graph-tool January 2019

graph-tool@skewed.de

12 participants
18 discussions

Image segmentation with graph cut in graph-tool
by Hakim 23 Jan '19

23 Jan '19

Hi, I've just started reading about Graph cut and Boykov-Kolmogorov algorithm in particular, which is implemented in Graph-tool. I need it to perform an object-based segmentation of an image that was previously thresholded to getting rid of the noise. I was wondering if it was possible to go from an image to a graph (and the other way around) in graph-tool? and what would be an efficient way to do it? Thanks. Hakim. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Make error when looking for libsigc-2.0.la
by getzinmw 21 Jan '19

21 Jan '19

Hello, I recently had to repartition my hard-drive and went with the new Ubuntu build. I have spent the last many few hours trying to build graph-tool with all of the correct dependencies. I thought I had made it as the make file was being prepared, however, while it was "Making all in draw" I got the following error: /bin/grep: /home/getzinmw/anaconda3/lib/libsigc-2.0.la: No such file or directory /bin/sed: can't read /home/getzinmw/anaconda3/lib/libsigc-2.0.la: No such file or directory libtool: error: '/home/getzinmw/anaconda3/lib/libsigc-2.0.la' is not a valid libtool archive I have done quite a bit of digging and it seems like, despite having libsigc-2.0.so.0 file(s) the libtool archive that it is looking for does not exist. Can you help me get past this? Thanks in advance...Sorry for an inconvenience. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Make error when looking for libsigc-2.0.la
by getzinmw 19 Jan '19

19 Jan '19

Hello, I recently had to repartition my hard-drive and went with the new Ubuntu build. I have spent the last many few hours trying to build graph-tool with all of the correct dependencies. I thought I had made it as the make file was being prepared, however, while it was "Making all in draw" I got the following error: /bin/grep: /home/getzinmw/anaconda3/lib/libsigc-2.0.la: No such file or directory /bin/sed: can't read /home/getzinmw/anaconda3/lib/libsigc-2.0.la: No such file or directory libtool: error: '/home/getzinmw/anaconda3/lib/libsigc-2.0.la' is not a valid libtool archive I have done quite a bit of digging and it seems like, despite having libsigc-2.0.so.0 file(s) the libtool archive that it is looking for does not exist. Can you help me get past this? Thanks in advance...Sorry for an inconvenience. config.log <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Edge property map for int type
by ashutosh 11 Jan '19

11 Jan '19

pdat = pd.DataFrame({'source':['A','B','C'],'target':['p','q','r'],'weight':[1,-1,2]}) graph = gt.Graph(directed=True) eprop = graph.new_edge_property("vector<int>") vprop = graph.add_edge_list(pdat[['source','target','weight']].values.tolist(), hashed=True,string_vals=True,eprops=[eprop]) I get the error TypeError: 'int' object is not iterable But not when the eprop is <string> I know I am missing something, but the property map page in the documentation doesn't elaborate clearly. -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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graph-tool example failure
by Moritz Warning 11 Jan '19

11 Jan '19

Hi, I tried to following: $ docker run -it -u user -w /home/user tiagopeixoto/graph-tool ipython Python 3.6.5 (default, May 11 2018, 04:00:52) Type 'copyright', 'credits' or 'license' for more information IPython 6.3.1 -- An enhanced Interactive Python. Type '?' for help. In [1]: from graph_tool.all import * Unable to init server: Could not connect: Connection refused Unable to init server: Could not connect: Connection refused In [2]: g = Graph() In [3]: v1 = g.add_vertex() In [4]: v2 = g.add_vertex() In [5]: e = g.add_edge(v1, v2) In [6]: graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18, ...: output_size=(200, 200), output="two-nodes.png") Out[6]: <PropertyMap object with key type 'Vertex' and value type 'vector<double>', for Graph 0x7f60e1fbadd8, at 0x7f60e1fbcd68> Do I make any obvious mistake? thanks, mwarning

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Getting negative entropy/positive Log likelihood for a weighted network with positive edge weights.
by isukritgupta 10 Jan '19

10 Jan '19

Dear Tiago, I am trying to model a weighted dense network with edge weights in the range 0 to 1, with the non-hierarchical SBM for both degree corrected and non-degree corrected versions. However, I get negative entropy for both dc and ndc SBMs. I have attached a sample network for your consideration along with a minimal working example from my code. Thanks for your time! Sukrit sukrit_network.gz <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> working_example_W_SBM.py <http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com…> -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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add_edge_list() and undirected graph
by Christopher Morris 07 Jan '19

07 Jan '19

Given an *undirected* graph g with four vertices, I add edges by g.add_edge_list([(0, 1), (0, 2), (0, 3), (1, 0), (1, 2), (1, 3), (2, 0), (2, 1), (2, 3), (3, 0), (3, 1), (3, 2)]) . When calling g.num_edges() the result is 12. In my opinion it should be 6, as the graph is undirected? Any ideas? -- Christopher Morris Algorithm Engineering, Department of Computer Science, TU Dortmund University https://ls11-www.cs.tu-dortmund.de/staff/morris

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Retrieving distances from shortest_distance
by elastica 06 Jan '19

06 Jan '19

Hi and happy new year graph coders! The shortest_distance function implements the Floyd's algorithm. I am carefully following the example provided by the docs <https://graph-tool.skewed.de/static/doc/topology.html#graph_tool.topology.s…> but the function doesn't return the expected result. Here is my trivial try: # ------------------- import graph_tool as gt from graph_tool.topology import shortest_distance import numpy as np wedges=[(2, 0, 6.0), (0, 3, 7.0), (0, 2, 2.0)] print(wedges) # Définition of the weighted graph g= gt.Graph(directed=True) weight = g.new_edge_property("double") g.add_edge_list(np.array(wedges), eprops=[weight]) # Floyd call dist=shortest_distance(g, dense=True) # I'm expecting the vector distance from vertex 2 print(dist[g.vertex(2)]) # ------------------- outputting : # ------------------- [(2, 0, 6.0), (0, 3, 7.0), (0, 2, 2.0)] array([ 1, 2147483647, 0, 2], dtype=int32) # ------------------- This not the correct distance vector from the 2-indexed node nor the correct predecessor vector. And I don't understand why I get an int32 vector since the weights have double type. Can somebody please correct my code in order to get the correct distances? Pascal -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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graph-tool January 2019