graph-tool October 2017

graph-tool@skewed.de

13 participants
23 discussions

GraphWidget with background image
by Paulo Nascimento 23 Oct '17

23 Oct '17

Hello Tiago, I finished implementing the background image in GraphWidget. I attached the files so you can see the result. You just need to run the file named test_window.py within an environment with graph-tool installed. I think that it only works with PNG image files, because I used the method cairo.ImageSurface.create_from_png() During this development I have found some difficult to use the key press events when the GraphWidget is inside a Gtk container. I was trying to set a GraphWidget inside the Gtk.Overlay, which is set inside a Gtk.Notebook page. In this configuration all the events with scroll and control key worked perfectly, but when I press the keys 'a', 's' or 'r' nothing happens. Do you have any idea why this occurs? I had another problem related with the docker image when I was developing the GUI. All the text outside the GraphWidget was shown as a undefined character, like small squares. I thought that happened because the Arch Linux is messing with the fonts. So I created a new Dockerfile using Ubuntu 16.04 and compiled with graph-tool. This way I had no problem with the font. I hope this help in some way. :) Regards, Paulo Nascimento

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v2.22 crashes when zooming-in or out on graph
by Evangelos Petsalis 17 Oct '17

17 Oct '17

Hi, I recently upgraded to v2.22 (from v2.19) and I noticed that with the new version when I use the roller button on the mouse to zoom in or out, the application crashes with a segmentation fault - this was NOT the case with v2.19. I was wondering if anybody else has experienced similar issues or have any ideas how to resolve the issue. Regards, Vaggelis -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Question about how to deal with weighted networks in SBM
by Henrique Ferraz de Arruda 16 Oct '17

16 Oct '17

Dear all, I have been using the lasted version of graph-tools, compiled from master and I'm not having much success with using weighted networks on the method "minimize_nested_blockmodel_dl" I'm passing the weights as the "recs" argument. The code executes the entire task, but when I visualize the communities doesn't seem to be correctly assigned. I would appreciate if someone could, please, show an example of use, or take a look at my code, as follow: ... gtGraph = gt.Graph(directed=True) gtGraph.add_edge_list(edges) #load the weight prop = gtGraph.new_edge_property("double") for i,e in enumerate(edges): prop[gtGraph.edge(e[0],e[1])] = w[i] state = gt.minimize_nested_blockmodel_dl(gtGraph, state_args={"recs":[prop], "rec_types":['real-normal']}) ... Tank you. Best regards. Henrique.

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Unable to use subplots with mplfig
by Snehal Shekatkar 15 Oct '17

15 Oct '17

Hello all, I am trying to use mplfig parameter of the graph_draw to draw 4 graphs on the same plot. My code is given below. However, this only produces graphs in first and second subplots. What am I missing? import graph_tool.all as gt import matplotlib.pyplot as plt plt.switch_backend('cairo') '''Load a graph''' g = gt.collection.data['karate'] for ind in range(4): ax = plt.subplot(2, 2, ind+1) gt.graph_draw(g, mplfig = ax) plt.savefig('karate4states.pdf') Thank you -- Snehal M. Shekatkar Pune India

3 12

Overlapping nodes in drawing
by ilyco 15 Oct '17

15 Oct '17

I was wondering whether anyone used the drawing capabilities and ran into the issue of overlapping nodes after calculating layout in various ways? On the same note, did anyone find a solution for increasing the size of some of the nodes, say based on their degree, and ensuring that they won't then overlap with other nodes? I am trying to find a solution without using the graphviz_draw function. I also have a large network: 7000 nodes and 150000 edges which makes it more difficult to manually manipulate values of position of overlapping nodes. Thanks! -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Garph-tool v2.24 on Ubuntu 17.04
by Evangelos Petsalis 14 Oct '17

14 Oct '17

I installed graph-tool v2.24 on Ubuntu 17.04 from the repository and get the following error every time I try to use an interactive window: from graph_tool.all import * import graph_tool as gt g = gt.collection.data["celegansneural"] interactive_window(g) python3: symbol lookup error: /usr/lib/python3/dist-packages/graph_tool/draw/libgraph_tool_draw.so: undefined symbol: _ZN5boost7context12stack_traits12default_sizeEv Are there any specific requirements with the boost library. The one installed by 1.62.0.1, which is the newest version available, according to apt-get Thanks -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

2 1

gt.scalar_assortativity returns wrong values
by Snehal Shekatkar 09 Oct '17

09 Oct '17

Hello Tiago, I am using gt.scalar_assortativity and I observed that it returns non-zero values and big variance values even when the values on the nodes are exactly same. g = gt.collection.data['karate'] s = g.new_vertex_property('float') for v in g.vertices(): s[v] = 0.9999 gt.scalar_assortativity(g, deg = s) This returns : (1.0, 8.889098493616578) I expect to see (0, 0) here. What am I missing? Thank you Snehal Shekatkar -- Snehal M. Shekatkar Pune India

2 20

Displaying Overlapping Communities for Networks Without Clustering with SBMs
by isukritgupta 07 Oct '17

07 Oct '17

Hi, I am trying to generate plots for communities detected by another algorithm (outside graph-tool). The communities are overlapping and I wanted to display something like nodes with multiple colors (like we have for SBMs). For this I set a new vertex property and assign nodal memberships to it. I assign a matrix which contains one hot vectors for each node's community membership. So the matrix has shape n x g where n is the number of nodes and g is the number of communities. When I use graph_draw like: graph_draw(g, vertex_shape="pie", vertex_pie_fractions=pv, edge_gradient=None, output="lesmis-sbm-marginals.svg") where pv is the property map, I get: python3: ../../../../src/cairo-arc.c:189: _cairo_arc_in_direction: Assertion `angle_max >= angle_min' failed. I want to show overlapping clusters with graph-tool, but the clustering hasn't been performed by graph-tool. Any ideas as to how to go about this? Thanks! -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

4 6

Save state to disk for long running nested block state analysis
by Felix Victor Münch 06 Oct '17

06 Oct '17

G'day! Just wondering whether it would be possible to implement, e.g. as a parameter of the minimize_nested_block_model function, a way to save intermediate results to disk at certain intervals and to resume the analysis, e.g. after a forced shut-down, or any other interruption. If I'd have some hints I might try to have a go at this feature myself. Or is this already possible with some lower level functions? Cheers! Felix --

2 1

Help with GraphWidget
by Paulo Nascimento 04 Oct '17

04 Oct '17

Hello Tiago, I am trying to set a background image in GraphWidget. I already tried to use the Gtk.Image overlaied by GraphWidget with bg_color = [1, 1, 1, 0], but it not worked. Is possible to set the background without modifing the gtk_draw.py source file? Best, Paulo Nascimento

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graph-tool October 2017