Re: [graph-tool] efficiency of graph creation

27 Apr 2015

      I solved this once by making a NoDupesGraph where you could add edges with
just the names of vertices .

class NoDupesGraph(Graph):
    '''Add nodes without worrying if it is a duplicate.
       Add edges without worrying if nodes exist   '''

    def __init__(self,*args,**kwargs):
        Graph.__init__(self,*args,**kwargs)
        self._nodes = {}

    def add_nodupe_vertex(self,label,*args,**kwargs):
      '''Return a node with label. Create node if label is new'''
      try:
          n = self._nodes[label]
      except KeyError:
          n = self.add_vertex()
          self._nodes[label]=n
      return n

    def add_nodupe_edge(self, n1_label, n2_label,directed=False):
      """
      Get or create edges using get_or_create_node
      """
      #there may be two if graph is directed but edge isn't
      edges = []

      n1 = self.add_nodupe_vertex(n1_label)
      n2 = self.add_nodupe_vertex(n2_label)
      edges.append(self.add_edge(n1,n2))
      if self.is_directed() and not directed:
          edges.append(self.add_edge(n2,n1))
      return edges

    def flush_empty_nodes(self):
        '''not implemented'''
        pass

    def condense_edges(self):
        '''if a node connects to only two edges, combine those
        edges and delete the node.

        not implemented
        '''
        pass

This could be easily modified to suit your need.

On Mon, Apr 27, 2015 at 3:23 PM, Krister <thekswenson@gmail.com> wrote:
...
Thanks for the quick response Thiago!
In this code all the edges and vertices are created by graph-tool and the
result is something much faster...
   is this the best I can do?
It's somewhat annoying to have to keep track of the vertices that will be
created like this:
def graph_tool_create_all_at_once():
  """ Create a graph_tool graph given a list of pairs. """
  G = Graph(directed=False)
  objectTOi = {}
  vertexpairs = []
  counter = 0
  for o1,o2 in get_pairs_of_ints():
    if(o1 in objectTOi):
      u = objectTOi[o1]
    else:
      u = counter
      counter += 1
      objectTOi[o1] = u
    if(o2 in objectTOi):
      v = objectTOi[o2]
    else:
      v = counter
      counter += 1
      objectTOi[o2] = v
vertexpairs.append((u,v))
G.add_edge_list(vertexpairs)
On 27 April 2015 at 16:39, Tiago de Paula Peixoto <tiago@skewed.de> wrote:
...
On 27.04.2015 14:29, thekswenson wrote:
...
I've been using networkx to simply create a graph and check the
connected
components.  The bottleneck of the operation is the creation of the
edges.
I've heard that graph-tool is very efficient so I've replaces the code
with
a graph-tool graph.
To my surprise, the creation of a graph-tool graph is MUCH slower than
that
of a networkx graph.
Am I doing something wrong?
How does the performance change if you create the necessary edges
beforehand?
In graph-tool things are faster than in networkx when they are delegated
to C++, otherwise this should be comparable in speed. In the case of
adding many edges, this is done by using the Graph.add_edge_list()
function, which runs in C++ internally. In your example, this should
provide a massive speed-up.
Best,
Tiago
--
Tiago de Paula Peixoto <tiago@skewed.de>
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