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

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 mpicbg.models.AbstractAffineModel2D<A>> - Class in mpicbg.trakem2.align
 
AbstractAffineTile2D(A, Patch) - Constructor for class mpicbg.trakem2.align.AbstractAffineTile2D
 
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 from http://forum.java.sun.com/thread.jspa?threadID=296255&start=0&tstart=0
AbstractTreeTransferHandler(DNDTree, int, boolean) - Constructor for class ini.trakem2.tree.AbstractTreeTransferHandler
 
accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchAndEndNodeIterator
 
accept(Node<I>) - Method in class ini.trakem2.display.Node.BranchNodeIterator
 
accept(Node<I>) - Method in class ini.trakem2.display.Node.EndNodeIterator
 
accept(Node<I>) - 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
 
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, float, float) - 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
 
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.
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(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
 
addDependent(double[]) - Method in class ini.trakem2.vector.VectorString3D
Add an array that will get resampled along; must be of the same length as the value returned by length()
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, Selection) - Method in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
 
addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.Param
 
addFields(GenericDialog) - Method in class mpicbg.trakem2.align.Align.ParamOptimize
 
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.
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.
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.
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 is an AreaNode.
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.
adjustmentValueChanged(AdjustmentEvent) - Method in class ini.trakem2.display.Displayable.SliderListener
 
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
 
AffineModel2D - Class in mpicbg.trakem2.transform
 
AffineModel2D() - Constructor for class mpicbg.trakem2.transform.AffineModel2D
 
AffineModel3D - Class in mpicbg.trakem2.transform
 
AffineModel3D() - Constructor for class mpicbg.trakem2.transform.AffineModel3D
 
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.ExtractFeaturesThread(Align.Param, List<AbstractAffineTile2D<?>>, AtomicInteger, AtomicInteger, int) - Constructor for class mpicbg.trakem2.align.Align.ExtractFeaturesThread
 
Align.MatchFeaturesAndFindModelThread - Class in mpicbg.trakem2.align
 
Align.MatchFeaturesAndFindModelThread(Align.Param, List<AbstractAffineTile2D<?>>, List<AbstractAffineTile2D<?>[]>, AtomicInteger, AtomicInteger, int) - Constructor for class mpicbg.trakem2.align.Align.MatchFeaturesAndFindModelThread
 
Align.Param - Class in mpicbg.trakem2.align
 
Align.Param() - Constructor for class mpicbg.trakem2.align.Align.Param
 
Align.ParamOptimize - Class in mpicbg.trakem2.align
 
Align.ParamOptimize() - Constructor for class mpicbg.trakem2.align.Align.ParamOptimize
 
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
 
alignLayersLinearlyJob(Layer, int, int, boolean, Rectangle) - Static method in class mpicbg.trakem2.align.AlignLayersTask
 
alignLayersNonLinearlyJob(Layer, int, int, boolean, Rectangle) - 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
 
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>, List<Patch>) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignPatches(Align.ParamOptimize, List<Patch>, List<Patch>, boolean, boolean, boolean, boolean) - Static method in class mpicbg.trakem2.align.AlignTask
 
alignPatchesTask(List<Patch>, List<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) - 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<?>>, 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) - Static method in class mpicbg.trakem2.align.AlignTask
 
alpha - Variable in class ini.trakem2.display.Displayable
 
always_interpolate_areas_with_distance_map - Static variable in class ini.trakem2.utils.AreaUtils
Project property key.
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.
append(StringBuilder, HashSet<String>, String) - Static method in class mpicbg.trakem2.transform.DTD
 
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
 
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 lineage.Identify
 
applies(Object) - Method in class treeline.TreelineGraphEditor
 
apply(float[]) - 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(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.LayerSet.DoChangeTrees
 
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<I>) - 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, float[]) - Static method in class ini.trakem2.utils.M
Reuses the @param fp to apply in place.
apply(float[]) - Method in class lenscorrection.NonLinearTransform
 
apply(float[]) - 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(float[]) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
 
applyInPlace(float[]) - Method in class lenscorrection.NonLinearTransform
 
applyInPlace(float[]) - Method in class lenscorrection.PolynomialModel2D
 
applyInverseInPlace(float[]) - Method in class mpicbg.trakem2.transform.TransformMesh
Catch non-invertible locations outside of the meshes boundaries and transfer them with the affine defined by the `closest' affine (the affine whose summed up control points distances to location are smallest).
applyLayerWise(Collection<Layer>) - Method in class ini.trakem2.imaging.ContrastEnhancerWrapper
 
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
 
area - Variable in class ini.trakem2.display.Patch.TransformProperties
 
AREA_AVERAGING - Static variable in class ini.trakem2.persistence.Loader
 
area_color_cues - Variable in class ini.trakem2.display.LayerSet
 
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.
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
 
AreaTree.AreaNode(float, float, Layer) - Constructor for class ini.trakem2.display.AreaTree.AreaNode
 
AreaTree.AreaNode(HashMap<String, String>) - Constructor for class ini.trakem2.display.AreaTree.AreaNode
To reconstruct from XML, without a layer.
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
 
AreaWrapper.PaintParameters() - Constructor for class ini.trakem2.display.AreaWrapper.PaintParameters
 
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
 
asContent(Display3D) - Method in class ini.trakem2.display.Display3D.VectorStringContent
 
asHexRGBColor(Color) - Static method in class ini.trakem2.utils.Utils
 
asHexRGBColor(StringBuilder, Color) - Static method in class ini.trakem2.utils.Utils
 
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
 
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.
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
 
attrs - Static variable in class lineage.LineageClassifier
 
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
 
AVG_PHYS_DIST - Static variable in class ini.trakem2.analysis.Compare
 

B

background - Variable in class ini.trakem2.tree.DNDTree
 
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.
BICUBIC - Static variable in class ini.trakem2.persistence.Loader
 
BigBrother - Class in ini.trakem2.utils
Supervise all threads, and report uncaught exceptions.
BigBrother(String) - Constructor for class ini.trakem2.utils.BigBrother
 
BILINEAR - Static variable in class ini.trakem2.persistence.Loader
 
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
 
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).
Blending - Class in ini.trakem2.imaging
Utility functions for blending images together, to remove contrast seams.
Blending() - Constructor for class ini.trakem2.imaging.Blending
 
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
 
BLUE - Static variable in class ini.trakem2.display.Channel
 
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
 
boundingBox - Variable in class mpicbg.trakem2.transform.TransformMesh
 
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.
branches - Variable in class ini.trakem2.analysis.Centrality.EtchingStep
 
branchWise(Collection<Vertex<T>>, int) - Static method in class ini.trakem2.analysis.Centrality
 
BRUSH - Static variable in class ini.trakem2.utils.ProjectToolbar
A tool to align objects from two different layers.
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.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.

C

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
 
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.
calibrate(Calibration) - Method in class ini.trakem2.vector.VectorString2D
Scale to match cal.pixelWidth, cal.pixelHeight and computed depth.
calibrate(Calibration) - Method in class ini.trakem2.vector.VectorString3D
Scale to match cal.pixelWidth, cal.pixelHeight and computed depth.
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.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.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
Join all given Trees by using the first one as the receiver, 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.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
 
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.ManualAlignMode
 
canZoom() - Method in interface ini.trakem2.display.Mode
 
cc_scale - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
 
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>) removed.
Centrality.EtchingStep(int, Set<Collection<Vertex<T>>>) - Constructor for class ini.trakem2.analysis.Centrality.EtchingStep
 
chain(VectorString3D) - Method in class ini.trakem2.vector.VectorString3D
Returns a new VectorString3D which is the result of the optimal chaining of this and the given VectorString.
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
 
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.
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.
checkYN(String) - Static method in class ini.trakem2.utils.Utils
 
children - Variable in class ini.trakem2.display.Node
 
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.
classify(double[]) - Static method in class lineage.LineageClassifier
 
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.History
Remove all steps from the list and return them.
clearCache() - Method in class ini.trakem2.display.Tree
 
clearColumnScreenshots(LayerSet) - Static method in class ini.trakem2.display.Display
 
clearColumnScreenshots() - Method in class ini.trakem2.display.Display
 
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) - 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) - 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 ini.trakem2.vector.VectorString2D
Does NOT clone the vector arrays, which are initialized to NULL; only the x,y,delta,z.
clone() - Method in class ini.trakem2.vector.VectorString3D
 
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 mpi.fruitfly.math.datastructures.FloatArrayND
 
clone() - Method in class mpicbg.trakem2.align.Align.Param
 
clone() - Method in class mpicbg.trakem2.align.Align.ParamOptimize
 
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.
closed - Variable in class ini.trakem2.vector.Editions
 
CLOSED - Static variable in class ini.trakem2.vector.VectorString3D
 
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
 
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.CATAParameters() - Constructor for class ini.trakem2.analysis.Compare.CATAParameters
 
Compare.Chain - Class in ini.trakem2.analysis
Represents a list of concatenated pipes, where each pipe is parent of the next within the ProjectTree.
Compare.Chain(Line3D) - Constructor for class ini.trakem2.analysis.Compare.Chain
 
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
 
complexConjugate(float[]) - Static method in class mpi.fruitfly.fft.pffft
 
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.
computeAverage(double[]) - Static method in class mpi.fruitfly.analysis.FitLine
 
computeBinaryFilter3(FloatArray3D, float) - Static method in class mpi.fruitfly.registration.ImageFilter
 
computeBinaryPlusSobelFilter3(FloatArray3D, float) - Static method in class mpi.fruitfly.registration.ImageFilter
 
computeCenterOfMass() - Method in class ini.trakem2.vector.VectorString3D
 
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, float) - 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()
computeLength() - Method in class ini.trakem2.vector.VectorString3D
The physical length of this sequence of points.
computeLogPowerSpectrum(float[]) - Static method in class mpi.fruitfly.fft.pffft
 
computeMedian(double[]) - Static method in class mpi.fruitfly.math.General
 
computeMedian(float[]) - Static method in class mpi.fruitfly.math.General
 
computePhaseCorrelation() - Method in class mpi.fruitfly.registration.PhaseCorrelation2D
 
computePhaseCorrelationMatrix(float[], float[], boolean) - Static method in class mpi.fruitfly.fft.pffft
 
computePhaseSpectrum(float[]) - Static method in class mpi.fruitfly.fft.pffft
 
computePowerSpectrum(float[]) - Static method in class mpi.fruitfly.fft.pffft
 
computeSegmentsIntersection(float, float, float, float, float, float, float, float) - Static method in class ini.trakem2.utils.M
 
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
 
computeVariance(double[]) - Static method in class mpi.fruitfly.analysis.FitLine
 
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
 
Connector.ConnectorNode(float, float, Layer) - Constructor for class ini.trakem2.display.Connector.ConnectorNode
 
Connector.ConnectorNode(float, float, Layer, float) - Constructor for class ini.trakem2.display.Connector.ConnectorNode
 
Connector.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) - 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, int, int) - Method in class ini.trakem2.display.AreaList
Returns whether the point x,y is contained in this object at the given Layer.
contains(Layer, int, int) - 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(int, int) - 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, int, int) - 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, int, int) - Method in class ini.trakem2.display.Dissector
 
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 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(int, int) - Method in class ini.trakem2.display.Patch
Considers the alpha mask.
contains(Layer, int, int) - Method in class ini.trakem2.display.Pipe
Test whether the Pipe contains the given point at the given layer.
contains(Layer, int, int) - 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, int, int) - 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
 
containsLocal(Layer, int, int, 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.
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
 
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.persistence.FSLoader
 
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.
CoordinateTransform - Interface in mpicbg.trakem2.transform
InvertibleCoordinateTransform with String import and export as used in TrakEM2.
CoordinateTransformList<E extends CoordinateTransform> - Class in mpicbg.trakem2.transform
 
CoordinateTransformList() - Constructor for class mpicbg.trakem2.transform.CoordinateTransformList
 
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(double[], int) - Static method in class ini.trakem2.vector.Util
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(double[], int, int) - Static method in class ini.trakem2.vector.Util
 
copy() - Method in class lenscorrection.NonLinearTransform
 
copy() - Method in class lenscorrection.PolynomialModel2D
 
copy() - Method in class mpicbg.trakem2.transform.AffineModel2D
 
copy() - Method in class mpicbg.trakem2.transform.AffineModel3D
 
copy() - Method in interface mpicbg.trakem2.transform.CoordinateTransform
 
copy() - Method in class mpicbg.trakem2.transform.CoordinateTransformList
 
copy() - Method in interface mpicbg.trakem2.transform.InvertibleCoordinateTransform
 
copy() - Method in class mpicbg.trakem2.transform.InvertibleCoordinateTransformList
 
copy() - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform
 
copy() - Method in class mpicbg.trakem2.transform.RigidModel2D
 
copy() - Method in class mpicbg.trakem2.transform.SimilarityModel2D
 
copy() - Method in class mpicbg.trakem2.transform.TranslationModel2D
 
copy() - Method in class mpicbg.trakem2.transform.TranslationModel3D
 
copyAs(Tree<?>, Class<A>, Class<B>) - 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
 
correctDistortionFromSelection(Selection) - Static method in class lenscorrection.DistortionCorrectionTask
 
correctDistortionFromSelectionParam - Static variable in class lenscorrection.DistortionCorrectionTask
 
correctDistortionFromSelectionTask(Selection) - Static method in class lenscorrection.DistortionCorrectionTask
 
correctImages() - Method in class lenscorrection.Distortion_Correction
 
correlate(Patch, Patch, float, float, int, double, double, float) - 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.
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.TaskFactory
Generates a Callable task for an ExecutorService to process @param input.
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 ini.trakem2.persistence.Loader
 
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
 
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
 
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<I>>, double, int, String) - Method in class ini.trakem2.persistence.Loader
Returns an ImageStack, one slice per region.
createGaussianKernel1D(float, 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
 
createInterpolated(Editions, double) - Static method in class ini.trakem2.vector.VectorString3D
 
createInterpolated(VectorString3D, Editions, double) - Method in class ini.trakem2.vector.VectorString3D
Create an interpolated VectorString3D between this and the given one, with the proper weight 'alpha' which must be 0 <= weight <= 1 (otherwise returns null)
createInterpolatedPoints(Editions, double) - Static method in class ini.trakem2.vector.VectorString3D
Create a new VectorString3D which is the weighted average between the two VectorString3D that make the Editions.
createInterpolatedPoints(Editions, double, int, int) - Static method in class ini.trakem2.vector.VectorString3D
Create a new VectorString3D which is the weighted average between the two VectorString3D that make the Editions.
createInverse() - Method in class mpicbg.trakem2.transform.AffineModel2D
TODO Not yet tested
createInverse() - Method in class mpicbg.trakem2.transform.AffineModel3D
 
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.
createInverseMappedImage(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping
 
createInverseMappedImageInterpolated(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping
 
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<I>>, 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.
createMappedImage(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping
 
createMappedImageInterpolated(ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping
 
createMappedMaskedImage(ImageProcessor, ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping
 
createMappedMaskedImageInterpolated(ImageProcessor, ImageProcessor) - Method in class mpicbg.trakem2.transform.TransformMeshMapping
 
createMaskedByteImage() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
 
createMesh(ProjectThing, Displayable, int) - Method in class ini.trakem2.display.Display3D
Returns a function that returns a Content object.
createMipMapRelPath(Patch, String) - Static method in class ini.trakem2.persistence.FSLoader
For Patch id=12345 creates 12/34/5.${filename}.jpg
createMLST(Collection<PointMatch>, float) - Static method in class mpicbg.trakem2.align.Align
Temporary helper method that creates
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
 
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
 
createRandom(int, double, boolean) - Static method in class ini.trakem2.vector.VectorString3D
 
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.
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.
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) - 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.
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(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
 
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
 
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 mpi.fruitfly.math.datastructures.FloatArray
 
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.
Methods to add to, update in and remove from a database are called anyway for XML projects, and can thus be used to perform tasks on updating a specific object.
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() - Method in class ini.trakem2.vector.VectorString3D
 
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_STROKE - Static variable in class ini.trakem2.display.DisplayCanvas
Paints a handle on the offscreen x,y.
DefaultGraphicsSource - Class in ini.trakem2.display.graphics
Handles default mode, i.e.
DefaultGraphicsSource() - Constructor for class ini.trakem2.display.graphics.DefaultGraphicsSource
 
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 from http://forum.java.sun.com/thread.jspa?threadID=296255&start=0&tstart=0
DefaultTreeTransferHandler(Project, DNDTree, int) - Constructor for class ini.trakem2.tree.DefaultTreeTransferHandler
 
deform - Static variable in class mpicbg.trakem2.align.AlignTask
 
deleteAll() - Method in class ini.trakem2.display.Selection
Delete all selected objects from their Layer.
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
 
DELETION - Static variable in class ini.trakem2.vector.Editions
 
delta - Variable in class ini.trakem2.analysis.Compare.CATAParameters
 
delta - Variable in class ini.trakem2.vector.Editions
 
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.
deserializePointMatches(Align.Param, AbstractAffineTile2D<?>, AbstractAffineTile2D<?>) - Static method in class mpicbg.trakem2.align.Align
 
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
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
 
Dispatcher.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.GridOverlay - Class in ini.trakem2.display
 
Display.GridOverlay() - Constructor for class ini.trakem2.display.Display.GridOverlay
 
Display3D - Class in ini.trakem2.display
One Display3D instance for each LayerSet (maximum).
Display3D.ControlClickBehavior - Class in ini.trakem2.display
A class to provide the behavior on control-clicking on content in the 3D viewer.
Display3D.VectorStringContent - Class in ini.trakem2.display
 
Display3D.VectorStringContent(VectorString3D, String, Color, double[], float) - Constructor for class ini.trakem2.display.Display3D.VectorStringContent
 
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.DoTransforms() - Constructor for class ini.trakem2.display.Displayable.DoTransforms
 
Displayable.SliderListener - Class in ini.trakem2.display
 
Displayable.SliderListener() - Constructor for class ini.trakem2.display.Displayable.SliderListener
 
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(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 - Variable in class ini.trakem2.vector.Editions
Levenshtein's distance between vs1 and vs2.
distance(int, VectorString, int) - Method in interface ini.trakem2.vector.VectorString
 
distance(int, VectorString, int) - Method in class ini.trakem2.vector.VectorString2D
Distance from point i in this to point j in vs2.
distance(double, double, double, double) - Static method in class ini.trakem2.vector.VectorString2D
 
distance(double, double, double, double, double, double) - Static method in class ini.trakem2.vector.VectorString3D
 
distance(VectorString3D, int, VectorString3D, int) - Static method in class ini.trakem2.vector.VectorString3D
 
distance(int, VectorString, int) - Method in class ini.trakem2.vector.VectorString3D
Distance from point i in this to point j in vs2.
distance(int, Point3d) - Method in class ini.trakem2.vector.VectorString3D
Distance from the point at i to p.
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.BasicParam() - Constructor for class lenscorrection.Distortion_Correction.BasicParam
 
Distortion_Correction.PluginParam - Class in lenscorrection
 
Distortion_Correction.PluginParam() - Constructor for class lenscorrection.Distortion_Correction.PluginParam
 
Distortion_Correction.PointMatchCollectionAndAffine - Class in lenscorrection
 
Distortion_Correction.PointMatchCollectionAndAffine(AffineTransform, Collection<PointMatch>) - Constructor for class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine
 
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.AppendCoordinateTransformThread(List<Patch>, CoordinateTransform, AtomicInteger) - Constructor for class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
 
DistortionCorrectionTask.CorrectDistortionFromSelectionParam - Class in lenscorrection
 
DistortionCorrectionTask.CorrectDistortionFromSelectionParam() - Constructor for class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
 
DistortionCorrectionTask.SetCoordinateTransformThread - Class in lenscorrection
Sets a CoordinateTransform to a list of patches.
DistortionCorrectionTask.SetCoordinateTransformThread(List<Patch>, CoordinateTransform, AtomicInteger) - Constructor for class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
 
distortSamplingX(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
 
distortSamplingY(FloatArray2D) - Static method in class mpi.fruitfly.registration.ImageFilter
 
divide(float[], float[], boolean) - Static method in class mpi.fruitfly.fft.pffft
 
divideComplexImg(float, float, float, float) - Static method in class mpi.fruitfly.fft.pffft
 
divideComplexReal(float, float, float, float) - Static method in class mpi.fruitfly.fft.pffft
 
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
 
DNDTree.NodeRenderer() - Constructor for class ini.trakem2.tree.DNDTree.NodeRenderer
 
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
 
DONOTOVERWRITE - Static variable in class mpi.fruitfly.fft.pffft
 
DONOTSCALE - Static variable in class mpi.fruitfly.fft.pffft
 
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.Display3D.ControlClickBehavior
 
DoStep - Interface in ini.trakem2.display
 
DOT - Static variable in class ini.trakem2.display.DLabel
 
DoubleArrayToStack(double[], int, int, int, String, float, float) - Static method in class mpi.fruitfly.general.ImageArrayConverter
 
DOWN - Static variable in class ini.trakem2.display.LayerSet
 
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
 
DTD - Static variable in class ini.trakem2.io.XMLFileFilter
 
DTD - Class in mpicbg.trakem2.transform
 
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(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
 
Editions - Class in ini.trakem2.vector
To extract and represent the sequence of editions that convert any N-dimensional vector string to any other of the same number of dimensions.
Editions(VectorString, VectorString, double, boolean) - Constructor for class ini.trakem2.vector.Editions
 
Editions(VectorString, VectorString, double, boolean, double, double, double) - Constructor for class ini.trakem2.vector.Editions
 
editions - Variable in class ini.trakem2.vector.Editions
In the form [length][3]
Editions.Chunk - Class in ini.trakem2.vector
 
elapsed(String) - Method in class ini.trakem2.utils.StopWatch
Time elapsed since last call to this method or the start.
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
 
end_nodes - Variable in class ini.trakem2.display.Tree
 
endElement(String, String, String) - Method in class ini.trakem2.persistence.TMLHandler
 
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(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.
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.
equalize(double) - Method in class ini.trakem2.vector.VectorString3D
Expand or shrink the points in this 3D path so that the average point interdistance becomes delta.
equals(Object) - Method in class ini.trakem2.display.DisplayCanvas.ScreenshotProperties
 
equals(Object) - Method in class ini.trakem2.display.Tag
 
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
 
ERROR - Static variable in class ini.trakem2.imaging.StitchingTEM
 
ERROR_PATH_NOT_FOUND - Static variable in class ini.trakem2.persistence.Loader
 
errorMapImp - Variable in class mpi.fruitfly.registration.PhaseCorrelation2D.CrossCorrelationResult
 
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
 
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
 
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
 
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.
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.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) - Method in class ini.trakem2.persistence.Loader
 
export(Project, File, boolean) - 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.
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.
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.
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.
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
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.AreaList
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Ball
Similar to exportSVG but the layer_id is saved instead of the z.
exportXML(Project, Writer, String, Object) - Static method in class ini.trakem2.display.Display
Export all displays of the given project as XML entries.
exportXML(StringBuilder, String, Object) - 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, Object) - Method in class ini.trakem2.display.DisplayCanvas
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Dissector
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.DLabel
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Layer
 
exportXML(Writer, String, Object) - Method in class ini.trakem2.display.LayerSet
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Patch
Opens and closes the tag and exports data.
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Pipe
Exports data, the tag is not opened nor closed.
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Polyline
Exports data.
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Profile
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Stack
Opens and closes the tag and exports data.
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.Tree
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.display.ZDisplayable
 
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.persistence.DBObject
Subclasses can override this method to store the instance as XML.
exportXML(StringBuilder, String, Object) - Method in class ini.trakem2.Project
 
exportXML(Writer, String, Object) - 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, Object) - Method in class ini.trakem2.tree.ProjectThing
Expects a HashMap as @param any.
exportXML(StringBuilder, String, HashMap<? extends Thing, Boolean>) - Method in class ini.trakem2.tree.ProjectThing
 
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
 
extendImageMirror(FloatArray2D, int, int) - Static method in class mpi.fruitfly.registration.PhaseCorrelation2D
 
extractAmiraLabels(ImagePlus, AmiraParameters, Layer, double, double) - Static method in class ini.trakem2.io.AmiraImporter
Returns an ArrayList containing all AreaList objects.
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.
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
 
FallLine - Class in ini.trakem2.display
 
FallLine(Display, ZDisplayable) - Constructor for class ini.trakem2.display.FallLine
 
FALSE - Static variable in class ini.trakem2.display.Node
 
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
 
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
 
fatalError(SAXParseException) - Method in class ini.trakem2.persistence.TMLHandler
 
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
 
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
Returns null.
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
 
fileAccess - Class in mpi.fruitfly.general
 
fileAccess() - Constructor for class mpi.fruitfly.general.fileAccess
 
fileParsing - Class in mpi.fruitfly.general
 
fileParsing() - Constructor for class mpi.fruitfly.general.fileParsing
 
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
 
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
find(int, int) - Method in class ini.trakem2.display.Layer
 
find(int, int, boolean) - Method in class ini.trakem2.display.Layer
Find the Displayable objects that contain the point.
find(Class<?>, int, int) - Method in class ini.trakem2.display.Layer
 
find(Class<?>, int, int, boolean) - Method in class ini.trakem2.display.Layer
Find the Displayable objects of Class c that contain the point, with class equality.
find(Class<?>, int, int, 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(float, float, 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
 
findLargestMutationChunk(int) - Method in class ini.trakem2.vector.Editions
 
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
 
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<I>, Node<I>) - 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.
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
 
fireNodeRemoved(Node<T>) - Method in class ini.trakem2.display.Tree
 
firstImageIndex - Variable in class lenscorrection.Distortion_Correction.PluginParam
 
firstLayerIndex - Variable in class lenscorrection.DistortionCorrectionTask.CorrectDistortionFromSelectionParam
 
fit(Collection<P>) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
 
fit(double[][], double[][], double) - Method in class lenscorrection.NonLinearTransform
 
fit(Collection<P>) - Method in class lenscorrection.PolynomialModel2D
 
FitLine - Class in mpi.fruitfly.analysis
Title: Line Fitter
FitLine() - Constructor for class mpi.fruitfly.analysis.FitLine
 
fitLine(double[]) - Static method in class mpi.fruitfly.analysis.FitLine
Fits the line to a point cloud and returns fitted line (m*x + n) and regression coefficient and Standard Deviation
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
Title: 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
Title: 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
 
FloatArrayND - Class in mpi.fruitfly.math.datastructures
Title: N-Dimensional Array Access
FloatArrayND(int[]) - Constructor for class mpi.fruitfly.math.datastructures.FloatArrayND
Create N-dimensional float array
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
 
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.
A null pointer as argument is accepted.
flush() - Static method in class lineage.LineageClassifier
Removes all threads and Instances from the cache tables.
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
 
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

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
 
General - Class in mpi.fruitfly.math
 
General() - Constructor for class mpi.fruitfly.math.General
 
generateAllReviewStacks() - Method in class ini.trakem2.display.Tree
 
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 and the corresponding List.
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.
Such images are stored as jpeg 85% quality in a folder named trakem2.mipmaps.
The Patch id and the right extension will be appended to the filename in all cases.
Any equally named files will be overwritten.
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.
generateTriangles(VectorString2D[], int, double, boolean) - Static method in class ini.trakem2.vector.SkinMaker
From an array of VectorString2D, obtain a list of Point3f which define, every three, a triangle of a skin.
generateTriangles(boolean) - Method in class ini.trakem2.vector.SkinMaker.Match
Generate a list of Point3f points, every three defining a triangle, between vs1 and vs2 using the given sequence of editions.
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(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(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
 
get(int[]) - Method in class mpi.fruitfly.math.datastructures.FloatArrayND
Return the value for a given positions in the nth-dimension
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
 
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
 
getAlphaPath(Patch) - Method in class ini.trakem2.persistence.FSLoader
 
getAlphaPath(Patch) - Method in class ini.trakem2.persistence.Loader
 
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.
getAngle(double, double) - Static method in class ini.trakem2.vector.Util
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 .
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
 
getAverageDelta() - Method in class ini.trakem2.vector.VectorString2D
 
getAverageDelta() - Method in class ini.trakem2.vector.VectorString3D
Return the average point interdistance.
getAverageVectorLength(int[], VectorString3D[]) - Static method in class ini.trakem2.vector.VectorString3D
 
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 If the list is empty, there is no bounding box, so it returns null.
getBoundingBox(Rectangle) - Method in class ini.trakem2.display.DLabel
Saves one allocation, returns the same Rectangle, modified (or a new one if null).
getBoundingBox() - Method in class mpicbg.trakem2.transform.TransformMesh
 
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<Node<Area>>) - Method in class ini.trakem2.display.AreaTree
 
getBounds(Collection<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(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<Node<T>>) - Method in class ini.trakem2.display.Tree
 
getBounds(Collection<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.
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.
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
 
getCalibrationCopy() - Method in class ini.trakem2.vector.VectorString2D
 
getCalibrationCopy() - Method in class ini.trakem2.vector.VectorString3D
 
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 @param 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.
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
 
getCoordinateTransformBoundingBox() - Method in class ini.trakem2.display.Patch
Get the bounding rectangle of the transformed image relative to the original image.
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.
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.LayerSet.DoChangeTrees
 
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.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
 
getDelta() - Method in interface ini.trakem2.vector.VectorString
 
getDelta() - Method in class ini.trakem2.vector.VectorString2D
If not resampled, returns zero.
getDelta() - Method in class ini.trakem2.vector.VectorString3D
If not resampled, the returned delta is zero.
getDependent(int) - Method in class ini.trakem2.vector.VectorString3D
 
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.
getDiffVectorLength(int, int, VectorString) - Method in interface ini.trakem2.vector.VectorString
 
getDiffVectorLength(int, int, VectorString) - Method in class ini.trakem2.vector.VectorString2D
Subtracts vs2 vector j to this vector i and returns its length, without changing any data.
getDiffVectorLength(int, int, VectorString) - Method in class ini.trakem2.vector.VectorString3D
Subtracts vs2 vector j to this vector i and returns its length, without changing any data.
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.
getDimensions() - Method in interface ini.trakem2.vector.VectorString
 
getDimensions() - Method in class ini.trakem2.vector.VectorString2D
 
getDimensions() - Method in class ini.trakem2.vector.VectorString3D
 
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<?>, 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.
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
 
getDistance() - Method in class ini.trakem2.vector.Editions
 
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
 
getEditions() - Method in class ini.trakem2.vector.Editions
 
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
 
getExpandedStates() - Method in class ini.trakem2.tree.DNDTree
Get the map of Thing vs.
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
 
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.
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.
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.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
 
getHeight() - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks
 
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
 
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<?>) - 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.
getLastNodeCoordiantes() - 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() - Method in class ini.trakem2.display.FallLine
 
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 betweeh 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
 
getLocalCalibration() - Method in class ini.trakem2.imaging.PatchStack
 
getLocation() - Method in class ini.trakem2.display.Display
 
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.imaging.PatchStack
 
getMasksFolder() - Method in class ini.trakem2.persistence.FSLoader
 
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
 
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 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: MIPMAP_JPEG, MIPMAP_PNG
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.
Requires 0 < mag <= 1.0
Returns -1 if the magnification is NaN or negative or zero.
As explanation:
mag = 1 / Math.pow(2, level)
so that 100% is 0, 50% is 1, 25% is 2, and so on, but represented in values between 0 and 1.
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.
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
 
getMode(String) - Static method in class ini.trakem2.persistence.Loader
 
getMorphedPerimeter(VectorString2D, VectorString2D, double, Editions) - Static method in class ini.trakem2.vector.SkinMaker
Returns a weighted VectorString2D.
getMorphedPerimeters(VectorString2D, VectorString2D, int, Editions) - Static method in class ini.trakem2.vector.SkinMaker
From two VectorString2D, return an array of x,y points ( in the form [2][n] ) defining all necessary intermediate, morphed perimeters that describe a skin between them (not including the two VectorString2D)
getMorphedPerimeters(VectorString2D[], int, double, boolean) - Static method in class ini.trakem2.vector.SkinMaker
From an array of VectorString2D, return a new array of VectorString2D defining all necessary intermediate, morphed perimeters that describe a skin between each consecutive pair; includes the originals inserted at the proper locations.
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.
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.
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
 
getNSources() - Method in class ini.trakem2.vector.VectorString3D
Returns the number of VectorString3D that have contributed to this VectorString3D, via merging with createInterpolated(...).
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
 
getOrCreateFront(Project) - Static method in class ini.trakem2.display.Display
 
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.
getPath() - Method in class ini.trakem2.display.Tree.MeasurePathDistance
 
getPath(ImagePlus) - Static method in class ini.trakem2.persistence.Cache
Returns null if the ImagePlus was preprocessed.
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.
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.
getPhaseCorrelationImage() - Method in class mpi.fruitfly.registration.PhaseCorrelation2D
 
getPhysicalDistance(boolean, int, float, boolean) - Method in class ini.trakem2.vector.Editions
Returns the distance between all points involved in a mutation; if average is false, then it returns the cummulative.
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, were 1<=n<=nslices.
getPixelsMaxDimension() - Method in class ini.trakem2.display.LayerSet
 
getPlugins(String) - Method in class ini.trakem2.Project
 
getPoint(int, int) - Method in interface ini.trakem2.vector.VectorString
Get the value at index i for dimension dim; dimensions start at 0 and go up to n-dimensions -1, for example for VectorString3D, 0=X, 1=Y, 2=Z; to get y[32] call getPoint(1, 32);
getPoint(int, int) - Method in class ini.trakem2.vector.VectorString2D
 
getPoint(int, int) - Method in class ini.trakem2.vector.VectorString3D
 
getPointCount() - Method in class ini.trakem2.display.Profile
Returns the number of backbone points.
getPoints(int) - Method in interface ini.trakem2.vector.VectorString
Get the array at dimension dim which ranges from 0 to n-dimensions -1; 0=X, 1=Y, 2=Z, et cetera depending on how many dimensions this VectorString supports.
getPoints(int) - Method in class ini.trakem2.vector.VectorString2D
 
getPoints(int) - Method in class ini.trakem2.vector.VectorString3D
 
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
 
getPolygonsByRounding(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
 
getPos(int[]) - Method in class mpi.fruitfly.math.datastructures.FloatArrayND
Return the position in a 1-dimensional array for a given positions in the nth-dimension
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, were 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
 
getQuicksortValue() - Method in interface mpi.fruitfly.math.Quicksortable
 
getQuicksortValue() - Method in class mpi.fruitfly.registration.PhaseCorrelation2D.CrossCorrelationResult
 
getRawBalls() - Method in class ini.trakem2.display.Ball
Returns the raw data for the balls, sorted by Layer ID versus double[]{z,y,r} .
getRelativeVector(int, int) - Method in class ini.trakem2.vector.VectorString3D
 
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.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.
getResult() - Method in class mpi.fruitfly.registration.PhaseCorrelation2D
 
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
 
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
 
getShape(ShapeRoi) - Static method in class ini.trakem2.utils.M
 
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()
getSimilarity(boolean, int, float) - Method in class ini.trakem2.vector.Editions
A mutation is considered an equal or near equal, and thus does not count.
getSimilarity() - Method in class ini.trakem2.vector.Editions
 
getSimilarity2() - Method in class ini.trakem2.vector.Editions
 
getSimilarity2(boolean, int, float) - Method in class ini.trakem2.vector.Editions
Returns the number of mutations / max(len(vs1), len(vs2)) : 1.0 means all are mutations and the sequences have the same lengths.
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
 
getSource() - Method in class ini.trakem2.vector.VectorString3D
Returns a list of lists of Point3d, one list of lists for each point in this VectorString3D; may be null.
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
 
getStatistics(boolean, int, float, boolean) - Method in class ini.trakem2.vector.Editions
Returns {average distance, cummulative distance, stdDev, median, prop_mut} which are: [0] - average distance: the average physical distance between mutation pairs [1] - cummulative distance: the sum of the distances between mutation pairs [2] - stdDev: of the physical distances between mutation pairs relative to the average [3] - median: the average medial physical distance between mutation pairs, more robust than the average to extreme values [4] - prop_mut: the proportion of mutation pairs relative to the length of the queried sequence vs1.
getStdDev(boolean, int, float) - Method in class ini.trakem2.vector.Editions
 
getStdDevAtEachPoint() - Method in class ini.trakem2.vector.VectorString3D
If null != source, compute the StdDev at each point in this VectorString3D, by comparing it with its associated source points.
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
 
getTags() - Method in class ini.trakem2.vector.VectorString3D
 
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
 
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
 
getTranslation() - Method in class mpi.fruitfly.registration.PhaseCorrelation2D
 
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
 
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.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
 
getVector(int, int) - Method in interface ini.trakem2.vector.VectorString
 
getVector(int, int) - Method in class ini.trakem2.vector.VectorString2D
 
getVector(int, int) - Method in class ini.trakem2.vector.VectorString3D
 
getVectors(int) - Method in interface ini.trakem2.vector.VectorString
 
getVectors(int) - Method in class ini.trakem2.vector.VectorString2D
 
getVectors(int) - Method in class ini.trakem2.vector.VectorString3D
 
getVirtualizationScale() - Method in class ini.trakem2.display.LayerSet
From 0.000...
getVirtualMatches() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
 
getVS1() - Method in class ini.trakem2.vector.Editions
 
getVS2() - Method in class ini.trakem2.vector.Editions
 
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
 
getWidth() - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks
 
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
 
getZeroPadingSizeForInPlace(int) - Static method in class mpi.fruitfly.fft.pffft
 
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
 
go(Layer) - Method in class ini.trakem2.display.FallLine
 
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
 
gridoverlay - Variable in class ini.trakem2.display.Display
 
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.GroupedGraphicsSource() - Constructor for class ini.trakem2.display.GroupingMode.GroupedGraphicsSource
 
GroupingMode.Painter - Class in ini.trakem2.display
 
GroupingMode.Painter() - Constructor for class ini.trakem2.display.GroupingMode.Painter
 
GroupingMode.PatchRange - Class in ini.trakem2.display
 
GroupingMode.PatchRange() - Constructor for class ini.trakem2.display.GroupingMode.PatchRange
 
GroupingMode.ScreenPatchRange<T> - Class in ini.trakem2.display
 
GroupingMode.SimpleThread - Class in ini.trakem2.display
 
gs - Variable in class ini.trakem2.display.GroupingMode
 

H

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
 
hasAlphaMask() - Method in class ini.trakem2.display.Patch
Caching system to avoid repeated checks.
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
 
hashCode() - Method in class ini.trakem2.display.DisplayCanvas.ScreenshotProperties
 
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
 
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 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
 
Identify - Class in lineage
 
Identify() - Constructor for class lineage.Identify
 
identify(Object...) - Static method in class lineage.Identify
Takes 2 arg (the Pipe or Polyline and the lib-name) or 5 args: Line3D pipe, String lib-name, double delta, boolean direct and boolean substring
identify(Line3D) - Method in class lineage.Identify
 
identityTolerance - Variable in class mpicbg.trakem2.align.Align.Param
 
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
 
ImageArrayConverter - Class in mpi.fruitfly.general
 
ImageArrayConverter() - Constructor for class mpi.fruitfly.general.ImageArrayConverter
 
imageClosed(ImagePlus) - Method in class ini.trakem2.display.Display
 
ImageData - Interface in ini.trakem2.display
An interface to label Displayable objects as containing images.
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
 
ImageFilter - Class in mpi.fruitfly.registration
 
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.
The role of the preprocessor is to do whatever is necessary to the given ImagePlus object before TrakEM2 ever sees the pixels of its ImageProcessor.
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
 
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
 
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) - Method in class ini.trakem2.persistence.Loader
Import images from the given text file, which is expected to contain 4 columns:
- column 1: image file path (if base_dir is not null, it will be prepended)
- column 2: x coord
- column 3: y coord
- column 4: z coord (layer_thickness will be multiplied to it if not zero)
This function implements the "Import from text file" command.
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
 
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
 
ini.trakem2 - package ini.trakem2
 
ini.trakem2.analysis - package ini.trakem2.analysis
 
ini.trakem2.display - package ini.trakem2.display
 
ini.trakem2.display.graphics - package ini.trakem2.display.graphics
 
ini.trakem2.imaging - package ini.trakem2.imaging
 
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
 
ini.trakem2.vector - package ini.trakem2.vector
 
init(String) - Method in class bunwarpj.trakem2.transform.CubicBSplineTransform
Initialize cubic B-spline transform from the parameters of a string
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(String) - Method in class lenscorrection.NonLinearTransform
 
init(String) - Method in class mpicbg.trakem2.transform.AffineModel2D
 
init(String) - Method in class mpicbg.trakem2.transform.AffineModel3D
 
init(String) - Method in interface mpicbg.trakem2.transform.CoordinateTransform
Initialize the properties of the CoordinateTransform from a data string as generated by #toString().
init(String) - Method in class mpicbg.trakem2.transform.CoordinateTransformList
 
init(String) - Method in class mpicbg.trakem2.transform.InvertibleCoordinateTransformList
 
init(String) - Method in class mpicbg.trakem2.transform.MovingLeastSquaresTransform
 
init(String) - Method in class mpicbg.trakem2.transform.RigidModel2D
 
init(String) - Method in class mpicbg.trakem2.transform.SimilarityModel2D
 
init(String) - Method in class mpicbg.trakem2.transform.TranslationModel2D
 
init(String) - Method in class mpicbg.trakem2.transform.TranslationModel3D
 
initModel() - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
 
initModel() - Method in class mpicbg.trakem2.align.AffineTile2D
 
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
 
INSERTION - Static variable in class ini.trakem2.vector.Editions
 
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
 
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.
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 to it.
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(Area) - Method in class ini.trakem2.display.Node
Expects Area in local coords.
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<?>) - Method in class mpicbg.trakem2.align.AbstractAffineTile2D
 
intersectsOrigin(Area, Layer) - Method in class ini.trakem2.display.Connector
 
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
 
InvertibleCoordinateTransform - Interface in mpicbg.trakem2.transform
InvertibleCoordinateTransform with String import and export as used in TrakEM2.
InvertibleCoordinateTransformList<E extends InvertibleCoordinateTransform> - Class in mpicbg.trakem2.transform
 
InvertibleCoordinateTransformList() - Constructor for class mpicbg.trakem2.transform.InvertibleCoordinateTransformList
 
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 lineage.Identify
 
invoke(Object...) - Method in class treeline.TreelineGraphEditor
 
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.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks
 
isActive() - Method in class ini.trakem2.display.Channel
 
isActive() - Method in class ini.trakem2.utils.Bureaucrat
 
isActiveWindow() - Method in class ini.trakem2.display.Display
 
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
 
isCalibrated() - Method in class ini.trakem2.vector.VectorString2D
 
isCalibrated() - Method in class ini.trakem2.vector.VectorString3D
 
isCancelled() - Method in class ini.trakem2.utils.TaskOnEDT
 
isClosed() - Method in class ini.trakem2.display.FakeImageWindow
 
isClosed() - Method in class ini.trakem2.display.Profile
 
isClosed() - Method in interface ini.trakem2.vector.VectorString
 
isClosed() - Method in class ini.trakem2.vector.VectorString2D
 
isClosed() - Method in class ini.trakem2.vector.VectorString3D
 
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.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
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.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 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.LayerSet.DoChangeTrees
 
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.
isMirroredX() - Method in class ini.trakem2.vector.VectorString3D
 
isMirroredY() - Method in class ini.trakem2.vector.VectorString3D
 
isMirroredZ() - Method in class ini.trakem2.vector.VectorString3D
 
isNear(VectorString3D, double) - Method in class ini.trakem2.vector.VectorString3D
Determine if any point of the given VectorString3D falls within a radius of any of the points in this VectorString3D.
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.
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
 
isReversed() - Method in class ini.trakem2.vector.VectorString3D
 
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
 
isSignalImage(Image) - Static method in class ini.trakem2.persistence.Loader
Returns true if the awt is a signaling image like NOT_FOUND or REGENERATING.
isSnapPaintable(long) - Method in class ini.trakem2.persistence.Loader
Check if an awt exists to paint as a snap.
isSource(ZDisplayable) - Method in class ini.trakem2.display.FallLine
 
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.
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
 
iterator() - Method in class ini.trakem2.display.Node.NodeCollection
 

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

kernelExpand(double[]) - Method in class lenscorrection.NonLinearTransform
 
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
 
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
largestGraphOnly - Static variable in class mpicbg.trakem2.align.AlignTask
 
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
 
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_set - Variable in class ini.trakem2.display.ZDisplayable
 
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.
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.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.DoChangeTrees(LayerSet) - Constructor for class ini.trakem2.display.LayerSet.DoChangeTrees
 
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.
LayerTree - Class in ini.trakem2.tree
 
LayerTree(Project, LayerThing) - Constructor for class ini.trakem2.tree.LayerTree
 
LayerTree.LayerThingNodeRender - Class in ini.trakem2.tree
 
LayerTree.LayerThingNodeRender() - Constructor for class ini.trakem2.tree.LayerTree.LayerThingNodeRender
 
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
 
length() - Method in class ini.trakem2.vector.Editions
 
length() - Method in interface ini.trakem2.vector.VectorString
 
length() - Method in class ini.trakem2.vector.VectorString2D
 
length() - Method in class ini.trakem2.vector.VectorString3D
The length of this string, that is, the number of points (and vectors) in it.
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.
lineage - package lineage
 
LineageClassifier - Class in lineage
Lineage classifier class 2009 Ignacio Arganda-Carreras and Sergio Jimenez-Celorrio This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation (http://www.gnu.org/licenses/gpl.txt ) This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
LineageClassifier() - Constructor for class lineage.LineageClassifier
 
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) - 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.ImageLoadingLock - Class in ini.trakem2.persistence
 
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
 
logNormalizeComplexVectors(float[]) - Static method in class mpi.fruitfly.fft.pffft
 
low_frequency_threshold - Variable in class ini.trakem2.imaging.Segmentation.FastMarchingParam
 
luminance(Color) - Static method in class ini.trakem2.utils.Utils
0.3 * R + 0.6 * G + 0.1 * B

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.ManualAlignMode
 
magnificationUpdated(Rectangle, double) - Method in interface ini.trakem2.display.Mode
 
main(String[]) - Static method in class ini.trakem2.tree.DTDParser
 
main(String[]) - Static method in class lineage.TestClassifier
 
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.
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
If the srcRect is null, makes a flat 8-bit or RGB image of the entire layer.
makeFlatImage(int, Layer, Rectangle, double, ArrayList<Patch>, Color) - Method in class ini.trakem2.persistence.Loader
Creates an ImageProcessor of the specified type.
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, double, int, int) - Method in class ini.trakem2.persistence.Loader
 
makePrescaledTiles(Layer[], Class<?>, Rectangle, double, int, int, String, boolean) - Method in class ini.trakem2.persistence.Loader
Generate 256x256 tiles, as many as necessary, to cover the given srcRect, starting at max_scale.
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.
makeReversedCopy() - Method in class ini.trakem2.vector.VectorString3D
 
makeStripe(Patch, Roi, float) - Static method in class ini.trakem2.imaging.StitchingTEM
 
makeStripe(Patch, Roi, float, 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
 
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") Then concatenate all good words with underscores.
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
 
ManualAlignMode.Landmarks(Layer) - Constructor for class ini.trakem2.display.ManualAlignMode.Landmarks
 
manyToManyInterpolation(Area, Area, int) - Static method in class ini.trakem2.utils.AreaUtils
 
map(TransformMeshMappingWithMasks.ImageProcessorWithMasks, TransformMeshMappingWithMasks.ImageProcessorWithMasks) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks
 
mapInterpolated(TransformMeshMappingWithMasks.ImageProcessorWithMasks, TransformMeshMappingWithMasks.ImageProcessorWithMasks) - Method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks
 
mapTriangle(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks
 
mapTriangle(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks
 
mapTriangleInterpolated(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks
 
mapTriangleInterpolated(TransformMesh, AffineModel2D, ImageProcessor, ImageProcessor, ImageProcessor, ImageProcessor, ByteProcessor) - Static method in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks
 
markNear(float, float, Layer, double) - Method in class ini.trakem2.display.Tree
 
mask - Variable in class ini.trakem2.display.Patch.PatchImage
The alpha mask, coordinate-transformed if null != ct.
mask - Variable in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks
 
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
 
mawts - Variable in class ini.trakem2.persistence.Loader
 
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_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_RETRIES - Variable in class ini.trakem2.persistence.Loader
 
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.Align.Param
Maximal allowed alignment error in px
maxIterations - Variable in class mpicbg.trakem2.align.Align.ParamOptimize
Maximal number of iteration allowed for the optimizer.
maxPlateauwidth - Variable in class mpicbg.trakem2.align.Align.ParamOptimize
Maximal number of iterations allowed to not change the parameter to be optimized.
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
 
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.
measureSize(ImagePlus) - Static method in class ini.trakem2.persistence.Loader
 
MEDIAN_PHYS_DIST - Static variable in class ini.trakem2.analysis.Compare
 
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.
Merger - Class in ini.trakem2.utils
 
Merger() - Constructor for class ini.trakem2.utils.Merger
 
mergeTargets(Connector) - Method in class ini.trakem2.display.Connector
 
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_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.Align.Param
Inlier/candidates ratio
minNumInliers - Variable in class mpicbg.trakem2.align.Align.Param
Minimal absolute number of inliers
MIPMAP_FORMATS - Static variable in class ini.trakem2.persistence.FSLoader
 
MIPMAP_JPEG - Static variable in class ini.trakem2.persistence.FSLoader
 
MIPMAP_PNG - Static variable in class ini.trakem2.persistence.FSLoader
 
MIPMAP_TIFF - Static variable in class ini.trakem2.persistence.FSLoader
 
mipmaps_regen - Variable in class ini.trakem2.persistence.Loader
If mipmaps regeneration is enabled or not.
mirror(int) - Method in class ini.trakem2.vector.VectorString3D
Where axis is any of VectorString.X_AXIS, .Y_AXIS or .Z_AXIS, and the mirroring is done relative to the local 0,0 of this VectorString.
MIRROR_X - Static variable in class ini.trakem2.vector.VectorString3D
 
MIRROR_Y - Static variable in class ini.trakem2.vector.VectorString3D
 
MIRROR_Z - Static variable in class ini.trakem2.vector.VectorString3D
 
mix(Color, Color) - Static method in class ini.trakem2.utils.Utils
Mix colors visually: red + green = yellow, etc.
Mode - Interface in ini.trakem2.display
 
modelStrings - Static variable in class lenscorrection.Distortion_Correction.BasicParam
Implemeted transformation models for choice
modelStrings - Static variable in class mpicbg.trakem2.align.Align.Param
Implemeted transformation models for choice
modes - Static variable in class ini.trakem2.persistence.Loader
 
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) - Static method in class mpicbg.trakem2.align.AlignTask
 
montageLayersTask(List<Layer>) - Static method in class mpicbg.trakem2.align.AlignTask
Montage each layer independently, with SIFT.
montageWithPhaseCorrelation(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.
montageWithPhaseCorrelation(List<Layer>) - 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
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, 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) - 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.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) - 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.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.
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.
MovingLeastSquaresTransform - Class in mpicbg.trakem2.transform
 
MovingLeastSquaresTransform() - Constructor for class mpicbg.trakem2.transform.MovingLeastSquaresTransform
 
mpi.fruitfly.analysis - package mpi.fruitfly.analysis
 
mpi.fruitfly.fft - package mpi.fruitfly.fft
 
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.transform - package mpicbg.trakem2.transform
 
multiply(float[], float[], boolean) - Static method in class mpi.fruitfly.fft.pffft
 
MultiplyARGBComposite - Class in ini.trakem2.display.graphics
 
multiplyComplexImg(float, float, float, float) - Static method in class mpi.fruitfly.fft.pffft
 
multiplyComplexReal(float, float, float, float) - Static method in class mpi.fruitfly.fft.pffft
 
MultiThreading - Class in mpi.fruitfly.general
Title: MultiThreading
MultiThreading() - Constructor for class mpi.fruitfly.general.MultiThreading
 
MUTATION - Static variable in class ini.trakem2.vector.Editions
 

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
NEAREST_NEIGHBOR - Static variable in class ini.trakem2.persistence.Loader
 
neighbors - Variable in class ini.trakem2.analysis.Vertex
 
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
 
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.
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
 
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<I> - Class in ini.trakem2.display
 
Node.BranchAndEndNodeIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.BranchAndEndNodeIterator
 
Node.BranchNodeIterator<I> - Class in ini.trakem2.display
 
Node.BranchNodeIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.BranchNodeIterator
 
Node.BreadthFirstSubtreeIterator<I> - Class in ini.trakem2.display
For a given starting node, iterates over the complete set of children nodes, recursively and breadth-first.
Node.BreadthFirstSubtreeIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.BreadthFirstSubtreeIterator
 
Node.EndNodeIterator<I> - Class in ini.trakem2.display
 
Node.EndNodeIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.EndNodeIterator
 
Node.FilteredIterator<I> - Class in ini.trakem2.display
 
Node.FilteredIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.FilteredIterator
 
Node.NodeCollection<I> - Class in ini.trakem2.display
Read-only Collection with a very expensive size().
Node.NodeCollection(Node<I>, Class<?>) - Constructor for class ini.trakem2.display.Node.NodeCollection
 
Node.NodeIterator<I> - Class in ini.trakem2.display
Stateful abstract Node iterator.
Node.NodeIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.NodeIterator
 
Node.Operation<I> - Interface in ini.trakem2.display
An operation to be applied to a specific Node.
Node.SlabIterator<I> - Class in ini.trakem2.display
For a given starting node, iterates all the way to the next end node or branch node, inclusive.
Node.SlabIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.SlabIterator
 
Node.SubtreeIterator<I> - Class in ini.trakem2.display
 
Node.SubtreeIterator(Node<I>) - Constructor for class ini.trakem2.display.Node.SubtreeIterator
 
NODE_FLAVOR - Static variable in class ini.trakem2.tree.TransferableNode
 
node_layer_map - Variable in class ini.trakem2.display.Tree
 
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(Vector3) - Method in class ini.trakem2.utils.Vector3
 
normalize(FloatArray) - Static method in class mpi.fruitfly.registration.ImageFilter
 
normalizeComplexVectorsToUnitVectors(float[]) - Static method in class mpi.fruitfly.fft.pffft
 
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
NUM_PROCESSORS - Static variable in class ini.trakem2.parallel.Process
 
numberOfImages - Variable in class lenscorrection.Distortion_Correction.PluginParam
 

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_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
 
openCompleteStack(String, String, String, int, int) - Static method in class mpi.fruitfly.general.fileAccess
 
openDBProject() - Static method in class ini.trakem2.Project
Open a TrakEM2 project from the database.
opener - Variable in class ini.trakem2.persistence.Loader
 
openFileRead(String) - Static method in class mpi.fruitfly.general.fileAccess
 
openFileWrite(String) - Static method in class mpi.fruitfly.general.fileAccess
 
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
 
openGreyJpeg(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.
openJpeg(String, boolean) - Static method in class ini.trakem2.io.ImageSaver
 
openJpegAlpha(String) - Static method in class ini.trakem2.io.ImageSaver
Open a jpeg file including the alpha channel if it has one.
openJpegFromStream(InputStream, boolean) - Static method in class ini.trakem2.io.ImageSaver
The stream IS NOT closed by this method.
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.
openStack(String, String, String, int, int, int) - Static method in class mpi.fruitfly.general.fileAccess
 
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.
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.BooleanSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.BooleanSetter
 
OptionPanel.BooleanSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.BooleanSetter
 
OptionPanel.ChoiceIntSetter - Class in ini.trakem2.utils
 
OptionPanel.ChoiceIntSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceIntSetter
 
OptionPanel.ChoiceIntSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceIntSetter
 
OptionPanel.ChoiceObjectSetter - Class in ini.trakem2.utils
 
OptionPanel.ChoiceObjectSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceObjectSetter
 
OptionPanel.ChoiceObjectSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceObjectSetter
 
OptionPanel.ChoiceStringSetter - Class in ini.trakem2.utils
 
OptionPanel.ChoiceStringSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceStringSetter
 
OptionPanel.ChoiceStringSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.ChoiceStringSetter
 
OptionPanel.DoubleSetter - Class in ini.trakem2.utils
 
OptionPanel.DoubleSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.DoubleSetter
 
OptionPanel.DoubleSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.DoubleSetter
 
OptionPanel.DoubleSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.DoubleSetter
 
OptionPanel.FloatSetter - Class in ini.trakem2.utils
 
OptionPanel.FloatSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.FloatSetter
 
OptionPanel.FloatSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.FloatSetter
 
OptionPanel.FloatSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.FloatSetter
 
OptionPanel.IntSetter - Class in ini.trakem2.utils
 
OptionPanel.IntSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.IntSetter
 
OptionPanel.IntSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.IntSetter
 
OptionPanel.IntSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.IntSetter
 
OptionPanel.NumericalSetter - Class in ini.trakem2.utils
 
OptionPanel.NumericalSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.NumericalSetter
 
OptionPanel.NumericalSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.NumericalSetter
 
OptionPanel.NumericalSetter(Object, String, Runnable, int, int) - Constructor for class ini.trakem2.utils.OptionPanel.NumericalSetter
 
OptionPanel.Setter - Class in ini.trakem2.utils
 
OptionPanel.Setter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.Setter
 
OptionPanel.Setter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.Setter
 
OptionPanel.StringSetter - Class in ini.trakem2.utils
 
OptionPanel.StringSetter(Object, String) - Constructor for class ini.trakem2.utils.OptionPanel.StringSetter
 
OptionPanel.StringSetter(Object, String, Runnable) - Constructor for class ini.trakem2.utils.OptionPanel.StringSetter
 
originalPatches - Variable in class ini.trakem2.display.GroupingMode
 
outside - Variable in class ini.trakem2.display.Patch.PatchImage
The outside mask, coordinate-transformed if null != ct.
outside - Variable in class mpicbg.trakem2.transform.TransformMeshMappingWithMasks.ImageProcessorWithMasks
 
overlap - Variable in class ini.trakem2.imaging.StitchingTEM.PhaseCorrelationParam
 
overlapImp - Variable in class mpi.fruitfly.registration.PhaseCorrelation2D.CrossCorrelationResult
 
overlappingPixels - Variable in class mpi.fruitfly.registration.PhaseCorrelation2D.CrossCorrelationResult
 
Overlay - Class in ini.trakem2.display
 
Overlay() - Constructor for class ini.trakem2.display.Overlay
 
OVERWRITE - Static variable in class mpi.fruitfly.fft.pffft
 

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 - 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) - 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) - 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
 
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
 
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) - 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.
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
 
pairOverlappingTiles(List<AbstractAffineTile2D<?>>, 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<?>[]>) - 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
 
param - Static variable in class mpicbg.trakem2.align.Align
 
paramOptimize - Static variable in class mpicbg.trakem2.align.Align
 
parent - Variable in class ini.trakem2.display.Node
 
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.
parseFilter(String) - Static method in class mpi.fruitfly.general.fileParsing
 
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.
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, 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.PatchImage - Class in ini.trakem2.display
 
Patch.TransformProperties - Class in ini.trakem2.display
 
Patch.TransformProperties(Patch) - Constructor for class ini.trakem2.display.Patch.TransformProperties
 
patches - Variable in class lenscorrection.DistortionCorrectionTask.AppendCoordinateTransformThread
 
patches - Variable in class lenscorrection.DistortionCorrectionTask.SetCoordinateTransformThread
 
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
 
PCMValue - Variable in class mpi.fruitfly.registration.PhaseCorrelation2D.CrossCorrelationResult
 
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.
pffft - Class in mpi.fruitfly.fft
 
pffft() - Constructor for class mpi.fruitfly.fft.pffft
 
pffft1D(float[], boolean) - Static method in class mpi.fruitfly.fft.pffft
 
pffft1DInPlace(float[], int) - Static method in class mpi.fruitfly.fft.pffft
 
pffft2D(FloatArray2D, boolean) - Static method in class mpi.fruitfly.fft.pffft
 
pffft2DInPlace(FloatArray2D, int, boolean) - Static method in class mpi.fruitfly.fft.pffft
 
pffft2DMT(FloatArray2D, boolean) - Static method in class mpi.fruitfly.fft.pffft
 
pffft3D(FloatArray3D, boolean) - Static method in class mpi.fruitfly.fft.pffft
 
pffft3DMT(FloatArray3D, boolean) - Static method in class mpi.fruitfly.fft.pffft
 
pffftInv1D(float[], int) - Static method in class mpi.fruitfly.fft.pffft
 
pffftInv2D(FloatArray2D, int) - Static method in class mpi.fruitfly.fft.pffft
 
pffftInv3D(FloatArray3D, int) - Static method in class mpi.fruitfly.fft.pffft
 
PhaseCorrelation2D - Class in mpi.fruitfly.registration
Title:
PhaseCorrelation2D(String, String, int, boolean, boolean, boolean) - Constructor for class mpi.fruitfly.registration.PhaseCorrelation2D
 
PhaseCorrelation2D(ImagePlus, ImagePlus, int, boolean, boolean, boolean) - Constructor for class mpi.fruitfly.registration.PhaseCorrelation2D
 
PhaseCorrelation2D(ImageProcessor, ImageProcessor, int, boolean, boolean, boolean) - Constructor for class mpi.fruitfly.registration.PhaseCorrelation2D
 
PhaseCorrelation2D.CrossCorrelationResult - Class in mpi.fruitfly.registration
 
PhaseCorrelation2D.CrossCorrelationResult() - Constructor for class mpi.fruitfly.registration.PhaseCorrelation2D.CrossCorrelationResult
 
PhaseCorrelationCalculator - Class in ini.trakem2.imaging
 
PhaseCorrelationCalculator(ImagePlus, ImagePlus) - Constructor for class ini.trakem2.imaging.PhaseCorrelationCalculator
 
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
 
pointMatches - Variable in class lenscorrection.Distortion_Correction.PointMatchCollectionAndAffine
 
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).
pow(int, int) - Static method in class mpi.fruitfly.math.General
 
PP - Static variable in class ini.trakem2.display.AreaWrapper
 
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.
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.
prettyPrint(String) - Method in class ini.trakem2.vector.Editions
Get the sequence of editions and matches in three lines, like: vs1: 1 2 3 4 5 6 7 8 9 M M D M M M I I M M M vs2: 1 2 3 4 5 6 7 8 9 With the given separator (defaults to tab if null)
previous(Layer) - Method in class ini.trakem2.display.LayerSet
 
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
 
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 - 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.
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, Stri