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

Use images as vertex symbols in graph_draw
by P-M 02 Feb '17

02 Feb '17

This is a somewhat general question but perhaps somebody can point me in a useful direction: I am trying to draw a small network of molecules. Ideally I would like to use the molecular structures (which I can save as image file) in the network representation as opposed to the normal little red circles. Is it possible to specify a separate file for each vertex that gets used as position marker? I have found "surface" as a vertex property in "graph_draw" but am not sure if that is what I am after. 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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Issue will gt.topology.all_paths()
by Evangelos Petsalis 01 Dec '16

01 Dec '16

Hi, I am running graph-too v2.18 on Ubuntu 15.10 and I was trying to to use the all_paths() function but when I run the example code (or any other code for that matter) I keep getting the following error: Traceback (most recent call last): File "/usr/lib/python3.4/code.py", line 90, in runcode exec(code, self.locals) File "<input>", line 1, in <module> File "/usr/lib/python3/dist-packages/graph_tool/topology/__init__.py", line 1732, in all_paths _prop("v", g, visited)) RuntimeError: This functionality is not available because boost::coroutine was not found at compile-time Did I compile the graph-tool the wrong way or is it a problem with the function itself? Regards, Vaggelis

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'grad_draw' is not defined
by attacc 30 Nov '16

30 Nov '16

Dear all I compiled graph-tool 2.19 with gcc 5.4 on linux, when I try to use it from graph_tool.all import * g = Graph() v1 = g.add_vertex() v2 = g.add_vertex() e = g.add_edge(v1, v2) graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18,output_size=(200, 200), output="test.png") I get the error: Traceback (most recent call last): File "<stdin>", line 1, in <module> NameError: name 'grad_draw' is not defined any suggestion is welcome regards Claudio -- 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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"in-out" correlations in graph-tool
by Snehal Shekatkar 30 Nov '16

30 Nov '16

Dear all, I want to calculate the "in-out" and "out-in" degree correlations in directed networks. However, I don't see any function in graph-tool that would do this for me. The usual "gt.scalar_assortativity" can do this only for "in-in" or "out-out" correlations. Can somebody please point out to me if there is any way around? Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

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Generating stochastic block model with different intra-group and inter-group probabilities
by Snehal Shekatkar 29 Nov '16

29 Nov '16

Dear all, I am trying to generate a stochastic block model in the graph_tool. Specifically, I am trying to construct a network with exactly 2 blocks such that the probabilities inside the groups are higher than that of the between the groups (assortative structure) but the probabilities inside the groups are not identical for two groups (say 0.9 for the first group and 0.6 for the second group). The extreme case of this would be to make the probability between the groups equal to zero which should give me two isolated modules. My code given below however fails to generate these two models. Can somebody kindly explain me my mistake? import numpy as np import graph_tool.all as gt N = 1000 ave_deg = 10 block = np.random.randint(1, 3, N) def f(): ave_deg = 5 return np.random.poisson(ave_deg) def corr(a, b): if a == 1 and b == 1: return 0.6 elif a == 2 and b == 2 : return 0.9 else: return 0. G, bm = gt.random_graph(N, deg_sampler = f, directed = False, model = "blockmodel-traditional", block_membership = block, vertex_corr = corr) largest_comp = gt.Graph(gt.GraphView(G, vfilt = gt.label_largest_component(G)), prune = True) gt.graph_draw(G) Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

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gt.assortativity vs gt.scalar_assortativity
by Snehal Shekatkar 27 Nov '16

27 Nov '16

Hello all, I am trying to use graph-tool to study the assortativity of certain graphs. I find that there are two functions in graph-tool that would do the job: "gt.assortativity" and "gt.scalar_assortativity". I initially thought that if the scalar property that I am interested in is the degree itself, I would get the same value for both. But I don't! I tried calculating assortativity for simple undirected Erdos-Renyi graphs and only "scalar assortativity" seems to give correct answer. In fact, "gt.assortativity" gives me quite high values even for ER graphs. Can somebody kindly explain the problem? Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

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graph_triangulation.cc:55:61: fatal error: CGAL/Periodic_3_Delaunay_triangulation_traits_3.h: No such file or directory
by P-M 24 Nov '16

24 Nov '16

Running `make` on the github version of graph-tool returns an error stating (it runs for a while first): graph_triangulation.cc:55:61: fatal error: CGAL/Periodic_3_Delaunay_triangulation_traits_3.h: No such file or directory compilation terminated. make[4]: *** [graph_triangulation.lo] Error 1 make[4]: Leaving directory `/home/pmj27/git/graph-tool/src/graph/generation' make[3]: *** [all-recursive] Error 1 make[3]: Leaving directory `/home/pmj27/git/graph-tool/src/graph' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/pmj27/git/graph-tool/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/pmj27/git/graph-tool' make: *** [all] Error 2 Does anybody know what this is caused by? 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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stackexchange site about the Complex networks
by Snehal Shekatkar 23 Nov '16

23 Nov '16

Dear all, I am sorry if this seems unimportant and please forgive me Tiago for using graph-tool's mailing list to find the right audience. As many of you must have been aware, there exists a famous question-answer website www.stackexchange.com which hosts several sites about extremely diverse topics like science, mathematics, computation, religion, history and so on. However, I find that the questions related to the various aspects of networks are spread over its various sister sites related to mathematics, computer science, statistics, biology etc. This is quite natural since the study of networks is an extremely interdisciplinary field. On the other hand, given the huge expanse of this field, it seems only natural to have a separate sister site for questions and answers related to "Complex networks" and in my opinion this would be extremely useful. Considering this, I have already officially put forth the proposal for such a site: http://area51.stackexchange.com/proposals/104390/complex-networks However, to actually make this proposal pass the first phase, we need *at least 60 followers and 40 example questions (each with 10 upvotes)* there. If you think that this should happen, I request you to kindly click the above link and follow it. Also, it would be great if you could upload some example questions there and try to upvote the existing ones. I would appreciate any discussion related to this in this thread. Also, I would highly appreciate if you could pass this to people interested in networks somehow (for example by posting on Facebook). Thank you Snehal -- Snehal Madhukar Shekatkar Pune India

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pickle error
by Peter Straka 23 Nov '16

23 Nov '16

Dear community, so I'm running the minimize_nested_blockmodel_dl() on a high performance computing cluster (due to RAM limitations on my laptop). My idea was save the output object via pickle, transfer it to my laptop and to analyse it there. But I get an error unpickling the object... see below. Would anybody know if this can be fixed? Many thanks, Peter (Both terminals are running Python 2.7.12.) *(remote) Pickling: * c = gt.is_bipartite(g, True)[1] state = gt.minimize_nested_blockmodel_dl(g, deg_corr=True, layers=True, state_args=dict(ec=g.ep.visits, layers=False, pclabel=c), B_min=200, B_max=2500, verbose=True) pickle.dump(state, open(outfile, "wb"), -1) *(local) Unpickling:* state = pickle.load(open(filename, "rb")) ---------------------------------------------------------------------------KeyError Traceback (most recent call last)<ipython-input-2-0c2db42e78d1> in <module>()----> 1 state = pickle.load(open(filename, "rb")) 2 state.print_summary() /usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.pyc in load(file) 1382 1383 def load(file):-> 1384 return Unpickler(file).load() 1385 1386 def loads(str): /usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.pyc in load(self) 862 while 1: 863 key = read(1)--> 864 dispatch[key](self) 865 except _Stop, stopinst: 866 return stopinst.value /usr/local/Cellar/python/2.7.12/Frameworks/Python.framework/Versions/2.7/lib/python2.7/pickle.pyc in load_build(self) 1221 setstate = getattr(inst, "__setstate__", None) 1222 if setstate:-> 1223 setstate(state) 1224 return 1225 slotstate = None /usr/local/lib/python2.7/site-packages/graph_tool/inference/nested_blockmodel.pyc in __setstate__(self, state) 144 def __setstate__(self, state): 145 conv_pickle_state(state)--> 146 self.__init__(**overlay(dmask(state, ["kwargs"]), **state["kwargs"])) 147 148 def get_bs(self): KeyError: 'kwargs'

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how to popup different right-click menus in GraphWidget when right-click on selected vertex and background area?
by Xun Xiao 18 Nov '16

18 Nov '16

Dear Tiago, I am extending the functions of GraphWidget that visualizes the Graph() object. By default, in graph-tool, when right-click on the widget, the self.picked vertex (closest to the pointer) will be unselected. However, i want to extend it so that 1) when right-click on the selected vertex, it popups a menu - let's say A, while 2) right-click on the background area, it first unselects the selected vertex and then popups another menu, let's say B. I know that i have to overwrite the button_press_event(), but at the branch of event.button == 3, i cannot successfully differentiate the above two cases. Thanks a lot. -- 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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