March 2016 - graph-tool - archives.skewed.de

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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Using graphviz "rank" feature with gt.graphviz_draw
by JHickey 20 Mar '16

20 Mar '16

Graphviz has a "rank" feature that allows nodes in a "subgraph" to be displayed at the same level. I would like to use this (or another feature?) to accomplish what I describe in the example below. Example: In the attached image, the number drawn in the centre of the node is its identifier. I assign a vertex property defining the hierarchical level ("lvl") for each node as follows: node 0; lvl = 0 node 1; lvl = 3 node 2; lvl = 2 node 3; lvl = 1 node 4; lvl = 0 I would like those nodes to be displayed at the same hierarchical level in the image. E.g., nodes 0 and 4 both have lvl=0 and should be drawn at the bottom of the image. Node 1 should stay at the top. <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> Note: the last example on the following page seems to show how to use Graphviz to do what I want (although I would like to define the subgraphs based on my lvl vertex property), but I am not sure how to implement this through graph_tool. URL: http://graphs.grevian.org/example Or, perhaps there is a simpler way of doing what I want to do? -- 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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Consistent colour scale and legend
by Alexandra Diem 17 Mar '16

17 Mar '16

Hi, I'm trying to use graph-tool to track concentrations on a network and was wondering what the best way would be to obtain consistent colour scales for a vertex property? I track the concentration of a substance as a vertex property and then use that as the vertex_fill_color in graph_draw because I would like to visualise the change in concentration over the network over time. This works great, but it appears that every time I plot the graph the colormap is rescaled to the minimum and maximum values in the vertex property. So if my values range from 0.0 to 0.4 and I use the Blues colormap 0.0 is white and 0.4 is dark blue. If in the next time step my values range from 0.0 to 0.6 then 0.6 is dark blue and 0.4 is now a different shade of blue. Instead, if I know 0.0 would be the minimum value and 1.0 would be the maximum I would like to consistently plot my graphs using that scaling, so that 0.4 always has the same shade of blue. I hope this all made sense. Thanks! Alexandra

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How is all_shortest_paths defined?
by Philipp-Maximilian Jacob 17 Mar '16

17 Mar '16

Hello, I was wondering how the all_shortest_paths function was defined. I have a large network ("g"). In that network there are two nodes ("source" and "target", say) for which I am interested as to how they interconnect. >From prior research I know that there is at least one set of connections between them. I have verified that this path actually exists in the network manually as far as I can tell. When I however run all_shortest_paths(g,source,target) this path is not part of the results set. Why is that? Does all_shortest_paths stop searching after it has found a certain number of results? If so, is it possible to change this cut-off criterion? Finally, is it possible to also obtain an edge descriptor as a result? Currently I think the documentation states that the result is an iterator over the sequence of vertices from source to target. Best wishes, Philipp

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graph-tool 2.13 Macports build throws dyld exception at gt.purge_vertices()
by stsmith＠ll.mit.edu 10 Mar '16

10 Mar '16

Tiego -- Is this an issue with 2.13, or the Macports build process? It fails consistently across several boxes with the underlying error "dyld: Symbol not found". Minimum code: # This code creates a little graph and filters out the largest connected component import graph_tool.all as gt g = gt.Graph() v0 = g.add_vertex() v1 = g.add_vertex() v2 = g.add_vertex() e01 = g.add_edge(v0,v1) e12 = g.add_edge(v1,v2) e20 = g.add_edge(v2,v0) comp, hist = gt.label_components(g) comp_sub = g.new_vertex_property('bool') k_sub = hist.argmax() for v in g.vertices(): if comp[v] == k_sub: comp_sub[v] = True g.set_vertex_filter(comp_sub) g.purge_vertices() Exception: dyld: lazy symbol binding failed: Symbol not found: __ZN10graph_tool6detail15action_dispatchIN5boost6lambda14lambda_functorINS3_19lambda_functor_baseINS3_12other_actionINS3_17assignment_actionEEENS2_6tuples5tupleINS4_INS3_8identityIRmEEEENS4_INS5_INS3_6actionILi2ENS3_15function_actionILi2EmEEEENSA_IKNS_15HardNumVerticesEKNS4_INS3_11placeholderILi1EEEEENS9_9null_typeESP_SP_SP_SP_SP_SP_SP_EEEEEESP_SP_SP_SP_SP_SP_SP_SP_EEEEEEN4mpl_5bool_ILb0EEEJNS0_15all_graph_viewsEEEC1ERKS10_ Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace dyld: Symbol not found: __ZN10graph_tool6detail15action_dispatchIN5boost6lambda14lambda_functorINS3_19lambda_functor_baseINS3_12other_actionINS3_17assignment_actionEEENS2_6tuples5tupleINS4_INS3_8identityIRmEEEENS4_INS5_INS3_6actionILi2ENS3_15function_actionILi2EmEEEENSA_IKNS_15HardNumVerticesEKNS4_INS3_11placeholderILi1EEEEENS9_9null_typeESP_SP_SP_SP_SP_SP_SP_EEEEEESP_SP_SP_SP_SP_SP_SP_SP_EEEEEEN4mpl_5bool_ILb0EEEJNS0_15all_graph_viewsEEEC1ERKS10_ Referenced from: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/graph_tool/libgraph_tool_core.so Expected in: flat namespace -- 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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Help troubleshoot edge_control_points
by itcarroll 10 Mar '16

10 Mar '16

The following snippet produces an output with nice curvey edges: ```` from graph_tool import load_graph, Graph from graph_tool.draw import graph_draw g = Graph() g.add_vertex(4) pos = g.new_vertex_property('vector<float>') pos[g.vertex(0)] = [0, 0] pos[g.vertex(1)] = [0, 1] pos[g.vertex(2)] = [1, 0] pos[g.vertex(3)] = [1, 1] g.add_edge(g.vertex(0), g.vertex(3)) g.add_edge(g.vertex(1), g.vertex(2)) g.vertex_properties['pos'] = pos ctl = g.new_edge_property('vector<float>') for e in g.edges(): ctl[e] = [0, 0, 0.25, 0.2, 0.75, 0.2, 1, 0] graph_draw(g, pos=g.vp.pos, edge_control_points=ctl, output='tmp.eps') ```` But when I replace the graph here with one loaded from the attached .gt file, I get no edges drawn at al. If I take out the `pos` argument though, the curvey edges come back. Suggestions for getting both positions and curvey edges? tmp.gt <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- 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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display_props for draw_hierarchy?
by Richard Ree 07 Mar '16

07 Mar '16

Hi, I'd like to be able to interactively identify vertices in the graph window produced by draw_hierarchy. I've used display_props to do this with normal graph windows but since the graph shown by draw_hierarchy is different from the original (the one passed to minimize_nested_blockmodel_dl), this doesn't seem possible - or am I missing something? Thanks -Rick

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Graphml dataset
by Kimon 04 Mar '16

04 Mar '16

Hi I installed graph-tools through brew and it works fine. Good work and thanks for the detailed info. I have a simple question about datasets. Except of the collection provided in graph-tools is there a dataset that provides graphml format of graphs? If not, is there a way to convert other formats, like txt from the snap dataset to graphml or gt? I googled for few hours and I couldn't find answer to the above sections. -- 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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Compiling v1.13 dev - configure: error: No usable boost::iostreams found
by Philipp-Maximilian Jacob 02 Mar '16

02 Mar '16

Hi, I am currently in the process of compiling v1.13 dev from source. I have generated the configure file using autogen.sh. I am running the configure script now using the command "./configure --enable-openmp CXX='g++-5'" however this returns the error "configure: error: No usable boost::iostreams found". I don't recall running into this error when I compiled v1.12 but maybe I just don't remember anymore. I have check the version of boost installed with Anaconda and it tells me that it is up-to-date so I presume I may just have to point the script to the correct location but have not found a solution that works for me online yet. What might I be doing wrong here? I have attached the config.log file. Best wishes, Philipp

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Compiling Error
by gaolongnuaa 01 Mar '16

01 Mar '16

Hi Tiago, I'm very interested in using graph-tools to do network analysis since my network is pretty large. After I installed those required dependency packages, I still got errors when I run make. The error message is as following which I could not figure out. ./configure CPPFLAGS="-I/home/gaol3/Software/Tools/boost/include -I/home/gaol3/Software/Tools/CGAL/include" LDFLAGS="-L/home/gaol3/Software/Tools/boost/lib -L/home/gaol3/Software/Tools/CGAL/lib" --disable-sparsehash make make[4]: *** [graph_hits.lo] Error 1 make[4]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph/centrality' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/mnt/isilon/cbmi/tan_lab/gaol3/Software/Downloads/graph-tool-2.12' make: *** [all] Error 2 Thanks, Long -- 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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