graph-tool June 2019

graph-tool@skewed.de

11 participants
15 discussions

How to control the orientation of the graph topology
by Xun Xiao 26 Feb '22

26 Feb '22

Hi Tiago, sometimes, when delete the graph and create a new one, then plot it, the plotted graph is shown upside down (in terms of the node text). So how could we control the orientation of the graph? Or which parameter we should use to always make node text shown in a correct orientation. 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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Upside down labels
by charlie 26 Feb '22

26 Feb '22

Hi, I'm suffering from the same issue mentioned in this post: https://git.skewed.de/count0/graph-tool/issues/174 Namely, I'm trying to draw a graph that includes a lot of self-looping edges, and my labels are being printed upside down. If I remove the self-loops the labels are shown the right way up. Is there a fix for it? Thanks, Charlie -- 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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random graph
by JM 01 Sep '21

01 Sep '21

Dear Tiago, I have a directed graph of about half a million nodes and approximately a million edges following scale free behaviour and a power law degree distribution. To test some of my hypothesis, I would like to generate random smaller graphs (about 50 up to 200 nodes) representative of the big one. When I used a sample function that samples straight away from the real distribution of the big network, I have following problems: - I generate unconnected nodes with both 0 in AND out degree. - I generate small sub parts of a few nodes that are not connected to the main graph. - If only sampling from nodes with at least 1 degree, the generated graph is coherent, but not representative anymore as I need a big portion of nodes with either only one in or one out degree. Here is the part of my script I used for that, where samples are drawn from dictionaries of the degrees: def sample_in(): a=np.random.randint(num) k_in = in_degrees[a] return k_in def sample_out(): if sample_in()==0: b=np.random.randint(num_out) k_out=out_zero_zeros.values()[b] return k_out else: b=np.random.randint(num) k_out=out_degrees[b] return k_out N=200 g=gt.random_graph(N, lambda:(sample_in(), sample_out()), model="constrained-configuration", directed=True) I also tried sampling from a list of tuples as you have mentioned before in the forum, but I didn't receive any results, as the tuples randomly drawn from my list might not be combinable. degs=[(7,1),(4,3),(5,6),(2,4),(6,8),(2,0),(3,5),(0,3),(2,7),(2,1)] g = gt.random_graph(4, lambda i: degs[i], directed=True) - Is there any option I could active that would help me in those cases I described above? - Is there a better way how to create representative small networks? Any help on that issue will be much appreciated. Best wishes, Jana -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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What formula is used for std in vertex_average and edge_average?
by VaSa 16 Jul '20

16 Jul '20

I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average >>> t2=gt.Graph() >>> t2.add_vertex(2) >>> t2.add_edge(t2.vertex(0), t2.vertex(1)) >>> gt.vertex_average(t2, "in") (0.5, 0.35355339059327373) Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ? also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710 0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some relation to that. A little bigger graph. >>> t3=gt.Graph() >>> t3.add_vertex(5) >>> t3.add_edge(t3.vertex(0), t3.vertex(1)) >>> gt.vertex_average(t3, "in") (0.2, 0.17888543819998318) Now, we should have 0,1,0,0,0 series for vertex incoming degree. So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854 come from ? Reason, I am asking because, I have a large graph, where the average looks quite alright but the std makes no sense, as going by the histogram, degree values are quite a bit more distributed than the std would indicate. -- 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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assigning vertex properties when adding edges
by m jadidi 04 Mar '20

04 Mar '20

Hi, I was wondering if there is any way to assign vertex properties while adding edges to the graph. for example using "add_edge_list" I can assign edge properties but later I have to iterate through all vertices again to assign their properties. I know this is not a problem when the vertex property is of the type "int" or "float" because then one can use "vprop.a = values", but in case of "string" and "object" this method doesn't work What would be the best/fastest way to handle this situation. I guess it would be very helpful to extend the "add_edge_list" function to accept vertex property in some way. cheers, -- Mohsen

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Nested Block State hierarchy level after mcmc_equilibrate
by ilyco 16 Jan '20

16 Jan '20

I ran mcmc_equilibrate on a nested block state model in a weighted graph. As per instructions, I copied the initially computed state in another object with increased hierarchy depth to 10. However, this fixed the depth to 10. Everything computed afterwards has depth 10 even if is clear that after 3 or 4 levels the nodes converge to one. There are many empty branches and when I try to plot it with empty_branches = False, I get an error stating it is not a tree. RuntimeError: Invalid hierarchical tree: No path from source to target. Did anybody perform any similar analyses? The hierarchy after mcmc_equilibrate: <NestedBlockState object, with base <BlockState object with 24 blocks (24 nonempty), degree-corrected, with 1 edge covariate, for graph <Graph object, undirected, with 230 vertices and 11230 edges, edges filtered by (<PropertyMap object with key type 'Edge' and value type 'bool', for Graph 0x7fc3a89f1210, at 0x7fc3a64911d0>, False), vertices filtered by (<PropertyMap object with key type 'Vertex' and value type 'bool', for Graph 0x7fc3a89f1210, at 0x7fc3a64912d0>, False) at 0x7fc3a89f1210>, at 0x7fc3a6491950>, and 10 levels of sizes [(230, 24), (24, 5), (5, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1)] at 0x7fc3a6491590> -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

4 4

Issue installing graph-tool due to cgal dependency
by David Jurgens 03 Jul '19

03 Jul '19

I've been struggling to get graph-tool installed on a standard 18.04 Ubuntu system for the past few hours (~5) due to the CGAL dependency. I first tried installing graph-tool from the packages, which ran fine but the library didn't actually seem to get installed (all the python import statements couldn't find it). I then tried installing from source and it makes it all the way to the end with the error: checking whether CGAL is available in /usr... no checking whether CGAL is available in /usr/local... no checking whether CGAL is available in /opt... no checking whether CGAL is available in /opt/local... no However, libcgal-dev is definitely installed: dpkg -L libcgal-dev | head -n10 /. /usr /usr/lib /usr/lib/x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/cmake /usr/lib/x86_64-linux-gnu/cmake/CGAL /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGAL_Macros.cmake /usr/lib/x86_64-linux-gnu/cmake/CGAL/FindTBB.cmake /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGAL_Common.cmake /usr/lib/x86_64-linux-gnu/cmake/CGAL/CGALExports-release.cmake No amount of futzing about with the LDFLAGS/CFLAGS seems to get it to work. Has anyone run into this before? This is probably the longest time I've spent trying to install a package in years :( -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

2 1

a RuntimeError I don't understand
by JeanPierre Paillet 26 Jun '19

26 Jun '19

Hello Tiago: While attempting to save a binary structure I encountered this error RuntimeError: Pickling of "graph_tool.libgraph_tool_core.Vertex" instances is not enabled (http://www.boost.org/libs/python/doc/v2/pickle.html) I don't understand why I was able to pickle.dump a stochastic block model (which contains vertices) and not this structure which contains a list of vertices. The url given in references returns a 404 Thanks in advance JP

2 3

Issue importing graph_tool into eclipse PyDev
by Leandro Radusky 20 Jun '19

20 Jun '19

When trying to import graph_tool into eclipse workbench, the library seems to be so big (or have a circular redundancy) and never finish to index it. I solved the problem by executing exec("from graph_tool.all import *") But with this i have no autocompletition and is really painful because all the calls to the library appears as not found functions and looses all the sense to use an IDE. Does anyone have this problem before (in eclipse or any other IDE)? Best, Leandro Radusky

1 0

A naive question
by JeanPierre Paillet 17 Jun '19

17 Jun '19

Hello: In the code for 'label_largest_component()' below, I can't make sense of the third line. What does it accomplish? label = g.new_vertex_property("bool") c, h = label_components(g, directed=directed) vfilt, inv = g.get_vertex_filter() label.fa = c.fa == h.argmax() return label

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graph-tool June 2019