Uses of Class
sc.fiji.snt.util.SWCPoint

Packages that use SWCPoint

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.io	Classes for importing reconstructions into SNT.
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.geditor	Classes implementing SNT's Graph Viewer

Uses of SWCPoint in sc.fiji.snt

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

Modifier and Type	Method	Description
List<SWCPoint>	Tree.getBPs()	Gets the branch points (junctions) of the graph.
List<SWCPoint>	Tree.getNodesAsSWCPoints()
List<SWCPoint>	PathAndFillManager.getSWCFor(Collection<Path> paths)	Converts a collection of connected Path objects into SWC points for export.
List<SWCPoint>	Tree.getTips()	Gets the end points (tips) of the graph.

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

Modifier and Type	Method	Description
static PathAndFillManager	PathAndFillManager.createFromNodes(Collection<SWCPoint> nodes)	Creates a PathAndFillManager instance from a collection of reconstruction nodes.
protected void	PathAndFillManager.flushSWCPoints(List<SWCPoint> swcPoints, PrintWriter pw, String commonFileHeader)
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)

Constructor parameters in sc.fiji.snt with type arguments of type SWCPoint

Modifier	Constructor	Description
	Tree(Collection<SWCPoint> nodes, String label)	Instantiates a Tree from a collection of reconstruction nodes.

Uses of SWCPoint in sc.fiji.snt.analysis

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

Modifier and Type	Method	Description
List<List<SWCPoint>>	PersistenceAnalyzer.getDiagramNodes(String descriptor)	Gets the tree nodes associated with each point in the persistence diagram.
protected Map<Integer,List<SWCPoint>>	StrahlerAnalyzer.getNodes()
NodeStatistics<SWCPoint>	TreeStatistics.getNodeStatistics()	Convenience method to initialize a NodeStatistics from all the nodes of the Tree being analyzed.
NodeStatistics<SWCPoint>	TreeStatistics.getNodeStatistics(String type)	Convenience method to initialize a NodeStatistics from a subset of the nodes of the Tree being analyzed.

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

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

Modifier and Type	Method	Description
SWCPoint	DirectedWeightedGraph.addVertex(double x, double y, double z)
SWCPoint	DirectedWeightedGraph.getRoot()	Gets the root of this graph.
SWCPoint	DirectedWeightedSubgraph.getRoot()	Gets the root of this graph.
SWCPoint	SWCWeightedEdge.getSource()
SWCPoint	SWCWeightedEdge.getTarget()

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

Modifier and Type	Method	Description
List<SWCPoint>	DirectedWeightedGraph.getBPs()	Gets the branch points (junctions) of the graph.
List<SWCPoint>	DirectedWeightedSubgraph.getBPs()	Gets the branch points (junctions) of the graph.
org.jgrapht.traverse.BreadthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedGraph.getBreadthFirstIterator()	Gets a BreadthFirstIterator, using the graph root as start vertex.
org.jgrapht.traverse.BreadthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedGraph.getBreadthFirstIterator(SWCPoint startVertex)	Gets a BreadthFirstIterator, using the specified start vertex.
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedGraph.getDepthFirstIterator()	Gets a DepthFirstIterator, using the graph root as start vertex.
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedGraph.getDepthFirstIterator(SWCPoint startVertex)	Gets a DepthFirstIterator, using the specified start vertex.
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedSubgraph.getDepthFirstIterator()
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedSubgraph.getDepthFirstIterator(SWCPoint startVertex)
Deque<SWCPoint>	DirectedWeightedGraph.getLongestPathVertices(boolean useDirected)	Return the sequence of nodes representing the longest shortest-path in the graph, as a Deque.
List<SWCPoint>	DirectedWeightedGraph.getNodesFromLeavesToRoot()
List<SWCPoint>	DirectedWeightedGraph.getNodesFromRootToLeaves()
NodeStatistics<SWCPoint>	DirectedWeightedGraph.getNodeStatistics()	Gets a NodeStatistics instance for the vertex set
NodeStatistics<SWCPoint>	DirectedWeightedGraph.getNodeStatistics(String type)	Gets a NodeStatistics instance for the nodes in the vertex set of the specified type
NodeStatistics<SWCPoint>	DirectedWeightedSubgraph.getNodeStatistics(String type)
Deque<SWCPoint>	DirectedWeightedGraph.getShortestPathVertices(SWCPoint v1, SWCPoint v2)	Gets the shortest path between source and target vertex as a Deque of SWCPoint objects.
List<SWCPoint>	DirectedWeightedGraph.getTips()	Gets the end points (tips) of the graph.
List<SWCPoint>	DirectedWeightedSubgraph.getTips()	Gets the end points (tips) of the subgraph.
org.jgrapht.traverse.TopologicalOrderIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedGraph.getTopologicalOrderIterator()	Gets a TopologicalOrderIterator for this graph.
Set<SWCPoint>	DirectedWeightedGraph.vertexSet(char lr)	Returns the subset of vertices contained in the given hemisphere

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

Modifier and Type	Method	Description
org.jgrapht.traverse.BreadthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedGraph.getBreadthFirstIterator(SWCPoint startVertex)	Gets a BreadthFirstIterator, using the specified start vertex.
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedGraph.getDepthFirstIterator(SWCPoint startVertex)	Gets a DepthFirstIterator, using the specified start vertex.
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>	DirectedWeightedSubgraph.getDepthFirstIterator(SWCPoint startVertex)
Path	DirectedWeightedGraph.getShortestPath(SWCPoint v1, SWCPoint v2)	Gets the shortest path between source and target vertex as a Path object.
Deque<SWCPoint>	DirectedWeightedGraph.getShortestPathVertices(SWCPoint v1, SWCPoint v2)	Gets the shortest path between source and target vertex as a Deque of SWCPoint objects.
void	DirectedWeightedGraph.setRoot(SWCPoint newRoot)	Sets the root of the tree.
void	DirectedWeightedSubgraph.setRoot(SWCPoint newRoot)	Sets the root of the tree.

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

Modifier and Type	Method	Description
static DirectedWeightedGraph	GraphUtils.createGraph(Collection<SWCPoint> nodes, boolean assignDistancesToWeights)	Deprecated.
static Tree	GraphUtils.createTree(org.jgrapht.Graph<SWCPoint,?> graph)	Deprecated.
DirectedWeightedSubgraph	DirectedWeightedGraph.getSubgraph(Set<SWCPoint> nodeSubset)	Returns the subgraph defined by the supplied subset of vertices, including their edges.
protected void	DirectedWeightedGraph.init(Collection<SWCPoint> nodes, boolean assignDistancesToWeights)

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

Modifier	Constructor	Description
	DirectedWeightedGraph(Collection<SWCPoint> nodes, boolean assignDistancesToWeight)	Creates a DirectedWeightedGraph from a collection of reconstruction nodes.
protected	DirectedWeightedGraph(Supplier<SWCPoint> vertexSupplier, Supplier<SWCWeightedEdge> edgeSupplier, org.jgrapht.GraphType type, org.jgrapht.graph.GraphSpecificsStrategy<SWCPoint,SWCWeightedEdge> specificsStrategy)	Subclass hook for installing a custom GraphSpecificsStrategy.
protected	DirectedWeightedGraph(Supplier<SWCPoint> vertexSupplier, Supplier<SWCWeightedEdge> edgeSupplier, org.jgrapht.GraphType type, org.jgrapht.graph.GraphSpecificsStrategy<SWCPoint,SWCWeightedEdge> specificsStrategy)	Subclass hook for installing a custom GraphSpecificsStrategy.
protected	DirectedWeightedSubgraph(DirectedWeightedGraph graph, Set<SWCPoint> nodeSubset)	Creates a subgraph from a sub-set of nodes.
	SparseDirectedWeightedGraph(Collection<SWCPoint> nodes, boolean assignDistancesToWeight)	Builds a CSR-backed graph from a collection of SWC nodes.

Uses of SWCPoint in sc.fiji.snt.io

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

Modifier and Type	Method	Description
SWCPoint	MouseLightLoader.getSomaLocation()	Gets the soma location for this neuron.

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

Modifier and Type	Method	Description
static Map<String,TreeSet<SWCPoint>>	MouseLightLoader.extractNodes(File jsonFile, String compartment)	Extracts reconstruction(s) from a JSON file.
static Map<String,TreeSet<SWCPoint>>	MouseLightLoader.extractNodes(InputStream stream, String compartment)
TreeSet<SWCPoint>	MouseLightLoader.getNodes()	Extracts the nodes (single-point soma, axonal and dendritic arbor) of the loaded neuron.
TreeSet<SWCPoint>	MouseLightLoader.getNodes(String compartment)	Script-friendly method to extract the nodes of a cellular compartment.

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

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

Modifier and Type	Method	Description
protected SWCPoint	AbstractAutoTracer.findGraphRoot(DirectedWeightedGraph graph)	Finds the root node of a graph.

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

Modifier and Type	Method	Description
protected double[]	AbstractGWDTTracer.computeIntensityWeightedJointCoverage(SWCPoint node, net.imglib2.RandomAccess<net.imglib2.type.numeric.integer.UnsignedShortType> countRA, net.imglib2.RandomAccess<? extends net.imglib2.type.numeric.RealType<?>> srcRA)	Computes INTENSITY-WEIGHTED joint coverage fraction (like APP2).
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 boolean	AbstractAutoTracer.isInsideSomaRoi(SWCPoint point)	Checks if a point is inside the soma ROI.
protected void	AbstractGWDTTracer.nodeToVoxelPos(SWCPoint node, long[] pos)	Converts an SWCPoint's physical coordinates to voxel position.
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).

Method parameters in sc.fiji.snt.tracing.auto with type arguments of type SWCPoint

Modifier and Type	Method	Description
protected double	AbstractAutoTracer.computeAverageRadius(Set<SWCPoint> nodes)	Computes average radius of a set of nodes.

Uses of SWCPoint in sc.fiji.snt.util

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

Modifier and Type	Method	Description
SWCPoint	SWCPoint.previous()	Returns the preceding node (if any)

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

Modifier and Type	Method	Description
List<SWCPoint>	SWCPoint.getNextPoints()	Returns the list holding the subsequent nodes in the reconstructed structure after this one.

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

Modifier and Type	Method	Description
int	SWCPoint.compareTo(SWCPoint o)
void	SWCPoint.setPrevious(SWCPoint previousNode)	Sets the preceding node in the reconstruction

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

Modifier and Type	Method	Description
static StringReader	SWCPoint.collectionAsReader(Collection<SWCPoint> points)	Converts a collection of SWC points into a Reader.
static void	SWCPoint.flush(Collection<SWCPoint> points, PrintWriter pw)	Prints a list of points as space-separated values.
void	BoundingBox.inferSpacing(Collection<SWCPoint> points)	Infers the voxel spacing of this box from the inter-node distances of a Collection of SWCPoints.

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

Methods in sc.fiji.snt.viewer.geditor with parameters of type SWCPoint

Modifier and Type	Method	Description
void	TreeGraphAdapter.setVertexColor(SWCPoint vertex, org.scijava.util.ColorRGB color)