- RADII - Static variable in class sc.fiji.snt.PathFitter
-
Flag specifying that the computed path should only inherit fitted radii
attributes
- RADII_AND_MIDPOINTS - Static variable in class sc.fiji.snt.PathFitter
-
Flag specifying that the computed path should inherit both midpoint
refinement of node coordinates and radii
- radius - Variable in class sc.fiji.snt.util.SWCPoint
-
The radius of reconstructed structure at this node
- randomPaths() - Static method in class sc.fiji.snt.SNTUtils
-
Generates a list of random paths.
- READY - Static variable in class sc.fiji.snt.SNTUI
-
Flag specifying that image data is available and the UI is not waiting on any
pending operations, thus 'ready to trace'
- realToString() - Method in class sc.fiji.snt.Path
-
- rebuildDisplayCanvases() - Method in class sc.fiji.snt.SNT
-
Rebuilds display canvases, i.e., the placeholder canvases used when no
valid image data exists (a single-canvas is rebuilt if only the XY view is
active).
- rebuildZYXZpanes() - Method in class sc.fiji.snt.SNT
-
- ReconstructionViewerCmd - Class in sc.fiji.snt.gui.cmds
-
Command for starting Reconstruction Viewer as a 'stand-alone' program
- ReconstructionViewerCmd() - Constructor for class sc.fiji.snt.gui.cmds.ReconstructionViewerCmd
-
- recordRotation(float, int, File) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Records an animated rotation of the scene as a sequence of images.
- RecViewerPrefsCmd - Class in sc.fiji.snt.gui.cmds
-
Command implementing Reconstruction Viewer 'Preferences...' command.
- RecViewerPrefsCmd() - Constructor for class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd
-
- reloadImage(int, int) - Method in class sc.fiji.snt.SNT
-
- reloadZYXZpanes(int) - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- RemoteSWCImporterCmd - Class in sc.fiji.snt.gui.cmds
-
Command for importing SWC reconstructions from remote databases
- RemoteSWCImporterCmd() - Constructor for class sc.fiji.snt.gui.cmds.RemoteSWCImporterCmd
-
- RemoteSWCLoader - Interface in sc.fiji.snt.io
-
Importers downloading remote SWC files should extend this interface.
- remove(Component) - Static method in class sc.fiji.snt.gui.FileDrop
-
Removes the drag-and-drop hooks from the component and optionally from
the all children.
- remove() - Method in class sc.fiji.snt.PathAndFillManager.AllPointsIterator
-
- remove(Path) - Method in class sc.fiji.snt.Tree
-
Removes a path from this tree.
- remove(Object) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Script friendly method to remove an object (
Tree,
OBJMesh,
AbstractDrawable, etc.) from this viewer's scene.
- removeAllMeshes() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Removes all loaded OBJ meshes from current viewer
- removeAllTrees() - Method in class sc.fiji.snt.viewer.Viewer3D
-
Removes all the Trees from current viewer
- removeFrom3DViewer(Image3DUniverse) - Method in class sc.fiji.snt.Path
-
- removeMesh(OBJMesh) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Removes the specified OBJ mesh.
- removeMesh(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Removes the specified OBJ mesh.
- removeMIPOverlayAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- removeNode(int) - Method in class sc.fiji.snt.Path
-
Removes the specified node if this path has at least two nodes.
- removeTree(Tree) - Method in class sc.fiji.snt.SciViewSNT
-
Removes the specified Tree.
- removeTree(Tree) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Removes the specified Tree.
- removeTree(String) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Removes the specified Tree.
- removeViewer(Viewer3D) - Static method in class sc.fiji.snt.SNTUtils
-
- repaintAllPanes() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanes
-
- replaceAll(List<Path>) - Method in class sc.fiji.snt.Tree
-
Replaces all Paths in this Tree.
- reportFinished(boolean) - Method in class sc.fiji.snt.SearchThread
-
- reportFinished(boolean) - Method in class sc.fiji.snt.TubularGeodesicsTracer
-
- reportProgress(float) - Method in class sc.fiji.snt.TubularGeodesicsTracer
-
- reportThreadStatus() - Method in class sc.fiji.snt.ManualTracerThread
-
- reportThreadStatus() - Method in class sc.fiji.snt.SearchThread
-
- requestStop() - Method in class sc.fiji.snt.ManualTracerThread
-
- requestStop() - Method in interface sc.fiji.snt.SearchInterface
-
- requestStop() - Method in class sc.fiji.snt.SearchThread
-
- requestStop() - Method in class sc.fiji.snt.TubularGeodesicsTracer
-
- resetListeners(Path) - Method in class sc.fiji.snt.PathAndFillManager
-
- resetRestrictions() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Removes any filtering restrictions that may have been set.
- restoreDefaultCursor() - Method in class sc.fiji.snt.hyperpanes.MultiDThreePanesCanvas
-
- restrictToLength(double, double) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Restricts analysis to paths sharing the specified length range.
- restrictToNamePattern(String) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Restricts analysis to Paths containing the specified string in their name.
- restrictToOrder(int...) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Restricts analysis to Paths sharing the specified branching order(s).
- restrictToSize(int, int) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Restricts analysis to paths having the specified number of nodes.
- restrictToSWCType(int...) - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Restricts analysis to Paths sharing the specified SWC flag(s).
- RoiConverter - Class in sc.fiji.snt.analysis
-
Converts SNT
Paths into (IJ1) ROIs.
- RoiConverter(Tree) - Constructor for class sc.fiji.snt.analysis.RoiConverter
-
Instantiates a new Converter.
- RoiConverter(Tree, ImagePlus) - Constructor for class sc.fiji.snt.analysis.RoiConverter
-
Instantiates a new Converter.
- ROIExporterCmd - Class in sc.fiji.snt.plugin
-
Command providing a GUI for
RoiConverter and allowing export of
Paths to the IJ1 ROI Manager.
- ROIExporterCmd() - Constructor for class sc.fiji.snt.plugin.ROIExporterCmd
-
- ROOT_NUMBER - Static variable in class sc.fiji.snt.analysis.MultiTreeColorMapper
-
Mapping property: Strahler root number
- rotate(int, double) - Method in class sc.fiji.snt.Tree
-
Rotates the tree.
- rotate(float) - Method in class sc.fiji.snt.viewer.Viewer3D
-
Rotates the scene.
- run() - Method in class sc.fiji.snt.analysis.PathProfiler
-
- run() - Method in class sc.fiji.snt.analysis.TreeAnalyzer
-
Generates detailed summaries in which measurements are grouped by SWC-type
flags
- run() - Method in class sc.fiji.snt.gui.cmds.ChooseDatasetCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.ColorMapReconstructionCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.CommonDynamicCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.CompareFilesCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.ComputeSecondaryImg
-
- run() - Method in class sc.fiji.snt.gui.cmds.ComputeTubenessImg
-
- run() - Method in class sc.fiji.snt.gui.cmds.CustomizeObjCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.CustomizeTreeCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.DistributionCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.EnableSciViewUpdateSiteCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.JSONImporterCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.LoadObjCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.LoadReconstructionCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.MLImporterCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.MultiSWCImporterCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.OpenDatasetCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.PathFitterCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.PrefsCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.ReconstructionViewerCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.RecViewerPrefsCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.RemoteSWCImporterCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.ShowCorrespondencesCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.SNTLegacyLoaderCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.SNTLoaderCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.SWCTypeFilterCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.SWCTypeOptionsCmd
-
- run() - Method in class sc.fiji.snt.gui.cmds.TranslateReconstructionsCmd
-
- run() - Method in class sc.fiji.snt.gui.SigmaPalette
-
- run() - Method in class sc.fiji.snt.ManualTracerThread
-
- run() - Method in class sc.fiji.snt.plugin.CallLegacyShollPlugin
-
- run() - Method in class sc.fiji.snt.plugin.LocalThicknessCmd
-
- run() - Method in class sc.fiji.snt.plugin.PlotterCmd
-
- run() - Method in class sc.fiji.snt.plugin.ROIExporterCmd
-
- run(String) - Method in class sc.fiji.snt.plugin.ShollAnalysisPlugin
-
Deprecated.
- run() - Method in class sc.fiji.snt.plugin.ShollTracingsCmd
-
- run() - Method in class sc.fiji.snt.plugin.SkeletonizerCmd
-
- run() - Method in class sc.fiji.snt.plugin.StrahlerCmd
-
- run() - Method in class sc.fiji.snt.plugin.TreeMapperCmd
-
- run() - Method in class sc.fiji.snt.SearchThread
-
- run() - Method in class sc.fiji.snt.TubularGeodesicsTracer
-
- runCommand(String) - Method in class sc.fiji.snt.PathManagerUI
-
- runCommand(String) - Method in class sc.fiji.snt.SNTUI
-
- RUNNING - Static variable in class sc.fiji.snt.SearchThread
-
- RUNNING_CMD - Static variable in class sc.fiji.snt.SNTUI
-