graph-tool May 2014

graph-tool@skewed.de

17 participants
24 discussions

return maps from clustering.motifs
by sandrine ollinger 05 May '14

05 May '14

Hello, I have a question about the Property maps returned by clustering.motif(). Practically, I have the following graph: >>> pprint(rlf) <Graph object, directed, with 22312 vertices and 44849 edges at 0x1007a3650> In this graph, vertex and edge have some properties. For example : >>> rlf.vertex_properties {'status': <PropertyMap object with key type 'Vertex' and value type 'string', for Graph 0x1007a3650, at 0x1007a36d0>, '_graphml_vertex_id': <PropertyMap object with key type 'Vertex' and value type 'string', for Graph 0x1007a3650, at 0x101057c10>, 'name': <PropertyMap object with key type 'Vertex' and value type 'string', for Graph 0x1007a3650, at 0x1007ac750>} Note that this graph occupies the memory space 0x1007a3650. I've asked to graph-tool the motifs of this graph, with the following instruction: >>> motifs, counts, vertex_maps = gt.clustering.motifs(gt.GraphView(rlf, directed=False), 4, return_maps=True) So far, so good. This instruction returned me 3 variables. The first one is a list of graphs (motifs), the second one a list of numbers of counts, but the third is a bit mysterious for me. So, it's a list of list of Property maps and it's ok that every one of this map correspond with a count of motif. However, I expected that this property maps refer to my original graph, but it does not. For example, if I'm looking for the first motif and the first map : >>> pprint(motifs[0]) <Graph object, undirected, with 4 vertices and 3 edges at 0x1007778d0> >>> case0 = vertex_maps[0] >>> graph0 = case0[0] >>> pprint(graph0) <PropertyMap object with key type 'Vertex' and value type 'int32_t', for Graph 0x1007778d0, at 0x10a2db7d0> The first PropertyMap object refer to the motif and not to my original graph. And here, I don't understand. For a motif which occurs 10 times in my graph, I obtain 10 property maps. If I use get_graph on this 10 maps, I obtain 10 identical graphs. What would be the value of returning the maps? I had hoped to obtain sub-graph with original vertex and edges properties. Is it something that I didn't understand? Is it possible to obtain sub-graph with original vertex and edges properties by using clustering.motifs? Best regards, Sandrine

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Something wrong with graph-tool documentation.
by Phyo Arkar Lwin 02 May '14

02 May '14

Its Math Processsing Error , Everywhere! http://graph-tool.skewed.de/static/doc/generation.html Examples This is a degree sampler which uses rejection sampling to sample from the distribution [Math Processing Error], up to a maximum. >>> def sample_k(max): ... accept = False ... while not accept: ... k = randint(1,max+1) ... accept = random() < 1.0/k ... return k ... The following generates a random undirected graph with degree distribution [Math Processing Error] (with k_max=40) and an *assortative*degree correlation of the form: [Math Processing Error] >>> g = gt.random_graph(1000, lambda: sample_k(40), model="probabilistic", ... vertex_corr=lambda i, k: 1.0 / (1 + abs(i - k)), directed=False, ... n_iter=100) >>> gt.scalar_assortativity(g, "out") (0.6321636468713748, 0.01082292099309249) The following samples an in,out-degree pair from the joint distribution: [Math Processing Error] with [Math Processing Error] and [Math Processing Error].

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How can I remove all nodes except the largest components in a graph?
by Liu 01 May '14

01 May '14

Hi, I have tried to simulate the phenomenen of cascading failures in interdependent networks. But I can't remove the nodes that don't belong to the largest component. Is there any simple solution for this task? Best, Liu

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largest connected component under attack, animation
by Николай Кинаш 01 May '14

01 May '14

Hello. import graph_tool.all as gt import numpy as np import sys, os, os.path from gi.repository import Gtk, Gdk, GdkPixbuf, GObject def random_attack(g): victim = g.vertex( np.random.randint( 0, g.num_vertices() ) ); g.remove_vertex( victim ); g = gt.price_network(100, directed=False); pos = gt.arf_layout(g) max_count = 50 if not os.path.exists("./frames"): os.mkdir("./frames"); win = Gtk.OffscreenWindow(); win.set_default_size(1000, 1000); win.graph = gt.GraphWidget(g, pos ); win.add(win.graph); count = 0; def update_state(): global count; count += 1; random_attack(g); gt.arf_layout(g, pos=pos, max_iter = 1); win.graph.regenerate_surface(lazy=False); win.graph.queue_draw(); pixbuf = win.get_pixbuf(); pixbuf.savev(r'./frames/dancing%06d.png' % count, 'png', [], []); if count > max_count: sys.exit(0); return True; cid = GObject.idle_add(update_state); win.connect("delete_event", Gtk.main_quit); win.show_all(); Gtk.main(); is there way to paint edges and vertex from largest connected component in different color? Somthing like this: vcmap = gt.label_largest_component(g) gt.GraphWidget(g, pos, vcmap );

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graph-tool May 2014