graph-tool November 2019

graph-tool@skewed.de

8 participants
17 discussions

cairo_draw ImportError libgraph_tool_draw.so: undefined symbol
by athanassios 29 Nov '19

29 Nov '19

Hi, I have just installed the latest release of graph-tool from anaconda. I would like to use your /graph_draw/ method to visualise graph but it fails to import the cairo_draw module. *from graph_tool.draw import cairo_draw* --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-e914249e8560> in <module> ----> 1 from graph_tool.draw import cairo_draw ~/anaconda3/envs/TRIADB/lib/python3.7/site-packages/graph_tool/draw/cairo_draw.py in <module> 87 88 from .. dl_import import dl_import ---> 89 dl_import("from . import libgraph_tool_draw") 90 try: 91 from .libgraph_tool_draw import vertex_attrs, edge_attrs, vertex_shape,\ ~/anaconda3/envs/TRIADB/lib/python3.7/site-packages/graph_tool/dl_import.py in dl_import(import_expr) 59 60 try: ---> 61 exec(import_expr, local_dict, global_dict) 62 finally: 63 sys.setdlopenflags(orig_dlopen_flags) # reset it to normal case to ~/anaconda3/envs/TRIADB/lib/python3.7/site-packages/graph_tool/draw/cairo_draw.py in <module> ImportError: /home/athan/anaconda3/envs/TRIADB/lib/python3.7/site-packages/graph_tool/draw/libgraph_tool_draw.so: undefined symbol: _ZN5Cairo7Context9show_textERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE My environment: ============ Ubuntu 18.04 (bionic) Anaconda3-2019.07-Linux-x86_64 Python 3.7.4 I have created my virtual environment and installed graph_tool with conda install -c conda-forge graph-tool graph-tool 2.29 The package has been successfully installed under ~/anaconda3/envs/TRIADB/lib/python3.7/site-packages and I have also tried to set LD_LIBRARY_PATH to solve the Imp ortError above echo $LD_LIBRARY_PATH /home/athan/anaconda3/envs/TRIADB/lib:/home/athan/anaconda3/envs/TRIADB/lib/python3.7/site-packages/graph_tool: Unfortunately this did not work, is there anything else I can try to enable drawing methods ? Thank you in advance for your time to answer my question and kudos for sharing this excellent code, graph network library with the rest of us. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Neighborhood of vertex
by Roaa Soloh 25 Nov '19

25 Nov '19

Kindly I want to determine the neighborhood for each vertex in my graph but it is undirected, and the function used in the website, not working in my case, any suggestions? Thanks,

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Question about configuration model for bipartite networks
by Patrick Kaminski 21 Nov '19

21 Nov '19

Hi, Is this the right way to maintain the bipartite property of a graph for using the configuration model? Node labels are stored in type (true/false for the two classes). gt.random_rewire(g, model ='constrained-configuration' , n_iter = 1, block_membership = g.vp.type) Best, Patrick

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Update add_edge_list vertex property map
by danoli 20 Nov '19

20 Nov '19

Hi, I'm using the function add_edge_list() to add vertices/edges to the graph. However, I have to do the operation more than once and I was wondering if there was a way of updating property maps. For example: g = Graph() edges = [(0, 1), (4, 6), (1, 2)] vertex_map = g.add_edge_list(edges, hashed=True) g.vp["vertex_map"] = vertex_map print([(g.vertex_index[v], g.vp["vertex_map"][v]) for v in g.vertices()]) # [(0, 0), (1, 1), (2, 4), (3, 6), (4, 2)] edges = [(1, 6), (7, 8)] vertex_map = g.add_edge_list(edges, hashed=True) print([(g.vertex_index[v], vertex_map[v]) for v in g.vertices()]) -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Building animations with Graph Tool
by James Ruffle 17 Nov '19

17 Nov '19

Dear Graph-Tool Community, I am trying to use a customised version of the animation script provided in the graph-tool cookbook where you can save iterated steps as frames to then convert to a short movie, as per the Dynamic Layout here: https://graph-tool.skewed.de/static/doc/demos/animation/animation.html The script [below] seems to works with finite numbers of nodes, e.g. 1000. However, with larger numbers of nodes, all output frames look the same (?not iterating through properly).To scale up, I want to apply this to a graph with 20,000 nodes. from graph_tool.all import * from numpy.random import * from numpy.linalg import norm import sys, os, os.path from gi.repository import GLib import graph_tool.all as gt; import matplotlib; import math; import numpy; from gi.repository import Gtk, Gdk, GdkPixbuf, GObject g = random_graph(500, lambda: 1 + poisson(5), directed=False) #step = 0.05 # move step step=0.05 K = 0.5 # preferred edge length pos = sfdp_layout(g, K=K, max_iter=1) # initial layout positions offscreen = sys.argv[1] == "offscreen" if len(sys.argv) > 1 else False max_count = 50 if offscreen and not os.path.exists("./frames"): os.mkdir("./frames") if not offscreen: win = GraphWindow(g, pos, geometry=(400, 400),bg_color=[0,0,0,1]) else: win = Gtk.OffscreenWindow() win.set_default_size(400, 400) win.graph = GraphWidget(g, pos) win.add(win.graph) count = 0 def update_state(): global count sfdp_layout(g, pos=pos, K=K, init_step=step, max_iter=1) count += 1 win.graph.fit_to_window(ink=True) win.graph.regenerate_surface() win.graph.queue_draw() # if doing an offscreen animation, dump frame to disk if offscreen: pixbuf = win.get_pixbuf() pixbuf.savev(r'./frames/dancing%06d.png' % count, 'png', [], []) if count > max_count: sys.exit(0) return True # Bind the function above as an 'idle' callback. cid = GLib.idle_add(update_state) # We will give the user the ability to stop the program by closing the window. win.connect("delete_event", Gtk.main_quit) # Actually show the window, and start the main loop. win.show_all() Gtk.main() I have tried modifying step, in addition to the number of iterations and k, but have had no success. Does anyone have advice how to get it working for large numbers of nodes - i.e. 20,000…? Thank you! James

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Random graph with degree sequence.
by Alvaro Sechinel 07 Nov '19

07 Nov '19

Hi, I'm using graph-tool to try to generate random graphs with a sequence of degrees. For example, in a 3-node graph, I generated a random graph with all nodes with input degrees 1 and output degrees 1. My code: >>> import graph_tool.all as gt>>> def deg_sampler():... return 1,1... >>> g = gt.random_graph(3,deg_sampler,parallel_edges=True, self_loops=False)>>> gt.graph_draw(g) Can I generate a random graph defining the input and output degrees of each node? For example, tree nodes with respectively the input degrees (1, 2, 0) and output degrees (1, 0, 2). Thanks, Alvaro

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graph-tool 2.29 breaks backward compatibility
by Adrien Dulac 01 Nov '19

01 Nov '19

Hello folks, I've discovered, while trying to fix and 'never seen before' bug in my code, after having installed graph-tool 2.29 from an Ubuntu repo, that some new features was not backward compatible. For example, my error came from that fact that now, the function `get_edges` returns by default a `Nx2` matrix, whereas it used to return a `Nx3` matrix in prior version. Another one is that edge property doesn't seem to accept node tuple anymore (e.g. g.ep['weights'][i,j]) After a quick search on the doc, changelog and mailing list, I didn't find mention of these changes, so I am wandering if there is a place to find such information, and if there may be other changes that affect the backward compatibility in new version ? Regards, adrien

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graph-tool November 2019