January 2017 - graph-tool - archives.skewed.de

Scalar Assortativity - Definition
by P-M 19 Jan '17

19 Jan '17

Hello Tiago, I have a quick question about how the scalar assortativity is calculated. You reference "M. E. J. Newman, “Mixing patterns in networks”, Phys. Rev. E 67, 026126 (2003)" as source for the equation. In the paper the equation seems to consider edges connecting nodes of indegree x to those of outdegree y (or rather "j" and "k"). In your implementation I am able to choose in-degree, out-degree or total as degree type. What does this do to the equation? If I choose, say, "in", will that mean the algorithm will look at edges connecting nodes of indegree x to those of indegree y? If so, is there a way for me to find the assortativity as per the definition in the paper? Best, Philipp -- 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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Many-to-all shortest path
by Pedro Camargo 19 Jan '17

19 Jan '17

Hi, I went over the documentation and some foruns but I was not able to find the answer for a question that is crucial for me. Can I compute many-to-all Shortest paths (about 5,000 origins in a 100,000 nodes network) taking advantage of all computer processors? Looking at the code, it looks like Dijkstra is computed with the GIL locked, but I was not sure how it goes for the other algorithms. Thanks, Pedro

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Increase resolution of graph_draw
by P-M 19 Jan '17

19 Jan '17

Hi, Is there a way of increasing the resolution of the graph_draw output? I am looking for something like a DPI setting as exists in e.g. matplotlib. I am trying to generate plots in publication quality but currently find myself having to scale the size of the plot up to then compress the final image back down to my required dimensions to increase the resolution which seems cumbersome. Does such an option exist? Or is there a better way of achieving this? Best, Philipp -- 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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Errors installing 2.19dev
by P-M 18 Jan '17

18 Jan '17

Hello, I am trying to compile the current git (2.19dev) version. As far as I can tell gcc 5.4 is being used. I am running Ubuntu 16.04. I have run: git clone gitlab@git.skewed.de:count0/graph-tool.git cd ./graph-tool/ ./autogen.sh sudo ./configure PYTHON="/home/pmj27/anaconda/bin/python2.7" --enable-openmp ./make -Wno-unused-local-typedefs That seemed to fail with the note "Makefile:500: recipe for target 'graph_cairo_draw.lo' failed" (I have attached the config.log config1.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> ). So I thought I would try again (after deleting all the files) and check the output of the config.log after running configure. So I ran: git clone gitlab@git.skewed.de:count0/graph-tool.git cd ./graph-tool/ ./autogen.sh That returned: libtoolize: putting auxiliary files in '.'. libtoolize: linking file './ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: linking file 'm4/libtool.m4' libtoolize: linking file 'm4/ltoptions.m4' libtoolize: linking file 'm4/ltsugar.m4' libtoolize: linking file 'm4/ltversion.m4' libtoolize: linking file 'm4/lt~obsolete.m4' libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. configure.ac:22: installing './compile' configure.ac:18: installing './config.guess' configure.ac:18: installing './config.sub' configure.ac:20: installing './install-sh' configure.ac:20: installing './missing' src/graph/Makefile.am: installing './depcomp' src/graph_tool/Makefile.am:3: installing './py-compile' I then ran "sudo ./configure PYTHON="/home/pmj27/anaconda/bin/python2.7" --enable-openmp" followed by "sudo chmod o+rw config.log" as I couldn't open config.log. "configure" did not print any error messages to the screen but config.log (attached config.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> ) seems to show some errors: configure:3811: gcc -V >&5 gcc: error: unrecognized command line option '-V' gcc: fatal error: no input files compilation terminated. configure:3811: gcc -qversion >&5 gcc: error: unrecognized command line option '-qversion' gcc: fatal error: no input files compilation terminated. configure:4588: gcc -E conftest.c conftest.c:11:28: fatal error: ac_nonexistent.h: No such file or directory compilation terminated. I unfortunately do not know what precisely I am looking for or what these error messages mean. Is anybody able to help me with this? Best wishes, Philipp -- 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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Changing default mouse hovering behavior in GTK interactive graphs
by mohit jangid 18 Jan '17

18 Jan '17

Hello, I've created a graph on graph-tool interactive window. I want to visually show the traversal of BFS or DFS. In this process, I want to update the node's and vertex's properties myself. By default, whenever the mouse is hovered over graphs nodes (drawn on GTK window) the node appears with blue halo color and all the connected nodes are highlighted with red edges and borders. I don't want any default highlighting. How can I turn off this default behavior? -- Mohit Kumar Jangid Mob# : +919530153503 “*The most powerful weapon on earth is the human soul on fire.” ~Field Marshal Ferdinand Foch*

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Annotating graph-tool graphs with graph_draw as a matplotlib subplot?
by Steve 18 Jan '17

18 Jan '17

I'm trying to annotate a graph plot with associated data and analysis. To do this, I'd like to use graph_plot as a subplot within a matplotlib graphic, ideally inline within a Jupyter notebook and "%matplotlib inline". Inline graph_plot works great by itself within Jupyter, but the graphs lack annotation or related content within the same output cell. Is there a way to get a graph_plot as a subplot within a matplotlib object? Or some equivalent approach that would allow for general graphical annotations of graph-tool graph plots? -- 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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Average neighbour-neighbour correlation
by P-M 08 Jan '17

08 Jan '17

I was wondering, how does avg_neighbour_corr define a neighbour? More specifically, if I look at "out" "out" correlation, does graph-tool look at all neighbours of a given vertex or only at those which are connected by an outgoing edge from the source vertex? Best, Philipp -- 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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