February 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

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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.

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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

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graph_union, unexpected behavior
by Stefan Klingelschmitt 20 Mar '14

20 Mar '14

Hey, I'm struggeling with the grap_union() function. It seems like the properties are only correctly passed to the union graph, if include=True. Is this how it supposed to work? Here a minimal example: import graph_tool.all as gt import graph_tool.topology as gt_topo from gi.repository import Gtk, Gdk, GdkPixbuf, GObject G = gt.Graph(directed=False) G_sub = gt.Graph(directed=False) v1 = G.add_vertex() v2 = G.add_vertex() v3 = G.add_vertex() v4 = G_sub.add_vertex() v5 = G_sub.add_vertex() e1 = G.add_edge(v2, v1) e2 = G.add_edge(v2, v3) e3 = G_sub.add_edge(v5, v4) G.vertex_properties['type'] = G.new_vertex_property("string") G_sub.vertex_properties['type'] = G_sub.new_vertex_property("string") G.vertex_properties['type'][v1] = 'Car' G.vertex_properties['type'][v2] = 'Crossing' G.vertex_properties['type'][v3] = 'Car' G_sub.vertex_properties['type'][v4] = 'Pedestrian' G_sub.vertex_properties['type'][v5] = 'Sidewalk' #ToDo: Function bug, why is include=True needed? G_union, prop = gt.graph_union(G, G_sub, props=[(G.vertex_properties['type'], \ G_sub.vertex_properties['type'])], include=True) pos = gt.sfdp_layout(G) gt.graph_draw(G_union, pos, vertex_text=G_union.vertex_properties['type']) Another point that I find a bit not so intuitive is that you have to specify every single property of the two graphs you would like to have in the new graph, wouldn't it be much more intuitive to copy all the properties into the new graph unless not told otherwise? P.S: This will probably not my last question as I'm planning to heavily use graph-tool for my research....

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Problem importing on Mac OS X 10.8, installed using MacPorts
by Uldis Bojars 07 Mar '14

07 Mar '14

Hi, When trying to import graph-tool the following error message is returned: >>> from graph_tool.all import * Fatal Python error: PyThreadState_Get: no current thread Could you help me solve this problem? graph-tool version py-graph-tool-2.2.18 was successfully installed using MacPorts but it fails during importing. Thanks, Uldis

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visualization of temporal networks
by hajons＠gmail.com 06 Mar '14

06 Mar '14

Hi, Any plans on supporting visualization of temporal dynamics? Or is there any way of doing that with the current feature set? Regards, Håkan

3 4

Graph_Draw error - PyCairo?
by CitSci 26 Feb '14

26 Feb '14

Hi, I have been having issues with graph_draw, notably there is a reference to certain parameters being 'unkown', it works for a while then kills the process. By graph_draw line is: pos=sfdp_layout(Graph) graph_draw(Graph, pos=pos,text=v_seq, output_size=(7000,7000), fmt='png',output="graph.png") Terminal output: /usr/lib/python2.7/dist-packages/graph_tool/draw/cairo_draw.py:417: UserWarning: Unknown parameter: text warnings.warn("Unknown parameter: " + k, UserWarning) Killed Is there something wrong with the pycairo installation? -- 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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