January 2013 - graph-tool - archives.skewed.de

graph-tool debian packages
by Johannes Schauer 14 Jan '13

14 Jan '13

Hi, I have some questions about the graph tool Debian package: Why does it depend on libboost-all-dev? Out of all ~38k binary packages in Debian, only libfeel++-dev depends on libboost-all-dev. I dont see a reason for the graph-tool package to depend on libboost-all-dev. Why does it? The graph-tool binary package also depends on expat. Why? The expat package only ships the program /usr/bin/xmlwf which I dont see being used by graph-tool at all? It also depends on python-dev. Why? Packages that are not *-dev packages should not need to depend on python-dev. It also depends on the g++ package. The g++ package only ships the binary /usr/bin/g++ which, as far as I can see, is never executed by graph-tool? I'm just asking because once I try to install the graph-tool package, apt-get tells me that it will fill 1036 MB of disk space with 323 new packages it needs to resolve graph-tool's dependencies. This seems somehow a bit like overkill to spend one gigabyte just to install graph-tool? cheers, josch PS: please dont forget to CC me as I'm not subscribed to this list

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Efficient mass removal of vertices possible?
by Va Sa 13 Jan '13

13 Jan '13

Greetings, Is it possible to somehow enter a list of vertices to be removed all at once? My naive approach for v in g.vertices(): if v.in_degree() == 0 and v.out_degree()==0: g.remove_vertex(v) is taking a while to run on a 3M Vertices graph, i.e. ~9 trillion memory shifts.. If one could avoid the memory shifting after each removal, the complexity would go down to just O(g.num_vertices) Sincerely, Val

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Thanks!
by Sirius Fuenmayor 10 Jan '13

10 Jan '13

Thanks for your help Giuseppe and Tiago, and for the fast response.

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Problem with pseudo_diameter() and GraphView object ()
by Sirius Fuenmayor 09 Jan '13

09 Jan '13

I get a 'Segmentation fault (core dumped)' error when I try to calculate the pseudo_diameter() of a GraphView object <class 'graph_tool.GraphView'>. I must convert the GraphView object to a Graph object <class 'graph_tool.Graph'> to perform this calculation? How do I make this conversion? My detailed problem is: I have a graph that is fragmented in several components and I want to calculate several measures on every component, so I must extract every component as a graph to be able to apply the different tools on it. To do this I use label_components() to create a vertex PropertyMap that label the components vprop_comps, size_comps = gt.label_components(g) from this Property Map (vprop_comps) I create one Boolean PropertyMap for every component, the Boolean Property Map for a component will have 1 for every vertex that belong to this component and 0 otherwise, finally I construct a GraphView object from the Boolean Property Map of a component, and then apply the different tools on this object. My code is: # for all components for i in range(size_comps.size): # create a boolean property map vprop_component_i = g.new_vertex_property("bool") # explore the property map that label the components 'vprop_comps' for j in range(vprop_comps.a.size): # if vprop_comps sugest that vertex j is in component i if (vprop_comps.a[j] == i): # put 'true' in the property of vertex j in the property map of component i vprop_component_i[g.vertex(j)] = True # With the boolean property map constructed for component i I can create a # GraphView object representing component i: c_i = gt.GraphView(g, vfilt=vprop_component_i) # and apply the different measures on it: clust_c_i = gt.global_clustering(c_i)[0] length_c_i = gt.pseudo_diameter(c_i)[0] Everything goes fine until I calculate the pseudo_diameter() of c_i, if I try to, I receive a 'Segmentation fault (core dumped)' error. Is there a more direct way to extract the components as graph objects?

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Using the values of a property (eg. g.edge_index)
by jcjveraa 09 Jan '13

09 Jan '13

Hey there, I have a list of labels which I'd like to attach to the rendering of a graph. I can get a PDF with labels on the edges using: import graph_tool.all as gt [[[make graph g with vertices and edges]]] gt.graphviz_draw(g, eprops={"label":g.edge_index},output="out.pdf") #produces a graph with edges labeled 0 to n-1 gt.graphviz_draw(g, eprops={"label":"test label"},output="out.pdf") #produces a graph with all edges labeled "test label", so labeling with strings is possible What I'd like to do is to use those edge_index values as index for an arary containing my labels as strings to be placed in the graph. eprops={"label":labelStrings[i]} # where i is equal to the numeric value of the edge_index How would I do that? edge_index is a PropertyMap so that can't be used as index, but getting the values out as an array fails too so apparently it is of type vector or object. Perhaps if I could see what a 'vector' is as defined here I might be able to figure it out, but it's not specified: http://projects.skewed.de/graph-tool/doc/graph_tool.html#graph_tool.Propert… Being able to assign a label at the moment the edge is created with add_egde would work too and is even preferable in my situation, so that might be a solution too if I'd know how. Thanks, Jelle -- 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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Energy optimization from scipy-optimize on a sub-graph
by Guillaume Gay 08 Jan '13

08 Jan '13

Hi all, I'm using graph-tool to represent a living tissue. The tissue grows and changes shape through successive local changes. For each of those changes, I need to optimize graph energy (as defined by a non trivial relation between graphs edge and vertices coordinates in 3D). My question is the following: Before the optimization, is it better to * Take a GraphView of the graph masked by filters: | local_view = gt.GrahView(graph, vfilt=is_local_v, efilt=is_local_e) ### ... optimize on local_view ...| * Work on the filtered graph: | graph.set_vertex_filter(is_local_v) graph.set_vertex_filter(efilt=is_local_e) ### optimize on local graph.set_vertex_filter(None) graph.set_vertex_filter(None)| * Do a copy of the local graph, | local_view = gt.GrahView(graph, vfilt=is_local_v, efilt=is_local_e) local = Graph(local_view, prune=True) ### ...optimize on local... graph.set_vertex_filter(is_local_v) graph.set_vertex_filter(efilt=is_local_e) for key, propin graph.vertex_properties: prop.fa = local.vertex_properties[key].fa| For now, I am doing it the second way... I suspect it's not the best, but don't have clue on which of the others is better. Any comments welcome! Thanks Guillaume

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Animations with graph-tool
by Tiago de Paula Peixoto 04 Jan '13

04 Jan '13

Hi there, I've just included a section in the documentation on how to do animations with graph-tool: http://projects.skewed.de/graph-tool/doc/dev/demos/animation.html This is the first on planned series of "cookbook" entries on how to do useful things with graph-tool, which I intend to do as time permits. Suggestions on further topics and comments are welcome, as well as contributed examples. Cheers, Tiago -- Tiago de Paula Peixoto <tiago(a)skewed.de>

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Getting the coordinates from vertex property map
by Kire Gasteovski 04 Jan '13

04 Jan '13

Guten Tag! I am making the following example http://projects.skewed.de/graph-tool/wiki/FrontpageExample . What I want to do is to extract the coordinates of the nodes into a list from the vertex property map (i.e. from the variable pos, I assume they are stored there). How do I do that? Please help me, because I am stuck on this problem for 2 days and I can't find the solution. Best regards, Kiril

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Error installing graph-tool on windows
by Jelle Veraa 04 Jan '13

04 Jan '13

Dear all, Happy new year! Starting of with what I'd actually like to do (building the program is of course a means to an end :) - I'd like to use the library for its subgraph isomorphism algorithm specifically - should you be able to provide me a binary of the library or know of another fast implementation for subgraph isomorphism that might help me as well. I'm trying to install the library on a 64 bit Windows 7 machine running 32 bit python 2.7. Installing the dependencies (from binaries) works, but running ./config from MinGW/MSys gives me an error. it exits with "Could not link test program to Python. Maybe the main Python library has been installed in some non-standard library path. If so, pass it to configure, via the LDFLAGS environment variable.", but the solution seems less straightforward - I've already tried all kinds of LDFLAGS versions pointing towards my Python folder (at C:\Python27, or /c/Python27 in MinGW). here is the log: http://bpaste.net/show/82ASZHcSnWmGsBIglFEo/ >From line 2055/configure:16996 things start going wrong (a bit is posted below). There is a reference to Lib\config, but the config directory does not exist. Furthermore the output 'None' at configure:17037 is injected into the command line for gcc.exe which also gives an error. I've been googling for an answer for some hours now bu no luck. I see that you need python-dev on linux for instance, but I've got Windows so 'apt-get python-dev' won't work :) Can anyone help me? thanks, Jelle configure:16996: result: -Lc:\Python27\Lib\config -lpython27 configure:17003: checking for Python site-packages path configure:17009: result: c:\Python27\Lib\site-packages configure:17016: checking python extra libraries configure:17023: result: configure:17030: checking python extra linking flags configure:17037: result: None configure:17044: checking consistency of all components of python development environment configure:17070: gcc -o conftest.exe -g -O2 -Ic:\Python27\include conftest.c -lm -Lc:\Python27\Lib\config -lpython27 None >&5 gcc.exe: error: None: No such file or directory

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