1. 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
  2. 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
  3. 13 Dec, 2007 1 commit
  4. 04 Nov, 2007 1 commit
  5. 07 Oct, 2007 1 commit
    • Tiago Peixoto's avatar
      Complete overhaul of command line parsing, and support for loading graph-tool... · cb61cc74
      Tiago Peixoto authored
      Complete overhaul of command line parsing, and support for loading graph-tool as whole as a python module
          
      The command line parsing was completely rewritten. It now supports
      better parsing of sub-options, with type checking and grouping
      support. Error reporting was also significantly improved, and it now
      warns of invalid options and option values, before the option is
      executed. Some syntax has changed, such as range filtering:
      --[vertex|edge]-range-filter was replaced by
      --exclude-[vertex|edge]-range and --keep-[vertex|edge]-range, which
      should have a clearer meaning. Ranges can also be specified now by
      comparison operators (>,<,>=,<=,=), such as ">=10", to indicate a
      range of (10, inf). In addition, ranges can now be easily open or
      closed at either end, by suffixing the specific end with '*', to
      indicate it is closed, ex: "10 700*" means (10,700].
          
      The graph-tool script can now be loaded as a python module (it must be
      renamed first to 'something.py'). All the command line options (except
      'for' and 'history' which become irrelevant) are available as
      functions, with full description and optional parameter support. In
      addition, pure function objects can be given as parameters where
      expressions are asked, instead of strings and files, which enables
      convenient extension of graph-tool.
      cb61cc74
  6. 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