添加节点和边时出现错误的 Networkx [英] Networkx with errors from adding nodes and edges

问题描述

这是一个生成网络图的简单python程序.当我将数据放入程序时一切正常，但是当我决定将数据放入两个输入文件时，事情开始变得有趣了.有两个输入文件:节点(或顶点)和边.当我从名为Step3-Vertices.txt"的输入文件中读取节点信息时，它没有给出任何错误，但我没有提供的节点中添加了额外的信息.以下是附加信息列表:'[', '{', "'", '0', '2', ',', ' ', '6', '8', 'W', '}', '.','1', '5', '3', '7', '4', 'O', 'X', 'D', ']', '\n'

This is a simple python program to generate a network graph. Everything was fine when I placed the data inside the program but when I decided to place the data in two input files, things started to get interesting. There are two input files: nodes (or vertices) and edges. When I read the nodes information from the input files called 'Step3-Vertices.txt', it did not give any error but additional information were added to the nodes which I did not supply. Here is a list of additional information : '[', '{', "'", '0', '2', ',', ' ', '6', '8', 'W', '}', '.', '1', '5', '3', '7', '4', 'O', 'X', 'D', ']', '\n'

然后我读入了名为Step3-Edges.txt"的第二个文件，这次我得到了一个我无法理解的错误消息列表.

I then read in the 2nd file called 'Step3-Edges.txt', this time I got a list of error messages which I could not comprehend.

错误消息 - 从文件中添加边缘信息时 NETWORKX 失败:

ERROR MESSAGES - NETWORKX FAILED WHEN EDGES INFORMATION ARE ADDED FROM FILE :

Traceback (most recent call last):
File "step4_test1.py", line 30, in <module>
G.add_edges_from(data_edges)
File "/home/desmond/anaconda3/lib/python3.6/site-packages/networkx/classes/graph.py", line 934, in add_edges_from
"Edge tuple %s must be a 2-tuple or 3-tuple." % (e,))
networkx.exception.NetworkXError: Edge tuple [ must be a 2-tuple or 3-tuple.

有人可以帮我吗?

这是我的程序:

""" THIS PROGRAM WORKS PROPERLY WHEN DATA ARE PASSED TO LOCAL VARIABLES CALLED "nodes" and "edges".  THE EXACT DATA ARE ALSO STORED IN TWO FILES: "nodes" in 'Step3-Vertices.txt' and "edges" in 'Step3-Edges.txt'.  PROBLEMS STARTED WHEN NODES AND EDGES ARE READ FROM BOTH FILES.  FIRST, RUN THIS PROGRAM AND IT SHOULD GENERATE A GRAPH.  THEN REPLACE THE "nodes" with "data_nodes" in "G.add_nodes_from" AND THIS WILL GENERATE UNEXPECTED ADDITIONAL NODES WHICH ARE NOT SUPPOSED TO BE THERE.  NEXT, REPLACE THE "edges" with "data_edges" in "G.add_nodes_from" AND ERROR MESSAGES ARE DISPLAYED."""  


import networkx as nx
import matplotlib.pyplot as plt



""" READ NODES INFORMATION FROM FILE """

with open('Step3-Vertices.txt', encoding='utf-8') as data_file:
    data_nodes = data_file.read()

print(data_nodes)

""" READ EDGESS INFORMATION FROM FILE """


with open('Step3-Edges.txt', encoding='utf-8') as data_file:
    data_edges = data_file.read()

print(data_edges)


G=nx.Graph()

"""  PASS NODES INFORMATION TO A VARIABLE CALLED 'nodes'   """

nodes = ['0000000002', '0000000101', '0000000111', '0000000200', '0000000502', '0000000600', '0000001000', '0000001001', '0000001069', '0000001253', '0000001462', '0000003013', '0000003200', '0000004100', '0000004305', '0000005100', '0000005460', '0000006600', '0000010021', '0000010101', '0000010200', '0000010314', '0000012000', '0000012151', '0000012600', '0000015201', '0000016100', '0000017002', '0000020002', '0000020050', '0000020100', '0000021001', '0000022044', '0000022100']


""" PASS EDGES INFORMATION TO A VARIABLE CALLED 'edges'   """

edges = [{'0000000002', '6080022W'}, {'80.015.012.210', '0000000002'}, {'80.015.012.210', '0000000502'}, {'0000012000', '0000000502'},{'0000000101', '012.105.123.127'}, {'0000000111', '2442032O'}, {'105.103.02.110', '0000000111'}, {'0604054X', '0000000200'}, {'100.001.008.002', '0000000200'}, {'0000000502', '1002567D'}, {'208.08.032.1', '0000000502'}]

"""THIS IS WHERE YOU ADD DATA TO THE NODES AND EDGES, BY DEFAULT, LOCAL VARIABLES ARE USED. TO ADD DATA FROM THE INPUT FILES - replace 'nodes' with 'data_nodes' and replace 'edges' with 'data_edges'   """




G.add_nodes_from(nodes)
G.add_edges_from(edges)

print("Nodes of graph: ")
print(G.nodes())


print("Edges of graph: ")
print(G.edges())

###  DRAW A GRAPH  ###

nx.draw(G)
plt.savefig("test1.png") # save as png
plt.show() # display

推荐答案

add_edges_from 是一个元组列表，其最基本的形式是要连接的 (u,v) 对列表.

The format expected by add_edges_from is a list of tuples, in its most basic form, as a list of (u,v) pairs to connect.

您的文件没有适当形式的数据，因此 networkx 不知道如何处理它们.如果文本与您在edges"变量中所写的完全相同，那么下面是一种将其添加到正确类型列表中的方法.你可以对节点处理做类似的事情，尽管这只需要一个元素列表，而不是一个元组列表，所以更简单.

Your files don't have the data in an appropriate form so networkx doesn't know what to do with them. If the text is exactly as you wrote in the "edges" variable, then below is one way to massage it into the right kind of list. You can do similar for the node processing, though this only needs a list of elements, not a list of tuples so is more straightforward.

with open("edgefile.txt") as data_file:
    data_edges = data_file.read()

# split on the comma, assuming this divides elements, remove the curly braces and quotes
elems = ([f.strip(" {}'") for f in data_edges.strip().split(',')])
# use zip to turn the flat list into a lst of pairs
edge_list = zip(elems[::2], elems[1::2])

# now we are in a form that nx.add_edges_from can handle
G = nx.Graph()
G.add_nodes_from(nodes)
G.add_edges_from(edge_list)

您应该在这里阅读有关阅读图表的文档:https://networkx.github.io/documentation/stable/reference/readwrite/index.html

You should read the docs on reading in graphs here: https://networkx.github.io/documentation/stable/reference/readwrite/index.html

描述了如何读取各种标准图形格式.

which describes how to read from various standard graph formats.

编辑在评论中跟随曲:

图中有许多意外"节点的原因是 nx.add_nodes_from 采用可迭代类型，当您将整个文件读入文本变量时，迭代该字符串一次需要一个字符.这会生成单字符节点，如 0、' 和 \n.因此，我们可以通过将字符串解析为列表来修复它，并遍历列表给出一个元素，例如 '0000000002'.

The reason that you have many "unexpected" nodes in the graph is because nx.add_nodes_from takes an iterable type, and when you read the whole file into a text variable, iterating over that string takes one character at at time. This produces the single-character nodes like 0, ', and \n. So we can fix it by parsing the string into a list, and iterating over a list gives one element, like '0000000002'.

这是一个例子:

# assume that the file describing nodes is read into this string:
node_txt = "'0000000002', '0000000101', '0000000111', '0000000200', '0000000502', '0000000600', '0000001000', '0000001001', '0000001069', '0000001253', '0000001462', '0000003013', '0000003200', '0000004100', '0000004305', '0000005100', '0000005460', '0000006600', '0000010021', '0000010101', '0000010200', '0000010314', '0000012000', '0000012151', '0000012600', '0000015201', '0000016100', '0000017002', '0000020002', '0000020050', '0000020100', '0000021001', '0000022044', '0000022100'\n"

G1 = nx.Graph()
G1.add_nodes_from(node_txt)
print(G1.nodes())
print(set(node_txt))
# output of these two commands shows that the node names are 1 char each:
>>> [' ', "'", '\n', ',', '1', '0', '3', '2', '5', '4', '7', '6', '9']
>>> set([' ', "'", '\n', ',', '1', '0', '3', '2', '5', '4', '7', '6', '9'])

# reference: what we really wanted    
node_list = ['0000000002', '0000000101', '0000000111', '0000000200', '0000000502', '0000000600', '0000001000', '0000001001', '0000001069', '0000001253', '0000001462', '0000003013', '0000003200', '0000004100', '0000004305', '0000005100', '0000005460', '0000006600', '0000010021', '0000010101', '0000010200', '0000010314', '0000012000', '0000012151', '0000012600', '0000015201', '0000016100', '0000017002', '0000020002', '0000020050', '0000020100', '0000021001', '0000022044', '0000022100']

G2  = nx.Graph()
G2.add_nodes_from(node_list)
print(G2.nodes())
print(set(node_list))

那么如何将node_txt转化为node_list的形式?我们对边缘遵循与上述相同的过程 - 这个过程稍微简单一些.

So how to transform node_txt into the form of node_list? We follow the same process as described above for the edges - this one is a bit simpler.

elems = [f.strip(" '") for f in node_txt.strip().split(',')]
print(elems == node_list)
# output: True -> so here we recovered the node names correctly from node_txt

这篇关于添加节点和边时出现错误的 Networkx的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！