Uses of Class
sc.fiji.snt.analysis.graph.DirectedWeightedGraph

Packages that use DirectedWeightedGraph

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.annotation	Classes handling neuropil annotations and atlases metadata.
sc.fiji.snt.tracing.auto	Automatic neuron tracing algorithms that reconstruct complete neuronal morphologies from images without user interaction.
sc.fiji.snt.tracing.auto.gwdt	Storage backends for the Gray-Weighted Distance Transform (GWDT) tracing algorithm.
sc.fiji.snt.viewer.geditor	Classes implementing SNT's Graph Viewer

Uses of DirectedWeightedGraph in sc.fiji.snt

Methods in sc.fiji.snt that return DirectedWeightedGraph

Modifier and Type	Method	Description
DirectedWeightedGraph	Tree.getGraph()	Assembles a DirectedGraph from this Tree.
DirectedWeightedGraph	Tree.getGraph(boolean simplify)	Assembles a DirectedGraph from this Tree.

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

Modifier and Type	Method	Description
static PathAndFillManager	PathAndFillManager.createFromGraph(DirectedWeightedGraph graph, boolean keepTreePathStructure)	Create a new PathAndFillManager instance from the graph.
protected void	PathAndFillManager.importGraph(DirectedWeightedGraph graph)
protected void	PathAndFillManager.importGraphWithPathStructure(DirectedWeightedGraph graph)
void	SNTService.loadGraph(DirectedWeightedGraph graph)

Constructors in sc.fiji.snt with parameters of type DirectedWeightedGraph

Modifier	Constructor	Description
	Tree(DirectedWeightedGraph graph, String label)	Instantiates a new Tree from a DirectedWeightedGraph with the specified label.
	Tree(DirectedWeightedGraph graph, String label, boolean keepTreePathStructure)	Instantiates a new Tree from a DirectedWeightedGraph with control over path structure preservation.

Uses of DirectedWeightedGraph in sc.fiji.snt.analysis

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

Modifier and Type	Method	Description
DirectedWeightedGraph	StrahlerAnalyzer.getGraph()
DirectedWeightedGraph	RootAngleAnalyzer.getTaggedGraph()

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

Modifier and Type	Method	Description
static void	StrahlerAnalyzer.classify(DirectedWeightedGraph graph, boolean reverseOrder)
protected static Map<BrainAnnotation,Double>	TreeStatistics.getAnnotatedLength(DirectedWeightedGraph graph, int level, char lr, boolean norm)
protected static Map<BrainAnnotation,double[]>	TreeStatistics.getAnnotatedLengthsByHemisphere(DirectedWeightedGraph graph, int level, boolean norm)

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

Subclasses of DirectedWeightedGraph in sc.fiji.snt.analysis.graph

Modifier and Type	Class	Description
class	SparseDirectedWeightedGraph	Memory-efficient variant of DirectedWeightedGraph backed by a compressed sparse-row (CSR) adjacency representation (CsrDirectedSpecifics).

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

Modifier and Type	Method	Description
static DirectedWeightedGraph	GraphUtils.createGraph(Collection<SWCPoint> nodes, boolean assignDistancesToWeights)	Deprecated.
static DirectedWeightedGraph	GraphUtils.createGraph(Tree tree)	Deprecated.
DirectedWeightedGraph	DirectedWeightedGraph.getSimplifiedGraph()	Returns a simplified graph in which slab nodes are removed and the graph is represented only by root, branch nodes and leaves.
static DirectedWeightedGraph	GraphUtils.getSimplifiedGraph(DirectedWeightedGraph graph)	Deprecated.

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

Modifier and Type	Method	Description
List<DirectedWeightedGraph>	DirectedWeightedGraph.getComponents()	Return the connected components of this graph as a list of new DirectedWeightedGraphs.

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

Modifier and Type	Method	Description
static DirectedWeightedGraph	GraphUtils.getSimplifiedGraph(DirectedWeightedGraph graph)	Deprecated.
static Window	GraphUtils.show(DirectedWeightedGraph graph)	Displays a graph in SNT's "Dendrogram Viewer" featuring UI commands for interactive visualization and export options.

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

Modifier	Constructor	Description
protected	DirectedWeightedSubgraph(DirectedWeightedGraph graph, Set<SWCPoint> nodeSubset)	Creates a subgraph from a sub-set of nodes.

Uses of DirectedWeightedGraph in sc.fiji.snt.annotation

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

Modifier and Type	Method	Description
static void	AllenUtils.assignHemisphereTags(DirectedWeightedGraph graph)	Assigns hemisphere tags to all nodes in a graph.
static List<DirectedWeightedSubgraph>	AllenUtils.splitByHemisphere(DirectedWeightedGraph graph)

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

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

Modifier and Type	Method	Description
DirectedWeightedGraph	BinaryTracer.getSingleGraph()	Generates a single DirectedWeightedGraphs by combining BinaryTracer.getGraphs()'s list into a single, combined graph.
abstract DirectedWeightedGraph	AbstractAutoTracer.traceToGraph()	Traces the structure and returns a DirectedWeightedGraph.
DirectedWeightedGraph	AbstractGWDTTracer.traceToGraph()

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

Modifier and Type	Method	Description
List<DirectedWeightedGraph>	BinaryTracer.getGraphs()	Generates a list of DirectedWeightedGraphs from the skeleton image.

Methods in sc.fiji.snt.tracing.auto with parameters of type DirectedWeightedGraph

Modifier and Type	Method	Description
protected void	AbstractAutoTracer.collapseSomaNodes(DirectedWeightedGraph graph, double cx, double cy, double cz)	Core method to collapse soma nodes to a centroid.
protected void	AbstractAutoTracer.collapseSomaToRoiCentroid(DirectedWeightedGraph graph)	Collapses all soma nodes to the geometric ROI centroid.
protected void	AbstractAutoTracer.collapseSomaToWeightedCentroid(DirectedWeightedGraph graph)	Collapses all soma nodes to their weighted centroid.
protected void	AbstractGWDTTracer.computeAndApplyScoreMap(DirectedWeightedGraph graph)	Computes or applies a score map and stamps each graph node's PointInImage.v with its score.
protected void	AbstractGWDTTracer.darkNodeAndSegmentPruning(DirectedWeightedGraph graph, double effectiveThreshold)	APP2-style dark node and segment pruning.
int	ComponentReconnector.extendTips(DirectedWeightedGraph graph, SWCPoint root, double backgroundThreshold)	Extends leaf tips of the tree across multi-voxel gaps by scanning for bright signal in each leaf's tangent direction and A*-bridging to it.
protected SWCPoint	AbstractAutoTracer.findGraphRoot(DirectedWeightedGraph graph)	Finds the root node of a graph.
protected void	AbstractGWDTTracer.hierarchicalPrune(DirectedWeightedGraph graph, double effectiveThreshold)	Performs hierarchical pruning using intensity-weighted coverage.
protected void	AbstractGWDTTracer.pruneParallelBranches(DirectedWeightedGraph graph)	Prunes parallel sibling branches, i.e., pairs of terminal branches that fork from the same branch point and then run alongside each other (their nodes stay within a radius-dependent proximity threshold).
protected void	AbstractGWDTTracer.recalculateRadiiFromImage(DirectedWeightedGraph graph, double effectiveThreshold)	Recalculates radii for all nodes using image-based method (like APP2).
int	ComponentReconnector.reconnect(DirectedWeightedGraph graph, SWCPoint root, double backgroundThreshold)	Attempts to reconnect disconnected components in the graph back to the main tree (the component containing the root).
protected void	AbstractAutoTracer.removeDisconnectedComponents(DirectedWeightedGraph graph)	Removes all vertices not connected to the root.
protected void	AbstractGWDTTracer.removeOvershoots(DirectedWeightedGraph graph)	Removes overshoot artifacts from the graph.
protected void	AbstractGWDTTracer.removeZigzags(DirectedWeightedGraph graph)	Removes zigzag artifacts from the graph.
protected void	AbstractGWDTTracer.resampleCurve(DirectedWeightedGraph graph, double stepSize)	Resamples the curve to have evenly spaced points.
protected void	AbstractGWDTTracer.smoothCurve(DirectedWeightedGraph graph, int windowSize)	Smooths the final curve using a moving average filter.
protected List<Tree>	AbstractAutoTracer.splitAtSomaBoundary(DirectedWeightedGraph graph)	Splits a graph at the soma boundary, creating separate trees for each neurite.
protected void	AbstractGWDTTracer.tuneBranches(DirectedWeightedGraph graph, double cosThreshold)	Tunes branch-point topology by re-parenting nodes adjacent to bifurcations.

Uses of DirectedWeightedGraph in sc.fiji.snt.tracing.auto.gwdt

Methods in sc.fiji.snt.tracing.auto.gwdt that return DirectedWeightedGraph

Modifier and Type	Method	Description
DirectedWeightedGraph	ArrayStorageBackend.buildGraph(long[] dims, double[] spacing, double threshold)
DirectedWeightedGraph	DiskBackedStorageBackend.buildGraph(long[] dims, double[] spacing, double threshold)
DirectedWeightedGraph	SparseStorageBackend.buildGraph(long[] dims, double[] spacing, double threshold)
DirectedWeightedGraph	StorageBackend.buildGraph(long[] dims, double[] spacing, double threshold)	Build graph from computed Fast Marching data.

Uses of DirectedWeightedGraph in sc.fiji.snt.viewer.geditor

Constructors in sc.fiji.snt.viewer.geditor with parameters of type DirectedWeightedGraph

Modifier	Constructor	Description
	TreeGraphAdapter(DirectedWeightedGraph graph)
protected	TreeGraphAdapter(DirectedWeightedGraph graph, String verticesColor)