March 2015 - graph-tool - archives.skewed.de

Efficient Bipartite Projection
by Carlos Andrade 17 Sep '15

17 Sep '15

Dear all, I have a bipartite graph, directed and with weightened edges. It is very large, I believe 36k nodes and 52k edges. I am trying to make a projection of it, but I could not find any function or way to do so with graph-tool. Is there any way I am not aware of? If there is no current way, where would you recommend try with such a big graph? I am currently trying to run this on a 8gb RAM 2012 macbook pro 15` (2.2 ghz or something like that). I started of from (1) Gephi plugin ( https://marketplace.gephi.org/plugin/multimode-networks-transformations-2/) which after running for a couple hours almost froze my computer and output no graph (I had to force quit it). My second attempt was (and is) on igraph ( http://igraph.org/python/doc/igraph.Graph-class.html#bipartite_projection ) I came across this post: http://stackoverflow.com/questions/606516/python-graph-library And read about graph-tool and how efficient it is compared to the igraph and networkx (which I was about to try but given up when I saw the time table). Thank you for your attention,

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graph-tool graphml and networkx
by tcb 17 Aug '15

17 Aug '15

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) <node id="n1"> <data key="key0">6</data> <data key="key1">0x1.5c71d0cb8d943p+3, 0x1.70db7f4083655p+3</data> </node> 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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Undefined symbol drawing function
by sasho.j.markov 20 Apr '15

20 Apr '15

Hi New to the graph-tool. Build it from src on Fedora 16 (64) . Built with cairomm enabled . Try to run as per the quick start , however when executing graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, ... output_size=(200, 200), output="two-nodes.pdf") i get undefined symbol _ZN5Cairo7ContextC1EP6_cairob However the symbol above is defined in : libcairomm-1.0.so see below nm command results nm /usr/local/lib/libcairomm-1.0.so | grep -i _ZN5Cairo7ContextC1EP6_cairob 0000000000014b90 T _ZN5Cairo7ContextC1EP6_cairob Interestingly the library libgraph_tool_draw.so has indeed have the undefined symbol U _ZN5Cairo7ContextC1EP6_cairob but does not depend on the cairomm libarary - see the ldd output . unless the library is dynamically load i do not understand why Any advise appreciated- regards Sasho ldd /usr/local/lib/python2.7/site-packages/graph_tool/draw/libgraph_tool_draw.so linux-vdso.so.1 => (0x00007fffc46da000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007f99fd6cd000) libpython2.7.so.1.0 => /usr/lib64/libpython2.7.so.1.0 (0x00007f99fd30e000) libboost_iostreams.so.1.49.0 => /usr/local/lib/libboost_iostreams.so.1.49.0 (0x00007f99fd0f6000) libboost_python.so.1.49.0 => /usr/local/lib/libboost_python.so.1.49.0 (0x00007f99fceaa000) libboost_regex.so.1.49.0 => /usr/local/lib/libboost_regex.so.1.49.0 (0x00007f99fcbc8000) libCGAL.so.9 => /usr/local/lib/libCGAL.so.9 (0x00007f99fc9a5000) libexpat.so.0 => /usr/local/lib/libexpat.so.0 (0x00007f99fc77c000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f99fc54d000) libm.so.6 => /lib64/libm.so.6 (0x00007f99fc2c9000) libc.so.6 => /lib64/libc.so.6 (0x00007f99fbf11000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f99fbcfb000) /lib64/ld-linux-x86-64.so.2 (0x00000030cea00000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f99fbadf000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f99fb8db000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f99fb6d7000) libz.so.1 => /lib64/libz.so.1 (0x00007f99fb4c0000) librt.so.1 => /lib64/librt.so.1 (0x00007f99fb2b8000) libgmpxx.so.4 => /usr/lib64/libgmpxx.so.4 (0x00007f99fb0b3000) libboost_thread.so.1.49.0 => /usr/local/lib/libboost_thread.so.1.49.0 (0x00007f99fae98000) libgmp.so.3 => /usr/lib64/libgmp.so.3 (0x00007f99fac41000) -- 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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Python<->C++ interface tutorial?
by maksimt 08 Apr '15

08 Apr '15

Hey, I'm a researcher without much experience in creating good graph algorithm implementations. I'm blown away with how much faster some algorithms are in C++ (for instance Dijkstra's shortest path) when compared to the implementation in python or matlab. Is there any chance you could create a tutorial of how you made the python interface to C++ code? Also as far as I can tell this is the best graph library out there, but it's relatively hard to install. As a result people like me are using inferior libraries for algorithms and visualization. Do you think you could work on making your library easier to install, or at least providing more instructions? I work with both Windows and Mac OS X, and I wasn't able to install your library on either. -- 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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Point Lables
by dartdog 28 Mar '15

28 Mar '15

I go the initial examples going in an IPython Notebook with no problem, looks great! The SIRS example, and the Price network I'd be happy to post the Gists of them at github. since so many are now using IPython notebooks for analysis. In the examples there are none with hover labels on the resulting plots. In doing visual exploration it is way helpful to be able to see the properties of a point in a cluster.. The pretty graphs alone are not so helpful? I'm sure it should be obvious but I am new to graph analysis... -- 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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rpm spec
by Gordon Messmer 24 Mar '15

24 Mar '15

I'm packaging graph-tool for RHEL. I'd like to contribute the spec for distribution so that your users can easily build packages on Red Hat systems, and you can offer them for distribution if you choose to do so. I did notice a couple of problems while packaging. First, your build scripts appear to install into the general library path(distutils.sysconfig.get_python_lib()) when it should install to the platform-dependent library path (distutils.sysconfig.get_python_lib(1)). According to the manual, I believe you should be using pyexecdir rather than pythondir. http://www.gnu.org/software/automake/manual/html_node/Python.html Second, numpy headers appear to be included incorrectly. >>> print numpy.get_include.__doc__ Return the directory that contains the NumPy \*.h header files. Extension modules that need to compile against NumPy should use this function to locate the appropriate include directory. $ python -c 'import numpy; print "-I" + numpy.get_include()' -I/usr/lib64/python2.7/site-packages/numpy/core/include However, arrayobject.h is included directly where the correct path should be numpy/arrayobject.h. Because the headers don't include that prefix, the spec file includes a static path for the headers. Similarly, the cairomm headers are included without a prefix. # pkg-config --cflags cairomm-1.0 -I/usr/include/cairomm-1.0 -I/usr/include/cairo -I/usr/include/sigc++-2.0 -I/usr/lib64/sigc++-2.0/include -I/usr/include/pixman-1 -I/usr/include/freetype2 -I/usr/include/libpng12 cairommconfig.h is included, when the correct path is cairomm/cairommconfig.h.

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issue with in_degree method
by ob 18 Mar '15

18 Mar '15

The in_degree method returns wrong values if it is called with the weight parameter. As far as I could trace down the issue, it seems the method weighted_in_degree is resposible with C++ signature: boost::python::api::object weighted_in_degree(graph_tool::PythonVertex {lvalue},boost::any). Below is a minimal example. Let's create a simple directed graph with two vertices and one edge. In [1]: import graph_tool.all as gt g=gt.Graph() v1 = g.add_vertex() v2 = g.add_vertex() e1 = g.add_edge(v1,v2) in-degree and out-degree look like expected In [2]: [[v.in_degree(),v.out_degree()] for v in g.vertices()] Out[2]: [[0, 1], [1, 0]] Now, let's add some weight. In [3]: g.ep['exposure'] = g.new_edge_property("double") g.ep['exposure'][e1] = 1.5 the results for out-degree look ok, however the in-degree array looks like it is shifted In [4]: [[v.in_degree(weight=g.ep['exposure']),v.out_degree(weight=g.ep['exposure'])] for v in g.vertices()] Out[4]: [[1.5, 1.5], [0.0, 0.0]] I am using py27-graph-tool @2.2.36_0+gtk3 and boost @1.57.0_1+no_single+no_static+python27 I wonder if anyone can reproduce this issue. in_degree_issue.json <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- 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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Multiple shorstest paths
by Flavien Lambert 16 Mar '15

16 Mar '15

Hi all, my apologies if the answer is in the doc, I did not find it. What is the output of graph_tool.topology.shortest_path when several shortest path are available between two vertices? Best, F.

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Common neighbors
by dushyanthbn 16 Mar '15

16 Mar '15

How can I find the number of immediate common neighbors between all the nodes in a given graph and represent it as a matrix. i have attached the graph. Please provide some inputs. connectivity11.gz <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- 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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Convert DOT or GDL graph to distance matrix
by kiarash 07 Mar '15

07 Mar '15

I am new in python and I found graph-tool interesting. I want to convert DOT or GDL graph to distance matrix. Is it possible in graph-tool? If yes, could u help me how can do that? -- 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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