Python example

other/pythonExample/README.md

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+# Working from Python Example
+
+
+### :warning: ALPHA: Package under construction (pre-release) :warning:
+Until I add tests, I make no guarantees as to the suitability of this code.
+
+While working from R meets the workflow of many people if you have a large
+amount of existing python code, or simply feel more productive working from
+python, then using these network comparison tools can be difficult.
+
+In the example file in this directory, we have included a simple way of calling the NetEMD code from python. 
+
+It should be noted that it is not fast (as data has to be passed between the
+runtimes), nor is it memory efficient as there are duplicate versions of data.
+However, for networks with a relatively small of nodes, it is a simple and
+relatively pain-free way of experimenting with this code. 
+
+To run this code the following python packages are required:
+
+* networkx - A python network library
+* numpy -  Python matrix and array library
+* rpy2 -  A library which allows R functions to be called from inside of python.
+
+Note: If you are using python 2.7, then you cannot install the current version
+of rpy2 as it is python 3 only, however the final version that is python 2.7
+compatible will be fine.

other/pythonExample/example.py

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+import numpy as np
+import networkx as nx
+import rpy2.robjects.numpy2ri
+rpy2.robjects.numpy2ri.activate()
+from rpy2 import robjects
+from rpy2.robjects.packages import importr
+import rpy2.robjects.numpy2ri
+orca=importr("orca")
+igraph = importr('igraph')
+netdist =importr('netdist')
+graphConstructor=rpy2.robjects.r['graph.adjacency']
+
+def makeRgdd(G):
+    B=nx.to_numpy_matrix(G)
+    B=np.array(B)
+    nr,nc = B.shape
+    Br = robjects.r.matrix(B, nrow=nr, ncol=nc)
+    Gr=graphConstructor(Br,mode ="undirected")
+    Ggdd=netdist.gdd(Gr)
+    return Ggdd
+
+G1=nx.Graph()
+G1.add_edges_from([[0,1],[1,2],[2,3]])
+G1gdd=makeRgdd(G1)
+
+
+G2=nx.Graph()
+G2.add_edges_from([[0,1],[1,2],[2,3],[3,4]])
+G2gdd=makeRgdd(G2)
+
+print netdist.net_emd(G1gdd,G1gdd)
+print netdist.net_emd(G2gdd,G2gdd)
+print netdist.net_emd(G1gdd,G2gdd)