March 2014 - graph-tool - archives.skewed.de

What formula is used for std in vertex_average and edge_average?
by VaSa 16 Jul '20

16 Jul '20

I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average >>> t2=gt.Graph() >>> t2.add_vertex(2) >>> t2.add_edge(t2.vertex(0), t2.vertex(1)) >>> gt.vertex_average(t2, "in") (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. >>> t3=gt.Graph() >>> t3.add_vertex(5) >>> t3.add_edge(t3.vertex(0), t3.vertex(1)) >>> gt.vertex_average(t3, "in") (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… Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.

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graph-tool can't find Graphviz renderer
by Mikhail Spivakov 07 Apr '16

07 Apr '16

Hello! I've got graphviz installed with python and python27 bindings. However, when I do: graph_draw(ug, vprops={"label": ug.vertex_index}, output="two-nodes.pdf", layout="fdp") I get the following error: graph G { graph [outputorder=edgesfirst, mode=major, overlap=true, ratio=fill, size="5.905512,5.905512", start=3019255687130444316]; node [label="\N", shape=circle, width="0.105", height="0.105", style=filled, color="#2e3436", fillcolor="#a40000"]; edge [arrowsize="0.3", color="#2e3436", penwidth="1.0"]; graph [bb="0,0,425,425"]; 0 [label=0, width="0.47", height="0.47", pos="330,101"]; 1 [label=1, width="0.47", height="0.47", pos="93,324"]; 0 -- 1 [pos="318,113 277,152 147,274 106,312"]; } Error: renderer for pdf is unavailable Out[8]: <PropertyMap object with key type 'Vertex' and value type 'vector<double>', for Graph 0x5ff3f90, at 0x6001290> At the same time, if I save the above dot expression as test1.dot and run the following command from the command line: $ dot -Tpng test1.dot -o graph1.png I get a beautiful graph1.png. Graphviz is installed in a non-standard location as I don't have admin rights. However, the graphviz folder is in LD_LIBRARY_PATH and gv.py is in PYTHONPATH. Would very much appreciate your advice on what else graph-tool might need to find the libraries and/or how to test it better. Many thanks, Mikhail

3 5

Segmentation fault using shortest_distance
by Juan Manuel Tirado 20 Mar '16

20 Mar '16

Hi Tiago, I am trying to calculate the shortest distances of a graph after applying a filter. I have a code that looks like this: g=gt.load_graph("myGraph.xml",format="xml") #for later use distances = gt.shortest_distance(g) #extract the components of the graph comp = g.label_components(g) #This splits the graph in several components #I want to calculate the shortest distances #for the component 2 for example filtering = g.new_vertex_property("boolean") for v in g.vertices(): if comp[v]==2: filtering[v]=True else: filtering[v]=False #set the vertex filter g.set_vertex_filter(filtering) distances_comp=gt.shortest_distance(g) The last line of code rises a segmentation fault. I have plotted the graph with the filtered graph and its correct, also I can calculate the local_clustering_coefficient without problems. Am I doing something wrong? Is there any other way to filter the graph and calculate the shortest distances? Is this a bug? Thanks so much, Juan

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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.

3 3

pycairo problem in ./configure
by Nikos Kouvaris 16 May '14

16 May '14

Hi all, I successfully compiled grpah-tool in my Mavericks OSX using homebrew for the dependencies optional or not (i.e. expat, boost, cairo,...) the configuration was ./configure LDFLAGS="-L/usr/local/Cellar" PYTHON_EXTRA_LDFLAGS="-L/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Python" CPPFLAGS="-I/usr/local/include/sparsehash" PYTHON_VERSION="2.7.6" --with-numpy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy --with-scipy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy --enable-cgal-valgrind --disable-cairo make and make install works fine here !! ---------------------------------------------------------------- No we I am coming into the problems... I need to be able also to draw my graphs, and so I need to install it again with cairo I had installed cairo, cairomm, py2cairo (for python2.7) before with homebrew, as you can see $ pkg-config cairomm-1.0 --libs -L/usr/local/Cellar/cairomm/1.10.0/lib -L/usr/local/Cellar/cairo/1.12.16/lib -L/usr/local/Cellar/libsigc++/2.3.1/lib -lcairomm-1.0 -lcairo -lsigc-2.0 $ pkg-config pycairo --libs -L/usr/local/Cellar/cairo/1.12.16/lib -lcairo $ pkg-config cairo --libs -L/usr/local/Cellar/cairo/1.12.16/lib -lcairo Now I am trying to configure the installation as: ./configure LDFLAGS="-L/usr/local/Cellar" PYTHON_EXTRA_LDFLAGS="-L/usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/Versions/2.7/Python" CPPFLAGS="-I/usr/local/include/sparsehash" PYTHON_VERSION="2.7.6" CAIROMM_LIBS="-L/usr/local/Cellar/cairomm/1.10.0/lib -L/usr/local/Cellar/cairo/1.12.16/lib -L/usr/local/Cellar/libsigc++/2.3.1/lib" CAIROMM_CFLAGS="-O3 -lcairomm-1.0 -lcairo -lsigc-2.0" --with-numpy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy --with-scipy=/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/scipy --enable-cgal-valgrind >> my_conf.log.txt and as you can see in the file my_conf.log.txt I take an error message: ....... checking pkg-config is at least version 0.9.0... yes checking for CAIROMM... yes checking python module: cairo... yes checking pycairo/pycairo.h usability... no checking pycairo/pycairo.h presence... no checking for pycairo/pycairo.h... no configure: error: pycairo headers not found The whole files my_conf.log.txt as well as the config.log are attached here. Does anyone have the same problem or know how to solve it? Thanks in advance, Nikos

4 7

Building graph from adjacency matrix
by Pietro Battiston 05 Apr '14

05 Apr '14

Hello, I tried graph-tool after some experience with networkx, in search for better efficiency (attracted by [1]) ... but unfortunately, it seems like it all depends on how data is stored! The (several) networks I play with are dense weighted networks of 1435 nodes. They are defined in terms of their adjacency matrices, which are pandas dataframes stored in a HDF5 store. In order to get the relative network with networkx, I would do dg = nx.from_numpy_matrix(hstore['my_df'].as_matrix(), create_using=nx.DiGraph()) which took around 18 seconds. In graph-tool, the best alternative I found, based on [2] and [3], is: # Since the bottleneck is given by the calls to g.add_edge(), # numba actually slows down things a bit. #from numba import autojit # #@autojit def graph_from_adj_matrix(m): g = Graph() n = m.shape[0] edges = list(g.add_vertex(n=n)) c = Counter(every=10, until=n) for i in xrange(n): for j in xrange(n): if m[i,j]: g.add_edge(edges[i], edges[j]) c.count() return g g = graph_from_adj_matrix(hstore['my_df'].as_matrix()) ... which takes around 200 seconds (and is still not even weighted!). Is there anything trivial (or simply new) I'm missing (apart from the possibility, mentioned in [3], of writing my code in C++)? [1] : http://graph-tool.skewed.de/performance [2] : http://lists.skewed.de/pipermail/graph-tool/2011-September/000438.html [3] : http://graph-tool.skewed.de/trac/ticket/106 Thanks, Pietro

3 8

Graphtool segfaulted
by Phyo Arkar Lwin 31 Mar '14

31 Mar '14

$ python Python 2.7.5 (default, Oct 14 2013, 09:13:45) [GCC 4.7.3] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from graph_tool.all import * Segmentation fault I am on Sabayon Linux 64bit, alll ./configure options met including optionals.

3 9

How can i retrived graph's coordinates of vertices?
by Phyo Arkar Lwin 28 Mar '14

28 Mar '14

I wanted to export those info into json but GraphML do not stores coordinates info. As sigmajs can support coords and do not want to strain browser side performance calculating layout. I want to get already generated coordinates by sfdp_layout of the graph. How can i do that? Thanks Phyo.

1 1

How can i retrived graph's coordinates of vertices?
by Phyo Arkar Lwin 28 Mar '14

28 Mar '14

I wanted to export those inforation into json but GraphML do not stores Positions. I want to get already generated coordinates by sfdp_layout of the graph. How can i do that? Thanks Phyo.

1 0