImagePlus
setSlice(int) - Method in class ini.trakem2.imaging.PatchStack
setSliceLabel(String, int) - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
setSnapshotsMode(int) - Method in class ini.trakem2.display.LayerSet
setSnapshotsQuality(boolean) - Method in class ini.trakem2.display.LayerSet
setSource(Displayable) - Method in class ini.trakem2.display.AreaWrapper
setSrcRect(int, int, int, int) - Method in class ini.trakem2.display.DisplayCanvas: Set the srcRect - used by the DisplayNavigator.
setStack(String, ImageStack) - Method in class ini.trakem2.imaging.PatchStack
setTaskName(String) - Method in class ini.trakem2.utils.Worker
setTempLoader(Loader) - Method in class ini.trakem2.Project
Setter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.Setter
Setter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.Setter
setText(String, boolean) - Method in class ini.trakem2.display.DLabel
setText(String) - Method in class ini.trakem2.tree.DNDTree.NodeRenderer: Override to show tooltip text as well.
setThickness(double) - Method in class ini.trakem2.display.Layer
setTitle(String) - Method in class ini.trakem2.display.Displayable: Does not accept null or zero-length titles.
setTitle(String) - Method in class ini.trakem2.display.DLabel
setTitle(String) - Method in class ini.trakem2.imaging.PatchStack
setTitle(String) - Method in class ini.trakem2.Project
setTitle(String) - Method in class ini.trakem2.tree.LayerThing
setTitle(String) - Method in class ini.trakem2.tree.ProjectThing
setTitle(String) - Method in interface ini.trakem2.tree.TitledThing
setTool(int) - Static method in class ini.trakem2.utils.ProjectToolbar
setTransparency(Displayable, float) - Static method in class ini.trakem2.display.Display3D
setTransparencySlider(float) - Method in class ini.trakem2.display.Display
setTranspOverlayAreas(boolean) - Method in class ini.trakem2.display.Display
setTranspOverlayImages(boolean) - Method in class ini.trakem2.display.Display
setTranspOverlayTextLabels(boolean) - Method in class ini.trakem2.display.Display
setType(int) - Method in class ini.trakem2.display.DLabel
setType(int) - Method in class ini.trakem2.imaging.PatchStack
setup(boolean, String, boolean, boolean) - Method in class ini.trakem2.analysis.Compare.CATAParameters
setup() - Method in class ini.trakem2.display.AreaWrapper.PaintParameters
setup(double, Rectangle) - Method in class ini.trakem2.display.DisplayCanvas: Used for restoring properties from the database.
setup() - Method in class ini.trakem2.display.LayerSet: For reconstruction purposes: set the active layer to the ZDisplayable objects.
setup() - Method in class ini.trakem2.imaging.Segmentation.FastMarchingParam
setup(Layer) - Method in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam: Run setup on a Patch of the layer, if any.
setup(Patch) - Method in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam: Returns false when canceled.
setup(Object...) - Method in interface ini.trakem2.plugin.TPlugIn: Setup with optional parameters (may be null).
setup() - Method in class ini.trakem2.tree.LayerThing: Tell the attributes who owns them, and the children's attributes as well, and set the parent to the children; used to finish up reconstruction from the database.
setup() - Method in class ini.trakem2.tree.ProjectThing
setup(ArrayList<TemplateThing>) - Method in class ini.trakem2.tree.TemplateThing: For reconstruction purposes.
setup(ControlWindow) - Static method in class ini.trakem2.utils.Utils: Initialize house keeping threads.
setup(String) - Method in class lenscorrection.Distortion_Correction.BasicParam
setup(String) - Method in class lenscorrection.Distortion_Correction.PluginParam: Setup as a three step dialog.
setup(Selection) - Method in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
setup(String) - Method in class mpicbg.trakem2.align.Align.Param
setup(Rectangle) - Method in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
setup() - Method in class mpicbg.trakem2.align.ElasticMontage.Param
setup() - Static method in class mpicbg.trakem2.align.ElasticMontage
setup(Rectangle) - Method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment.Param
setup(Object...) - Method in class org.janelia.intensity.MatchIntensities
setUpdateGraphics(Layer, Displayable) - Static method in class ini.trakem2.display.Display: Mark the canvas for updating the offscreen images if the given Displayable is NOT the active.
setUpdateGraphics(Layer, boolean) - Static method in class ini.trakem2.display.Display: Flag the DisplayCanvas of Displays showing the given Layer to update their offscreen images.
setUpdateGraphics(boolean) - Method in class ini.trakem2.display.Display: Whether to update the offscreen images or not.
setUpdateGraphics(boolean) - Method in class ini.trakem2.display.DisplayCanvas
setupMenuItems(JMenu, Project) - Method in class ini.trakem2.persistence.FSLoader: Adds a "Save" and "Save as" menu items.
setupMenuItems(JMenu, Project) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
setupPreloader(ControlWindow) - Static method in class ini.trakem2.persistence.Loader: Uses maximum 4 concurrent threads: higher thread number does not improve performance.
setupPreloaderThreads(int) - Static method in class ini.trakem2.persistence.Loader: Set to zero to disable; maximum recommended is 4 if you have more than 4 CPUs.
setupSIFT(String) - Method in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
setupSIFT(String) - Method in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
setValue(Set<Collection<Vertex<T>>>) - Method in class ini.trakem2.analysis.Centrality.EtchingStep
setValue(short) - Method in class ini.trakem2.display.paint.USHORTPaint: Will alter the value for this instance and for all USHORTPaintContext instances returned from USHORTPaint.createContext(ColorModel, Rectangle, Rectangle2D, AffineTransform, RenderingHints).
setValue(String) - Method in class ini.trakem2.tree.TemplateThing
setVisible(boolean) - Method in class ini.trakem2.display.Displayable
setVisible(boolean, boolean) - Method in class ini.trakem2.display.Displayable
setVisible(String, boolean, boolean) - Method in class ini.trakem2.display.Layer: Note: Not recursive into embedded LayerSet objects.
setVisible(String, boolean, boolean) - Method in class ini.trakem2.display.LayerSet: Returns the hash set of objects whose visibility has changed.
setVisible(boolean) - Method in class ini.trakem2.display.Selection: Set all selected objects visible/hidden; returns a collection of those that changed state.
setVisible(boolean, boolean) - Method in class ini.trakem2.display.ZDisplayable
setVisible(boolean) - Method in class ini.trakem2.tree.ProjectThing: Switch the visibility of the Displayable objects contained here or in the children.
setWaitingCursor() - Static method in class ini.trakem2.display.Display3D
setWeight(float) - Method in class ini.trakem2.imaging.BinaryInterpolation2D: After changing the weight, it's totally valid to call process() again, and then getResult().
setWindow(Window) - Method in class ini.trakem2.imaging.PatchStack
setXPlane(FloatArray2D, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
setXPlane(float[][], int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
setYPlane(FloatArray2D, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
setYPlane(float[][], int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
setZ(double) - Method in class ini.trakem2.display.Layer
setZPlane(FloatArray2D, int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
setZPlane(float[][], int) - Method in class mpi.fruitfly.math.datastructures.FloatArray3D
shallowCopy() - Method in class ini.trakem2.tree.LayerThing: A new copy with same template, same project, same id, same object and cloned table of same attributes, and same title, but no parent and no children.
shallowCopy() - Method in class ini.trakem2.tree.ProjectThing: A new copy with same template, same object and cloned table of same attributes, but no parent and no children.
shallowCopy() - Method in class ini.trakem2.tree.TemplateThing: A new copy with same type, same project, same id, but no parent and no children.
shallowCopy() - Method in interface ini.trakem2.tree.Thing
ShapeProxy - Class in ini.trakem2.display.inspect
ShapeProxy(Shape) - Constructor for class ini.trakem2.display.inspect.ShapeProxy: Create a new proxy for s.
shortest(float, float) - Static method in class ini.trakem2.utils.M: Returns the shortest possible String representation of a float number, according to the desired decimal @param precision.
ShortSetter(ShortProcessor) - Constructor for class mpicbg.trakem2.util.RobustNormalizeLocalContrast.ShortSetter
show(Layer, Displayable, boolean, boolean) - Method in class ini.trakem2.display.Display: Set this Display to show the specific layer, centered at the @param displ, and perhaps selected, adding to the selection instead of clearing it if @param shift_down is true.
show(ProjectThing) - Static method in class ini.trakem2.display.Display3D
show(ProjectThing, boolean, int) - Static method in class ini.trakem2.display.Display3D: Scan the ProjectThing children and assign the renderable ones to an existing Display3D for their LayerSet, or open a new one.
show(LayerSet, Collection<Content>) - Static method in class ini.trakem2.display.Display3D
show(ResultsTable) - Method in class ini.trakem2.display.Tree.MeasurePathDistance: Reuses @param rt unless it is null, in which case it creates a new one.
show() - Method in class ini.trakem2.imaging.PatchStack
show(String) - Method in class ini.trakem2.imaging.PatchStack
showAllTables(HashMap<Class<?>, ResultsTable>) - Static method in class ini.trakem2.utils.Utils
showAndResetView(ProjectThing) - Static method in class ini.trakem2.display.Display3D
showCentered(Layer, Displayable, boolean, boolean) - Static method in class ini.trakem2.display.Display: Show the given Displayable centered and selected.
showCentered(Rectangle) - Method in class ini.trakem2.display.DisplayCanvas: Center the srcRect around the given object(s) bounding box, zooming if necessary, so that the given r becomes a rectangle centered in the srcRect and zoomed out by a factor of 2.
showCentered2D(boolean) - Method in class ini.trakem2.analysis.Compare.Chain: Show centered, set visible and select.
showDialog() - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper: Uses the @param reference Patch as the one to extract the reference histogram from.
showFront(Layer) - Static method in class ini.trakem2.display.Display: Show the layer in the front Display, or in a new Display if the front Display is showing a layer from a different LayerSet.
showImages - Variable in class mpi.fruitfly.registration.CrossCorrelation2D
showInfo(ProjectThing) - Method in class ini.trakem2.tree.ProjectTree
showMessage(String) - Static method in class ini.trakem2.utils.Utils
showMessage(String, String) - Static method in class ini.trakem2.utils.Utils
showMessageT(String) - Static method in class ini.trakem2.utils.Utils: Runs the showMessage in a separate Thread.
showOrthoslices(Patch) - Static method in class ini.trakem2.display.Display3D
showOrthoslices(ImagePlus, String, int, int, float, Layer) - Static method in class ini.trakem2.display.Display3D
showPopup(Component, int, int) - Method in class ini.trakem2.display.Display
showProgress(double) - Static method in class ini.trakem2.utils.Utils
showStatus(String, boolean) - Static method in class ini.trakem2.utils.Utils
showStatus(String) - Static method in class ini.trakem2.utils.Utils
showVolume(Patch) - Static method in class ini.trakem2.display.Display3D
showWindow() - Static method in class ini.trakem2.utils.Search
shutdown() - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper: Waits until all tasks have finished executing.
SIDE - Static variable in class ini.trakem2.display.SnapshotPanel
sift - Variable in class lenscorrection.Distortion_Correction.BasicParam
sift - Variable in class mpicbg.trakem2.align.Align.Param
sift - Variable in class mpicbg.trakem2.align.AlignmentUtils.ParamPointMatch
sigma - Variable in class ini.trakem2.analysis.Vertex: Number of short paths passing through this vertex.
sigma - Variable in class ini.trakem2.imaging.filters.CorrectBackground: Sigma of the Gaussian
sigmaX - Variable in class ini.trakem2.imaging.filters.GaussianBlur
sigmaY - Variable in class ini.trakem2.imaging.filters.GaussianBlur
sign(double) - Static method in class mpi.fruitfly.math.General
SimilarityTile2D - Class in mpicbg.trakem2.align
SimilarityTile2D(SimilarityModel2D, Patch) - Constructor for class mpicbg.trakem2.align.SimilarityTile2D
SimilarityTile2D(Patch) - Constructor for class mpicbg.trakem2.align.SimilarityTile2D
simplify(double[], double[], long[], int, LayerSet) - Static method in class ini.trakem2.display.Polyline: Resample the curve to, first, a number of points as resulting from resampling to a point interdistance of delta, and second, as adjustment by random walk of those points towards the original points.
singularInterpolation(Area, Area, int) - Static method in class ini.trakem2.utils.AreaUtils: Interpolate areas only if they are made of a single shape each.
size() - Method in class ini.trakem2.display.LayerSet: The number of Layers in this LayerSet.
size() - Method in class ini.trakem2.display.Node.NodeCollection: WARNING: O(n) operation: will traverse the whole collection.
size() - Method in class ini.trakem2.persistence.Cache
size() - Method in class ini.trakem2.utils.FieldMapView
size() - Method in class ini.trakem2.utils.History
skip_ends - Variable in class ini.trakem2.analysis.Compare.CATAParameters
skippedEntity(String) - Method in class ini.trakem2.persistence.TMLHandler
SlabIterator(Node) - Constructor for class ini.trakem2.display.Node.SlabIterator
sleep(long) - Static method in class ini.trakem2.utils.Utils
slider - Variable in class ini.trakem2.display.LayerPanel
SliderListener() - Constructor for class ini.trakem2.display.Displayable.SliderListener
slope - Variable in class ini.trakem2.imaging.filters.CLAHE
sloppyOverlapTest - Static variable in class mpicbg.trakem2.align.AlignTask
snap(Patch) - Static method in class ini.trakem2.display.Display: Snap a Patch to the most overlapping Patch, if any.
snap(Patch, Align.ParamOptimize, boolean) - Static method in class mpicbg.trakem2.align.AlignTask: Find the most overlapping image to @param patch in the same layer where @param patch sits, and snap @param patch and all its linked Displayable objects.
snapshot_modes - Static variable in class ini.trakem2.display.LayerSet
SnapshotPanel - Class in ini.trakem2.display
SnapshotPanel(Display, Displayable) - Constructor for class ini.trakem2.display.SnapshotPanel
snapshotsQuality() - Method in class ini.trakem2.display.LayerSet: For creating snapshots, using a very slow but much better scaling algorithm (the Image.SCALE_AREA_AVERAGING method).
snapTo(int, int, int, int) - Method in class ini.trakem2.display.Displayable: Does nothing unless overriden.
snapTo(int, int, int, int) - Method in class ini.trakem2.display.Pipe: x,y is the cursor position in offscreen coordinates.
snapTo(int, int, int, int) - Method in class ini.trakem2.display.Profile: x,y is the cursor position in offscreen coordinates.
SNT_invert_image - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
softRemove() - Method in class ini.trakem2.display.Displayable: Calls remove(false) unless overriden.
softRemove() - Method in class ini.trakem2.display.Profile: Does nothing.
softRemove() - Method in class ini.trakem2.display.ZDisplayable: Does not remove from the LayerSet.
source_dir - Variable in class lenscorrection.Distortion_Correction.PluginParam
SOUTH - Static variable in class ini.trakem2.display.LayerSet
SOUTHEAST - Static variable in class ini.trakem2.display.LayerSet
SOUTHWEST - Static variable in class ini.trakem2.display.LayerSet
sp - Static variable in class lenscorrection.Distortion_Correction
specify() - Method in class ini.trakem2.display.Selection
split(List<Displayable>) - Static method in class ini.trakem2.display.AreaList: For each AreaList in the list, find disconnected volumes within each and make an AreaList out of each.
splitArea(Area, PolygonRoi, Rectangle) - Static method in class ini.trakem2.utils.M: Returns an array of two Area objects, or of 1 if the @param proi doesn't intersect @param a.
splitAt(Node<T>) - Method in class ini.trakem2.display.Tree
splitNear(float, float, Layer, double) - Method in class ini.trakem2.display.Tree: Split the Tree into new Tree at the point closest to the x,y,layer world coordinate.
springLengthSpringMesh - Variable in class mpicbg.trakem2.align.ElasticMontage.Param: Spring mesh
sq(double) - Static method in class mpi.fruitfly.math.General: simple square
sq(float) - Static method in class mpi.fruitfly.math.General
sqDistanceToEndPoints(double, double, long) - Method in class ini.trakem2.display.Polyline
srcRect - Variable in class ini.trakem2.display.GroupingMode
srcRectUpdated(Rectangle, double) - Method in class ini.trakem2.display.AffineTransformMode
srcRectUpdated(Rectangle, double) - Method in class ini.trakem2.display.DefaultMode
srcRectUpdated(Rectangle, double) - Method in class ini.trakem2.display.GroupingMode
srcRectUpdated(Rectangle, double) - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
srcRectUpdated(Rectangle, double) - Method in class ini.trakem2.display.ManualAlignMode
srcRectUpdated(Rectangle, double) - Method in interface ini.trakem2.display.Mode
Stack - Class in ini.trakem2.display
Stack(Project, String, double, double, Layer, String) - Constructor for class ini.trakem2.display.Stack
Stack(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Stack: Construct a Stack from an XML entry.
StackToDoubleArray1D(ImageStack) - Static method in class mpi.fruitfly.general.ImageArrayConverter
StackToDoubleArrayZeroPadding(ImageStack, int, int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
StackToFloatArray(ImageStack) - Static method in class mpi.fruitfly.general.ImageArrayConverter
StackToFloatArrayComplex(ImageStack) - Static method in class mpi.fruitfly.general.ImageArrayConverter
StackToFloatArrayComplexZeroPadding(ImageStack, int, int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
StackToFloatArrayDeprecated(ImageStack) - Static method in class mpi.fruitfly.general.ImageArrayConverter
StackToFloatArrayZeroPadding(ImageStack, int, int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
StaleFiles - Class in ini.trakem2.persistence: Methods to remove files that are no longer referenced from the current Patch instances of a Project.
StaleFiles() - Constructor for class ini.trakem2.persistence.StaleFiles
StaleFiles.AlphaMaskPath - Class in ini.trakem2.persistence
StaleFiles.CoordinateTransformPath - Class in ini.trakem2.persistence
StaleFiles.Path - Interface in ini.trakem2.persistence
start() - Method in class ini.trakem2.utils.RedPhone
start() - Static method in class ini.trakem2.utils.StdOutWindow
startAndJoin(Thread[]) - Static method in class mpi.fruitfly.general.MultiThreading
startedWorking() - Method in class ini.trakem2.utils.Worker
startElement(String, String, String, Attributes) - Method in class ini.trakem2.persistence.TMLHandler
startLargeUpdate() - Method in class ini.trakem2.persistence.DBLoader: Used in combination with commitLargeUpdate()
startLargeUpdate() - Method in class ini.trakem2.persistence.Loader
startTask(Runnable) - Static method in class mpi.fruitfly.general.MultiThreading
startTask(Runnable, int) - Static method in class mpi.fruitfly.general.MultiThreading
startWaitingCursor() - Static method in class ini.trakem2.ControlWindow: Appends to the buffer data relative to the viewport of the given tree.
STD_DEV - Static variable in class ini.trakem2.analysis.Compare
STD_DEV_ALL - Static variable in class ini.trakem2.analysis.Compare
StdOutWindow - Class in ini.trakem2.utils: Captures the last 10000 chars of StdOut and StdErr into two TextArea.
stds - Variable in class ini.trakem2.imaging.filters.NormalizeLocalContrast
stds1 - Variable in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
stds2 - Variable in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
steps - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
steps - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
stiffnessSpringMesh - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
stiffnessSpringMesh - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
stitch(Patch[], int, double, double, boolean, StitchingTEM.PhaseCorrelationParam) - Static method in class ini.trakem2.imaging.StitchingTEM: Returns the same Patch instances with their coordinates modified; the top-left image is assumed to be the first one, and thus serves as reference; so, after the first image, coordinates are ignored for each specific Patch.
StitchingTEM - Class in ini.trakem2.imaging: Given: - list of images - grid width - known percent overlap This class will attempt to find the optimal montage, by applying phase-correlation, and/or cross-correlation, and/or SIFT-based correlation) between neighboring images.
StitchingTEM() - Constructor for class ini.trakem2.imaging.StitchingTEM
StitchingTEM.PhaseCorrelationParam - Class in ini.trakem2.imaging: Phase correlation parameters class
StopWatch - Class in ini.trakem2.utils
StopWatch() - Constructor for class ini.trakem2.utils.StopWatch
StopWatch(String) - Constructor for class ini.trakem2.utils.StopWatch
storeAlphaMask(Patch, ByteProcessor) - Method in class ini.trakem2.persistence.Loader: Deprecated.
storeArrayForReuse(Image) - Static method in class ini.trakem2.utils.CachingThread
storeForReuse(byte[][]) - Static method in class ini.trakem2.utils.CachingThread
storeForReuse(byte[]) - Static method in class ini.trakem2.utils.CachingThread
storeForReuse(int[]) - Static method in class ini.trakem2.utils.CachingThread
storeLayerAlpha(LayerPanel, float) - Method in class ini.trakem2.display.Display: Add to layer_alpha table, or remove if alpha is zero.
stret - Variable in class ini.trakem2.imaging.filters.NormalizeLocalContrast
StringSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.StringSetter
StringSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.StringSetter
sub(int, int) - Method in class ini.trakem2.display.Polyline: Create a shorter Polyline, from start to end (inclusive); not added to the LayerSet.
subclone(Project) - Method in class ini.trakem2.tree.ProjectThing: Implicit id copying; assumes the ids of the object are also the same in the given project; the object, if it is a DBObject, is retrieved from the given project by matching its id.
substring_matching - Variable in class ini.trakem2.analysis.Compare.CATAParameters
subtract(long, ShapeRoi) - Method in class ini.trakem2.display.AreaList: Subtracts the given ROI, which is expected in world/LayerSet coordinates, to the area present at Layer with id layer_id, or set it if none present yet.
subtract(Area, Layer) - Method in class ini.trakem2.display.AreaWrapper: Subtract an area in world coordinates.
SubtractARGBComposite - Class in ini.trakem2.display.graphics
SubtractBackground - Class in ini.trakem2.imaging.filters: Subtract background with the rolling-ball algorithm.
SubtractBackground() - Constructor for class ini.trakem2.imaging.filters.SubtractBackground
SubtractBackground(int) - Constructor for class ini.trakem2.imaging.filters.SubtractBackground
SubtractBackground(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.SubtractBackground
SubtreeIterator(Node) - Constructor for class ini.trakem2.display.Node.SubtreeIterator
SUCCESS - Static variable in class ini.trakem2.imaging.StitchingTEM

T

Tag - Class in ini.trakem2.display
Tag(Object, int) - Constructor for class ini.trakem2.display.Tag
TAG_ATTR1 - Static variable in class ini.trakem2.display.Displayable
TAG_ATTR2 - Static variable in class ini.trakem2.display.Displayable
TAG_BACKGROUND - Static variable in interface ini.trakem2.display.Taggable
tagForMipmapRemoval(Patch, boolean) - Method in class ini.trakem2.persistence.FSLoader: Queue/unqueue for mipmap removal on shutdown without saving; the yes, when true, makes the p be queued, and when false, be removed from the queue.
tagForMipmapRemoval(Patch, boolean) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
Taggable - Interface in ini.trakem2.display
tags - Variable in class ini.trakem2.display.LayerSet: A set of unique tags, retrievable by their own identity.
target - Variable in class ini.trakem2.display.Patch.PatchImage: The image, coordinate-transformed if null != ct.
target_dir - Variable in class lenscorrection.Distortion_Correction.PluginParam
targetMean - Variable in class ini.trakem2.imaging.filters.Normalize
targetStdDev - Variable in class ini.trakem2.imaging.filters.Normalize
Task(String) - Constructor for class ini.trakem2.utils.Worker.Task
Task(String, boolean) - Constructor for class ini.trakem2.utils.Worker.Task
TaskFactory<I,O> - Class in ini.trakem2.parallel
TaskFactory() - Constructor for class ini.trakem2.parallel.TaskFactory
TaskOnEDT<V> - Class in ini.trakem2.utils
TaskOnEDT(Callable<V>) - Constructor for class ini.trakem2.utils.TaskOnEDT: The task @param fn should not be threaded; this class is intended to run small snippets of code under the event dispatch thread, while still being able to retrieve the result of the computation.
TemplateThing - Class in ini.trakem2.tree
TemplateThing(String) - Constructor for class ini.trakem2.tree.TemplateThing: Create a new non-database-stored TemplateThing.
TemplateThing(String, Project) - Constructor for class ini.trakem2.tree.TemplateThing: Create a new database-stored TemplateThing.
TemplateThing(String, Project, long) - Constructor for class ini.trakem2.tree.TemplateThing: Reconstruct a TemplateThing from the database.
TemplateTree - Class in ini.trakem2.tree
TemplateTree(Project, TemplateThing) - Constructor for class ini.trakem2.tree.TemplateTree
test(String) - Static method in class ini.trakem2.imaging.FastIntegralImage
testCreateOrigin(LayerSet, VectorString3D, VectorString3D, VectorString3D) - Static method in class ini.trakem2.analysis.Compare
TestGraphicsSource - Class in ini.trakem2.display.graphics
TestGraphicsSource() - Constructor for class ini.trakem2.display.graphics.TestGraphicsSource
TEXT - Static variable in class ini.trakem2.display.DLabel
textValueChanged(TextEvent) - Method in class ini.trakem2.display.Displayable.SliderListener
Thing - Interface in ini.trakem2.tree
TileConfiguration - Class in mpicbg.trakem2.align
TileConfiguration() - Constructor for class mpicbg.trakem2.align.TileConfiguration
tilePairs - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
tiles - Variable in class mpicbg.trakem2.align.Align.ExtractFeaturesThread
tiles - Variable in class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
tilesAreInPlace - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
tilesAreInPlace - Static variable in class mpicbg.trakem2.align.AlignTask
tilesAreInPlace - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
tileSequence(Layer, int, int, boolean) - Static method in class ini.trakem2.persistence.ProjectTiler: Return a lazy sequence of Rectangle instances, each specifying a tile that contains at least parts of one Patch.
tilesFromPatches(Align.Param, List<? extends Patch>, Collection<? extends Patch>, List<AbstractAffineTile2D<?>>, Collection<AbstractAffineTile2D<?>>) - Static method in class mpicbg.trakem2.align.Align: If a Patch is locked or in fixedPatches, its corresponding Tile is added to fixedTiles.
title - Variable in class ini.trakem2.analysis.Compare.Chain
title - Variable in class ini.trakem2.display.Displayable
TitledThing - Interface in ini.trakem2.tree
TMLHandler - Class in ini.trakem2.persistence: Creates the project objects from an XML file (TrakEM2 Markup Language Handler).
TMLHandler(String, FSLoader) - Constructor for class ini.trakem2.persistence.TMLHandler
toArray() - Method in class ini.trakem2.display.Node.NodeCollection: Override to avoid calling size(), which would iterate the whole list just for that.
toArray(Y[]) - Method in class ini.trakem2.display.Node.NodeCollection
toCalibration() - Method in class ini.trakem2.display.Tree.MeasurementPair: Concatenate the affine of the Tree and an affine that expresses the x,y calibration.
toClosestPaintedNode(Layer, float, float, double) - Method in class ini.trakem2.display.Tree: Also sets the last visited and the receiver node.
toDataString() - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform: Save cubic B-spline transform information into String
toDouble(int[], int) - Static method in class ini.trakem2.utils.Utils
toFront() - Static method in class ini.trakem2.ControlWindow
toggleClosed() - Method in class ini.trakem2.display.Profile: Toggle curve closed/open.
toInt(double[], int) - Static method in class ini.trakem2.utils.Utils
toLayer(Layer) - Method in class ini.trakem2.display.Display: Calls setLayer(la) on the SetLayerThread.
toolChanged(String) - Static method in class ini.trakem2.display.Display
toolChanged(int) - Static method in class ini.trakem2.display.Display
toolChanged(String) - Static method in class ini.trakem2.utils.ProjectToolbar: Called by macro tools.
TOP - Static variable in class ini.trakem2.display.LayerSet
TOP_BOTTOM - Static variable in class ini.trakem2.imaging.StitchingTEM
toPatchCoordinate(double, double) - Method in class ini.trakem2.display.Layer: Transfer the world coordinate specified by world_x,world_y in pixels, to the local coordinate of the Patch immediately present under it.
toPixelCoordinate(double, double) - Method in class ini.trakem2.display.Patch: Transfer a world coordinate (in pixels, uncalibrated) to the coordinate space of the original image.
toPixelCoordinate(double, double, AffineTransform, CoordinateTransform, int, int, int) - Static method in class ini.trakem2.display.Patch
toResultsTable(ResultsTable, int, double, int) - Method in class ini.trakem2.display.Tree.MeasurementPair
toShapesFile(StringBuffer, String, String, double) - Method in class ini.trakem2.display.Ball: Writes the data of this object as a Ball object in the .shapes file represented by the 'data' StringBuffer.
toShapesFile(StringBuffer, String, String, double) - Method in class ini.trakem2.display.Pipe: Writes the data of this object as a Pipe object in the .shapes file represented by the 'data' StringBuffer.
toShapesFile(StringBuffer, String, String, double) - Method in class ini.trakem2.display.Profile: Writes the data of this object as a Bezier object in the .shapes file represented by the 'data' StringBuffer.
toString() - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
toString() - Method in class ini.trakem2.analysis.Compare.Chain
toString() - Method in class ini.trakem2.display.Bucket
toString() - Method in class ini.trakem2.display.Displayable: Minimal info that identifies this object as unique, for display on a JTree node.
toString() - Method in class ini.trakem2.display.DisplayablePanel
toString() - Method in class ini.trakem2.display.DLabel
toString() - Method in class ini.trakem2.display.Layer
toString() - Method in class ini.trakem2.display.LayerPanel
toString() - Method in class ini.trakem2.display.LayerSet
toString() - Method in interface ini.trakem2.display.Line3D
toString() - Method in class ini.trakem2.display.Node
toString() - Method in class ini.trakem2.display.Tag
toString() - Method in class ini.trakem2.Project
toString() - Method in class ini.trakem2.tree.LayerThing
toString() - Method in class ini.trakem2.tree.ProjectThing
toString() - Method in class ini.trakem2.tree.TemplateThing
toString() - Method in interface ini.trakem2.tree.Thing
toString(Object) - Static method in class ini.trakem2.utils.Utils: Print an object; if it's an array, print each element, recursively, as [0, 1, 2] or [[0, 1, 2], [3, 4, 5]], etc, same for Iterable and Map objects.
toString() - Method in class lenscorrection.PolynomialModel2D
totalAreaOfTruncatedCone(double, double, double) - Static method in class ini.trakem2.utils.M: The lateral area plus the two circles.
toXML(String) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
toXML(String) - Method in class ini.trakem2.imaging.filters.CLAHE
toXML(String) - Method in class ini.trakem2.imaging.filters.CorrectBackground
toXML(String) - Method in class ini.trakem2.imaging.filters.DefaultMinAndMax
toXML(String) - Method in class ini.trakem2.imaging.filters.EnhanceContrast
toXML(String) - Method in class ini.trakem2.imaging.filters.EqualizeHistogram
toXML(String) - Method in class ini.trakem2.imaging.filters.GaussianBlur
toXML(String) - Method in interface ini.trakem2.imaging.filters.IFilter: Create an XML representation of this Filter.
toXML(String) - Method in class ini.trakem2.imaging.filters.Invert
toXML(String) - Method in class ini.trakem2.imaging.filters.LUTBlue
toXML(String) - Method in class ini.trakem2.imaging.filters.LUTCustom
toXML(String) - Method in class ini.trakem2.imaging.filters.LUTCyan
toXML(String) - Method in class ini.trakem2.imaging.filters.LUTGreen
toXML(String) - Method in class ini.trakem2.imaging.filters.LUTMagenta
toXML(String) - Method in class ini.trakem2.imaging.filters.LUTRed
toXML(String) - Method in class ini.trakem2.imaging.filters.LUTYellow
toXML(String) - Method in class ini.trakem2.imaging.filters.Normalize
toXML(String) - Method in class ini.trakem2.imaging.filters.NormalizeLocalContrast
toXML(String) - Method in class ini.trakem2.imaging.filters.RankFilter
toXML(String) - Method in class ini.trakem2.imaging.filters.ResetMinAndMax
toXML(String) - Method in class ini.trakem2.imaging.filters.RobustNormalizeLocalContrast
toXML(String) - Method in class ini.trakem2.imaging.filters.SubtractBackground
toXML(String) - Method in class ini.trakem2.imaging.filters.ValueToNoise
TPlugIn - Interface in ini.trakem2.plugin
tr_map - Static variable in class ini.trakem2.display.Polyline
TrakEM2MLParser - Class in ini.trakem2.tree: A class to parse a file in TrakEM2 XML format.
TrakEM2MLParser(String) - Constructor for class ini.trakem2.tree.TrakEM2MLParser
TrakEM2MLParser(InputStream) - Constructor for class ini.trakem2.tree.TrakEM2MLParser: Note: will close the xml_stream.
TRANS_ROT - Static variable in class ini.trakem2.analysis.Compare
TRANS_ROT_SCALE - Static variable in class ini.trakem2.analysis.Compare
TRANS_ROT_SCALE_SHEAR - Static variable in class ini.trakem2.analysis.Compare
TransferableNode - Class in ini.trakem2.tree: Adapted from freely available code by DeuDeu.
TransferableNode(DefaultMutableTreeNode) - Constructor for class ini.trakem2.tree.TransferableNode
transferVectorStrings(List<VectorString3D>, List<Tuple3d>, List<Tuple3d>, Class<AffineModel3D>) - Static method in class ini.trakem2.analysis.Compare: Transform all points of all VectorString3D in vs using a Moving Least Squares Transform defined by the pairing of points in source to those in target.
transferVectorStrings(List<VectorString3D>, Map<String, Tuple3d>, Map<String, Tuple3d>) - Static method in class ini.trakem2.analysis.Compare: Transfer vs via a moving least squares transform by matching source named points into equally named target named points.
transferVectorStrings(List<VectorString3D>, ProjectThing, ProjectThing) - Static method in class ini.trakem2.analysis.Compare
transform(AffineTransform) - Method in class ini.trakem2.display.Displayable: Concatenate the given affine to this and all its linked objects.
transform(AffineTransform, double, double) - Static method in class ini.trakem2.utils.M
transform(CoordinateTransform, Area) - Static method in class ini.trakem2.utils.M: Return a new Area resulting from applying @param ict to @param a; assumes areas consists of paths with moveTo, lineTo and close operations.
transform - Variable in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
transform - Variable in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
transform(ImageProcessor) - Method in class lenscorrection.NonLinearTransform
transform_type - Variable in class ini.trakem2.analysis.Compare.CATAParameters
TransformationStep - Class in ini.trakem2.display
transformData(AffineTransform) - Method in class ini.trakem2.display.AreaTree.AreaNode
transformData(AffineTransform) - Method in class ini.trakem2.display.Node: Apply @param aff to the data, not to the x,y position.
transformData(AffineTransform) - Method in class ini.trakem2.display.Treeline.RadiusNode
transformPatchesAndVectorData(Layer, AffineTransform) - Static method in class mpicbg.trakem2.align.AlignTask
transformPatchesAndVectorData(Collection<Patch>, AffineTransform) - Static method in class mpicbg.trakem2.align.AlignTask
transformPatchesAndVectorData(Collection<Patch>, Runnable) - Static method in class mpicbg.trakem2.align.AlignTask: For registering within the same project instance.
transformPoint(double[][], int, double, double, double, double, double) - Static method in class ini.trakem2.display.Displayable: Transform in place only the 'i' point in the points array.
transformPoint(double, double) - Method in class ini.trakem2.display.Displayable: Apply this Displayable's AffineTransform to the given point.
transformPoints(Layer, double, double, double, double, double) - Method in class ini.trakem2.display.AreaList
transformPoints(double[][]) - Method in class ini.trakem2.display.Displayable: Returns the argument if this Displayable's AffineTransform is the identity; otherwise returns a new double[][] with all points from @param p transformed according to the AffineTransform.
transformPoints(double[][], int) - Method in class ini.trakem2.display.Displayable
transformPoints(double[][], AffineTransform) - Method in class ini.trakem2.display.Displayable
transformPoints(double[][], int, AffineTransform) - Method in class ini.trakem2.display.Displayable: Will crop second dimension of the given array at the given length.
transformPoints(AffineTransform, double[][], int) - Static method in class ini.trakem2.display.Displayable: Will crop second dimension of the given array at the given length.
transformPoints(double[], AffineTransform) - Method in class ini.trakem2.display.Displayable
transformPoints(AffineTransform, double[]) - Static method in class ini.trakem2.display.Displayable
transformPoints(double[]) - Method in class ini.trakem2.display.Displayable: Transforms the points represented as X1,Y1,X2,Y2...
transformPoints(float[]) - Method in class ini.trakem2.display.Displayable: Transforms the points represented as X1,Y1,X2,Y2...
transformPoints(Layer, double, double, double, double, double) - Method in class ini.trakem2.display.ZDisplayable: Deprecated.
TransformProperties(Patch) - Constructor for class ini.trakem2.display.Patch.TransformProperties
transformRectangle(Rectangle) - Method in class ini.trakem2.display.Displayable: Returns a new Rectangle which encloses completly the given rectangle after transforming it with this Displayable's AffineTransform.
transforms - Variable in class ini.trakem2.display.VectorDataTransform
transformVectorData(AlignTask.ReferenceData, Collection<Displayable>, LayerSet) - Static method in class mpicbg.trakem2.align.AlignTask
translate(double, double) - Method in class ini.trakem2.display.AffineTransformMode: Translate all selected objects and their links by the given differentials.
translate(double, double, boolean) - Method in class ini.trakem2.display.Displayable: Translate this Displayable and its linked ones if linked=true.
translate(double, double) - Method in class ini.trakem2.display.Displayable
translate(float, float) - Method in class ini.trakem2.display.Node: Only this node, not any of its children.
translate(double, double) - Method in class ini.trakem2.display.Selection: Translate all selected objects and their links by the given differentials.
translateAffine(Rectangle, AffineTransform) - Static method in class mpicbg.trakem2.align.RegularizedAffineLayerAlignment
translation - Variable in class org.janelia.intensity.LinearIntensityMap
TranslationTile2D - Class in mpicbg.trakem2.align
TranslationTile2D(TranslationModel2D, Patch) - Constructor for class mpicbg.trakem2.align.TranslationTile2D
TranslationTile2D(Patch) - Constructor for class mpicbg.trakem2.align.TranslationTile2D
Tree<T> - Class in ini.trakem2.display: A sequence of points ordered in a set of connected branches.
Tree(Project, String) - Constructor for class ini.trakem2.display.Tree
Tree(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Tree: Reconstruct from XML.
Tree(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Tree: For cloning purposes, does not call addToDatabase(), neither creates any root node.
Tree.MeasurementPair - Class in ini.trakem2.display
Tree.MeasurePathDistance - Class in ini.trakem2.display
Tree.MeshData - Class in ini.trakem2.display: One color per vertex.
Tree.NodePath - Class in ini.trakem2.display
Tree.Pair - Class in ini.trakem2.display
treeCollapsed(TreeExpansionEvent) - Method in class ini.trakem2.tree.DNDTree: Sense node expansion events (the method name is missleading).
TreeConnectorsView - Class in ini.trakem2.display: List all connectors whose origins intersect with the given tree.
TreeConnectorsView(Tree<?>) - Constructor for class ini.trakem2.display.TreeConnectorsView
treeExpanded(TreeExpansionEvent) - Method in class ini.trakem2.tree.DNDTree
Treeline - Class in ini.trakem2.display
Treeline(Project, String) - Constructor for class ini.trakem2.display.Treeline
Treeline(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.Treeline: Reconstruct from XML.
Treeline(Project, long, String, float, float, float, boolean, Color, boolean, AffineTransform) - Constructor for class ini.trakem2.display.Treeline: For cloning purposes, does not call addToDatabase()
Treeline.RadiusNode - Class in ini.trakem2.display
trim() - Method in class ini.trakem2.imaging.LayerStack: Does nothing.
trim(CharSequence) - Static method in class ini.trakem2.utils.Utils
trimProcessor() - Method in class ini.trakem2.imaging.PatchStack
tryAddNewConnector(Displayable, boolean) - Method in class ini.trakem2.tree.ProjectTree: If the parent node of active can accept a Connector or has a direct child node that can accept a Connector, add a new Connector and return it.
twoDimArrayToOneDimArray(float[][]) - Static method in class mpi.fruitfly.general.ArrayConverter
twoDimArrayToOneDimArray(double[][]) - Static method in class mpi.fruitfly.general.ArrayConverter
type - Variable in class ini.trakem2.imaging.filters.RankFilter: See RankFilters.
type - Variable in class ini.trakem2.io.ImageFileHeader
TypedHashMap<K,V> - Class in ini.trakem2.utils: An extended HashMap that throws UnsupportedOperationException for calls to HashMap.get(Object), HashMap.remove(Object), HashMap.containsKey(Object) and HashMap.containsValue(Object).
TypedHashMap() - Constructor for class ini.trakem2.utils.TypedHashMap
TypedHashMap(int) - Constructor for class ini.trakem2.utils.TypedHashMap
TypedHashMap(Map<? extends K, ? extends V>) - Constructor for class ini.trakem2.utils.TypedHashMap
TypedHashMap(int, float) - Constructor for class ini.trakem2.utils.TypedHashMap
typeExists(String) - Method in class ini.trakem2.Project

U

unbound(Iterable, TaskFactory<I, O>, Collection<O>, int) - Static method in class ini.trakem2.parallel.Process: Takes a Collection of inputs, applies a function to each created by the generator, and places their output in outputs in the same order as each input was retrieved from inputs; will not wait for executing tasks to finish before creating and submitting new tasks.
unbound(Iterable, TaskFactory<I, O>) - Static method in class ini.trakem2.parallel.Process
unbound(Iterable, TaskFactory<I, O>, int) - Static method in class ini.trakem2.parallel.Process
uncaughtException(Thread, Throwable) - Method in class ini.trakem2.utils.BigBrother
UNDO - Static variable in interface ini.trakem2.display.DoStep
undoOneStep() - Method in class ini.trakem2.display.AffineTransformMode
undoOneStep() - Method in class ini.trakem2.display.DefaultMode
undoOneStep() - Method in class ini.trakem2.display.GroupingMode
undoOneStep() - Method in class ini.trakem2.display.inspect.InspectPatchTrianglesMode
undoOneStep() - Method in class ini.trakem2.display.LayerSet: Undoes one step of the ongoing transformation history, otherwise of the overall LayerSet history.
undoOneStep() - Method in class ini.trakem2.display.ManualAlignMode
undoOneStep() - Method in interface ini.trakem2.display.Mode
undoOneStep() - Method in class ini.trakem2.utils.History: Returns null if there aren't any more steps to undo.
uniquePathExists(String) - Method in class ini.trakem2.tree.ProjectThing: Check if any of the possible children of this Thing can have the given Thing as child, or any of they children can, recursing down.
uniquePathExists(String) - Method in class ini.trakem2.tree.TemplateThing: Check if a unique path exists through the child trees until reaching a Thing of the given type.
universe - Variable in class ini.trakem2.display.d3d.ControlClickBehavior
unlink() - Method in class ini.trakem2.display.Displayable: Remove all links held by this Displayable.
unlink(Displayable) - Method in class ini.trakem2.display.Displayable: Remove the link with the given Displayable, and tell the given Displayable to remove the link with this.
unlinkAll(Class<?>) - Method in class ini.trakem2.display.Displayable: Unlink all Displayable objects of the given type linked by this.
unlock() - Method in class ini.trakem2.utils.Lock
unmark() - Method in class ini.trakem2.display.Tree
unzipTiff(InputStream, String) - Method in class ini.trakem2.persistence.Loader: Retrieves a zipped ImagePlus from the given InputStream.
UP - Static variable in class ini.trakem2.display.LayerSet
update() - Static method in class ini.trakem2.display.Display: Update the entire GUI: 1 - The layer scroller 2 - The visible tab panels 3 - The toolbar 4 - The navigator 5 - The canvas
update(Layer) - Static method in class ini.trakem2.display.Display: Find all Display instances that contain the layer and repaint them, in the Swing GUI thread.
update(LayerSet) - Static method in class ini.trakem2.display.Display
update(LayerSet, boolean) - Static method in class ini.trakem2.display.Display: Find all Display instances showing a Layer of this LayerSet, and update the dimensions of the navigator and canvas and snapshots, and repaint, in the Swing GUI thread.
update(Displayable) - Static method in class ini.trakem2.display.Display3D: Remake the mesh for the Displayable in a separate Thread, if it's included in a Display3D (otherwise returns null).
update() - Method in class ini.trakem2.display.Displayable.SliderListener
update(Graphics) - Method in class ini.trakem2.display.DisplayCanvas
update(Graphics) - Method in class ini.trakem2.display.DisplayNavigator
update(T) - Method in class ini.trakem2.display.GroupingMode.ScreenPatchRange
update(Graphics) - Method in class ini.trakem2.display.RollingPanel
update(Graphics) - Method in class ini.trakem2.display.SnapshotPanel
update() - Method in class ini.trakem2.display.TreeConnectorsView
update(Graphics) - Method in class ini.trakem2.imaging.ContrastPlot
update(double, double) - Method in class ini.trakem2.imaging.ContrastPlot: Set new min and max (of the image, not of the plot) and repaint.
updateAndDraw() - Method in class ini.trakem2.imaging.PatchStack
updateAndRepaintWindow() - Method in class ini.trakem2.display.FakeImagePlus
updateAndRepaintWindow() - Method in class ini.trakem2.imaging.PatchStack
updateBucket(Displayable, Layer) - Method in interface ini.trakem2.display.Bucketable
updateBucket() - Method in class ini.trakem2.display.Displayable: Commands the parent container (a Layer or a LayerSet) to update the bucket position of this Displayable.
updateBucket(Displayable, Layer) - Method in class ini.trakem2.display.Layer: Update buckets of a position change for the given Displayable.
updateBucket(Displayable, Layer) - Method in class ini.trakem2.display.LayerSet
updateBucket(Layer) - Method in class ini.trakem2.display.ZDisplayable
updateBucket() - Method in class ini.trakem2.display.ZDisplayable: Update buckets for all Layers.
updateCache() - Method in class ini.trakem2.display.Tree: Update the internal Node cache; you want to invoke this operation after altering programmatically the Layer pointers of any of the Node of this Tree.
updateCheckbox(int, boolean) - Method in class ini.trakem2.display.DisplayablePanel
updateCheckbox(int) - Method in class ini.trakem2.display.DisplayablePanel
updateCheckboxes(Displayable, int, boolean) - Static method in class ini.trakem2.display.Display: Used by the Displayable to update the visibility and locking state checkboxes in other Displays.
updateCheckboxes(Collection<Displayable>, int, boolean) - Static method in class ini.trakem2.display.Display: Set the checkbox @param cb state to @param state value, for each Displayable.
updateCheckboxes(Collection<Displayable>, int) - Static method in class ini.trakem2.display.Display: Update the checkbox @param cb state to an appropriate value for each Displayable.
updateComponent(Component) - Static method in class ini.trakem2.utils.Utils: Repaint the given Component on the swing repaint thread (aka "SwingUtilities.invokeLater").
updateComponentTreeUI() - Static method in class ini.trakem2.display.Display
updateFrameTitle() - Method in class ini.trakem2.display.Display: Set a new title in the JFrame, showing info on the layer 'z' and the magnification.
updateImage(ImagePlus) - Method in class ini.trakem2.display.FakeImageWindow
updateImage() - Method in class ini.trakem2.imaging.PatchStack
updateImagePlusPath(String, String) - Method in class ini.trakem2.persistence.Cache
updateInDatabase(String) - Method in class ini.trakem2.display.Displayable
updateInDatabase(DBObject, String) - Method in class ini.trakem2.persistence.DBLoader
updateInDatabase(DBObject, Set<String>) - Method in class ini.trakem2.persistence.DBLoader
updateInDatabase(String) - Method in class ini.trakem2.persistence.DBObject
updateInDatabase(Set<String>) - Method in class ini.trakem2.persistence.DBObject
updateInDatabase(DBObject, String) - Method in class ini.trakem2.persistence.FSLoader
updateInDatabase(DBObject, Set<String>) - Method in class ini.trakem2.persistence.FSLoader
updateInDatabase(DBObject, String) - Method in class ini.trakem2.persistence.Loader
updateInDatabase(DBObject, Set<String>) - Method in class ini.trakem2.persistence.Loader
updateLayerScroller(LayerSet) - Static method in class ini.trakem2.display.Display
updateLayerTree() - Method in class ini.trakem2.display.Layer: Recursive into nested LayerSet objects.
updateLayerTree() - Method in class ini.trakem2.display.LayerSet: Recursive into nested LayerSet objects.
updateList() - Method in class ini.trakem2.display.RollingPanel
updateList(Thing) - Method in class ini.trakem2.tree.DNDTree: Rebuilds the part of the tree under the given node, one level deep only, for reordering purposes.
updateList(DefaultMutableTreeNode) - Method in class ini.trakem2.tree.DNDTree: Rebuilds the part of the tree under the given node, one level deep only, for reordering purposes.
updateList(LayerSet) - Method in class ini.trakem2.tree.LayerTree: Remove all layer nodes from the given layer_set, and add them again according to the layer's Z value.
updateMipMaps() - Method in class ini.trakem2.display.Patch: Recreate mipmaps and flush away any cached ones.
updateMipMapsFormat(int, int) - Method in class ini.trakem2.persistence.FSLoader: Removes all mipmap files and recreates them with the currently set mipmaps format.
updateMipMapsFormat(int, int) - Method in class ini.trakem2.persistence.Loader: Does nothing unless overriden.
updateMultiPaint() - Method in class ini.trakem2.display.Display
updatePanel(Layer, Displayable) - Static method in class ini.trakem2.display.Display
updatePanelIndex(Layer, Displayable) - Static method in class ini.trakem2.display.Display: Deprecated.
updatePatch() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
updatePixelProperties(ImagePlus) - Method in class ini.trakem2.display.Patch: Update type, original dimensions and min,max from the ImagePlus.
updater - Variable in class ini.trakem2.display.GroupingMode
updateSelection() - Static method in class ini.trakem2.display.Display
updateSelection(Display) - Static method in class ini.trakem2.display.Display
updateTitle(Project) - Static method in class ini.trakem2.ControlWindow
updateTitle(Layer, Displayable) - Static method in class ini.trakem2.display.Display: Update the title of the given Displayable in its DisplayablePanel, if any.
updateTitle(Layer) - Static method in class ini.trakem2.display.Display: Update the Display's title in all Displays showing the given Layer.
updateTitle(Project) - Static method in class ini.trakem2.display.Display
updateTitle(LayerSet) - Static method in class ini.trakem2.display.Display: Update the Display's title in all Displays showing a Layer of the given LayerSet.
updateTitle() - Method in class ini.trakem2.display.DisplayablePanel
updateTitle() - Method in class ini.trakem2.tree.ProjectThing: Recursive into children and object (to update it's DisplayablePanel title).
updateTransform(Displayable) - Static method in class ini.trakem2.display.Display: Update in all displays the Transform for the given Displayable if it's selected.
updateTransform(Displayable) - Method in class ini.trakem2.display.Selection: Update the bounding box of the whole selection.
updateType(String, String) - Method in class ini.trakem2.tree.ProjectThing: Recursive into children, changes the type column in the ab_things table.
updateTypeName(String, String) - Method in class ini.trakem2.Project
updateUILater() - Method in class ini.trakem2.tree.DNDTree: Overriding to fix synchronization issues: the path changes while the multithreaded swing attempts to repaint it, so we "invoke later".
updateView() - Method in class ini.trakem2.display.Tree
updateViewData(Node<?>) - Method in class ini.trakem2.display.Tree
updateVisibleTabs() - Static method in class ini.trakem2.display.Display
updateVisibleTabs(Project) - Static method in class ini.trakem2.display.Display
use_color_cue_colors - Variable in class ini.trakem2.display.LayerSet
useLegacyOptimizer - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
useLegacyOptimizer - Variable in class mpicbg.trakem2.align.ElasticMontage.Param
useLocalSmoothnessFilter - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
usesMipMapsFolder() - Method in class ini.trakem2.persistence.FSLoader
usesMipMapsFolder() - Method in class ini.trakem2.persistence.Loader: Does nothing and returns false unless overriden.
useTps - Variable in class mpicbg.trakem2.align.ElasticLayerAlignment.Param
USHORTPaint - Class in ini.trakem2.display.paint
USHORTPaint(short) - Constructor for class ini.trakem2.display.paint.USHORTPaint
Util - Class in mpicbg.trakem2.align
Util() - Constructor for class mpicbg.trakem2.align.Util
Util.Features - Class in mpicbg.trakem2.align
Util.PointMatches - Class in mpicbg.trakem2.align
Utils - Class in ini.trakem2.utils: Utils class: stores generic widely used methods.
Utils() - Constructor for class ini.trakem2.utils.Utils

V

v1 - Variable in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
v2 - Variable in class mpicbg.trakem2.align.concurrent.BlockMatchPairCallable.BlockMatchResults
v_loaders - Static variable in class ini.trakem2.persistence.Loader
value - Variable in class ini.trakem2.imaging.filters.ValueToNoise
valueOf(String) - Static method in enum org.janelia.intensity.LinearIntensityMap.Interpolation: Returns the enum constant of this type with the specified name.
values() - Method in class ini.trakem2.utils.FieldMapView
values() - Static method in enum org.janelia.intensity.LinearIntensityMap.Interpolation: Returns an array containing the constants of this enum type, in the order they are declared.
ValueToNoise - Class in ini.trakem2.imaging.filters
ValueToNoise() - Constructor for class ini.trakem2.imaging.filters.ValueToNoise
ValueToNoise(double, double, double) - Constructor for class ini.trakem2.imaging.filters.ValueToNoise
ValueToNoise(Map<String, String>) - Constructor for class ini.trakem2.imaging.filters.ValueToNoise
variabilityAnalysis(Project, String, String[], boolean, boolean, boolean, String, boolean, boolean, boolean, Map<Project, Color>, boolean, float, double, int, boolean, boolean, Map<String, VectorString3D>, Project[]) - Static method in class ini.trakem2.analysis.Compare
Vector3 - Class in ini.trakem2.utils
Vector3(double, double, double) - Constructor for class ini.trakem2.utils.Vector3: creates vector from x,y,z
Vector3() - Constructor for class ini.trakem2.utils.Vector3: creates null vector
Vector3(Vector3) - Constructor for class ini.trakem2.utils.Vector3: creates vector from v
VectorData - Interface in ini.trakem2.display: An interface to represent Displayable objects that are not images.
VectorDataTransform - Class in ini.trakem2.display
VectorDataTransform(Layer) - Constructor for class ini.trakem2.display.VectorDataTransform
VectorDataTransform.ROITransform - Class in ini.trakem2.display
VectorStringContent(VectorString3D, String, Color, double[], float) - Constructor for class ini.trakem2.display.Display3D.VectorStringContent
version - Static variable in class ini.trakem2.utils.Utils
Vertex<T> - Class in ini.trakem2.analysis: A class to express a Vertex in a graph.
Vertex(T) - Constructor for class ini.trakem2.analysis.Vertex
verts - Variable in class ini.trakem2.display.Tree.MeshData
virtualMatches - Variable in class mpicbg.trakem2.align.AbstractAffineTile2D: A set of virtual point correspondences that are used to connect a tile to the rest of the TileConfiguration assuming that the initial layout was correct.
VISIBILITY_STATE - Static variable in class ini.trakem2.display.DisplayablePanel
visible - Variable in class ini.trakem2.display.Displayable
visualize - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
visualize() - Method in class lenscorrection.NonLinearTransform
visualize - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
visualize - Variable in class mpicbg.trakem2.align.ElasticMontage.Param: Visualize spring mesh optimization
visualizeResults - Variable in class lenscorrection.Distortion_Correction.PluginParam
visualizeSmall(double) - Method in class lenscorrection.NonLinearTransform
volumeOfTruncatedCone(double, double, double) - Static method in class ini.trakem2.utils.M
vs - Variable in class ini.trakem2.analysis.Compare.Chain

W

W - Static variable in class ini.trakem2.analysis.Compare
wait(Collection<Future<?>>) - Static method in class ini.trakem2.utils.Utils
waitForOffs() - Method in class ini.trakem2.display.AbstractRepaintThread: Waits until the offscreen thread is finished with the current cycle.
waitForRepaint() - Method in class ini.trakem2.display.DisplayCanvas
waitIfAlive(Collection<Future<?>>, boolean) - Static method in class ini.trakem2.utils.Utils
waitOnRepaintCycle() - Method in class ini.trakem2.display.AbstractOffscreenThread
WAND - Static variable in class ini.trakem2.utils.ProjectToolbar
warning(SAXParseException) - Method in class ini.trakem2.persistence.TMLHandler
WEST - Static variable in class ini.trakem2.display.LayerSet
widestSetOnly - Variable in class mpicbg.trakem2.align.AbstractLayerAlignmentParam
width - Variable in class ini.trakem2.display.Displayable.DataPackage
width - Variable in class ini.trakem2.display.Displayable: Width and height of the data, not the bounding box.
width - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam: In pixels, of the the underlying image to copy around the mouse.
width - Variable in class ini.trakem2.io.ImageFileHeader
width - Variable in class ini.trakem2.persistence.ImageBytes
width - Variable in class mpi.fruitfly.math.datastructures.FloatArray2D
width - Variable in class mpi.fruitfly.math.datastructures.FloatArray3D
willPaint(Displayable) - Static method in class ini.trakem2.display.Display: Check if any display will paint the given Displayable within its srcRect.
with_source - Variable in class ini.trakem2.analysis.Compare.CATAParameters
Worker - Class in ini.trakem2.utils
Worker(String) - Constructor for class ini.trakem2.utils.Worker
Worker(String, boolean) - Constructor for class ini.trakem2.utils.Worker
Worker(String, boolean, boolean) - Constructor for class ini.trakem2.utils.Worker
Worker.Task - Class in ini.trakem2.utils: A class that calls run() wrapped properly for task monitoring; Create it like this: Bureaucrat b = Bureaucrat.createAndStart(new Worker.Task("Title") { public void exec() { doSomething(); doSomethingElse(); }}, project);
WORKING - Static variable in class ini.trakem2.imaging.StitchingTEM
wrap(AffineTransform, CoordinateTransform, AffineTransform) - Static method in class ini.trakem2.utils.M: The @param ict is expected to transform the data as if this data was expressed in world coordinates, so this method returns a transformation list that prepends the transform from local to world, then the @param ict, then from world to local.
writeXMLTo(Project, Writer, XMLOptions) - Method in class ini.trakem2.persistence.Loader: Write the project as XML.
wrongImageJVersion() - Static method in class ini.trakem2.utils.Utils

X

x - Variable in class ini.trakem2.display.Coordinate
x - Variable in class ini.trakem2.display.Node
x - Variable in class ini.trakem2.utils.Vector3
XML - Static variable in class ini.trakem2.io.XMLFileFilter
xmlError(String, Object) - Method in class ini.trakem2.display.Displayable
xmlError(DBObject, String, Object) - Static method in class ini.trakem2.display.Displayable
XMLFileFilter - Class in ini.trakem2.io: Accepts .dtd and/or .xml extensions.
XMLFileFilter(int) - Constructor for class ini.trakem2.io.XMLFileFilter
XMLOptions - Class in ini.trakem2.persistence
XMLOptions() - Constructor for class ini.trakem2.persistence.XMLOptions

Y

y - Variable in class ini.trakem2.display.Coordinate
y - Variable in class ini.trakem2.display.Node
y - Variable in class ini.trakem2.utils.Vector3
YesNoDialog - Class in ini.trakem2.display: A modal dialog box with a one line message and "Yes" and "No" buttons.
YesNoDialog(String, String) - Constructor for class ini.trakem2.display.YesNoDialog
YesNoDialog(Frame, String, String) - Constructor for class ini.trakem2.display.YesNoDialog
YesNoDialog(Frame, String, String, boolean) - Constructor for class ini.trakem2.display.YesNoDialog
yesPressed() - Method in class ini.trakem2.display.YesNoDialog: Returns true if the user dismissed dialog by pressing "Yes".

Z

z - Variable in class ini.trakem2.utils.Vector3
ZDisplayable - Class in ini.trakem2.display: For Pipes and other objects that must be shown in all Layers of a LayerSet.
ZDisplayable(Project, String, double, double) - Constructor for class ini.trakem2.display.ZDisplayable
ZDisplayable(Project, long, String, boolean, AffineTransform, float, float) - Constructor for class ini.trakem2.display.ZDisplayable: For reconstruction from the database.
ZDisplayable(Project, long, HashMap<String, String>, HashMap<Displayable, String>) - Constructor for class ini.trakem2.display.ZDisplayable: For reconstruction from an XML file.
zeroPad(ImagePlus) - Static method in class ini.trakem2.utils.MCTriangulator
zeroPad(int, int) - Static method in class ini.trakem2.utils.Utils: Zero-pad a number, so that '1' becomes '001' if n_digits is 3.
zeroPad(FloatArray2D, int, int) - Static method in class mpi.fruitfly.general.ImageArrayConverter
zoomIn() - Method in class ini.trakem2.display.DisplayCanvas: Zoom in using the current mouse position, or the center if the mouse is out.
zoomIn(int, int) - Method in class ini.trakem2.display.DisplayCanvas: Overriding to repaint the DisplayNavigator as well.
zoomOut() - Method in class ini.trakem2.display.DisplayCanvas: Zoom out using the current mouse position, or the center if the mouse is out.
zoomOut(int, int) - Method in class ini.trakem2.display.DisplayCanvas: Overriding to repaint the DisplayNavigator as well.
zoomToFit() - Method in class ini.trakem2.display.DisplayCanvas

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