Here is my function that creates the igraph instance.
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import numpy as np
import igraph as ig
def buildIGraphFromAdjCost(adj, cost, names):
"""
Build an igraph with adj, cost and names.
Parameters
----------
adj: ndarray, int
NxK array specifying the adjacency relations.
adj[i, k] is the k^th nearest neighbor of the i^th node.
Each entry of adj is an integer between 0 and N-1 (inclusive).
cost: ndarry, double
NxK array specifying the cost of each edge
cost[i, k] is the cost of the edge connecting the i^th node and
its k^th nearest neighbor (i.e., edge between i and adj[i, k])
names: node names
Returns
-------
G: igraph
An igraph instance with N nodes.
"""
N, K = adj.shape
adjInd = np.tile(np.arange(N)[:, None], (1, K))
es = np.dstack((adjInd, adj[:, :K])).reshape((N*K, 2))
# es.shape at this point is (N*K, 2)
G = ig.Graph()
G.add_vertices(names)
G.add_edges(es)
G.es['weight'] = cost.ravel()
# At this point all the nodes have a degree around 2*K
G.simplify(multiple=True, loops=True, combine_edges=dict(weight="mean"))
# Now every node has degree around K
return G
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Before calling this function, the adj and cost arrays are built from a set
of points so that adj holds the k nearest neighbors of each point and cost
holds the distances of that point to its k nearest neighbors. I ran this
code on several data sets and I am observing multiple edges between pairs
of nodes before simplifying the graph.
Thanks,
Ram
On Fri, Jul 18, 2014 at 3:47 PM, Tamás Nepusz <[email protected]> wrote:
> Hi,
>
> Show us a small, self-contained example that reproduces the issue,
> otherwise we cannot tell you what you are doing wrong.
>
> T.
>
> > On 18 Jul 2014, at 07:57, Ram MS <[email protected]> wrote:
> >
> > Hi,
> >
> > I am creating an instance of igraph in Python and adding some vertices
> and edges using add_vertices and add_edges methods of the Graph object. All
> the vertices and edges are created in one go. I have a 'name' attribute on
> the vertices and a 'weight' attribute on the edges. Strangely, I am
> observing multiple edges added between some vertices with the same weight.
> >
> > Currently I am calling graph.simplify() to remove the unwanted multiple
> edges after the graph is constructed. But I am wondering why it is creating
> multiple edges at all. Could someone help me see what might be going on?
> >
> > Thanks,
> > Ram
> >
> >
> > _______________________________________________
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> > [email protected]
> > https://lists.nongnu.org/mailman/listinfo/igraph-help
>
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