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 = {}

'''Return a node with label. Create node if label is new'''
try:
n = self._nodes[label]
except KeyError:
self._nodes[label]=n
return n

"""
Get or create edges using get_or_create_node
"""
#there may be two if graph is directed but edge isn't
edges = []

if self.is_directed() and not directed:
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 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))

On 27 April 2015 at 16:39, Tiago de Paula Peixoto 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
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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