Hello,
I'm writing an application with heavy graph operations. It's written in python, so i've tried networkx, igraph and lately i've tried to use boost graph library bindings to python (BGL-PY).
Thanks god i ran into graph-tool which looks very complete and also is doing a transition into something very handy for me (python accessible boost-based library).
I'm having a look at the API i found here: http://projects.forked.de/graph-tool/doc/quickstart.html#creating-and-manipu...
and i see i add vertices with g = Graph() g.add_vertices() and calculate the betweeness centrality with graph_tool.centrality.betweeness_centrality().
As i was looking for an implementation of a minimum spanning tree i realized i couldn't find it in the reference i pointed a couple of lines above.
So i had a look at the graph_tool.py that uses the library and realized that the interface is different there.
Graph = GraphInterface() Graph.GetBetweennessCentrality() or Graph.GetMinimumSpanningTree() etc, and i cannot find any add_vertex() in this API.
I'm a bit confused, so i'm trying to understand what i should use to have full power over the graph-tool API.
TIA
Claudio Martella
Hello Claudio,
Claudio Martella wrote:
Hello,
I'm writing an application with heavy graph operations. It's written in python, so i've tried networkx, igraph and lately i've tried to use boost graph library bindings to python (BGL-PY).
Thanks god i ran into graph-tool which looks very complete and also is doing a transition into something very handy for me (python accessible boost-based library).
Great. ;-)
I'm having a look at the API i found here: http://projects.forked.de/graph-tool/doc/quickstart.html#creating-and-manipu...
and i see i add vertices with g = Graph() g.add_vertices() and calculate the betweeness centrality with graph_tool.centrality.betweeness_centrality().
As i was looking for an implementation of a minimum spanning tree i realized i couldn't find it in the reference i pointed a couple of lines above.
So i had a look at the graph_tool.py that uses the library and realized that the interface is different there.
Graph = GraphInterface() Graph.GetBetweennessCentrality() or Graph.GetMinimumSpanningTree() etc, and i cannot find any add_vertex() in this API.
I'm a bit confused, so i'm trying to understand what i should use to have full power over the graph-tool API.
The minimum spanning tree code has not yet been ported to the new scheme, so it does not work at the moment. If you dig in the source code you will find the old code, but as you noticed it will not make much sense. Right now, you cannot really use it, sorry. :-(
The interface from graph-tool with C++ (with the BGL) is also something I plan to document, so that it will be easy for people to write extensions. There is even a module called run_action which allows inline embedding of C++ code, which is automatically compiled and run (via scipy's weave).
I'm currently finishing the documentation of the features which are implemented. I will then include more algorithms from BGL (such as minimum spanning tree, which is a high priority), which are relatively easy.
I cannot promise any time schedule, but hopefully all this will be done soon, as I'm working at it regularly. I'll post something in this list when it is done.
Cheers, Tiago
Tiago de Paula Peixoto wrote:
Hello Claudio,
Claudio Martella wrote:
Hello,
I'm writing an application with heavy graph operations. It's written in python, so i've tried networkx, igraph and lately i've tried to use boost graph library bindings to python (BGL-PY).
Thanks god i ran into graph-tool which looks very complete and also is doing a transition into something very handy for me (python accessible boost-based library).
Great. ;-)
I'm having a look at the API i found here: http://projects.forked.de/graph-tool/doc/quickstart.html#creating-and-manipu...
and i see i add vertices with g = Graph() g.add_vertices() and calculate the betweeness centrality with graph_tool.centrality.betweeness_centrality().
As i was looking for an implementation of a minimum spanning tree i realized i couldn't find it in the reference i pointed a couple of lines above.
So i had a look at the graph_tool.py that uses the library and realized that the interface is different there.
Graph = GraphInterface() Graph.GetBetweennessCentrality() or Graph.GetMinimumSpanningTree() etc, and i cannot find any add_vertex() in this API.
I'm a bit confused, so i'm trying to understand what i should use to have full power over the graph-tool API.
The minimum spanning tree code has not yet been ported to the new scheme, so it does not work at the moment. If you dig in the source code you will find the old code, but as you noticed it will not make much sense. Right now, you cannot really use it, sorry. :-(
The interface from graph-tool with C++ (with the BGL) is also something I plan to document, so that it will be easy for people to write extensions. There is even a module called run_action which allows inline embedding of C++ code, which is automatically compiled and run (via scipy's weave).
I'm currently finishing the documentation of the features which are implemented. I will then include more algorithms from BGL (such as minimum spanning tree, which is a high priority), which are relatively easy.
I cannot promise any time schedule, but hopefully all this will be done soon, as I'm working at it regularly. I'll post something in this list when it is done.
Just to make some things more clear about your question: If you want to calculate the betweenness centrality, for instance, you should do the following:
vbet, ebet = graph_tool.centrality.betweeness(g)
and then vbet and ebet are property maps with the vertex and edge betweeness centrality. All documented functions have short examples, and they show how you should use them. When minimum spanning tree is implemented, it will also work in a similar fashion.
Best regards, Tiago
Hello Tiago,
thanks for the answer. I'm really looking forward to contribute to your project with some porting, as I need minimum spanning tree capabilities and bellman-ford/dijkstra algorithms. I'll try to understand a bit the architecture you've put in place in order to do some implementations. In the meanwhile i wanted to run some benchmarking scripts to see how quicker graph_tool with openmp is compared to both networkx and and to igraph (ATM i can just compare the betweenness centrality).
So i gitted the development code and tried to build it but i had some compile time errors. I attach both the output of make and the config.log. I added ubuntu's gcc-snapshot package (which provides gcc 4.4) and overrid the system compiler by using CC and CXX pointint to the snapshot bins.
TIA
Claudio
On Thu, Aug 6, 2009 at 4:19 PM, Tiago de Paula Peixototiago@forked.de wrote:
Tiago de Paula Peixoto wrote:
Hello Claudio,
Claudio Martella wrote:
Hello,
I'm writing an application with heavy graph operations. It's written in python, so i've tried networkx, igraph and lately i've tried to use boost graph library bindings to python (BGL-PY).
Thanks god i ran into graph-tool which looks very complete and also is doing a transition into something very handy for me (python accessible boost-based library).
Great. ;-)
I'm having a look at the API i found here: http://projects.forked.de/graph-tool/doc/quickstart.html#creating-and-manipu...
and i see i add vertices with g = Graph() g.add_vertices() and calculate the betweeness centrality with graph_tool.centrality.betweeness_centrality().
As i was looking for an implementation of a minimum spanning tree i realized i couldn't find it in the reference i pointed a couple of lines above.
So i had a look at the graph_tool.py that uses the library and realized that the interface is different there.
Graph = GraphInterface() Graph.GetBetweennessCentrality() or Graph.GetMinimumSpanningTree() etc, and i cannot find any add_vertex() in this API.
I'm a bit confused, so i'm trying to understand what i should use to have full power over the graph-tool API.
The minimum spanning tree code has not yet been ported to the new scheme, so it does not work at the moment. If you dig in the source code you will find the old code, but as you noticed it will not make much sense. Right now, you cannot really use it, sorry. :-(
The interface from graph-tool with C++ (with the BGL) is also something I plan to document, so that it will be easy for people to write extensions. There is even a module called run_action which allows inline embedding of C++ code, which is automatically compiled and run (via scipy's weave).
I'm currently finishing the documentation of the features which are implemented. I will then include more algorithms from BGL (such as minimum spanning tree, which is a high priority), which are relatively easy.
I cannot promise any time schedule, but hopefully all this will be done soon, as I'm working at it regularly. I'll post something in this list when it is done.
Just to make some things more clear about your question: If you want to calculate the betweenness centrality, for instance, you should do the following:
vbet, ebet = graph_tool.centrality.betweeness(g)
and then vbet and ebet are property maps with the vertex and edge betweeness centrality. All documented functions have short examples, and they show how you should use them. When minimum spanning tree is implemented, it will also work in a similar fashion.
Best regards, Tiago
graph-tool mailing list graph-tool@forked.de http://lists.forked.de/mailman/listinfo/graph-tool
Hi Claudio,
Claudio Martella wrote:
So i gitted the development code and tried to build it but i had some compile time errors. I attach both the output of make and the config.log. I added ubuntu's gcc-snapshot package (which provides gcc 4.4) and overrid the system compiler by using CC and CXX pointint to the snapshot bins.
It seems to me the problem lies with boost, or with your boost + gcc combination. You have boost 1.34 apparently. Can you install version 1.39?
Cheers, Tiago
I installed 1.37 which is the latest boost on the latest ubuntu. the compilation goes on further but it dies anyway. I wanted to keep the system clean of scratch compilation but i'll work out a way to compile the system on my MacOSX.
I'll let you know ASA I manage.
On Fri, Aug 14, 2009 at 10:45 AM, Tiago de Paula Peixototiago@forked.de wrote:
Hi Claudio,
Claudio Martella wrote:
So i gitted the development code and tried to build it but i had some compile time errors. I attach both the output of make and the config.log. I added ubuntu's gcc-snapshot package (which provides gcc 4.4) and overrid the system compiler by using CC and CXX pointint to the snapshot bins.
It seems to me the problem lies with boost, or with your boost + gcc combination. You have boost 1.34 apparently. Can you install version 1.39?
Cheers, Tiago
graph-tool mailing list graph-tool@forked.de http://lists.forked.de/mailman/listinfo/graph-tool
Claudio Martella wrote:
I installed 1.37 which is the latest boost on the latest ubuntu. the compilation goes on further but it dies anyway. I wanted to keep the system clean of scratch compilation but i'll work out a way to compile the system on my MacOSX.
I'll let you know ASA I manage.
Please try the following if you have boost < 1.39:
git checkout 9587bf8f5b7 src/graph/read_graphviz_spirit.cpp
This might help.
Cheers, Taigo
-
Claudio Martella -
Tiago de Paula Peixoto