graph-tool April 2014

graph-tool@skewed.de

17 participants
19 discussions

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

5 9

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

Something wrong with graph-tool documentation.
by Phyo Arkar Lwin 02 May '14

02 May '14

Its Math Processsing Error , Everywhere! http://graph-tool.skewed.de/static/doc/generation.html Examples This is a degree sampler which uses rejection sampling to sample from the distribution [Math Processing Error], up to a maximum. >>> def sample_k(max): ... accept = False ... while not accept: ... k = randint(1,max+1) ... accept = random() < 1.0/k ... return k ... The following generates a random undirected graph with degree distribution [Math Processing Error] (with k_max=40) and an *assortative*degree correlation of the form: [Math Processing Error] >>> g = gt.random_graph(1000, lambda: sample_k(40), model="probabilistic", ... vertex_corr=lambda i, k: 1.0 / (1 + abs(i - k)), directed=False, ... n_iter=100) >>> gt.scalar_assortativity(g, "out") (0.6321636468713748, 0.01082292099309249) The following samples an in,out-degree pair from the joint distribution: [Math Processing Error] with [Math Processing Error] and [Math Processing Error].

2 1

How can I remove all nodes except the largest components in a graph?
by Liu 01 May '14

01 May '14

Hi, I have tried to simulate the phenomenen of cascading failures in interdependent networks. But I can't remove the nodes that don't belong to the largest component. Is there any simple solution for this task? Best, Liu

3 9

largest connected component under attack, animation
by Николай Кинаш 01 May '14

01 May '14

Hello. import graph_tool.all as gt import numpy as np import sys, os, os.path from gi.repository import Gtk, Gdk, GdkPixbuf, GObject def random_attack(g): victim = g.vertex( np.random.randint( 0, g.num_vertices() ) ); g.remove_vertex( victim ); g = gt.price_network(100, directed=False); pos = gt.arf_layout(g) max_count = 50 if not os.path.exists("./frames"): os.mkdir("./frames"); win = Gtk.OffscreenWindow(); win.set_default_size(1000, 1000); win.graph = gt.GraphWidget(g, pos ); win.add(win.graph); count = 0; def update_state(): global count; count += 1; random_attack(g); gt.arf_layout(g, pos=pos, max_iter = 1); win.graph.regenerate_surface(lazy=False); win.graph.queue_draw(); pixbuf = win.get_pixbuf(); pixbuf.savev(r'./frames/dancing%06d.png' % count, 'png', [], []); if count > max_count: sys.exit(0); return True; cid = GObject.idle_add(update_state); win.connect("delete_event", Gtk.main_quit); win.show_all(); Gtk.main(); is there way to paint edges and vertex from largest connected component in different color? Somthing like this: vcmap = gt.label_largest_component(g) gt.GraphWidget(g, pos, vcmap );

2 1

How can i set minimun distance between nodes (so they do not overlap each other)
by Phyo Arkar Lwin 30 Apr '14

30 Apr '14

I am using sfdp_layout. How can i modify it so nodes do not overlap each other alot and can show edges? Graph going to be huge (Millon of nodes) so what is best algorithm for it ? below is my result and code of 70k nodes (email conversation) : <https://lh3.googleusercontent.com/-mp9AYfKCLN8/U0WHfv93LiI/AAAAAAAAAvE/46g3…> > def draw_graph(userdict,edges): > g = Graph() > g.add_vertex(len(userdict)) > for edg in edges: > g.add_edge(*edg) > > #pos = sfdp_layout(g, C=0.8 , K=4, cooling_step=0.69) > pos = sfdp_layout(g,p=10, cooling_step=0.69) > for vertex in g.vertices(): > print pos[vertex] > return g Thanks Phyo.

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graph-tool April 2014