I need to make an adjacency metrics
I have the edges information.
edges = numpy.array([[0,1],[0,3],[1,2],[1,4],[2,5],[3,4],[3,5],[4,5]])
I need a python code to generate the adjacency metrics using NumPy only from the edges information. Can someone help?
It depends what type of adjacency matrix you want, but here's an example with 0 for not connected and 1 for connected, rows are from and columns are to.
import numpy
edges = numpy.array([[0,1],[0,3],[1,2],[1,4],[2,5],[3,4],[3,5],[4,5]])
matrix = numpy.zeros((edges.max()+1, edges.max()+1))
matrix[edges[:,0], edges[:,1]] = 1
gives
array([[0., 1., 0., 1., 0., 0.],
[0., 0., 1., 0., 1., 0.],
[0., 0., 0., 0., 0., 1.],
[0., 0., 0., 0., 1., 1.],
[0., 0., 0., 0., 0., 1.],
[0., 0., 0., 0., 0., 0.]])
If you want the connections to be bidirectional (ie. 0->1 also connects 1->0), then add another line of code to do the reverse connection.
import numpy
edges = numpy.array([[0,1],[0,3],[1,2],[1,4],[2,5],[3,4],[3,5],[4,5]])
matrix = numpy.zeros((edges.max()+1, edges.max()+1))
matrix[edges[:,0], edges[:,1]] = 1
matrix[edges[:,1], edges[:,0]] = 1
gives
array([[0., 1., 0., 1., 0., 0.],
[1., 0., 1., 0., 1., 0.],
[0., 1., 0., 0., 0., 1.],
[1., 0., 0., 0., 1., 1.],
[0., 1., 0., 1., 0., 1.],
[0., 0., 1., 1., 1., 0.]])
The easiest way to get the job done would be using the NetworkX package (if you are allowed to).
In [72]: import networkx as nx
In [73]: edges = [[0, 1], [0, 3], [1, 2], [1, 4], [2, 5], [3, 4], [3, 5], [4, 5]]
In [74]: nodes = sorted(set(node for edge in edges for node in edge))
In [75]: G = nx.Graph()
In [76]: G.add_nodes_from(nodes)
In [77]: G.add_edges_from(edges)
In [78]: A = nx.adjacency_matrix(G)
In [79]: A.toarray()
Out[79]:
array([[0, 1, 0, 1, 0, 0],
[1, 0, 1, 0, 1, 0],
[0, 1, 0, 0, 0, 1],
[1, 0, 0, 0, 1, 1],
[0, 1, 0, 1, 0, 1],
[0, 0, 1, 1, 1, 0]], dtype=int32)
