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 <[email protected]> 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 <[email protected]> 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 <[email protected]>
>>
>>
>> _______________________________________________
>> graph-tool mailing list
>> [email protected]
>> http://lists.skewed.de/mailman/listinfo/graph-tool
>>
>>
>
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>
>
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