Graphs

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The aim of the graphs package is to provides functions to easily create, modify and display geometric graphs (geometric in a sense position nodes are associated to geometric position in 2D or 3D).

Data Representation

Graph structure is represented by at least two arrays:

  • NODES, which contains coordinates of each vertex
  • EDGES, which contains indices of start and end vertex.

Others arrays may sometimes be used:

  • FACES, which contains indices of vertices of each face (either a double array, or a cell array)
  • CELLS, which contains indices of faces of each cell.

An alternative representation is to use a structure, with fields:

  • 'nodes'
  • 'edges'

corresponding to the data described above.

Note that topological description of 2D graph is entirely contained in EDGES array, and that NODES array is used only to display the graph.

Caution: this type of data structure is easy to create and to manage, but may be very inefficient for some algorithms.

Graphs are usually considered as non-oriented in this package.

Function List

Graph creation

  • knnGraph - Create the k-nearest neighbors graph of a set of points
  • delaunayGraph - Graph associated to Delaunay triangulation of input points
  • gabrielGraph - Gabriel Graph of a set of points
  • euclideanMST - Build euclidean minimal spanning tree of a set of points
  • prim_mst - Minimal spanning tree by Prim's algorithm

Create graph from images

  • imageGraph - Create equivalent graph of a binary image
  • boundaryGraph - Get boundary of image as a graph
  • gcontour2d - Creates contour graph of a 2D binary image.
  • gcontour3d - Create contour graph of a 3D binary image.

Graph information

  • grNodeDegree - Degree of a node in a (undirected) graph
  • grNodeInnerDegree - Inner degree of a node in a graph
  • grNodeOuterDegree - Outer degree of a node in a graph
  • grAdjacentNodes - Find list of nodes adjacent to a given node
  • grAdjacentEdges - Find list of edges adjacent to a given node
  • grOppositeNode - Return opposite node in an edge
  • grLabel - Associate a label to each connected component of the graph

Graph management (low level operations)

  • grRemoveNode - Remove a node in a graph
  • grRemoveNodes - Remove several nodes in a graph
  • grRemoveEdge - Remove an edge in a graph.
  • grRemoveEdges - Remove several edges from a graph

Graph processing (general applications)

  • mergeGraphs - Merge two graphs, by adding nodes, edges and faces lists.
  • grMergeNodes - Merge two (or more) nodes in a graph.
  • grMergeMultipleNodes - Simplify a graph by merging multiple nodes
  • grMergeMultipleEdges - Remove all edges sharing the same extremities
  • grSimplifyBranches - Replace branches of a graph by single edges

Filtering operations on Graph

  • grMean - Compute mean from neihgbours
  • grMedian - Compute median from neihgbours
  • grDilate - Morphological dilation on graph
  • grErode - Morphological erosion on graph
  • grClose - Morphological closing on graph
  • grOpen - Morphological opening on graph

Geodesic and shortest path operations

  • grShortestPath - Find a shortest path between two nodes in the graph
  • grPropagateDistance - Propagates distances from a vertex to other vertices
  • grVertexEccentricity - Eccentricity of vertices in the graph
  • graphDiameter - Diameter of a graph
  • graphPeripheralVertices - Peripheral vertices of a graph
  • graphCenter - Center of a graph
  • graphRadius - Radius of a graph
  • grFindGeodesicPath - Find a geodesic path between two nodes in the graph
  • grFindMaximalLengthPath - Find a path that maximizes sum of edge weights

Operations for geometric graphs

  • grEdgeLengths - Compute length of edges in a geometric graph
  • grMergeNodeClusters - Merge cluster of connected nodes in a graph
  • grMergeNodesMedian - Replace several nodes by their median coordinate
  • clipGraph - Clip a graph with a rectangular area
  • clipGraphPolygon - Clip a graph with a polygon
  • addSquareFace - Add a (square) face defined from its vertices to a graph
  • grFaceToPolygon - Compute the polygon corresponding to a graph face
  • graph2Contours - Convert a graph to a set of contour curves

Voronoi Graphs

  • voronoi2d - Compute a voronoi diagram as a graph structure
  • boundedVoronoi2d - Return a bounded voronoi diagram as a graph structure
  • centroidalVoronoi2d - Centroidal Voronoi tesselation within a polygon
  • boundedCentroidalVoronoi2d - Create a 2D Centroidal Voronoi Tesselation in a box
  • cvtUpdate - Update germs of a CVT with given points
  • cvtIterate - Update germs of a CVT using random points with given density

Graph display

  • drawGraph - Draw a graph, given as a set of vertices and edges
  • drawGraphEdges - Draw edges of a graph
  • drawGraphFaces - Draw faces of a graph
  • drawDigraph - Draw a directed graph, given as a set of vertices and edges
  • drawDirectedEdges - Draw edges with arrow indicating direction
  • drawEdgeLabels - Draw values associated to graph edges
  • drawNodeLabels - Draw values associated to graph nodes
  • drawSquareMesh - Draw a 3D square mesh given as a graph
  • patchGraph - Transform 3D graph (mesh) into a patch handle

Input/Output

  • readGraph - Read a graph from a text file
  • writeGraph - Write a graph to an ascii file