NetworkX largest component no longer working?
Question:
according to networkx documentation, connected_component_subgraphs(G) returns a sorted list of all components. Thus the very first one should be the largest component.
However, when I try to get the largest component of a graph G using the example code on the documentation page
G=nx.path_graph(4)
G.add_edge(5,6)
H=nx.connected_component_subgraphs(G)[0]
I get
TypeError: 'generator' object has no attribute '__getitem__'
It used to work on my other computer with earlier versions of networkx (1.7 I think, not 100% sure)
Now I am using a different computer with python 2.7.7 and networkx 1.9. Is it a version problem?
I have written a small function with a couple lines myself to find the largest component, just wondering why this error came out.
BTW, I can get the components by converting the generator object to a list.
components = [comp for comp in nx.connected_components(G)]
But the list is not sorted by component size as stated in the documentation.
example:
G = nx.Graph()
G.add_edges_from([(1,2),(1,3),(4,5)])
G.add_nodes_from(range(6,20))
components = [comp for comp in nx.connected_components(G)]
component_size = [len(comp) for comp in components]
print G.number_of_nodes(), G.number_of_edges(), component_size
G = nx.Graph()
G.add_edges_from([(1000,2000),(1000,3000),(4000,5000)])
G.add_nodes_from(range(6,20))
components = [comp for comp in nx.connected_components(G)]
component_size = [len(comp) for comp in components]
print G.number_of_nodes(), G.number_of_edges(), component_size
output:
19 3 [3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
19 3 [2, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
looks like when the node names are large numbers and when there are a bunch of single nodes, the returned subgraphs are not sorted properly
Answers:
The networkx-1.9 documentation is here http://networkx.github.io/documentation/networkx-1.9/reference/generated/networkx.algorithms.components.connected.connected_components.html#networkx.algorithms.components.connected.connected_components
The interface was changed to return a generator (as you figured out). The example in the documentation shows how to do what you ask.
Generate a sorted list of connected components, largest first.
>> G = nx.path_graph(4)
>>> G.add_path([10, 11, 12])
>>> sorted(nx.connected_components(G), key = len, reverse=True)
[[0, 1, 2, 3], [10, 11, 12]]
or
>>> sorted(nx.connected_component_subgraphs(G), key = len, reverse=True)
As for version 2.4:
nx.connected_component_subgraphs(G) is removed.
Instead to get the same result use:
connected_subgraphs = [G.subgraph(cc) for cc in nx.connected_components(G)]
And to get the giant component:
gcc = max(nx.connected_components(G), key=len)
giantC = G.subgraph(gcc)
according to networkx documentation, connected_component_subgraphs(G) returns a sorted list of all components. Thus the very first one should be the largest component.
However, when I try to get the largest component of a graph G using the example code on the documentation page
G=nx.path_graph(4)
G.add_edge(5,6)
H=nx.connected_component_subgraphs(G)[0]
I get
TypeError: 'generator' object has no attribute '__getitem__'
It used to work on my other computer with earlier versions of networkx (1.7 I think, not 100% sure)
Now I am using a different computer with python 2.7.7 and networkx 1.9. Is it a version problem?
I have written a small function with a couple lines myself to find the largest component, just wondering why this error came out.
BTW, I can get the components by converting the generator object to a list.
components = [comp for comp in nx.connected_components(G)]
But the list is not sorted by component size as stated in the documentation.
example:
G = nx.Graph()
G.add_edges_from([(1,2),(1,3),(4,5)])
G.add_nodes_from(range(6,20))
components = [comp for comp in nx.connected_components(G)]
component_size = [len(comp) for comp in components]
print G.number_of_nodes(), G.number_of_edges(), component_size
G = nx.Graph()
G.add_edges_from([(1000,2000),(1000,3000),(4000,5000)])
G.add_nodes_from(range(6,20))
components = [comp for comp in nx.connected_components(G)]
component_size = [len(comp) for comp in components]
print G.number_of_nodes(), G.number_of_edges(), component_size
output:
19 3 [3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
19 3 [2, 1, 1, 1, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]
looks like when the node names are large numbers and when there are a bunch of single nodes, the returned subgraphs are not sorted properly
The networkx-1.9 documentation is here http://networkx.github.io/documentation/networkx-1.9/reference/generated/networkx.algorithms.components.connected.connected_components.html#networkx.algorithms.components.connected.connected_components
The interface was changed to return a generator (as you figured out). The example in the documentation shows how to do what you ask.
Generate a sorted list of connected components, largest first.
>> G = nx.path_graph(4)
>>> G.add_path([10, 11, 12])
>>> sorted(nx.connected_components(G), key = len, reverse=True)
[[0, 1, 2, 3], [10, 11, 12]]
or
>>> sorted(nx.connected_component_subgraphs(G), key = len, reverse=True)
As for version 2.4:
nx.connected_component_subgraphs(G) is removed.
Instead to get the same result use:
connected_subgraphs = [G.subgraph(cc) for cc in nx.connected_components(G)]
And to get the giant component:
gcc = max(nx.connected_components(G), key=len)
giantC = G.subgraph(gcc)