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.curation	Classes for curation of reconstructions, as implemented by the "Curation Assistant".
sc.fiji.snt.analysis.graph	Classes for handling neuronal reconstructions as graphs
sc.fiji.snt.analysis.sholl.parsers	Parsers to retrieve Sholl profiles from multiple sources (2D/3D images, reconstructions, and tables)
sc.fiji.snt.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.gui	Customizations and commands for SNT's GUI.
sc.fiji.snt.gui.cmds	Scijava-based GUIs for SNT built-in commands.
sc.fiji.snt.io	Classes for importing reconstructions into SNT.
sc.fiji.snt.plugin	SNT add-ons as IJ2 commands
sc.fiji.snt.tracing.auto	Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.
sc.fiji.snt.util	Miscellaneous SNT utilities, including classes defining reconstruction nodes.
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	Description
Tree	Tree.clone()	Creates a deep copy of this Tree.
Tree	SNTService.demoTree()	Deprecated.
Tree	SNTService.demoTree(String tree)	Returns a demo tree.
static Tree	Tree.fromFile(String filePath)	Script-friendly method for loading a Tree from a reconstruction file.
Tree	PathManagerUI.geSelectedPathsAsTree()	Gets the collection of paths listed in the Path Manager as a Tree object.
protected Tree	PathManagerUI.getSingleTree()
Tree	PathAndFillManager.getTree(int treeId)	Returns the specified Tree.
Tree	PathAndFillManager.getTree(String treeLabel)	Returns the specified Tree.
Tree	SNTService.getTree()	Gets the collection of paths listed in the Path Manager as a Tree object.
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(String... swcTypes)	Extracts the subset of paths matching the specified criteria (script friendly method)
Tree	Tree.transformedCopy(String transformOptions)	Retrieves a transformed duplicate of this tree.

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

Modifier and Type	Method	Description
List<Tree>	SNTService.demoTrees()	Returns a collection of four demo reconstructions (dendrites from pyramidal cells from the MouseLight database).
protected List<Tree>	SNTService.demoTreesSWC()
protected Collection<Tree>	PathManagerUI.getMultipleTrees()
Map<String,Tree>	PathManagerUI.getSelectedPathsOrganizedByTrees(boolean ifNoneSelectedGetAll)	Gets the paths currently selected in the Manager's JTree list as Trees.
Collection<Tree>	PathAndFillManager.getTrees()	Returns all the paths associated with this PathAndFillManager instance, grouped by Tree.
Collection<Tree>	SNTService.getTrees()	Gets the collection of paths listed in the Path Manager as a Tree object.
Map<String,Tree>	PathAndFillManager.importNeurons(Map<String,TreeSet<SWCPoint>> map, org.scijava.util.ColorRGB color, String spatialUnit)	Import neuron(s) as a collection of reconstruction nodes (SWC points)
List<Tree>	PathAndFillManager.importSWCs(Map<String,String> swcs, org.scijava.util.ColorRGB color)	Imports a group of SWC files (Remote URLs supported).
static List<Tree>	Tree.listFromDir(String dir)	Retrieves a list of Trees from reconstruction files stored in a common directory.
static List<Tree>	Tree.listFromDir(String dir, String pattern)	Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.
static List<Tree>	Tree.listFromDir(String dir, String pattern, String... swcTypes)	Retrieves a list of Trees from reconstruction files stored in a common directory matching the specified criteria.
static Collection<Tree>	Tree.listFromFile(String tracesOrJsonFile)	Retrieves a list of Trees from a single file.
static Collection<Tree>	Tree.transform(Collection<Tree> trees, String transformOptions, boolean inPlace)	Transforms a collection of trees using standardized flags.

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

Modifier and Type	Method	Description
void	PathAndFillManager.addTree(Tree tree)	Adds a Tree.
void	PathAndFillManager.addTree(Tree tree, String commonTag)	Adds a Tree.
void	SciViewSNT.addTree(Tree tree)	Adds a tree to the associated SciView instance.
void	Tree.applyProperties(Tree tree)	Applies properties from another Tree to this Tree.
graphics.scenery.Node	SciViewSNT.getTreeAsSceneryNode(Tree tree)	Gets the specified Tree as a Scenery Node.
static boolean	DelineationsManager.hasDelineationLabels(Tree tree)	Checks if the given tree has any delineation labels.
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.

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

Modifier and Type	Method	Description
void	PathAndFillManager.addTrees(Collection<Tree> trees)	Adds a collection of Trees.
void	PathAndFillManager.addTrees(Collection<Tree> trees, String commonTag)	Adds a collection of Trees.
static void	Tree.assignUniqueColors(Collection<Tree> trees)	Deprecated. use TreeUtils.assignUniqueColors(Collection)
static void	Tree.assignUniqueColors(Collection<Tree> trees, String excludedHue)	Deprecated. use TreeUtils.assignUniqueColors(Collection, String)
void	CurationManager.calibrateFromTrees(List<Tree> trees)	Calibrates thresholds from the given in-memory trees, enables live monitoring, runs a full scan, and switches SNTUI to the Assistant tab.
static boolean	DelineationsManager.hasDelineationLabels(Collection<Tree> trees)	Checks if the given trees have any delineation labels.
void	SNTService.loadTrees(Collection<Tree> trees)	Loads the specified collection of trees.
static Collection<Tree>	Tree.transform(Collection<Tree> trees, String transformOptions, boolean inPlace)	Transforms a collection of trees using standardized flags.

Uses of Tree in sc.fiji.snt.analysis

Fields in sc.fiji.snt.analysis declared as Tree

Modifier and Type	Field	Description
protected Tree	TreeStatistics.tree

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

Modifier and Type	Method	Description
Tree	TreeStatistics.getParsedTree()	Returns the set of parsed Paths.
Tree	RootAngleAnalyzer.getTaggedTree()
Tree	RootAngleAnalyzer.getTaggedTree(String lutName, double min, double max)	Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.
Tree	RootAngleAnalyzer.getTaggedTree(net.imglib2.display.ColorTable colorTable)	Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.
Tree	RootAngleAnalyzer.getTaggedTree(net.imglib2.display.ColorTable colorTable, double min, double max)	Returns a recolored copy of the analyzed tree with the root angles assigned to its node values.
Tree	ConvexHullAnalyzer.getTree()	Gets the tree being analyzed.

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

Modifier and Type	Method	Description
Collection<Tree>	MultiTreeStatistics.getGroup()	Gets the collection of Trees being analyzed.
List<Tree>	MultiTreeColorMapper.sortedMappedTrees()

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

Modifier and Type	Method	Description
void	NodeStatistics.assignBranches(Tree tree)	Associates the nodes being analyzed to the branches of the specified tree
protected AbstractConvexHull	ConvexHullAnalyzer.computeHull(Tree tree)
Map<BrainAnnotation,int[]>	NodeStatistics.getAnnotatedFrequenciesByHemisphere(int level, Tree tree)
SNTChart	NodeStatistics.getAnnotatedFrequencyHistogram(int depth, String hemisphere, Tree tree)	Retrieves the histogram of count frequencies across brain areas of the specified ontology level across the specified hemisphere.
static String	AnalysisUtils.getMetricLabel(String standardMetric, Tree tree)	Assembles a label from a measurements metric and a spatial unit
static PCAnalyzer.PrincipalAxis[]	PCAnalyzer.getPrincipalAxes(Tree tree)	Computes the principal axes for a Tree structure.
static PCAnalyzer.PrincipalAxis[]	PCAnalyzer.getPrincipalAxes(Tree tree, boolean excludeRoot)	Computes the principal axes for a Tree structure with option to exclude root.
void	TreeColorMapper.map(Tree tree, String measurement, String lut)	Colorizes a tree after the specified measurement.
void	TreeColorMapper.map(Tree tree, String measurement, net.imglib2.display.ColorTable colorTable)	Colorizes a tree after the specified measurement.
void	TreeColorMapper.map(Tree tree, LinearProfileStats stats, net.imglib2.display.ColorTable colorTable)	Colorizes a tree using Sholl data.
void	TreeColorMapper.map(Tree tree, Profile profile, net.imglib2.display.ColorTable colorTable)	Colorizes a tree using Sholl data.
static PCAnalyzer.PrincipalAxis[]	PCAnalyzer.orientTowardTips(PCAnalyzer.PrincipalAxis[] axes, Tree tree)	Convenience method to orient existing principal axes toward a tree's tips centroid.
static int	MultiSpectralRefiner.refineTree(ij.ImagePlus imp, Tree tree)	Refines all paths in a tree, processing each path in parallel.
static int	MultiSpectralRefiner.refineTree(ij.ImagePlus imp, Tree tree, MultiSpectralRefiner.Parameters params)	Refines all paths in a tree with custom parameters.
static <T extends net.imglib2.type.numeric.NumericType<T>> int	MultiSpectralRefiner.refineTree(net.imagej.ImgPlus<T> img, Tree tree)	Refines all paths in a tree, processing each path in parallel.
static <T extends net.imglib2.type.numeric.NumericType<T>> int	MultiSpectralRefiner.refineTree(net.imagej.ImgPlus<T> img, Tree tree, MultiSpectralRefiner.Parameters params)	Refines all paths in a tree with custom parameters.
static void	ColorMapper.unMap(Tree tree)	Removes color mapping from all paths in the specified tree.

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

Modifier and Type	Method	Description
void	GroupedTreeStatistics.addGroup(Collection<Tree> group, String groupLabel)	Adds a comparison group to the analysis queue.
void	GroupedTreeStatistics.addGroup(Collection<Tree> group, String groupLabel, String... swcTypes)	Adds a comparison group to the analysis queue.
static TreeStatistics	TreeStatistics.fromCollection(Collection<Tree> trees, String metric)	Creates a TreeStatistics instance from a group of Trees and a specific metric for convenient retrieval of histograms
void	TreeColorMapper.mapTrees(List<Tree> trees, 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

Modifier	Constructor	Description
	ConvexHullAnalyzer(Tree tree)	Instantiates a new convex hull analyzer.
	NodeStatistics(Collection<T> points, Tree tree)	Performs statistics on a collection of nodes.
	PathProfiler(Tree tree, ij.ImagePlus imp)	Deprecated. Use PathProfiler(Tree, Dataset)
	PathProfiler(Tree tree, net.imagej.Dataset dataset)	Instantiates a new Profiler.
	PersistenceAnalyzer(Tree tree)	Creates a new PersistenceAnalyzer for the specified neuronal tree.
	RoiConverter(Tree tree)	Instantiates a new Converter.
	RoiConverter(Tree tree, ij.ImagePlus imp)	Instantiates a new Converter.
	RootAngleAnalyzer(Tree tree)	Constructs a RootAngleAnalyzer for the given tree.
	ShollAnalyzer(Tree tree)	Instantiates a new Sholl analyzer using default settings, i.e., focused on Tree's root; using sampling step size of average inter-node distance; curve fitting enabled; and all other parameters left to defaults/auto-discovery.
	ShollAnalyzer(Tree tree, TreeStatistics statistics)
	StrahlerAnalyzer(Tree tree)
	TreeAnalyzer(Tree tree)	Deprecated. Use TreeStatistics constructors instead
	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

Modifier	Constructor	Description
	MultiTreeColorMapper(Collection<Tree> trees)	Instantiates the MultiTreeColorMapper.
	MultiTreeStatistics(Collection<Tree> group)	Instantiates a new instance from a collection of Trees.
	MultiTreeStatistics(Collection<Tree> group, String... swcTypes)	Instantiates a new instance from a collection of Trees.

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

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

Modifier and Type	Method	Description
static CurationTags.Partition	CurationTags.partitionByReviewStatus(Tree tree)	Splits a Tree's paths into four buckets by review status: positive, negative, unsure, and unreviewed (no cur:* tag).

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

Modifier	Constructor	Description
	PlausibilityCalibrator(Collection<Tree> trees)	Creates a calibrator from a collection of reference trees.

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

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

Modifier and Type	Method	Description
static Tree	GraphUtils.createTree(org.jgrapht.Graph<SWCPoint,?> graph)	Deprecated.
Tree	DirectedWeightedGraph.getTree()	Returns a new tree associated with this graph, using the current state of the graph to build the tree.
Tree	DirectedWeightedGraph.getTree(boolean createNewTree)	Returns a tree associated with this graph.
Tree	DirectedWeightedSubgraph.getTree()	Returns the tree associated with the parent's graph
Tree	DirectedWeightedGraph.getTreeWithSamePathStructure()	Attempt to build a new Tree with the same Path hierarchy as the source Tree.

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

Modifier and Type	Method	Description
List<Tree>	AnnotationGraph.getTrees()
List<Tree>	DirectedWeightedGraph.getTrees()	Return the connected components of this graph as a list of Trees

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

Modifier and Type	Method	Description
static DirectedWeightedGraph	GraphUtils.createGraph(Tree tree)	Deprecated.

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

Modifier	Constructor	Description
	DirectedWeightedGraph(Tree tree)	Creates a DirectedWeightedGraph from a Tree with edge weights corresponding to inter-node distances.
	DirectedWeightedGraph(Tree tree, boolean assignDistancesToWeight)	Creates a DirectedWeightedGraph from a Tree, with the option to assign edge weights corresponding to inter-node distances.
	SparseDirectedWeightedGraph(Tree tree)	Builds a CSR-backed graph from a Tree.
	SparseDirectedWeightedGraph(Tree tree, boolean assignDistancesToWeight)	Builds a CSR-backed graph from a Tree, with an option to skip Euclidean edge-weight assignment.

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

Modifier	Constructor	Description
	AnnotationGraph(Collection<Tree> trees, String metric, double threshold, int maxOntologyDepth)	Constructs an annotation graph from a collection of trees using specified parameters.
	AnnotationGraph(Collection<Tree> trees, Collection<BrainAnnotation> annotations, String metric)	Constructs an annotation graph from trees and annotations using a specified metric.
	AnnotationGraph(Collection<Tree> trees, Collection<BrainAnnotation> annotations, String metric, double threshold)	Constructs an annotation graph from trees and annotations with specified parameters.

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

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

Modifier and Type	Method	Description
Tree	TreeParser.getTree()	Returns the tree associated with this parser

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

Modifier	Constructor	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	Description
static void	AllenUtils.assignAnnotationsFromNodeValues(Tree tree)	Assigns brain annotations (interpreted as CCF IDs) to node values for all paths in a Tree.
static void	AllenUtils.assignHemisphereTags(Tree tree)
static void	AllenUtils.assignToLeftHemisphere(Tree tree)	Assigns a tree to the left hemisphere by mirroring it if necessary.
static void	AllenUtils.assignToRightHemisphere(Tree tree)	Assigns a tree to the right hemisphere by mirroring it if necessary.
static String	AllenUtils.getHemisphere(Tree tree)	Checks the hemisphere a neuron belongs to.
static boolean	AllenUtils.isLeftHemisphere(Tree tree)	Checks the hemisphere a neuron belongs to.
static void	AllenUtils.transferAnnotationIdsToNodeValues(Tree tree)	Transfers brain annotation IDs to node values for all paths in a Tree.

Uses of Tree in sc.fiji.snt.gui

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

Modifier and Type	Method	Description
List<Tree>	DemoRunner.Demo.getTrees()

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

Modifier	Constructor	Description
	MeasureUI(Collection<Tree> trees)
	MeasureUI(SNT plugin, Collection<Tree> trees)

Uses of Tree in sc.fiji.snt.gui.cmds

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

Modifier and Type	Method	Description
static Object	FigCreatorCmd.render(Collection<Tree> trees, String renderOptions)	Convenience method to quickly display a collection of Trees

Uses of Tree in sc.fiji.snt.io

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

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

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

Modifier and Type	Method	Description
static List<Tree>	MouseLightLoader.demoTrees()	Returns a collection of four demo reconstructions NB: Data is cached locally.
static Map<String,Tree>	MouseLightLoader.extractTrees(File jsonFile, String compartment)	Extracts reconstruction(s) from a JSON file.
static Map<String,Tree>	MouseLightLoader.extractTrees(InputStream stream, String compartment)
Collection<Tree>	NDFImporter.getTrees()	Extracts tracings from the specified file path
Collection<Tree>	NeurolucidaImporter.getTrees()	Returns the parsed trees (one per <tree> element in the file).

Uses of Tree in sc.fiji.snt.plugin

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

Modifier and Type	Method	Description
List<Tree>	StrahlerCmd.getInvalidTrees()	Returns the Tree(s) that could not be parsed (i.e., topologically invalid)
List<Tree>	StrahlerCmd.getValidTrees()	Returns the Tree(s) successfully parsed (i.e., topologically valid)

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

Modifier and Type	Method	Description
protected void	AutotraceFromBinaryTipsCmd.handleTracedTrees(List<Tree> trees)	Intercepts the trees produced by the parent's binary-tracer flow, prunes each one to keep only the paths on a root-to-tip route, and forwards the pruned result to the parent's standard tree-handling (which adds them to the Path Manager, optionally with proofreading and color assignment, per the "After tracing" choice).
protected void	BinaryTracerCmd.handleTracedTrees(List<Tree> trees)
protected void	BinaryTracerCommonCmd.handleTracedTrees(List<Tree> trees)	Called after tracing completes with valid trees.
protected void	BinaryTracerFileCmd.handleTracedTrees(List<Tree> trees)
protected void	GWDTMultiSomaFileCmd.handleTracedTrees(List<Tree> trees)
protected void	GWDTTracerCommonCmd.handleTracedTrees(List<Tree> trees)	Called after tracing completes with valid trees.
protected void	GWDTTracerFileCmd.handleTracedTrees(List<Tree> trees)

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

Modifier	Constructor	Description
	PathOrderAnalysisCmd(Tree tree)
	RootAngleAnalyzerCmd(Tree tree)	Instantiates a new RootAngleAnalyzerCmd for a single Tree
	StrahlerCmd(Tree tree)	Instantiates a new StrahlerCmd for a single Tree

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

Modifier	Constructor	Description
	RootAngleAnalyzerCmd(Collection<Tree> trees)	Instantiates a new RootAngleAnalyzerCmd.
	StrahlerCmd(Collection<Tree> trees)	Instantiates a new StrahlerCmd.

Uses of Tree in sc.fiji.snt.tracing.auto

Methods in sc.fiji.snt.tracing.auto that return Tree

Modifier and Type	Method	Description
Tree	BinaryTracer.getSingleTree()	Generates a single Tree from BinaryTracer.getSingleGraph().
Tree	AbstractGWDTTracer.trace()	Traces the neuron and returns a Tree.
default Tree	AutoTracer.trace()	Traces the neuronal structure and returns a single merged Tree.

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

Modifier and Type	Method	Description
List<Tree>	BinaryTracer.getTrees()	Generates a list of Trees from the skeleton image.
protected List<Tree>	AbstractAutoTracer.splitAtSomaBoundary(DirectedWeightedGraph graph)	Splits a graph at the soma boundary, creating separate trees for each neurite.
List<Tree>	AbstractGWDTTracer.traceMultiSoma(List<SomaUtils.SomaResult> somas)	Traces multiple somas in a single image using a NeuTube-style recovery pass strategy.
List<Tree>	AbstractGWDTTracer.traceTrees()	Traces the neuron and returns a list of Trees.
List<Tree>	AutoTracer.traceTrees()	Traces the neuronal structure and returns a list of Trees.
List<Tree>	BinaryTracer.traceTrees()

Uses of Tree in sc.fiji.snt.util

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

Modifier and Type	Method	Description
static Tree	TreeUtils.getConnectedTree(Path path)	Gets the connected tree (component) containing the given path.
static Tree	TreeUtils.merge(Collection<Tree> trees)	Combines all trees into a single Tree container.

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

Modifier and Type	Method	Description
static List<Tree>	TreeUtils.filterByCableLength(Collection<Tree> trees, double minLength, double maxLength)	Returns the subset of trees whose cable length falls within the specified range.
static List<Tree>	TreeUtils.filterBySize(Collection<Tree> trees, int minPaths, int maxPaths)	Returns the subset of trees whose path count falls within the specified range.
static List<Tree>	TreeUtils.splitByPrimaryPaths(Tree tree)	Splits a tree with multiple primary paths into separate trees, one rooted at each primary path.

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

Modifier and Type	Method	Description
static void	TreeUtils.assignUniqueColors(Tree tree)	Assigns distinct colors to paths of a Tree.
static void	TreeUtils.assignUniqueColors(Tree tree, String excludedHue)	Assigns distinct colors to paths of a Tree.
static double	TreeUtils.computeUprightAngle(Tree tree, boolean useCentroid)	Computes the angle (in degrees) needed to make a tree appear upright in the XY viewing plane.
static int	TreeUtils.mergeContinuousPaths(Tree tree, double angleThreshold)	Merges paths that continue along the same trajectory at branch points, reducing fragmentation in auto-traced reconstructions.
static ij.ImagePlus	TreeUtils.rasterize(Tree tree)	Rasterizes a tree into a 3D image using frustum (truncated-cone) geometry with partial-volume supersampling.
static ij.ImagePlus	TreeUtils.rasterize(Tree tree, double lateralRes, double axialRes)	Rasterizes a tree into a 3D image with the specified voxel sizes.
static List<Tree>	TreeUtils.splitByPrimaryPaths(Tree tree)	Splits a tree with multiple primary paths into separate trees, one rooted at each primary path.

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

Modifier and Type	Method	Description
static void	TreeUtils.assignUniqueColors(Collection<Tree> trees)	Assigns distinct colors to a collection of Trees.
static void	TreeUtils.assignUniqueColors(Collection<Tree> trees, String excludedHue)	Assigns distinct colors to a collection of Trees.
static ij.ImagePlus	ImpUtils.combineSkeletons(Collection<Tree> trees)
static ij.ImagePlus	ImpUtils.combineSkeletons(Collection<Tree> trees, boolean asMontage)
static List<Tree>	TreeUtils.filterByCableLength(Collection<Tree> trees, double minLength, double maxLength)	Returns the subset of trees whose cable length falls within the specified range.
static List<Tree>	TreeUtils.filterBySize(Collection<Tree> trees, int minPaths, int maxPaths)	Returns the subset of trees whose path count falls within the specified range.
static Tree	TreeUtils.merge(Collection<Tree> trees)	Combines all trees into a single Tree container.

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

Modifier	Constructor	Description
	TreeToRaster(Tree tree)	Constructs a new rasterizer for the given tree.

Uses of Tree in sc.fiji.snt.viewer

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

Modifier and Type	Method	Description
Tree	Viewer3D.getTree(String label)	Gets the tree associated with the specified label.

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

Modifier and Type	Method	Description
Collection<Tree>	Bvv.getRenderedTrees()	Gets all the trees currently rendered.
List<Tree>	Viewer3D.getTrees()	Returns all trees added to this viewer.
List<Tree>	Viewer3D.getTrees(boolean visibleOnly)	Returns all trees added to this viewer.

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

Modifier and Type	Method	Description
void	Viewer2D.add(Tree tree, String color)	Appends a tree to the viewer.
void	Viewer2D.add(Tree tree, String measurement, String lut)	Appends a tree to the viewer rendered after the specified measurement.
void	Viewer2D.add(Tree tree, String measurement, String lut, double min, double max)	Appends a tree to the viewer rendered after the specified measurement.
void	Viewer2D.add(Tree tree, String measurement, net.imglib2.display.ColorTable colorTable, double min, double max)	Appends a tree to the viewer rendered after the specified measurement.
void	Viewer2D.add(Tree tree, org.scijava.util.ColorRGB color)	Appends a tree to the viewer.
void	Bvv.addTree(Tree tree)	Adds a Tree to the viewer as overlay
void	Viewer2D.addTree(Tree tree)	Deprecated. Use Viewer2D.add(Object) instead
void	Viewer3D.addTree(Tree tree)	Adds a tree to this viewer.
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	Description
void	Viewer2D.add(List<Tree> trees, String lut)	Adds a list of trees while assigning each tree to a LUT index.
void	Viewer2D.addTrees(Collection<Tree> trees)	Deprecated. use Viewer2D.add(Object) instead
void	Viewer3D.addTrees(Collection<Tree> trees, boolean assignUniqueColors)	Deprecated. use Viewer3D.addTrees(Collection, String) instead
void	Viewer3D.addTrees(Collection<Tree> trees, String color)	Adds a collection of trees.
void	Viewer3D.addTrees(Collection<Tree> trees, String color, double transparencyPercent)	Adds a collection of trees.
void	Viewer3D.addTrees(Collection<Tree> trees, String color, String... commonTags)	Adds a collection of trees.

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

Modifier	Constructor	Description
	MultiViewer2D(Collection<Tree> trees)
	MultiViewer3D(Collection<Tree> trees)	Assembles a multi-panel viewer from a list of trees (1 per panel)