June 2012 - graph-tool - archives.skewed.de

Second largest component
by Julien Arino 07 Jun '12

07 Jun '12

Hi all, I continue with the probably silly questions.. I have a graph that is relatively large (1.6 million vertices, 2.4 million arcs). I extract the largest strong component, but it is still quite large (~400,000 vertices) and while the "analysis" algos work smoothly, when it comes to representing it, it's very sparsely connected, so essentially a huge cloud of points. So I am trying to extract the second largest strong component, which is way smaller. I do the following: comp, hist = label_components(g) idx = argsort(hist) idx_second_largest = idx[-2] idx_vertices_second_largest = find(comp.a == idx_second_largest) u = GraphView(g, vfilt=idx_vertices_second_largest) To make things easier, I'll paraphrase the example from the doc. >>> g2=random_graph(100, lambda: (1,1)) >>> comp,hist=label_components(g2) >>> print hist [11 28 41 17 3] So my second largest strong component should be the one with elements labelled 1. >>> print comp.a [0 1 1 2 3 2 2 0 0 2 1 3 3 0 3 1 4 0 2 2 1 3 2 1 2 2 2 2 2 1 2 1 3 1 2 2 1 2 3 2 2 0 2 2 4 2 3 2 2 3 1 1 2 1 1 2 1 1 2 4 2 1 0 1 2 1 1 3 2 2 2 1 3 3 1 2 1 1 0 0 2 2 2 3 3 3 2 2 2 2 1 2 3 0 1 1 2 1 0 3] Using the code above gives, finally >>> print idx_vertices_second_largest [ 1 2 10 15 20 23 29 31 33 36 50 51 53 54 56 57 61 63 65 66 71 74 76 77 90 94 95 97] But when I use this as u = GraphView(g2, vfilt=idx_vertices_second_largest), I get an error that ends with File "/usr/local/lib/python2.7/dist-packages/graph_tool/__init__.py", line 527, in __get_set_f_array a[:] = v ValueError: operands could not be broadcast together with shapes (100) (4) So as far as picking up the indices, I seem to be right, but after that, problem.. Where am I being silly? (Coming from classic C, my first reaction is "what should I typecast to?".) Thanks! -- J.

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Pickling of "graph_tool.libgraph_tool_core.Edge" instances is not enabled
by Héctor Urbina 04 Jun '12

04 Jun '12

Hello, I got this error when trying to save a graph to a file: Traceback (most recent call last): File "/usr/local/bin/graphanalyze.py", line 123, in <module> network.save(outFN) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/__init__.py", line 1443, in save self.__graph.WriteToFile(file_name, None, fmt, props) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/io.py", line 62, in pickler pickle.dump(obj, sstream, -1) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 1370, in dump Pickler(file, protocol).dump(obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 224, in dump self.save(obj) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 600, in save_list self._batch_appends(iter(obj)) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 633, in _batch_appends save(x) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 286, in save f(self, obj) # Call unbound method with explicit self File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 548, in save_tuple save(element) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.py", line 306, in save rv = reduce(self.proto) RuntimeError: Pickling of "graph_tool.libgraph_tool_core.Edge" instances is not enabled (http://www.boost.org/libs/python/doc/v2/pickle.html) my code is: filename = basename(outputFile) + '_' + str(cutoff) + '.xml.gz' network.save(filename) -- Héctor Urbina S. Ingeniero en Bioinformática Fono: 82049138

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Vertex variable name from a string
by jarino 04 Jun '12

04 Jun '12

Hi, I am wondering: is it possible to generate a vertex variable name from a string. Let me explain: I need to read a set of vertices from a csv file, and a set of arcs from another file. My vertices have names of the form XYZ, and my arcs then indicate whether there is a connection between XYZ and, say, ABC. Of course, I could define a property "name", assign it to the vertex, then find the indices of the origin and end vertices when I browsing my connection file. But I am wondering.. From the examples, I would like to do something like v1 = g.add_vertex() v2 = g.add_vertex() e = g.add_edge(v1, v2) but where v1, v2, etc., would be replaced by vertexName[i] (in a loop). Probably it is my incompetence with python, but I don't seem to be able to do that. A call to for i in range(1, len(vertexName)): vertexName[i] = g.add_vertex() does not give an error. But when I try to assign an edge using the "same" method, for i in range(1, len(listVertices)): e = g.add_edge(origVertex[i], destVertex[i]) I get Traceback (innermost last): File "<stdin>", line 1, in <module> File "import_graph.py", line 59, in <module> e = g.add_edge(origVertex[i], destVertex[i]) File "/usr/local/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1109, in add_edge e = libcore.add_edge(weakref.ref(self), source, target) TypeError: No registered converter was able to extract a C++ reference to type graph_tool::PythonVertex from this Python object of type str I am guessing that, if at all possible, then some typecasting is needed.. So, is it possible and if so, how? Thanks! -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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warning when importing graph_tool.all
by shakira 03 Jun '12

03 Jun '12

Hi, all I install graph tool and when I passed the following command I am having the above warning message, what is that? I am using ipython In [1]: from graph_tool.all import * /usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed import gobject._gobject Cheers Shakira -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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shortest distance in filtered graph doesn't work properly
by Héctor Urbina 03 Jun '12

03 Jun '12

Hello, I'm using a graph filtered with the minimum spanning tree and calculating the shortest distance for all the vertices. when capturing the array of distances for the vertex with index 0 it gives me: >>> dist1 array([ 0, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 1, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 1, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647, 2147483647], dtype=int32) as if the algorithm were checking for a direct edge between each pair of vertices instead of searching for the shortest path and giving the appropriate distance. Is there another way to get the right values? -- Héctor Urbina S. Ingeniero en Bioinformática Fono: 82049138

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how to use a python object saved in a graph property map
by Héctor Urbina 03 Jun '12

03 Jun '12

Hello, I have the following code: sortedEdges = [] g = Graph() g.graph_properties["sortedEdges"] = self._graph.new_graph_property("object", sortedEdges) then I fill the sortedEdges list with the appropriate values and return g. Now, how can I get the list of sorted edges from g? I'm also saving a dictionary that uses the names of the vertices as keys and the graph vertices as values in a internal graph property map; so, in general, I want to learn how to use any python object after it is saved as graph_property Thanks, -- Héctor Urbina S. Ingeniero en Bioinformática Fono: 82049138

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max flow min cut
by BWIND 03 Jun '12

03 Jun '12

hi, I'm relatively new to Python but i managed to get the build the graph and attach the capacities to the edges and got some results from the Maxflow algorithm. I what to used to implement the min cut and separate the graph in two. Did anybody tried this? Bernardo Mota

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