Commit fd63f857 authored by Kelvin Rodriguez's avatar Kelvin Rodriguez
Browse files

Merge pull request #86 from jlaura/master 

Fixes subgraphs from node lists and add subgraph extract from edge lists
parents 501db9d2 302d3fdb

autocnet/graph/network.py

+78 −22
Original line number Diff line number Diff line
@@ -40,8 +40,6 @@ class CandidateGraph(nx.Graph): 
    ----------

    """







    def __init__(self, *args, basepath=None, **kwargs):

        super(CandidateGraph, self).__init__(*args, **kwargs)

        self.node_counter = 0
@@ -66,7 +64,6 @@ class CandidateGraph(nx.Graph): 
        for s, d, edge in self.edges_iter(data=True):

            self.edge[s][d] = Edge(self.node[s], self.node[d])





    @classmethod

    def from_graph(cls, graph):

        """
@@ -85,7 +82,6 @@ class CandidateGraph(nx.Graph): 
            graph = pickle.load(f)

        return graph





    @classmethod

    def from_filelist(cls, filelist, basepath=None):

        """
@@ -609,7 +605,7 @@ class CandidateGraph(nx.Graph): 
        with open(filename, 'wb') as f:

            pickle.dump(self, f, protocol=pickle.HIGHEST_PROTOCOL)



    def plot(self, ax=None, **kwargs):

    def plot(self, ax=None, **kwargs): # pragma: no cover

        """

        Plot the graph object
@@ -625,20 +621,80 @@ class CandidateGraph(nx.Graph): 
        """

        return plot_graph(self, ax=ax,  **kwargs)



    @singledispatch

    def create_subgraph(self, arg, key=None):

        if not hasattr(self, 'clusters'):

            raise AttributeError('No clusters have been computed for this graph.')

        nodes_in_cluster = self.clusters[arg]

        edges_in_cluster = [(u,v) for u,v in self.edges() if u in nodes_in_cluster and v in nodes_in_cluster]

        subgraph = self.subgraph(edges_in_cluster)

        return subgraph



    @create_subgraph.register(pd.DataFrame)

    def _(self, arg, g, key=None):

        if key == None:

            return

        col = arg[key]

        nodes = col[col == True].index

        subgraph = g.subgraph(nodes)

        return subgraph
 
    def create_edge_subgraph(self, edges):

        """

        Create a subgraph using a list of edges.

        This is pulled directly from the networkx dev branch.



        Parameters

        ----------

        edges : list

                A list of edges in the form [(a,b), (c,d)] to retain

                in the subgraph



        Returns

        -------

        H : object

            A networkx subgraph object

        """

        H = self.__class__()

        adj = self.adj

        # Filter out edges that don't correspond to nodes in the graph.

        edges = ((u, v) for u, v in edges if u in adj and v in adj[u])

        for u, v in edges:

            # Copy the node attributes if they haven't been copied

            # already.

            if u not in H.node:

                H.node[u] = self.node[u]

            if v not in H.node:

                H.node[v] = self.node[v]

            # Create an entry in the adjacency dictionary for the

            # nodes u and v if they don't exist yet.

            if u not in H.adj:

                H.adj[u] = H.adjlist_dict_factory()

            if v not in H.adj:

                H.adj[v] = H.adjlist_dict_factory()

            # Copy the edge attributes.

            H.edge[u][v] = self.edge[u][v]

            H.edge[v][u] = self.edge[v][u]

        H.graph = self.graph

        return H



    def create_node_subgraph(self, nodes):

        """

        Given a list of nodes, create a sub-graph and

        copy both the node and edge attributes to the subgraph.

        Changes to node/edge attributes are propagated back to the

        parent graph, while changes to the graph structure, i.e.,

        the topology, are not.



        Parameters

        ----------

        nodes : iterable

                An iterable (list, set, ndarray) of nodes to subset

                the graph



        Returns

        -------

        H : object

            A networkX graph object



        """

        bunch = set(self.nbunch_iter(nodes))

        # create new graph and copy subgraph into it

        H = self.__class__()

        # copy node and attribute dictionaries

        for n in bunch:

            H.node[n] = self.node[n]

        # namespace shortcuts for speed

        H_adj = H.adj

        self_adj = self.adj

        for i in H.node:

            adj_nodes = set(self.adj[i].keys()).intersection(bunch)

            H.adj[i] = {}

            for j, edge in self.adj[i].items():

                if j in adj_nodes:

                    H.adj[i][j] = edge



        H.graph = self.graph

        return H

autocnet/graph/tests/test_network.py

+6 −1
Original line number Diff line number Diff line
@@ -97,7 +97,6 @@ class TestCandidateGraph(unittest.TestCase): 
                os.remove(i)

            except: pass





    def test_fromlist(self):

        mock_list = ['AS15-M-0295_SML.png', 'AS15-M-0296_SML.png', 'AS15-M-0297_SML.png',

                     'AS15-M-0298_SML.png', 'AS15-M-0299_SML.png', 'AS15-M-0300_SML.png']
@@ -107,7 +106,13 @@ class TestCandidateGraph(unittest.TestCase): 
        n = network.CandidateGraph.from_filelist(get_path('adjacency.lis'), get_path('Apollo15'))

        self.assertEqual(len(n.nodes()), 6)



    def test_subset_graph(self):

        g = self.graph

        edge_sub = g.create_edge_subgraph([(0,2)])

        self.assertEqual(len(edge_sub.nodes()), 2)



        node_sub = g.create_node_subgraph([0,1])

        self.assertEqual(len(node_sub), 2)



    def tearDown(self):

        pass