http://blog.gmane.org/gmane.comp.science.graph.graph-tool.general hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/935 <pre>I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average (0.5, 0.35355339059327373) Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ? also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710 0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some relation to that. A little bigger graph. (0.2, 0.17888543819998318) Now, we should have 0,1,0,0,0 series for vertex incoming degree. So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854 come from ? Reason, I am asking because, I have a large graph, where the average looks quite alright but the std makes no sense, as going by the histogram, degree values are quite a bit more distributed than the std would indicate. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/What-formula-is-used-for-std-in-vertex-average-and-edge-average-tp4025055.html Sent from the Main discussion list for</pre> VaSa 2013-05-21T11:37:19 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/931 <pre>Hey guys! I'm trying to build graph-tool and I'm using: OSX 10.8 brew The latest Anaconda python distribution from Continuum. When building the blockmodel I'm getting the following error: graph_blockmodel.hh:910: error: no matching function for call to 'get(const boost::tuples::tuple&lt;boost::UndirectedAdaptor&lt;boost::filtered_graph&lt;boost::adj_list&lt;long unsigned int&gt;, graph_tool::detail::MaskFilter&lt;boost::unchecked_vector_property_map&lt;unsigned char, boost::adj_edge_index_property_map&lt;long unsigned int&gt; &gt; &gt;, graph_tool::detail::MaskFilter&lt;boost::unchecked_vector_property_map&lt;unsigned char, boost::typed_identity_property_map&lt;long unsigned int&gt; &gt; &gt; &gt; boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type, boost::tuples::null_type&gt;&amp;)' The (now complex) configure command I'm using is: LDFLAGS=-L/usr/local/opt/boost149/lib CPPFLAGS="-I/usr/local/opt/boost149/include -I/usr/local/include/sparsehash" CC=gcc-4.7 PKG_CONFIG_PATH=/opt/X11/lib/pkg</pre> Eric Jonas 2013-05-20T17:42:18 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/928 <pre>Hi guys, when I import graph_tool I get an error. It complains graph filtering was disabled at compile time. Well, I can't set it enable because for some reason compiling with flag enabled drains out my memory. I have 4GB RAM and I am using Arch. I get package from AUR repository and made makepkg on it(I had to modify it slightly to get rid of openmp and graph-filtering). My stack trace from ipython: In [1]: from graph_tool.all import * --------------------------------------------------------------------------- RuntimeError Traceback (most recent call last) &lt;ipython-input-1-100bbe2bc9d9&gt; in &lt;module&gt;() ----&gt; 1 from graph_tool.all import * /usr/lib/python2.7/site-packages/graph_tool/__init__.py in &lt;module&gt;() 2010 e.__class__.__doc__ = _edge_doc 2011 -&gt; 2012 init_edge_classes() 2013 2014 # some shenanigans to make it seem there is only a single edge class /usr/lib/python2.7/site-packages/graph_tool/__init__.py in init_edge_classes() </pre> piwonski.kris< at >gmail.com 2013-05-17T10:19:01 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/927 <pre>I am encountering the same errors others have: configure:16482: checking for main in -lbz2 configure:16501: g++ -o conftest.exe -Wall -Wextra -ftemplate-depth-150 -Wno-deprecated -Wno-unknown-pragmas -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-unknown-pragmas conftest.cpp -lbz2 -lm c:/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe: cannot find -lbz2 configure:16522: checking for main in -lexpat configure:16541: g++ -o conftest.exe -Wall -Wextra -ftemplate-depth-150 -Wno-deprecated -Wno-unknown-pragmas -O3 -fvisibility=default -fvisibility-inlines-hidden -Wno-unknown-pragmas conftest.cpp -lexpat -lm &gt;&amp;5 c:/mingw/bin/../lib/gcc/mingw32/4.7.2/../../../../mingw32/bin/ld.exe: cannot find -lexpat And finally: configure:17109: checking consistency of all components of python development environment configure:17135: gcc -o conftest.exe -g -O2 -Ic:\Python2.7\include conftest.c -lm -Lc:\Python2.7\Lib\config -lpython27 None &gt;&amp;5 gcc.exe: error: None: No such file or direct</pre> Brian Ball 2013-05-02T21:07:54 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/921 <pre>Hi all, In general which graph format is fastest when writing/reading graphs? I am also getting errors when I load pickled and cpickled graphs...That is something like: "TypeError: No registered converter was able to produce a C++ rvalue of type std::string from this Python object of type unicode" Cheers, Anatol </pre> Anatol Wegner 2013-04-29T12:16:13 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/918 <pre>Hello, I am using Debian and I have two versions of graph-tool available. I have a program we would like to distribute using graph-tool but it turns out that it runs fine with version graph-tool_2.2.19-1 but it does not with version 2.2.23-1. File "process.py", line 168, in &lt;module&gt; main() File "process.py", line 126, in main processor.process_text((input_text, parse_tree)) File "process.py", line 100, in process_text self.reset_graph() File "process.py", line 37, in reset_graph self.graph = self.graph_builder.new_graph() File "/home/ragerri/pythoncode/corefgraph-en-opener/corefgraph/graph/graph_builder.py", line 92, in new_graph GraphWrapper.set_properties(graph=graph, graph_properties={'graph_builder': self}) File "/home/ragerri/pythoncode/corefgraph-en-opener/corefgraph/graph/utils.py", line 82, in set_properties graph.graph_properties[name][graph] = property_value TypeError: 'NoneType' object does not support item assignment This error does not arise if I remove [gra</pre> Rodrigo Agerri 2013-04-28T21:01:01 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/915 <pre>Can anyone give step by step installation procedure, directed towards noob, for graph-tool in Fedora 18._______________________________________________ graph-tool mailing list graph-tool&lt; at &gt;skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool </pre> mij.rafee.1344< at >gmail.com 2013-04-24T08:28:22 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/912 <pre>Hi all, what is the best way to generate a random graph from a given degree sequence? ``gt.random_graph`` has lots of features, but I can't find a way to provide a degree sequence. I appreciate your help, Matthias _______________________________________________ graph-tool mailing list graph-tool&lt; at &gt;skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool </pre> Matthias Ekman 2013-04-16T15:18:05 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/907 <pre>Hi all, I'm trying to verify that I'm looking at bugs in graph_tool, and not my own user error. A little background: I'm using graph_tool to search over graphs that have been generated by graph_tool.generation.geometric_graph(). The graph represents an occupancy grid that some simulated robots are traversing. The robots do not know apriori which vertices are occupied, so they have to update their own internal maps of the world as they try to move. They do this by updating an internal edge filter (one for each robot) which filters out untraversable edges. In this way, I have one graph, and multiple edge filters, which works fairly well when I'm trying to use either graph_tool.search.dijkstra_search() or graph_tool.search.astar_search() functions to decide where to go next (I swap filters more or less non-stop). To test out how well this works, I'm randomly generating graphs and occupied vertices, and then running my code on those randomly generated graphs. Sometimes I'll end up with 50-60 tests succes</pre> CFK 2013-04-11T01:00:41 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/898 <pre>Ni! I'd like to point out that this dude is answering bugs on this mailing list on his birthday, and even that is just a tiny demonstration of how awesome he is. (Though I suspect his girlfriend doesn't really understand why =D) Happy birthday Tiago! May your life be integer, your happiness double, your networks fully connected, and your property maps full of treasure =) Hugs, ale .~´ _______________________________________________ graph-tool mailing list graph-tool&lt; at &gt;skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool </pre> Alexandre Hannud Abdo 2013-03-19T19:16:45 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/892 <pre>Hi there I've just started using graph tool, and so far I'm very impressed with the ease of use and the thorough documentation. I'm currently trying to instantiate a fully connected graph with some 600 vertices, but I find that adding all the edges usually takes around 10 seconds on my system. The fastest way of doing it that I have come up with so far is to write: from itertools import combinations edges = [g.add_edge(v1,v2) for (v1,v2) in combinations(g.vertices(),2)] But I'm wondering if there is a faster method? Thanks for a great tool Jonas -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Fast-initialization-of-graph-tp4025012.html Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. </pre> arnfred 2013-03-19T08:39:11 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/891 <pre>As for 12.10 (quantal), python3-graph-tool depends on python3-matplotlib, but there is no such a package in quantal repositories. As for 13.04 (raring), there is no python3-graph-tool package at all. Is there a way to use graph-tool with python3 in ubuntu without building it from source and packing .deb myself? Or am I missing something? Thanks in advance, Anatol -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/python3-packages-aren-t-installable-in-ubuntu-tp4025011.html Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. </pre> anatol 2013-03-19T01:41:32 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/885 <pre>i have a very simple directed graph: V0 -&gt; V2 V1 -&gt; V2 i use BFS and DFS algorithms starting from V0 and get different results from `discover_vertex` function: for BFS it does not discover V1, that is correct - there is no path from V0 to V1 but for DFS it does discover V1 output: directed graph 0 2 BFS visited 2 // correct 0 2 1 DFS visited 3 // wrong undirected graph 0 2 1 BFS visited 3 // correct 0 2 1 DFS visited 3 // correct code: import graph_tool.all as gt class BFSCheck(gt.BFSVisitor): def __init__(self): self.visited = 0 def discover_vertex(self, u): self.visited += 1 print u, class DFSCheck(gt.DFSVisitor): def __init__(self): self.visited = 0 def discover_vertex(self, u): self.visited += 1 print u, def Cmp(graph): v0 = graph.add_vertex() v1 = graph.add_vertex() v2 = graph.add_vertex() e0 = graph.add_edge(v0, v2) e1 = graph.add_edge(v1, v2) bfs_check = BFSCheck() gt.bfs_search(graph, v0, bfs_check) print "BFS visited %d" % bfs_check.visited dfs_check = DFSC</pre> shpavel 2013-03-04T14:22:53 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/883 <pre>Dear Graph-toolers, thanks for this great library, I am really enjoying my first contact with it and might spread it for our research here in IFSC/USP (Brasil, we do Physics here as well :-). I am not being able to find out how to get the degrees calculated with the weights (i.e. strengths) and I need to get clustering coefficients (i.e. transitivity) for the same kind of graphs, that is, weighted digraphs. Is this possible in graph_tool? BTW: this is not possible in networkx and igraph. Gephi can do the job, but i can't automate it, even using scripting plugin. best regards and cheers, Renato </pre> Renato Fabbri 2013-03-02T01:51:37 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/877 <pre>I'm wondering if anyone has an idea for a work around with my problem. I've written a gui using pyqt which I guess uses gtk 3.x. When I import graph_tool.draw, I get an error message saying (main.py:3823): Gtk-ERROR **: GTK+ 2.x symbols detected. Using GTK+ 2.x and GTK+ 3 in the same process is not supported Trace/breakpoint trap (core dumped) I've been thinking that the easiest solution would be to call anything graph_tool related in a separate process. Thoughts on this? How would I import graph_tool without importing draw? More specifically, which submodule provides the core functionality? -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Gtk-Error-GTK-2-x-symbols-detected-ideas-for-work-around-tp4024997.html Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. </pre> mikeschneider 2013-02-18T00:58:11 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/875 <pre>Hi, I would like to draw all edges of a graph using dash lines. I use the following code : gt.graph_draw(g.g, vertex_text=g.vprop_nickname, vertex_font_size=18, edge_end_marker="square", edge_dash_style = [10.0,10.0,0.0], output="graph.svg") but get only plain lines for edges... Any clue ? -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/edge-dash-style-usage-example-tp4024995.html Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. </pre> rbarzic 2013-02-12T21:23:10 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/862 <pre>Hi, I am trying to read the graphml output of graph-tool's graphml using networkx. https://github.com/networkx/networkx/issues/843 Unfortunately this does not work with any of the vector_* type property maps which graph-tool uses. Have you encountered this issue before? It seems the right thing to do might be to extend your graphml to hold the vector_* attributes as detailed: http://graphml.graphdrawing.org/primer/graphml-primer.html#EXT Is there some reason why it was done the way it is? How do you manage read/writing graphml data to other tools? In the meantime, it might be possible to hack some read support for graph-tool's xml into networkx. To this end, could you please advise how to parse the 'key1' data (should be two floats) &lt;node id="n1"&gt; &lt;data key="key0"&gt;6&lt;/data&gt; &lt;data key="key1"&gt;0x1.5c71d0cb8d943p+3, 0x1.70db7f4083655p+3&lt;/data&gt; &lt;/node&gt; thanks - -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/graph-tool-graphml-a</pre> tcb 2013-02-09T17:02:59 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/855 <pre>hello, has the package for Ubuntu Raring been compiled with OpenMP support? I wanted to compute betweenness centrality in parallel on a machine with 8 cores, but only one was being used. Fetching the source package and compiling it explicitly with OpenMP support has solved the issue.. thanks, m -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/OpenMP-support-on-Ubuntu-Raring-tp4024975.html Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. </pre> marcov 2013-02-06T09:59:48 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/854 <pre>hi, is there any way to be periodically reported on the state of completion of a certain procedure, for instance, with a percentage of the total work that has been done so far? It would be good to have this feature to know whether an expensive task on a large is going to be completed anytime soon or if would be better to use a machine with more processors, or just give up thank you, m. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/progress-reporting-tp4024974.html Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. </pre> marcov 2013-02-06T09:50:35 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/844 <pre>Hi, I try to create a very large graph using random_graph function. My computer has 128 GB physical memory and 16 GB swap partition. When I try to create a graph with 50 million for number of vertices, and 80 for both numbers of incoming and outgoing edges, it consumes all memory space and then crashes. Do you have any idea how I can overcome the memory limit? Is there any way to make random_graph function more memory efficient? Thanks, Arash -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Memory-problem-tp4024963.html Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com. </pre> Arash 2013-02-01T16:04:33 http://comments.gmane.org/gmane.comp.science.graph.graph-tool.general/827 <pre>If I understand correctly the Floyd-Warshall and Johnson’s algorithms are only useful in weighted graphs, so I was looking for algorithms to compute the all-pairs-shortest-paths for unweighted and undirected graphs fastest than the usual breadth-first search (BFS) method, and I found these algorithms: Timothy M. Chan: All-pairs shortest paths for unweighted undirected graphs in o(mn) time. SODA 2006: 514-523 (https://www.waset.org/journals/ijcms/v3/v3-5-43.pdf) Raimund Seidel: On the All-Pairs-Shortest-Path Problem in Unweighted Undirected Graphs. J. Comput. Syst. Sci. 51(3): 400-403 (1995) ( www.mimuw.edu.pl/~mucha/teaching/alp2006/seidel92.pdf) Do you think it is plausible and possible to implement these algorithms? Any one have seen an implementation of these in any familiar language? _______________________________________________ graph-tool mailing list graph-tool&lt; at &gt;skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool </pre> Sirius Fuenmayor 2013-01-29T18:47:36 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.comp.science.graph.graph-tool.general