Questions tagged [graph-tool]

Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). http://graph-tool.skewed.de/

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How to get X Y coordinates of lattice graph using graph_tool

I am creating a lattice graph using graph_tool. I am trying to create a Property Map that represents X Y coordinates in the graph. For instance, if I create a lattice graph with a height of 5 and a ...
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41 views

Conda install graph-tool failed on win-64

I've tried to install graph-tool via anaconda for python 2.7: conda install -c kristanarmstrong graph-tool I got the following error: UnsatisfiableError: The following specifications were found to ...
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23 views

graph-tool Euler circuit

I am currently using the graph-tool library with Python (3.6) and I just noticed that there is no functionality to extract a Eulerian/Hamiltonian path/circuit. Is there a particular reason for this? I ...
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30 views

AttributeError: module 'graph_tool.draw' has no attribute 'draw_hierarchy' is returned when running my code, which is not true

I'm trying to run a script that uses graph tools, and the code returns: /usr/lib/python3/dist-packages/graph_tool/all.py:40: RuntimeWarning: Error importing draw module, proceeding nevertheless: No ...
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18 views

OpenMP on mac (Mojave) along with graph-tool python

I am trying to use multi-threading on mac with python graph-tool Currently when I import graph-tool and do: openmp_enabled() <---this returns False I want to know what steps I need to take to be ...
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28 views

Community detection with (nested and non-nested) stochastic block model for (weighted) bipartite networks using python package graph-tool

I'm new to Python and I would like to use the package graph-tool to estimate the optimal number of communities in my network using the stochastic block model (nested and non-nested) approach. I read ...
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32 views

How to generate a scale free network with a desired power law distribution and fixed average degrees via graph-tool?

I'm trying to reproduce the synthetic networks described in some papers. How to create scale-free networks with desired power-law degree distributions and fixed average degrees, P(k)=k^(-λ)? The ...
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15 views

Graph_Tool - Initialize edge properties more efficiently

I am using graph-tool to calculate some centrality measures. from graph_tool.all import * graph = Graph(directed=True) Before I do that, I need to initialize the edge properties. I am doing the ...
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70 views

Load an edge-list into graph-tool

I want to load an edge-list into graph-tool. The vertex-indices in my list are not sequential, so I would like them to be automatically added as vertex_properties. As far as I understand this should ...
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63 views

(Python graph-tool) graph-tool search using OpenMP? Can finding all paths between a source and target vertex be made parallel?

I am currently using graph_tool.topology.all_paths to find all paths between two vertices of a specific length, but the documentation doesn't explicitly say what algorithm is used. I assume it is ...
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27 views

(Python graph-tool) Find paths of a specific length using graph-tool?

Is there a way to find paths between two vertices in a graph of a specific length? I know I can find the shortest path using: graph_tool.topology.all_shortest_paths and that I can find paths of a ...
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47 views

Adding edges using add_edge_list (graph-tool) from Pandas dataframe in a loop writes zeros to property map

I am trying to create a directed graph from a very large data-set (200 million edges) using graph-tool. I am using chunksize in Pandas to work with the data because of memory constraints. The data (...
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2answers
73 views

Efficient shortest path in DAG with Python's graph-tool

Task: I want to compute a shortest path between a source and target node in a DAG (directed acyclic graph) using Python's graph-tool efficiently. My DAG has negative weights. In theory, this is a ...
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47 views

MacOS Sierra - brew installs graph-tool with openmp disabled

Running brew install graph-tool on MacOs 10.13.4 does install graph-tool but openmp seems disabled. Am I missing a brew option to have openmp enabled? I did run brew install libomp prior to ...
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32 views

How to I display a figure using graph-tool without the program blocking?

I am trying to write a program which dynamically updates a graph visualization as the state of the graph changes. Currently, the graph_draw method in graph-tool causes the program to halt until the ...
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60 views

conda error when installing geopandas and graph-tool

I'm trying to import geographic data using geopandas and process it with graph-tool, however when I try to install both of these packages with conda, when I import geopandas, I get libgdal.so.20: ...
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48 views

A node's contribution to its Katz centrality

Let G be n x n adjacency matrix of a weighted directed graph. Define the vector of Katz centralities by c = (I- a G)^{-1}.b where I is identity matrix, a is a positive scalar, b is a column vector, ...
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45 views

python graph-tool: Fastest way to add edges without duplicates?

What's the fastest/most performant way to add edges without duplicates to a digraph in Python's graph-tool? The naive solution would be to call g.edge(u, v) before adding edges, but that seems like ...
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94 views

How to attach graph-tool to Django using Docker

I need to use some graph-tool calculations in my Django project. So I started with docker pull tiagopeixoto/graph-tool and then added it to my Docker-compose file: version: '3' services: db: ...
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66 views

graph visualization: graph-tool package python

I have a high order graph that draw by graph-tool package python. but I need a graph visualization that make a better form. is it possible that draw the graph-tool graph by graphviz package? or some ...
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76 views

How can I calculate the girth of a graph using graph-tool?

Graph-tool offers a lot of tools for assessing a graph: https://graph-tool.skewed.de/static/doc/topology.html. However, I can't find any method for calculating the girth, i.e., the shortest cycle in ...
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151 views

python - computing weighted betweenness centrality for nodes of a huge graph

I have a huge graph (say for example 300,000 nodes and 1,000,000 edges) which I'm analyzing using Python on an Ubuntu machine with 32GB of RAM and 4 CPU cores. I found graph-tool to be a very ...
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244 views

Graph-tool installed, Import.all does not work

I have installed graph-tool: brew --prefix graph-tool '/usr/local/opt/graph-tool but when trying to import it: Python 3.6.4 |Anaconda, Inc.| (default, Jan 16 2018, 12:04:33) [GCC 4.2.1 Compatible ...
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67 views

Graph-tool: Dijkstra search with multiple weights constraints

I am using graph-tool library for python to find the shortest path between two vertex. I have multiple weights for the edges and based on the certain conditions the appropriate wight values is chosen ...
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1answer
34 views

minimize_blockmodel_dl with weighted graph

I am trying to use minimize_blockmodel_dl to identify communities in a weighted (undirected) graph. I found out that this method once supported a eweight parameter, but it doesn't anymore. Is there ...
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66 views

implementing Girvan-Newman in graph-tool

I'm trying to implement the Girvan-Newman algo in graph-tool and using igraph to cross-check the number of clusters. The problem is I'm getting more clusters, around 460, than the igraph version, 23. ...
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30 views

has_path equivalent in Graph-Tool

Does graph-tool have any equivalent function to NetworkX's has_path? I'd like to return True if there's a valid path between any given nodes.
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138 views

Finding all paths between source and target in graph-tool, return edges instead of vertices

Stack Overflow! I have a directed graph and need to find all paths between a source and target vertex. Between several vertices, there are multiple edges. Using graph-tool, one may suggest using ...
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1answer
46 views

Connecting subgraphs programmatically

I am looking for a graph theory package in Python or C++ that enables me to create edges between subgraphs/clusters and their nodes at will, as depicted in the accepted answer to this question, to ...
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150 views

How to check OpenMP usage in python graph-tool

I am using python graph-tool for this algorithm in order to find min-cut in a large graph. My algorithm needs several calls to this function, and it seems to be the bottleneck. So I want to ensure if ...
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2answers
62 views

BGL: Get initial direction of edge in undirected graph

In an undirected BGL graph: Can I get the information whether an edge (u,v) == (v,u) was initially added as (u,v) or as (v,u)? Background: I created a graph using Pythons graph-tool library which ...
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61 views

graph-tool: How do I maintain an ordered set of vertices?

I am working on a network using graph-tool. Within the set of all vertices, there are specific groups of vertices with a well defined order that I would like to keep track of. Until now, I have been ...
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1answer
87 views

Draw only biggest connected subgraph in graph-tool

In graph-tool, is there a way to only draw the biggest connected subgraph? I'm currently having one big connected subgraph and a few smaller connected subgraphs I'm not particularly interested in. I'm ...
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46 views

Multiple subplots using graph-tool

I'm currently trying to plot several graphs on the same figure using graph-tool, but I'm confronted with a weird bug. I'm using the fact that the graph_draw() function allows to specify a container ...
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42 views

Issue with python graph-tool TSP tour

I'm relatively new to Hamiltonian path and Travelling Salesman Problem (TSP). Particularly for my application, I was attracted to use graph-tool because of its built-in tsp_tour function that "returns ...
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1answer
162 views

Setting up graph-tool on Docker Toolbox for WIndows

I followed the graph-tool docker installation instructions here. I've set up Docker Toolbox (can't use Docker for Windows, not on Pro), and I've gotten jupyter running with the Docker image. However, ...
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160 views

graph-tool: How do I find vertices that fit a certain property value?

I have a class Node that I set as a property for a graph using graph-tool. from graph_tool.all import * class Node(object): def __init__(self, name, age): self.symbol = name self....
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90 views

How do I access Class fields in Python Graph-Tool property maps?

I'm trying to draw a graph with a class as a vertex property. How do I draw the graph with the vertex_text set to the name field of the classes they contain? from graph_tool.all import * class Node(...
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249 views

Graph-tool: compile and connect to local CGAL library, in Linux? (no sudo)

[Ubuntu] I have compiled CGAL locally: /path/to/cgal/ /lib/ libCGAL_Core.so libCGAL_Core.so.13.0.2 libCGAL_ImageIO.so.13 libCGAL.so libCGAL.so.13.0.2 ...
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54 views

Installing graph-tool with local BOOST

In order to install graph-tool, I must install dependencies with autoconf. Some of these dependencies use boost, and I link my local boost install to these dependencies with: export BOOST_ROOT=/my/...
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1answer
420 views

Installing graph-tool library on conda installed python 3.5, Mac OS

Precisely the same as here, which hasn't been resolved. Followed the sequential directions here; all channels added. Tried: Adding to .bash_profile export PKG_CONFIG_PATH=$PKG_CONFIG_PATH://...
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1answer
63 views

Is there a way to add a title or a caption to the drawing using graph_tool

At least some workaround would be appreciated. I am trying to save the figures as pdfs and then use it with latex as an animation. If there is a way to automatically add captions that will be really ...
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54 views

best library or framework to build heavy weight graph based interactive applications

My company asked me to start working on a project that needs to work(interactively) with graphs. It needs to handle creating and maintaining couple of thousands of graph nodes in a way that user can ...
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2answers
56 views

How can I retrieve a selected vertex in graph-tool?

I would like to be able to retrieve the vertex_index of a currently selected vertex (the vertex currently having the mouse over it). I have not found this question asked in StackOverflow, nor this ...
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1answer
37 views

graph-tool - Edges between separate graphs?

In graph-tool, I have a forest of graphs and I want to add special edges across the graphs from/to specific nodes without encapsulating all the graphs into a new bigger multi-graph. Is there a way to ...
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75 views

joblib parallel for with graph-tool filtering?

With graph-tool and joblib working together, do we need to send graph.copy() in the "Parallel" call like in the code below when using graph vertex filtering with .set_vertex_filter? graph.copy() makes ...
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165 views

How to compile graph-tool in ubuntu

I am trying to compile and install graph-tool version 2.26 in ubuntu using ./configure but I am getting following error checking for boostlib >= 1.55.0 (105500)... yes checking whether the Boost::...
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1answer
67 views

Align the node labels radially in draw_hierarchy

How is it possible to align the labels of nodes to oriente radially toward center using "draw_hierarchy"? The text file which contains my dataset about my network, in each row has the labels of two ...
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1answer
202 views

What installation dependencies/options are needed for graph-tool to include draw_hierarchy?

I've installed graph-tool 2.26 on ubuntu 14.04, python 3.5.4. I can use graph-tool, but it seems incomplete. For example I've seen this error: AttributeError: module 'graph_tool.draw' has no ...
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1answer
62 views

graph-tool draw function cannot show Chinese text

I am using graph-tool and trying to draw graphs with node property of Chinese words. However, when I draw it using # coding=utf-8 from graph_tool.all import * # English string as vertex name g = ...