使用networkx创建邻接矩阵时遇到麻烦

Question

在this question的答案中，有代码创建带有一定数量节点的所有树。

问题是，我尝试使用networkx nx.to_numpy_array中的内置函数创建相应的邻接矩阵，但由于某种原因它不起作用，因此代码如下：

#Function created by warped

import itertools
import numpy as np
import networkx as nx
import matplotlib.pyplot as plt 

def make_all_trees(nodes):
    # generate all pairwise combinations of nodes
    edges =  [a for a in itertools.product(range(nodes), range(nodes))]

    # use sets to lose..
    # ..symmetric edges: (0,1), (1,0) => keep only (0,1) 
    edges = list(set([tuple(set(e)) for e in edges]))
    # ..and self-loops: (0,0)
    edges = [e for e in edges if len(e)>1]

    trees = []
    # generate all graphs that have nodes-1 edges
    for o in itertools.combinations(edges, nodes-1):
        #make sure that all nodes are in the edgelist:
        flattened = [item for sublist in o for item in sublist]

        if len(set(flattened)) == nodes:
            G = nx.Graph()
            G.add_edges_from(o)
            # make sure all nodes are connected
            if len(list(nx.connected_components(G)))==1:
                trees.append(G)

    return trees

#This is what I added it to create the corresponding adjacency matrix

trees = make_all_trees(3) #This create all the graph trees with 3 nodes, so it creates 3 trees

adjaux = []
for i in trees:
    adjaux.append(nx.to_numpy_array(i))

print(np.array(adjaux))

#Draws the graph
for p, tree in enumerate(trees):
    plt.subplot(4,4, p+1)
    nx.draw_networkx(tree)
plt.show()

输出如下

#Adjacency matrix created 

adjaux = [[[0. 1. 0.]   [[0. 1. 1.]     [[0. 1. 0.] 
           [1. 0. 1.]    [1. 0. 0.]      [1. 0. 1.]
           [0. 1. 0.]]   [1. 0. 0.]]     [0. 1. 0.]]]

您可以看到，尽管所有树图都是正确的，并且前两个邻接矩阵是正确的，最后一个是不正确的，输出应该是：

adjaux = [[[0. 1. 0.]   [[0. 1. 1.]     [[0. 0. 1.] 
           [1. 0. 1.]    [1. 0. 0.]      [0. 0. 1.]
           [0. 1. 0.]]   [1. 0. 0.]]     [1. 1. 0.]]]

我试图逐步重新创建代码，但是我看不到什么以及为什么它不起作用，一切似乎都很好，因此，任何帮助将不胜感激，谢谢！

Answer 1

nx.to_numpy_array的文档：

[...] 节点列表（列表，可选）–行和列按以下顺序排序 到节点列表中的节点。如果nodelist为None，则排序为 由G.nodes（）产生。 [...]

检查图形的顺序：

trees = make_all_trees(3)
for tree in trees:
    print(tree.nodes())

#output:
[0, 1, 2] # first tree
[0, 1, 2] # second tree
[1, 2, 0] # third tree, node order is changed

因此，邻接矩阵在所有情况下都是正确的（图形显示正确，因此边缘必须正确记录），但是顺序混乱。您需要在nodelist参数中明确指定节点的顺序：

adjaux=[]
for tree in trees:
    adjaux.append(nx.to_numpy_array(tree, nodelist=sorted(tree.nodes())))

for a in adjaux:
    print('-'*10)
    print(a)

----------
[[0. 1. 0.]
 [1. 0. 1.]
 [0. 1. 0.]]
----------
[[0. 1. 1.]
 [1. 0. 0.]
 [1. 0. 0.]]
----------
[[0. 0. 1.]
 [0. 0. 1.]
 [1. 1. 0.]]