Uses of Class
sc.fiji.snt.Tree

Packages that use Tree

Package	Description
sc.fiji.snt	SNT core classes
sc.fiji.snt.analysis	Analysis of Trees.
sc.fiji.snt.analysis.graph	Classes for handling neuronal reconstructions as graphs
sc.fiji.snt.analysis.sholl	Sholl analysis of Trees.
sc.fiji.snt.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.io	Classes for importing reconstructions into SNT.
sc.fiji.snt.plugin	SNT add-ons as IJ2 commands
sc.fiji.snt.viewer	Visualization of reconstructions

Uses of Tree in sc.fiji.snt

Methods in sc.fiji.snt that return Tree

Modifier and Type	Method and Description
Tree	Tree.clone()
Tree	SNTService.demoTree() Returns a toy reconstruction (fractal tree).
static Tree	Tree.fromFile(java.lang.String filePath) Script-friendly method for creating a Tree from a reconstruction file.
Tree	SNTService.getTree(boolean selectedPathsOnly) Gets the collection of paths listed in the Path Manager as a Tree object.
Tree	Tree.subTree(int... swcTypes) Extracts the subset of paths matching the specified criteria.
Tree	Tree.subTree(java.lang.String... swcTypes) Extracts the subset of paths matching the specified criteria (script friendly method)

Methods in sc.fiji.snt that return types with arguments of type Tree

Modifier and Type	Method and Description
java.util.List<Tree>	SNTService.demoTrees() Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database).
java.util.Map<java.lang.String,Tree>	PathAndFillManager.importNeurons(java.util.Map<java.lang.String,java.util.TreeSet<SWCPoint>> map, org.scijava.util.ColorRGB color, java.lang.String spatialUnit) Import neuron(s) as a collection of reconstruction nodes (SWC points)
java.util.List<Tree>	PathAndFillManager.importSWCs(java.util.Map<java.lang.String,java.lang.String> swcs, org.scijava.util.ColorRGB color) Imports a group of SWC files (Remote URLs supported).
static java.util.List<Tree>	Tree.listFromDir(java.lang.String dir) Retrieves a list of Trees from reconstruction files stored in a common directory.
static java.util.List<Tree>	Tree.listFromDir(java.lang.String dir, java.lang.String pattern) Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.

Methods in sc.fiji.snt with parameters of type Tree

Modifier and Type	Method and Description
void	SciViewSNT.addTree(Tree tree) Adds a tree to the associated SciView instance.
void	PathAndFillManager.addTree(Tree tree) Adds a Tree.
graphics.scenery.Node	SciViewSNT.getTreeAsSceneryNode(Tree tree) Gets the specified Tree as a Scenery Node.
void	SNTService.loadTree(Tree tree) Loads the specified tree.
boolean	Tree.merge(Tree tree) Appends all paths of a specified Tree to this one.
boolean	SciViewSNT.removeTree(Tree tree) Removes the specified Tree.

Uses of Tree in sc.fiji.snt.analysis

Methods in sc.fiji.snt.analysis that return Tree

Modifier and Type	Method and Description
Tree	TreeAnalyzer.getParsedTree() Returns the set of parsed Paths.

Methods in sc.fiji.snt.analysis that return types with arguments of type Tree

Modifier and Type	Method and Description
java.util.List<Tree>	MultiTreeColorMapper.sortedMappedTrees()

Methods in sc.fiji.snt.analysis with parameters of type Tree

Modifier and Type	Method and Description
void	TreeColorMapper.map(Tree tree, sholl.math.LinearProfileStats stats, net.imglib2.display.ColorTable colorTable) Colorizes a tree using Sholl data.
void	TreeColorMapper.map(Tree tree, java.lang.String measurement, net.imglib2.display.ColorTable colorTable) Colorizes a tree after the specified measurement.
void	TreeColorMapper.map(Tree tree, java.lang.String measurement, java.lang.String lut) Colorizes a tree after the specified measurement.

Method parameters in sc.fiji.snt.analysis with type arguments of type Tree

Modifier and Type	Method and Description
void	TreeColorMapper.mapTrees(java.util.List<Tree> trees, java.lang.String lut) Colorizes a list of trees, with each tree being assigned a LUT index.

Constructors in sc.fiji.snt.analysis with parameters of type Tree

Constructor and Description
PathProfiler(Tree tree, ij.ImagePlus imp) Instantiates a new Profiler
RoiConverter(Tree tree) Instantiates a new Converter.
RoiConverter(Tree tree, ij.ImagePlus imp) Instantiates a new Converter.
TreeAnalyzer(Tree tree) Instantiates a new Tree analyzer.
TreeStatistics(Tree tree) Instantiates a new instance from a collection of Paths

Constructor parameters in sc.fiji.snt.analysis with type arguments of type Tree

Constructor and Description
MultiTreeColorMapper(java.util.Collection<Tree> trees) Instantiates the MultiTreeColorMapper.

Uses of Tree in sc.fiji.snt.analysis.graph

Methods in sc.fiji.snt.analysis.graph that return Tree

Modifier and Type	Method and Description
static Tree	GraphUtils.createTree(org.jgrapht.graph.DefaultDirectedGraph<SWCPoint,?> graph) Creates a Tree from a graph.

Methods in sc.fiji.snt.analysis.graph with parameters of type Tree

Modifier and Type	Method and Description
static org.jgrapht.graph.DefaultDirectedGraph<SWCPoint,org.jgrapht.graph.DefaultWeightedEdge>	GraphUtils.createGraph(Tree tree) Creates a DirectedGraph from a Tree.

Uses of Tree in sc.fiji.snt.analysis.sholl

Constructors in sc.fiji.snt.analysis.sholl with parameters of type Tree

Constructor and Description
TreeParser(Tree tree) Instantiates a new Tree Parser.

Uses of Tree in sc.fiji.snt.annotation

Methods in sc.fiji.snt.annotation with parameters of type Tree

Modifier and Type	Method and Description
static void	AllenUtils.assignToLeftHemisphere(Tree tree)
static void	AllenUtils.assignToRightHemisphere(Tree tree)
static boolean	AllenUtils.isLeftHemisphere(Tree tree) Checks the hemisphere a neuron belongs to.

Uses of Tree in sc.fiji.snt.io

Methods in sc.fiji.snt.io that return Tree

Modifier and Type	Method and Description
Tree	MouseLightLoader.getTree() Script-friendly method to extract the entire neuron as a collection of Paths.
Tree	RemoteSWCLoader.getTree(java.lang.String cellId)
Tree	NeuroMorphoLoader.getTree(java.lang.String cellId) Gets the collection of Paths for the specified cell ID
Tree	FlyCircuitLoader.getTree(java.lang.String cellId) Gets the collection of Paths for the specified cell ID
Tree	MouseLightLoader.getTree(java.lang.String compartment) Script-friendly method to extract a compartment as a collection of Paths.
Tree	MouseLightLoader.getTree(java.lang.String compartment, org.scijava.util.ColorRGB color) Extracts a cell compartment as a collection of Paths.

Methods in sc.fiji.snt.io that return types with arguments of type Tree

Modifier and Type	Method and Description
static java.util.Map<java.lang.String,Tree>	MouseLightLoader.extractTrees(java.io.File jsonFile, java.lang.String compartment) Extracts reconstruction(s) from a JSON file.

Uses of Tree in sc.fiji.snt.plugin

Constructors in sc.fiji.snt.plugin with parameters of type Tree

Constructor and Description
StrahlerCmd(Tree tree)

Uses of Tree in sc.fiji.snt.viewer

Methods in sc.fiji.snt.viewer with parameters of type Tree

Modifier and Type	Method and Description
void	Viewer3D.addTree(Tree tree) Adds a tree to this viewer.
void	Viewer2D.addTree(Tree tree) Appends a tree to the viewer using default options.
void	Viewer2D.addTree(Tree tree, org.scijava.util.ColorRGB color) Appends a tree to the viewer.
void	Viewer2D.addTree(Tree tree, java.lang.String measurement, net.imglib2.display.ColorTable colorTable, double min, double max) Appends a tree to the viewer rendered after the specified measurement.
void	Viewer2D.addTree(Tree tree, java.lang.String measurement, java.lang.String lut) Appends a tree to the viewer rendered after the specified measurement.
void	Viewer2D.addTree(Tree tree, java.lang.String measurement, java.lang.String lut, double min, double max) Appends a tree to the viewer rendered after the specified measurement.
boolean	Viewer3D.removeTree(Tree tree) Removes the specified Tree.
void	Viewer3D.translate(Tree tree, SNTPoint offset) Translates the specified Tree.

Method parameters in sc.fiji.snt.viewer with type arguments of type Tree

Modifier and Type	Method and Description
void	Viewer2D.addTrees(java.util.List<Tree> trees, java.lang.String lut) Adds a list of trees while assigning each tree to a LUT index.