DirectedWeightedGraph (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- org.jgrapht.graph.AbstractGraph<V,E>
- - org.jgrapht.graph.AbstractBaseGraph<V,E>
  - - sc.fiji.snt.analysis.graph.SNTGraph<SWCPoint,SWCWeightedEdge>
    - - sc.fiji.snt.analysis.graph.DirectedWeightedGraph

All Implemented Interfaces:

Serializable, Cloneable, org.jgrapht.Graph<SWCPoint,SWCWeightedEdge>
```
public class DirectedWeightedGraph
extends SNTGraph<SWCPoint,SWCWeightedEdge>
```
Class for accessing a reconstruction as a graph structure.

Author:

Tiago Ferreira, Cameron Arshadi

See Also:

Serialized Form

Field Summary
- Fields inherited from interface org.jgrapht.Graph
  DEFAULT_EDGE_WEIGHT

Constructor Summary

Constructors
Constructor and Description
`DirectedWeightedGraph()` Creates an empty DirectedWeightedGraph.
`DirectedWeightedGraph(Collection<SWCPoint> nodes, boolean assignDistancesToWeight)` Creates a DirectedWeightedGraph from a collection of reconstruction nodes.
`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.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`SWCPoint`	`addVertex(double x, double y, double z)`
`void`	`assignEdgeWeightsEuclidean()` For all edges, sets the Euclidean distance between the source and target vertex as the weight.
`List<SWCPoint>`	`getBPs()` Gets the branch points (junctions) of the graph.
`org.jgrapht.traverse.BreadthFirstIterator<SWCPoint,SWCWeightedEdge>`	`getBreadthFirstIterator()` Gets a `BreadthFirstIterator`, using the graph root as start vertex.
`org.jgrapht.traverse.BreadthFirstIterator<SWCPoint,SWCWeightedEdge>`	`getBreadthFirstIterator(SWCPoint startVertex)` Gets a `BreadthFirstIterator`, using the specified start vertex.
`List<DirectedWeightedGraph>`	`getComponents()` Return the connected components of this graph as a list of new `DirectedWeightedGraph`s.
`org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>`	`getDepthFirstIterator()` Gets a `DepthFirstIterator`, using the graph root as start vertex.
`org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge>`	`getDepthFirstIterator(SWCPoint startVertex)` Gets a `DepthFirstIterator`, using the specified start vertex.
`Path`	`getLongestPath(boolean useDirected)` Return the sequence of nodes representing the longest shortest-path in the graph, as a `Path`.
`Deque<SWCPoint>`	`getLongestPathVertices(boolean useDirected)` Return the sequence of nodes representing the longest shortest-path in the graph, as a `Deque`.
`NodeStatistics<SWCPoint>`	`getNodeStatistics()` Gets a NodeStatistics instance for the vertex set
`NodeStatistics<SWCPoint>`	`getNodeStatistics(String type)` Gets a NodeStatistics instance for the nodes in the vertex set of the specified type
`SWCPoint`	`getRoot()` Gets the root of this graph.
`Path`	`getShortestPath(SWCPoint v1, SWCPoint v2)` Gets the shortest path between source and target vertex as a `Path` object.
`Deque<SWCPoint>`	`getShortestPathVertices(SWCPoint v1, SWCPoint v2)` Gets the shortest path between source and target vertex as a `Deque` of SWCPoint objects.
`DirectedWeightedGraph`	`getSimplifiedGraph()` Returns a simplified graph in which slab nodes are removed and the graph is represented only by root, branch nodes and leaves.
`DirectedWeightedSubgraph`	`getSubgraph(Set<SWCPoint> nodeSubset)` Returns the subgraph defined by the supplied subset of vertices, including their edges.
`List<SWCPoint>`	`getTips()` Gets the end points (tips) of the graph.
`Tree`	`getTree()` Returns a new tree associated with this graph, using the current state of the graph to build the tree.
`Tree`	`getTree(boolean createNewTree)` Returns a tree associated with this graph.
`List<Tree>`	`getTrees()` Return the connected components of this graph as a list of `Tree`s
`Tree`	`getTreeWithSamePathStructure()` Attempt to build a new Tree with the same `Path` hierarchy as the source Tree.
`void`	`scale(double xScale, double yScale, double zScale, boolean updateEdgeWeightsEuclidean)` Scales the point coordinates of each vertex by the specified factors.
`void`	`setRoot(SWCPoint newRoot)` Sets the root of the tree.
`Window`	`show()` Displays this graph in a new instance of SNT's "Dendrogram Viewer".
`double`	`sumEdgeWeights()` Gets the sum of all edge weights.
`void`	`updateVertexProperties()` Re-assigns a unique Integer identifier to each vertex based on visit order during Depth First Search.
`Set<SWCPoint>`	`vertexSet(char lr)` Returns the subset of vertices contained in the given hemisphere

Methods inherited from class sc.fiji.snt.analysis.graph.SNTGraph
applyEdges, applyVertices, filterEdges, filterVertices, getEdgeColor, getEdgeColorRGBMap, getVertexColor, getVertexColorRGBMap, getVertexValue, getVertexValueMap, setEdgeColor, setVertexColor, setVertexValue

Methods inherited from class org.jgrapht.graph.AbstractBaseGraph
addEdge, addEdge, addVertex, addVertex, clone, containsEdge, containsVertex, degreeOf, edgeSet, edgesOf, getAllEdges, getEdge, getEdgeSource, getEdgeSupplier, getEdgeTarget, getEdgeWeight, getType, getVertexSupplier, incomingEdgesOf, inDegreeOf, outDegreeOf, outgoingEdgesOf, removeEdge, removeEdge, removeVertex, setEdgeSupplier, setEdgeWeight, setVertexSupplier, vertexSet

Methods inherited from class org.jgrapht.graph.AbstractGraph
assertVertexExist, containsEdge, equals, hashCode, removeAllEdges, removeAllEdges, removeAllEdges, removeAllVertices, toString, toStringFromSets

Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.jgrapht.Graph
containsEdge, removeAllEdges, removeAllEdges, removeAllVertices, setEdgeWeight

- Constructor Detail
  - DirectedWeightedGraph
```
public DirectedWeightedGraph(Tree tree)
```
    Creates a DirectedWeightedGraph from a Tree with edge weights corresponding to inter-node distances.
    
    Parameters:
    
    tree - the Tree to be converted
    
    Throws:
    
    IllegalArgumentException - if Tree contains multiple roots
  - DirectedWeightedGraph
```
public DirectedWeightedGraph(Tree tree,
                             boolean assignDistancesToWeight)
```
    Creates a DirectedWeightedGraph from a Tree, with the option to assign edge weights corresponding to inter-node distances.
    
    Parameters:
    
    tree - the Tree to be converted
    
    assignDistancesToWeight - whether to assign inter-node distances between adjacent points as edge weights
    
    Throws:
    
    IllegalArgumentException - if Tree contains multiple roots
  - DirectedWeightedGraph
```
public DirectedWeightedGraph()
```
    Creates an empty DirectedWeightedGraph. Edges added to the graph are unweighted until a weight is assigned manually.
    
    See Also:
    
    assignEdgeWeightsEuclidean(), Graph.setEdgeWeight(Object, Object, double), AbstractBaseGraph.setEdgeWeight(Object, double)
  - DirectedWeightedGraph
```
public DirectedWeightedGraph(Collection<SWCPoint> nodes,
                             boolean assignDistancesToWeight)
```
    Creates a DirectedWeightedGraph from a collection of reconstruction nodes.
    
    Parameters:
    
    nodes - the collections of SWC nodes
    
    assignDistancesToWeight - if true, inter-node Euclidean distances are used as edge weights
- Method Detail
  - getSimplifiedGraph
```
public DirectedWeightedGraph getSimplifiedGraph()
```
    Returns a simplified graph in which slab nodes are removed and the graph is represented only by root, branch nodes and leaves. An edge weight in this graph corresponds to the sum of edge weights along the path between the corresponding vertices in the base graph.
    
    Returns:
    
    the simplified graph
    
    Throws:
    
    IllegalStateException - if the base graph does not have exactly one root
  - addVertex
```
public SWCPoint addVertex(double x,
                          double y,
                          double z)
```
  - assignEdgeWeightsEuclidean
```
public void assignEdgeWeightsEuclidean()
```
    For all edges, sets the Euclidean distance between the source and target vertex as the weight.
  - scale
```
public void scale(double xScale,
                  double yScale,
                  double zScale,
                  boolean updateEdgeWeightsEuclidean)
```
    Scales the point coordinates of each vertex by the specified factors.
    
    Parameters:
    
    xScale - the scaling factor for x coordinates
    
    yScale - the scaling factor for y coordinates
    
    zScale - the scaling factor for z coordinates
    
    updateEdgeWeightsEuclidean - if true, update all edge weights with inter-node Euclidean distances
  - sumEdgeWeights
```
public double sumEdgeWeights()
```
    Gets the sum of all edge weights.
    
    Returns:
    
    the sum of all edge weights
  - getDepthFirstIterator
```
public org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge> getDepthFirstIterator()
```
    Gets a DepthFirstIterator, using the graph root as start vertex.
    
    Returns:
    
    the DepthFirstIterator
    
    Throws:
    
    IllegalStateException - if the graph does not have exactly one root
  - getDepthFirstIterator
```
public org.jgrapht.traverse.DepthFirstIterator<SWCPoint,SWCWeightedEdge> getDepthFirstIterator(SWCPoint startVertex)
```
    Gets a DepthFirstIterator, using the specified start vertex.
    
    Parameters:
    
    startVertex - the start vertex
    
    Returns:
    
    the DepthFirstIterator
  - getBreadthFirstIterator
```
public org.jgrapht.traverse.BreadthFirstIterator<SWCPoint,SWCWeightedEdge> getBreadthFirstIterator()
```
    Gets a BreadthFirstIterator, using the graph root as start vertex.
    
    Returns:
    
    the BreadthFirstIterator
    
    Throws:
    
    IllegalStateException - if the graph does not have exactly one root
  - getBreadthFirstIterator
```
public org.jgrapht.traverse.BreadthFirstIterator<SWCPoint,SWCWeightedEdge> getBreadthFirstIterator(SWCPoint startVertex)
```
    Gets a BreadthFirstIterator, using the specified start vertex.
    
    Parameters:
    
    startVertex - the start vertex
    
    Returns:
    
    the BreadthFirstIterator
  - getLongestPath
```
public Path getLongestPath(boolean useDirected)
```
    Return the sequence of nodes representing the longest shortest-path in the graph, as a Path.
    
    Parameters:
    
    useDirected - whether to treat the graph as directed. If true, the longest shortest-path will always include the root and a terminal node.
    
    Returns:
    
    the longest shortest-path
    
    Throws:
    
    IllegalStateException - if the graph does not have exactly one root
  - getLongestPathVertices
```
public Deque<SWCPoint> getLongestPathVertices(boolean useDirected)
```
    Return the sequence of nodes representing the longest shortest-path in the graph, as a Deque. This eliminates the computational overhead of converting the vertex sequence to a Path object, if a Path is not desired.
    
    Parameters:
    
    useDirected - whether to treat the graph as directed. If true, the longest shortest-path will always include the root and a terminal node.
    
    Returns:
    
    the longest shortest-path
    
    Throws:
    
    IllegalStateException - if the graph does not have exactly one root
  - getShortestPath
```
public Path getShortestPath(SWCPoint v1,
                            SWCPoint v2)
```
    Gets the shortest path between source and target vertex as a Path object. Since underlying edge direction is ignored, a shortest path will always exist between any two vertices that share a connected component.
    
    Parameters:
    
    v1 - the source vertex
    
    v2 - the target vertex
    
    Returns:
    
    the shortest Path between source v1 and target v2, or null if no path exists
    
    Throws:
    
    IllegalArgumentException - if the graph does not contain both v1 and v2
  - getShortestPathVertices
```
public Deque<SWCPoint> getShortestPathVertices(SWCPoint v1,
                                               SWCPoint v2)
```
    Gets the shortest path between source and target vertex as a Deque of SWCPoint objects. This eliminates the computational overhead of creating a Path object from the vertex sequence, if a Path is not desired. Since underlying edge direction is ignored, a shortest path will always exist between any two vertices that share a connected component.
    
    Parameters:
    
    v1 - the source vertex
    
    v2 - the target vertex
    
    Returns:
    
    the shortest path between source v1 and target v2, or null if no path exists
    
    Throws:
    
    IllegalArgumentException - if the graph does not contain both v1 and v2
  - updateVertexProperties
```
public void updateVertexProperties()
```
    Re-assigns a unique Integer identifier to each vertex based on visit order during Depth First Search. Also updates the parent and previousPoint fields of each SWCPoint vertex contained in the Graph.
    
    Throws:
    
    IllegalStateException - if the graph does not contain exactly one root
  - getBPs
```
public List<SWCPoint> getBPs()
```
    Gets the branch points (junctions) of the graph.
    
    Returns:
    
    the list of branch points
  - getTips
```
public List<SWCPoint> getTips()
```
    Gets the end points (tips) of the graph.
    
    Returns:
    
    the list of end points
  - getNodeStatistics
```
public NodeStatistics<SWCPoint> getNodeStatistics()
```
    Gets a NodeStatistics instance for the vertex set
    
    Returns:
    
    the NodeStatistics instance
  - getNodeStatistics
```
public NodeStatistics<SWCPoint> getNodeStatistics(String type)
```
    Gets a NodeStatistics instance for the nodes in the vertex set of the specified type
    
    Parameters:
    
    type - the vertex type (e.g., "tips"/"end-points", "junctions"/"branch points", "all")
    
    Returns:
    
    the NodeStatistics instance
  - getRoot
```
public SWCPoint getRoot()
```
    Gets the root of this graph.
    
    Returns:
    
    the root node.
    
    Throws:
    
    IllegalStateException - if the graph does not contain exactly one root
  - getTree
```
public Tree getTree()
```
    Returns a new tree associated with this graph, using the current state of the graph to build the tree.
    
    Returns:
    
    the tree
    
    Throws:
    
    IllegalStateException - if the graph does not have exactly one root
  - getTree
```
public Tree getTree(boolean createNewTree)
```
    Returns a tree associated with this graph.
    
    Parameters:
    
    createNewTree - If true, reassembles a tree from this graph's data. If false, returns the cached tree if it exists or null if it does not exist
    
    Returns:
    
    the tree
  - getTreeWithSamePathStructure
```
public Tree getTreeWithSamePathStructure()
```
    Attempt to build a new Tree with the same Path hierarchy as the source Tree.
    
    Returns:
    
    the tree
  - getComponents
```
public List<DirectedWeightedGraph> getComponents()
```
    Return the connected components of this graph as a list of new DirectedWeightedGraphs.
    
    Returns:
    
    the list of DirectedWeightedGraph objects
  - getTrees
```
public List<Tree> getTrees()
```
    Return the connected components of this graph as a list of Trees
    
    Returns:
    
    the list of Tree objects
  - getSubgraph
```
public DirectedWeightedSubgraph getSubgraph(Set<SWCPoint> nodeSubset)
```
    Returns the subgraph defined by the supplied subset of vertices, including their edges.
    
    Parameters:
    
    nodeSubset - a subset of this graph's vertex set
    
    Returns:
    
    the subgraph
  - vertexSet
```
public Set<SWCPoint> vertexSet(char lr)
```
    Returns the subset of vertices contained in the given hemisphere
    
    Parameters:
    
    lr - the hemisphere (i.e., BrainAnnotation.LEFT_HEMISPHERE, BrainAnnotation.RIGHT_HEMISPHERE ,BrainAnnotation.ANY_HEMISPHERE
    
    Returns:
    
    the vertex subset
  - setRoot
```
public void setRoot(SWCPoint newRoot)
```
    Sets the root of the tree. This modifies the edge directions such that all other nodes in the graph have the new root as ancestor.
    
    Parameters:
    
    newRoot - the new root of the tree, which must be an existing vertex of the graph
    
    Throws:
    
    IllegalArgumentException - if the graph does not contain newRoot
  - show
```
public Window show()
```
    Displays this graph in a new instance of SNT's "Dendrogram Viewer".
    
    Returns:
    
    a reference to the displayed window.
    
    Throws:
    
    IllegalStateException - if the graph does not have exactly one root

Class DirectedWeightedGraph

Field Summary

Fields inherited from interface org.jgrapht.Graph

Constructor Summary

Method Summary

Methods inherited from class sc.fiji.snt.analysis.graph.SNTGraph

Methods inherited from class org.jgrapht.graph.AbstractBaseGraph

Methods inherited from class org.jgrapht.graph.AbstractGraph

Methods inherited from class java.lang.Object

Methods inherited from interface org.jgrapht.Graph

Constructor Detail

DirectedWeightedGraph

DirectedWeightedGraph

DirectedWeightedGraph

DirectedWeightedGraph

Method Detail

getSimplifiedGraph

addVertex

assignEdgeWeightsEuclidean

scale

sumEdgeWeights

getDepthFirstIterator

getDepthFirstIterator

getBreadthFirstIterator

getBreadthFirstIterator

getLongestPath

getLongestPathVertices

getShortestPath

getShortestPathVertices

updateVertexProperties

getBPs

getTips

getNodeStatistics

getNodeStatistics

getRoot

getTree

getTree

getTreeWithSamePathStructure

getComponents

getTrees

getSubgraph

vertexSet

setRoot

show