| 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.util |
Miscellaneous SNT utilities, including classes defining reconstruction nodes.
|
| sc.fiji.snt.viewer.geditor |
| Modifier and Type | Method and Description |
|---|---|
List<SWCPoint> |
Tree.getNodesAsSWCPoints() |
List<SWCPoint> |
PathAndFillManager.getSWCFor(Collection<Path> paths) |
List<SWCPoint> |
PathAndFillManager.getSWCForOld(Collection<Path> paths)
Gets the list of SWCPoints associated with a collection of Paths.
|
| Modifier and Type | Method and 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) |
Map<String,Tree> |
PathAndFillManager.importNeurons(Map<String,TreeSet<SWCPoint>> map,
ColorRGB color,
String spatialUnit)
Import neuron(s) as a collection of reconstruction nodes (SWC points)
|
| Constructor and Description |
|---|
Tree(Collection<SWCPoint> nodes,
String label)
Instantiates a Tree from a collection of reconstruction nodes.
|
| Modifier and Type | Method and Description |
|---|---|
ArrayList<ArrayList<SWCPoint>> |
PersistenceAnalyzer.getDiagramNodes(String descriptor)
Gets the persistence diagram nodes.
|
protected Map<Integer,List<SWCPoint>> |
StrahlerAnalyzer.getNodes() |
NodeStatistics<SWCPoint> |
TreeStatistics.getNodeStatistics() |
NodeStatistics<SWCPoint> |
TreeStatistics.getNodeStatistics(String type) |
| Modifier and Type | Method and Description |
|---|---|
SWCPoint |
DirectedWeightedGraph.addVertex(double x,
double y,
double z) |
SWCPoint |
DirectedWeightedSubgraph.getRoot()
Gets the root of this graph.
|
SWCPoint |
DirectedWeightedGraph.getRoot()
Gets the root of this graph.
|
SWCPoint |
SWCWeightedEdge.getSource() |
SWCPoint |
SWCWeightedEdge.getTarget() |
| Modifier and Type | Method and Description |
|---|---|
List<SWCPoint> |
DirectedWeightedSubgraph.getBPs()
Gets the branch points (junctions) of the graph.
|
List<SWCPoint> |
DirectedWeightedGraph.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> |
DirectedWeightedSubgraph.getDepthFirstIterator() |
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge> |
DirectedWeightedGraph.getDepthFirstIterator()
Gets a
DepthFirstIterator, using the graph root as start vertex. |
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge> |
DirectedWeightedSubgraph.getDepthFirstIterator(SWCPoint startVertex) |
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge> |
DirectedWeightedGraph.getDepthFirstIterator(SWCPoint startVertex)
Gets a
DepthFirstIterator, using the specified start vertex. |
Deque<SWCPoint> |
DirectedWeightedGraph.getLongestPathVertices(boolean useDirected)
Return the sequence of nodes representing the
longest shortest-path
in the graph, as a
Deque. |
NodeStatistics<SWCPoint> |
DirectedWeightedGraph.getNodeStatistics()
Gets a NodeStatistics instance for the vertex set
|
NodeStatistics<SWCPoint> |
DirectedWeightedSubgraph.getNodeStatistics(String type) |
NodeStatistics<SWCPoint> |
DirectedWeightedGraph.getNodeStatistics(String type)
Gets a NodeStatistics instance for the nodes in the vertex set of the specified 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> |
DirectedWeightedSubgraph.getTips()
Gets the end points (tips) of the subgraph.
|
List<SWCPoint> |
DirectedWeightedGraph.getTips()
Gets the end points (tips) of the graph.
|
Set<SWCPoint> |
DirectedWeightedGraph.vertexSet(char lr)
Returns the subset of vertices contained in the given hemisphere
|
| Modifier and Type | Method and 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> |
DirectedWeightedSubgraph.getDepthFirstIterator(SWCPoint startVertex) |
org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge> |
DirectedWeightedGraph.getDepthFirstIterator(SWCPoint startVertex)
Gets a
DepthFirstIterator, using the specified start vertex. |
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.
|
| Modifier and Type | Method and 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.
|
| Constructor and Description |
|---|
DirectedWeightedGraph(Collection<SWCPoint> nodes,
boolean assignDistancesToWeight)
Creates a DirectedWeightedGraph from a collection of reconstruction nodes.
|
DirectedWeightedSubgraph(DirectedWeightedGraph graph,
Set<SWCPoint> nodeSubset)
Creates a subgraph from a sub-set of nodes.
|
| Modifier and Type | Method and Description |
|---|---|
SWCPoint |
MouseLightLoader.getSomaLocation() |
| Modifier and Type | Method and 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.
|
| Modifier and Type | Method and Description |
|---|---|
SWCPoint |
SWCPoint.getPreviousPoint()
Returns the preceding node (if any)
|
| Modifier and Type | Method and Description |
|---|---|
List<SWCPoint> |
SWCPoint.getNextPoints()
Returns the list holding the subsequent nodes in the reconstructed structure
after this one.
|
| Modifier and Type | Method and Description |
|---|---|
int |
SWCPoint.compareTo(SWCPoint o) |
void |
SWCPoint.setPreviousPoint(SWCPoint previousPoint)
Sets the preceding node in the reconstruction
|
| Modifier and Type | Method and 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. |
| Modifier and Type | Method and Description |
|---|---|
void |
TreeGraphAdapter.setVertexColor(SWCPoint vertex,
ColorRGB color) |
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