updating networkx from_numpy_{matrix,array}

Author: TheChymera

nipype/interfaces/cmtk/cmtk.py

@@ -264,7 +264,7 @@ def cmat(
         )
         intersection_matrix = np.matrix(intersection_matrix)
         I = G.copy()
-        H = nx.from_numpy_matrix(np.matrix(intersection_matrix))
+        H = nx.from_numpy_array(np.matrix(intersection_matrix))
         H = nx.relabel_nodes(H, lambda x: x + 1)  # relabel nodes so they start at 1
         I.add_weighted_edges_from(
             ((u, v, d["weight"]) for u, v, d in H.edges(data=True))

nipype/interfaces/cmtk/nbs.py

@@ -150,8 +150,8 @@ def _run_interface(self, runtime):
             pADJ[x, y] = PVAL[idx]
 
         # Create networkx graphs from the adjacency matrix
-        nbsgraph = nx.from_numpy_matrix(ADJ)
-        nbs_pval_graph = nx.from_numpy_matrix(pADJ)
+        nbsgraph = nx.from_numpy_array(ADJ)
+        nbs_pval_graph = nx.from_numpy_array(pADJ)
 
         # Relabel nodes because they should not start at zero for our convention
         nbsgraph = nx.relabel_nodes(nbsgraph, lambda x: x + 1)

nipype/interfaces/cmtk/tests/test_nbs.py

@@ -18,7 +18,7 @@ def creating_graphs(tmpdir):
     graphnames = ["name" + str(i) for i in range(6)]
     for idx, name in enumerate(graphnames):
         graph = np.random.rand(10, 10)
-        G = nx.from_numpy_matrix(graph)
+        G = nx.from_numpy_array(graph)
         out_file = tmpdir.strpath + graphnames[idx] + ".pck"
         # Save as pck file
         with open(out_file, 'wb') as f: