python - 使用NetworkX将图形导出到带有节点位置的graphml

我正在使用NetworkX 1.9.1。

我有一个需要按位置组织的图形，然后将其导出为graphml格式。

我已经在this question中尝试过代码。它不起作用，这是我的例子

import networkx as nx
import matplotlib.pyplot as plt

G = nx.read_graphml("colored.graphml")

pos=nx.spring_layout(G) # an example of quick positioning
nx.set_node_attributes(G, 'pos', pos)

nx.write_graphml(G, "g.graphml")

nx.draw_networkx(G, pos)
plt.savefig("g.pdf")

这是我遇到的错误，问题是位置的保存方式（graphml不接受数组）。

C:\Anaconda\python.exe C:/Users/sturaroa/Documents/PycharmProjects/node_labeling_test.py
Traceback (most recent call last):
  File "C:/Users/sturaroa/Documents/PycharmProjects/node_labeling_test.py", line 11, in <module>
    nx.write_graphml(G, "g.graphml")
  File "<string>", line 2, in write_graphml
  File "C:\Anaconda\lib\site-packages\networkx\utils\decorators.py", line 220, in _open_file
    result = func(*new_args, **kwargs)
  File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 82, in write_graphml
    writer.add_graph_element(G)
  File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 350, in add_graph_element
    self.add_nodes(G,graph_element)
  File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 307, in add_nodes
    self.add_attributes("node", node_element, data, default)
  File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 300, in add_attributes
    scope=scope, default=default_value)
  File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 288, in add_data
    '%s as data values.'%element_type)
networkx.exception.NetworkXError: GraphML writer does not support <type 'numpy.ndarray'> as data values.

我的印象是，最好将位置定义为2个单独的节点属性x和y，然后分别保存它们，并以graphml格式like this为其定义一个键。

但是，我对Python不太熟悉，在我来回弄乱之前，请先征求您的意见。

谢谢。

最佳答案

没错，GraphML想要更简单的属性（没有numpy数组或列表）。

您可以将节点的x和y位置设置为这样的属性

G = nx.path_graph(4)
pos = nx.spring_layout(G)

for node,(x,y) in pos.items():
    G.node[node]['x'] = float(x)
    G.node[node]['y'] = float(y)

nx.write_graphml(G, "g.graphml")