python graph-tool access vertex properties

Question

For my current project I want to use the graph-tool library since they claim being the fastest: https://graph-tool.skewed.de/performance. I have some algorithms (shortest path, etc.) to run on really large networks, so the faster the better!

First question: Is this claim 'being the fastest' true? ;)

While trying to build a graph-tool graph fitting my needs, I figured out that its not possible to access vertex properties in a efficient way. Maybe I missed something?

My question is now, can the function "getVertexFromGraph(graph, position)" be written in a more efficient way? Or more in general: Can I check efficiently if a vertex (given by its position property) is already in the graph or not.

Thanks in advance!

import graph_tool as gt
#from graph_tool.all import *

edgeList = [[(0.5,1),(2.1,4.3)],[(2.1,4.3),(5.4,3.3)],[(5.4,3.3),(1.3,3.5)],[(4.4,3.3),(2.3,3.5)]] #A lot more coordinate values....

# Initialize the graph
routableNetwork = gt.Graph()

# Initialize the vertex property "position" to store the vertex coordinates
vpPosition = routableNetwork.new_vertex_property("vector<double>")
routableNetwork.vertex_properties["position"] = vpPosition

def getVertexFromGraph(graph, position):
    """
    This method checks if a vertex, identified by its position, is in the given graph or not.
    :param graph:       The graph containing all vertices to check  
    :param position:    The vertex/position to check
    :return:            The ID of the vertex if the vertex is already in the graph, 'None' otherwise
    """
    for v in graph.vertices():
        if graph.vp.position[v] == position:
            return v
    return None

def main():
    """
    This method creates the graph by looping over all given edges, inserting every: 
        - non existent vertex in the graph with its coordinates (property 'position')  
        - edge with its corresponding length (property 'distance')
    :return: -
    """
    for e in edgeList:
        vertex0 = getVertexFromGraph(routableNetwork,e[0])
        vertex1 = getVertexFromGraph(routableNetwork,e[1])
        if vertex0 == None:
            vertex0 = routableNetwork.add_vertex()
            routableNetwork.vertex_properties['position'][vertex0] = e[0]
        if vertex1 == None:
            vertex1 = routableNetwork.add_vertex()
            routableNetwork.vertex_properties['position'][vertex1] = e[1]

        edge = routableNetwork.add_edge(vertex0,vertex1)
        #routableNetwork.edge_properties['distance'][edge] = calculateDistance(e[0][0],e[0][1],e[1][0],e[1][1])

    #saveRoutableNetwork(routableNetwork)
    #graph_draw(routableNetwork, vertex_text=routableNetwork.vertex_index, vertex_font_size=18, output_size=(200, 200), output="two-nodes.png")

if __name__ == "__main__":
    main()

Answer 1

The function you are looking for is find_vertex():

https://graph-tool.skewed.de/static/doc/util.html#graph_tool.util.find_vertex

It is important to realize that graph-tool achieves its speed by off-loading performance-sensitive loops from Python to C++. So whenever you iterate through the vertices, like you did in your code, you lose any advantage.

Note also that, although find_vertex() is implemented in C++, and hence many times faster than the equivalent in pure Python, it is still an O(N) operation. For large graphs, you are better off creating a good old python dictionary that maps property values to vertices, which has an O(1) cost for lookup.