October 2015 - graph-tool - archives.skewed.de

Simple Cycle Finder
by tanzairatier 25 Mar '16

25 Mar '16

Hello all, I'm wondering if anyone can suggest a strategy for finding elementary cycles with Graph-Tool. I'm working also with Network X, and they have a function for this, called simple_cycles(G). That function essentially runs Tarjan's Algorithm to find all strongly connected components, and then detects cycles within each of those components (this approach is called Johnson's Algorithm). I've tried to port the Network X code to Graph-Tool, but there are un-matching parallels in the data structures of both tools. e.g. Graph-Tool prefers to label with property maps. Since I've only begun using Graph-Tool a short while ago, this task is difficult for me. Any help would be appreciated, many thanks in advance. -- 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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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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Help regarding -enable-openMP
by Shubham Bhushan 11 Nov '15

11 Nov '15

Hi I asked earlier as to how utilize the parallel processing in my code. Now I installed it using the precompiled packages for Ubuntu. does that mean I'll have to reinstall it from source using the openmp option in the configure command? Shubham -- http://about.me/shubham.bhushan

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Any chance of having labels in Unicode?
by Yannis Haralambous 28 Oct '15

28 Oct '15

dear all, I would like to use math symbols (such as ∈, ⊆ and ∡) and Greek letters into labels (vertex properties and edge properties), so that they can appear in graph-tool-made or graphviz-made graphs. How can I use graph-tool in a Unicode-compliant way? thanks in advance Yannis H. -- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous(a)telecom-bretagne.eu Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas) Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)

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Customizing mouse functionality
by Evangelos Petsalis 28 Oct '15

28 Oct '15

Hi Tiago, I was wondering if there is a way to customize what happens when a mouse button is clicked. In particular I am interested in the following: 1) Disabling the feature that allows user to move vertices around by using the mouse 2) Any callbacks that might be available when a mouse button is pressed/released 3) If you could point out the part of your code (name of file/function) that is being called upon a mouse click (that would be the code that gets the screen coordinates and from there extracts which vertex has been selected). Thanks in advance, Vaggelis -- 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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Long node labels are hidden by neighboring nodes
by yannis panagis 27 Oct '15

27 Oct '15

Dear all, I am trying to draw a graph the labels of which are rather long and overlap with neighboring nodes. Because of that some labels are hidden apparently according to the drawing order of the nodes. You can reproduce the effect by running the attached script in the same directory with the graph file. Is there any workaround for that issue. Do z-coordinates help at all? Cheers Yannis Panagis

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Installation issues
by soumajyoti 27 Oct '15

27 Oct '15

Hi, I tried building graph tool from source and it gave me an error after running configure. I have attached the log file. Can somebody please help me with it? I am using Red Hat Enterprise Edition Linux. Thanks, Soumajyoti. config.log <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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Gephi
by Yannis Haralambous 25 Oct '15

25 Oct '15

Just a short question: is there a way to visualize graph-tool graphs with gephi? Thanks in advance Yannis -- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous(a)telecom-bretagne.eu Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas) Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)

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Graphviz vertex/edge properties
by Yannis Haralambous 15 Oct '15

15 Oct '15

Sorry for disturbing again, but I’m trying to draw a graph (with graphviz) with labels on vertices and on edges. I saw in the documentation that vprops and eprops are Python attributes with values that are dictionaries containing key-value pairs, where key is a graphviz attribute and value is either a string or a property map. So I tried the following: graphviz_draw(g, vcolor=typev, vprops={label: labelv}, eprops={label: labele}, output=fname+".pdf ») where label is a graphviz property (as explained in http://www.graphviz.org/doc/info/attrs.html#d:label <http://www.graphviz.org/doc/info/attrs.html#d:label>) and labelv and labele are property maps defined as labelv = g.new_vertex_property("string") labele = g.new_edge_property("string ») This doesn’t work and I get the error message Traceback (most recent call last): File "build-graph.py", line 459, in <module> graphviz_draw(g, vcolor=typev, vprops={label: labelv}, eprops={label: labele}, output=fname+".pdf") NameError: name 'label' is not defined But label is indeed a graphviz property, no doubt upon that. What am I doing wrong? Thanks in advance Yannis -- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous(a)telecom-bretagne.eu <mailto:yannis.haralambous@telecom-bretagne.eu> Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ <http://omega.enstb.org/yannis> ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas) Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)

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Efficient way to have unique edges (with given vertices and type)
by Yannis Haralambous 14 Oct '15

14 Oct '15

Hi, I would like to know if there is a computationally efficient way of creating edges only if an edge with the same extremities and the same type (= a given edge property, in the sense of graph-tool edge properties) does not exist already. Of course I can use the following algorithm: before creating edge (v1,v2) of type t1: take all edges out-going from v1: check how many of them have v2 as target, among them: check whether one of them has type t1 if yes do not create a new edge and return this one if not, create a new edge As this seems to be a bit slow (I have to do many such edge creations) I was wondering if there is a more efficient « create-only-if-doesnt-exist-already » method, of maybe simply a query method including the type (a single method for checking if there exists an edge of a given type between two given vertices). Thanks in advance Yannis -- ------------------------------------------------------- Yannis Haralambous Professor Institut Mines-Télécom, Télécom Bretagne Computer Science Department UMR CNRS 6285 Lab-STICC Technopôle Brest Iroise CS 83818, 29238 Brest Cedex 3, France Email: yannis.haralambous(a)telecom-bretagne.eu Internet: http://perso.telecom-bretagne.eu/yannisharalambous/ ICBM address: 48°21'31.57"N 4°34'16.76"W Twitter: y_haralambous ------------------------------------------------------- ...the ball I threw while playing in the park has not yet reached the ground (Dylan Thomas) Es gab eine Zeit, wo ich nur ungern über Schubert sprechen, nur Nächtens den Bäumen und Sternen von ihm vorerzählen mögen. (Robert Schumann)

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