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  1. 27 Mar, 2008 1 commit
    • Tiago Peixoto's avatar
      Port graph I/O to new filtering engine, enable graph pickling, and fix several issues · 99bf21c8
      Tiago Peixoto authored 
      Now graphml files properly contain all the supported value types, which
are all perfectly preserved when read (floating point data is now saved
in hexadecimal format). Several other improvements were made, such as
the ability to read and write to python file-like objects.

It is also now possible to have arbitrary python object properties, and
store them persistently (which is done internally with the pickling
interface).

vector<bool> was totally abolished, since its implementation is quite
broken. See: http://www.gotw.ca/publications/N1211.pdf and
http://www.gotw.ca/publications/N1185.pdf Now a uint8_t (aka. char) is
used in graph properties instead of a bool.

Graph types can now be fully pickled (this may not be feasible
memory-wise if the graph is too large, since the whole XML
representation is dumped to a string before it is saved on disc).
      99bf21c8
  3. 17 Feb, 2008 1 commit
    • Tiago Peixoto's avatar
      Split libgraph_tool into sub-modules and add test cases · 3cfff0cb
      Tiago Peixoto authored 
      This commit splits libraph_tool into different libraries:
 
   - libgraph_tool_core
   - libgraph_tool_clustering (*)
   - libgraph_tool_community (*)
   - libgraph_tool_correlations (*)
   - libgraph_tool_distance (*)
   - libgraph_tool_generation (*)
   - libgraph_tool_layout (*)
   - libgraph_tool_misc (*)
   - libgraph_tool_stats (*)

It also adds the python sub-module 'test', which provides extensive unit
testing of the core functionality. The core library is fully functional
and all test pass successfully.

(*) -> module needs to be ported to new refactoring, and does not yet build
      3cfff0cb
  5. 10 Feb, 2008 1 commit
    • Tiago Peixoto's avatar
      Refactor metaprogramming engine · 0b66e272
      Tiago Peixoto authored 
      This is a huge commit which completely refactors the metaprogramming
engine which generates and selects (at run time) the graph view type and
the desired algorithm implementation (template instantiation) that runs
on it.

Things are laid out now as following. There exists a main underlying
graph type (GraphInterface::multigraph_t) and several other template
classes that mask it some way or another, in a hierarchic fashion:

     multigraph_t -> filtered_graph (edges only, vertices only, both)
         |                               |           |           |
         |                               |           |           |
         |-------(reversed_graph)--------|-----------|-----------|
         |                               |           |           |
         \------(UndirectedAdaptor)------------------------------/

The filtered_graph filters out edges and/or vertices from the graph
based on some scalar boolean property. The reversed_graph reversed the
direction of the edges and, finally, the UndirectedAdaptor treats the
original directed graphs as undirected, transversing the in- and
out-edges of each vertex indifferently. Thus, the total number of graph
view types is 12. (The option --disable-graph-filtering can be passed to
the configure script, which will disable graph filtering altogether and
bring the total number down to 3, to reduce compile time and memory
usage)

In general, some specific algorithm, implemented as a template function
object, needs to be instantiated for each of those types. Furthermore,
the algorithm may also depend on other types, such as specific
property_maps. Thus, the following scheme is used:

    struct my_algorithm // algorithm to be implemented
    {
        template <class Graph, class PropertyMap>
        void operator()(Graph *g, PropertyMap p, double& result) const
        {
            // ...
        }
    };

    // in order for the above code to be instantiated at compile time
    // and selected at run time, the run_action template function object
    // is used from a member function of the GraphInterface class:

    double GraphInterface::MyAlgorithm(string prop_name)
    {
        double result;
        boost::any vprop = prop(property, _vertex_index, _properties);
        run_action<>()(*this, bind<void>(my_algorithm(), _1, _2,
                                         var(result)),
                       vertex_scalar_properties())(vprop);
        return result;
    }

The whole code was changed to reflect this scheme, but now things are
more centralized and less ad-hoc code needed to be
written. Unfortunately, due to GCC's high memory usage during template
instantiations, some of the code (namely all the degree correlation
things) had to be split in multiple compilation units... Maybe this will
change in the future if GCC gets optimized.

This commit also touches other parts of code. More specifically, the way
filtering gets done is very different. Now we only filter on boolean
properties, and with the above scheme, the desired implementation runs
with the correct chosen type, and no implicit type conversions should
ever happen, which would have a bad impact on performance.
      0b66e272
  7. 17 Dec, 2007 1 commit
    • Tiago Peixoto's avatar
      Fix visibility/RTTI problem with run_action() · 0c1f0df2
      Tiago Peixoto authored 
      Some visibility voodoo is necessary to ensure that RTTI work properly
across DSO boundaries, which is necessary to properly handle dynamic
property maps and such. Additionally, the action template must have a
different name each time the action code changes, to avoid additional
weirdness.

This also adds some other utility functions/typedefs to make writing
"inline" c++ code easier.
      0c1f0df2
  9. 14 Dec, 2007 1 commit
    • Tiago Peixoto's avatar
      Add support for running arbitrary C++ code from python · 866bb994
      Tiago Peixoto authored 
      It is now possible to run arbitrary "inline" C++ code from python, using
scipy.weave, as such:

        g = graph_tool.Graph()
        g.load("foo.xml")
        value = 2.0
        g.run_action('cout << num_vertices(g) << " " << value << endl;',
                     ["value"]);

The code gets compiled the first time, and is reused after that. Python
local and global variables can be passed to C++, as shown above, by
specifying a list of passed variables as the second argument.
      866bb994
  11. 13 Dec, 2007 1 commit
  13. 06 Dec, 2007 1 commit
  15. 30 Nov, 2007 1 commit
    • Tiago Peixoto's avatar
      Further improvements of the python interface · 1a0e9b5f
      Tiago Peixoto authored 
      Property maps can now be obtained as such:

         weight = g.edge_properties['weight']
         print weight[v] # v is a Vertex object
         weight[v] = 2.0
         # and so on...

The list of properties is obtained from g.vertex_properties,
g.edge_properties and g.graph_properties, which can be read as
dictionaries. The last can be set also, as such:

         g.graph_properties = {foo:"bar", baz:42}

Functions to add and remove vertices or adges were also added
(add_{vertex|edge}, remove_{vertex|edgge}).

Vertex and Edge types can also now be printed for convenience, as such:

       for v in g.vertices():
           print v
       for e in g.edges():
           print e

which results, for example, in:
0
1
2
3
4
5
6
(0,1)
(1,2)
(2,6)
(3,4)
(4,5)
(4,2)
(5,6)
(6,1)

(this also adds the forgotten graph_tool.py file, which was previously
on .gitignore)
      1a0e9b5f
  17. 26 Nov, 2007 1 commit
    • Tiago Peixoto's avatar
      Further improvement of python interface · 06358b7c
      Tiago Peixoto authored 
      Vertices and edges can be accessed from the graph class, as such:

    import graph_tool
    g = graph_tool.Graph()
    for v in g.vertices():
        for e in v.out_edges():
           # do something...

Additionally, the --edit-{vertex|edge|graph}-property was ported to the
new interface, and is working again, as it used to.

The Vertex and Edge class no longer have the 'get_property' and
'set_property' method. They'll be replaced by a new method of accessing
property maps.
      06358b7c
  19. 04 Nov, 2007 1 commit
  21. 23 Oct, 2007 2 commits
  23. 12 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      Added --purge-edges and --purge-vertices option · 23e319bf
      Tiago Peixoto authored 
          
Filtered vertices and edges can be permanently removed from the graph
with --purge-vertices and --purge-edges, respectively. The edge or
vertex filter is automatically removed, afterwards. This is useful if
maximum speed is necessary, and saving and reloading the graph without
filtering is not desired.
    
(this commit also removes some trailing whitespaces)
      23e319bf
  25. 07 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      Remove graph rewiring · f618944c
      Tiago Peixoto authored 
      Remove graph rewiring for now, since it's quite buggy. It will be
re-commited when ready.
      f618944c
  27. 04 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      · 8e962092
      Tiago Peixoto authored 
      Simplify range filtering, and definitely remove python filtering
    
Simplify range filtering of vertices and edges, by always filtering
both at once, even if all vertices or edges are being considered. This
severely reduces compilation time and memory, at a small potential
cost in run-time speed, which will probably be overshadowed by other
things, such as dynamic_map look-ups ("premature optimization is the
root of all evil"). Also, remove python-filtering, since, in the end,
it is just code bloat, since it is quite slow for most uses and can be
replaced, generally, by python property editing + range filtering.
      8e962092
  29. 12 Sep, 2007 1 commit
  31. 09 Aug, 2007 1 commit
    • Tiago Peixoto's avatar
      * src/graph-tool: change layout and community graph options. · c3a6567d
      Tiago Peixoto authored 
      	* src/boost-workaround/boost/graph/kamada_kawai_spring_layout.hpp: annotated code with openmp constructs.

	* src/graph/graph_adaptor.hh: graph_type should be a typedef to the original graph.

	* src/graph/graph_properties.hh, src/graph/graph_properties.cc: added pos_t type.

	* src/boost-workaround/boost/graph/fruchterman_reingold.hpp: annotated code with openmp constructs.

	* src/graph/graph_layout.cc: new file with graph layout routines.

	* src/graph/graph.cc: removed graph layout routines.

	* src/graph/graph_community_network.cc (struct get_community_network): fixed inversion of directedness test.

	* src/graph/graph.cc (GraphInterface::LabelComponents): use vector_property_map instead of HashedDescriptor. Don't use a static map!

	* src/graph/graph_adaptor.hh: fixed edge descriptor equality comparison, which must rely on underlying edge, regardless of whether it's inverted or not.


git-svn-id: https://svn.forked.de/graph-tool/trunk@121 d4600afd-f417-0410-95de-beed9576f240
      c3a6567d
  33. 11 Jul, 2007 1 commit
    • Tiago Peixoto's avatar
      · 32990eb6
      Tiago Peixoto authored 
              * ChangeLog: updated ChangeLog file with svn history

        * src/graph/graph_filtering.hh: added add_edge() and remove_edge() functions for filtered graphs

        * src/graph/shared_map.hh: included SharedContainer

        * src/graph/graph_rewiring.cc: initial support for random graph rewiring



git-svn-id: https://svn.forked.de/graph-tool/trunk@114 d4600afd-f417-0410-95de-beed9576f240
      32990eb6
  35. 02 Jul, 2007 1 commit
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