How can I remove all nodes except the largest components in a graph?
Hi, I have tried to simulate the phenomenen of cascading failures in interdependent networks. But I can't remove the nodes that don't belong to the largest component. Is there any simple solution for this task? Best, Liu
Hello Liu, there is an example code of what you are looking for in the "label_largest_component" documentation: http://graph-tool.skewed.de/static/doc/topology.html#graph_tool.topology.lab... Best, Giuseppe 2014-04-29 9:15 GMT+02:00 Liu <boxiliu.hust@gmail.com>:
Hi,
I have tried to simulate the phenomenen of cascading failures in interdependent networks. But I can't remove the nodes that don't belong to the largest component. Is there any simple solution for this task?
Best, Liu
_______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
Thanks for your help. But I was still confused by the graph filter. My aim is to to remove the nodes that don't belong to largest component of subnetwork consisted of type A nodes while the corresponding type B nodes are remained in the graph. I wrote the script like this, p = 0.02 G = gt.load_graph(File) pos = G.vertex_properties['pos'] v_type = G.vertex_properties['v_type'] e_type = G.edge_properties['e_type'] exist = G.new_vertex_property('bool') G.vertex_properties['exsit'] = exist exist.a = True for v in G.vertices(): if v_type[v]: if np.random() < p: exist[v] =False for n in v.all_neighbours(): if not v_type[n]: exist[n] = False G.set_vertex_filter(prop=exist) G.purge_vertices() pos = G.vertex_properties['pos'] v_type = G.vertex_properties['v_type'] exist = G.vertex_properties['tag'] gt.graph_draw(G, pos=pos) # step 1 largest component in network A UA = gt.GraphView(G, vfilt=v_type) LCA = gt.label_largest_component(UA) exist.a = False for v in G.vertices(): if LCA[v]: exist[v] = True for n in v.all_neighbours(): if not v_type[n]: exist[v] = True G.set_vertex_filter(exist) line 56: G.purge_vertices() Console warns that , Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 56, in <module> G.purge_vertices() File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1867, in purge_vertices new_g = Graph(self, prune=(True, False, False)) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1133, in __init__ _prop("v", gv, vorder)) ValueError: Cannot find property map type. Very appreciate for your help. best, Liu 在 2014年4月29日星期二UTC+8下午5时02分02秒，Giuseppe Profiti写道：
Hello Liu, there is an example code of what you are looking for in the "label_largest_component" documentation:
http://graph-tool.skewed.de/static/doc/topology.html#graph_tool.topology.lab...
Best, Giuseppe
2014-04-29 9:15 GMT+02:00 Liu <boxili...@gmail.com <javascript:>>:
Hi,
I have tried to simulate the phenomenen of cascading failures in interdependent networks. But I can't remove the nodes that don't belong to the largest component. Is there any simple solution for this task?
Best, Liu
_______________________________________________ graph-tool mailing list graph...@skewed.de <javascript:> http://lists.skewed.de/mailman/listinfo/graph-tool
On 04/29/2014 03:52 PM, Liu wrote:
Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 56, in <module> G.purge_vertices() File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1867, in purge_vertices new_g = Graph(self, prune=(True, False, False)) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1133, in __init__ _prop("v", gv, vorder)) ValueError: Cannot find property map type.
This is a bug in graph-tool. It has been fixed in the most recent git version. As a workaround, you can use G.purge_vertices(in_place=True). Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Dear Tiago, I used G.purge_vertices(in_place=True). But the vertex filter didn't work. G.set_vertex_filter(prop=exist) G.purge_vertices(in_place=True) gt.graph_draw(G, pos=pos) # step 1 largest component in network A UA = gt.GraphView(G, vfilt=v_type) line 45：LCA = gt.label_largest_component(UA) exist.a = False for v in G.vertices(): if LCA[v]: exist[v] = True for n in v.all_neighbours(): if not v_type[n]: exist[v] = True G.set_vertex_filter(exist) G.purge_vertices(in_place=True) Console warns that, Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 45, in <module> LCA = gt.label_largest_component(UA) File "/usr/lib/python2.7/dist-packages/graph_tool/topology/__init__.py", line 814, in label_largest_component label.a = (c.a == h.argmax()) & (vfilt.a ^ inv) ValueError: operands could not be broadcast together with shapes (248) (256) Thanks for your help! Best, Liu 在 2014年4月29日星期二UTC+8下午11时13分06秒，Tiago Peixoto写道：
On 04/29/2014 03:52 PM, Liu wrote:
Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 56, in <module> G.purge_vertices() File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1867, in purge_vertices new_g = Graph(self, prune=(True, False, False)) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1133, in __init__ _prop("v", gv, vorder)) ValueError: Cannot find property map type.
This is a bug in graph-tool. It has been fixed in the most recent git version.
As a workaround, you can use G.purge_vertices(in_place=True).
Best, Tiago
-- Tiago de Paula Peixoto <ti...@skewed.de <javascript:>>
On 04/30/2014 03:28 AM, Liu wrote:
Dear Tiago,
I used G.purge_vertices(in_place=True). But the vertex filter didn't work.
G.set_vertex_filter(prop=exist) G.purge_vertices(in_place=True)
gt.graph_draw(G, pos=pos) # step 1 largest component in network A UA = gt.GraphView(G, vfilt=v_type)
line 45：LCA = gt.label_largest_component(UA) exist.a = False for v in G.vertices(): if LCA[v]: exist[v] = True for n in v.all_neighbours(): if not v_type[n]: exist[v] = True
G.set_vertex_filter(exist) G.purge_vertices(in_place=True)
Console warns that, Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 45, in <module> LCA = gt.label_largest_component(UA) File "/usr/lib/python2.7/dist-packages/graph_tool/topology/__init__.py", line 814, in label_largest_component label.a = (c.a == h.argmax()) & (vfilt.a ^ inv) ValueError: operands could not be broadcast together with shapes (248) (256)
This seems to be something else. Could you please provide a full working example, so I can investigate? Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
On 04/30/2014 09:37 AM, Tiago de Paula Peixoto wrote:
On 04/30/2014 03:28 AM, Liu wrote:
Dear Tiago,
I used G.purge_vertices(in_place=True). But the vertex filter didn't work.
G.set_vertex_filter(prop=exist) G.purge_vertices(in_place=True)
gt.graph_draw(G, pos=pos) # step 1 largest component in network A UA = gt.GraphView(G, vfilt=v_type)
line 45：LCA = gt.label_largest_component(UA) exist.a = False for v in G.vertices(): if LCA[v]: exist[v] = True for n in v.all_neighbours(): if not v_type[n]: exist[v] = True
G.set_vertex_filter(exist) G.purge_vertices(in_place=True)
Console warns that, Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 45, in <module> LCA = gt.label_largest_component(UA) File "/usr/lib/python2.7/dist-packages/graph_tool/topology/__init__.py", line 814, in label_largest_component label.a = (c.a == h.argmax()) & (vfilt.a ^ inv) ValueError: operands could not be broadcast together with shapes (248) (256)
This seems to be something else. Could you please provide a full working example, so I can investigate?
I've fixed a related problem in the git version. Please try with that. If it does not work, please send the full working example, and I'll check it out. Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Dear Tiago, I just send full working example to you. The Network_Prepare.py is to generate a ER-ER interdependent network as it shows. The MAIN.py is to simulate the cascading failure in interdependent network. I will try the newest code on github later. Thank u. best, Liu 在 2014年4月30日星期三UTC+8下午3时44分48秒，Tiago Peixoto写道：
On 04/30/2014 09:37 AM, Tiago de Paula Peixoto wrote:
On 04/30/2014 03:28 AM, Liu wrote:
Dear Tiago,
I used G.purge_vertices(in_place=True). But the vertex filter didn't work.
G.set_vertex_filter(prop=exist) G.purge_vertices(in_place=True)
gt.graph_draw(G, pos=pos) # step 1 largest component in network A UA = gt.GraphView(G, vfilt=v_type)
line 45：LCA = gt.label_largest_component(UA) exist.a = False for v in G.vertices(): if LCA[v]: exist[v] = True for n in v.all_neighbours(): if not v_type[n]: exist[v] = True
G.set_vertex_filter(exist) G.purge_vertices(in_place=True)
Console warns that, Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 45, in <module> LCA = gt.label_largest_component(UA) File "/usr/lib/python2.7/dist-packages/graph_tool/topology/__init__.py", line 814, in label_largest_component label.a = (c.a == h.argmax()) & (vfilt.a ^ inv) ValueError: operands could not be broadcast together with shapes (248) (256)
This seems to be something else. Could you please provide a full working example, so I can investigate?
I've fixed a related problem in the git version. Please try with that. If it does not work, please send the full working example, and I'll check it out.
Best, Tiago
-- Tiago de Paula Peixoto <ti...@skewed.de <javascript:>>
Dear Tiago, The purge_vertices(in_place = False ) in he newest git version is OK. Best, Liu 在 2014年4月30日星期三UTC+8下午3时44分48秒，Tiago Peixoto写道：
On 04/30/2014 09:37 AM, Tiago de Paula Peixoto wrote:
On 04/30/2014 03:28 AM, Liu wrote:
Dear Tiago,
I used G.purge_vertices(in_place=True). But the vertex filter didn't work.
G.set_vertex_filter(prop=exist) G.purge_vertices(in_place=True)
gt.graph_draw(G, pos=pos) # step 1 largest component in network A UA = gt.GraphView(G, vfilt=v_type)
line 45：LCA = gt.label_largest_component(UA) exist.a = False for v in G.vertices(): if LCA[v]: exist[v] = True for n in v.all_neighbours(): if not v_type[n]: exist[v] = True
G.set_vertex_filter(exist) G.purge_vertices(in_place=True)
Console warns that, Traceback (most recent call last): File "/home/lockheed/PycharmProjects/cascade_failures/MAIN.py", line 45, in <module> LCA = gt.label_largest_component(UA) File "/usr/lib/python2.7/dist-packages/graph_tool/topology/__init__.py", line 814, in label_largest_component label.a = (c.a == h.argmax()) & (vfilt.a ^ inv) ValueError: operands could not be broadcast together with shapes (248) (256)
This seems to be something else. Could you please provide a full working example, so I can investigate?
I've fixed a related problem in the git version. Please try with that. If it does not work, please send the full working example, and I'll check it out.
Best, Tiago
-- Tiago de Paula Peixoto <ti...@skewed.de <javascript:>>
participants (3)
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Giuseppe Profiti -
Liu -
Tiago de Paula Peixoto