1. 10 Apr, 2008 1 commit
    • Tiago Peixoto's avatar
      Correlations algorithms refactoring · 360a3395
      Tiago Peixoto authored
      The whole histogram code has been redone, and the code has been
      simplified. The three-point vertex-edge-vertex correlation has been
      scrapped, since it's not frequently used, and would make compilation
      even more expensive.
      
      This also adds some missing files to the generation routine.
      360a3395
  2. 06 Apr, 2008 1 commit
  3. 04 Apr, 2008 1 commit
  4. 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
  5. 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
  6. 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. 21 Dec, 2007 1 commit
    • Tiago Peixoto's avatar
      Directory restructuring of graph_tool Python module (now a package) · 4a7da8a9
      Tiago Peixoto authored
      Everything was moved into the graph_tool directory, which should have,
      after installation, the following structure:
      
      graph_tool/                          Top-level package
            __init__.py                    Initialize the graph_tool package
            libgraph_tool.so               libgraph_tool submodule
            libgraph_tool.la               libtool file for libgraph_tool
            include/                       C++ include files for dynamically
                                           compiled code
      4a7da8a9
  8. 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
  10. 13 Dec, 2007 1 commit
  11. 06 Dec, 2007 1 commit
  12. 03 Dec, 2007 4 commits
  13. 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
  14. 28 Nov, 2007 1 commit
  15. 26 Nov, 2007 2 commits
    • Tiago Peixoto's avatar
      e1375c3c
    • 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
  16. 11 Nov, 2007 1 commit
  17. 10 Nov, 2007 2 commits
  18. 05 Nov, 2007 1 commit
    • Ale Abdo's avatar
      Correlated random rewiring functional · 0b15235f
      Ale Abdo authored
      Several changes in the random rewiring code, making it fully
      functional for the correlated case.
      The reshuffling operations lag in efficiency, even though already
      the algorithm runs in little time.
      0b15235f
  19. 04 Nov, 2007 2 commits
  20. 24 Oct, 2007 2 commits
    • Tiago Peixoto's avatar
      Fix Set{Vertex|Edge}FilterRange() when boundaries are -inf · 8ed48c65
      Tiago Peixoto authored
      This fixes the same problem as commit 6663be71, but which arises
      when a filter range boundary is -inf (such as "<=100").
      8ed48c65
    • Tiago Peixoto's avatar
      Fix vertex and edge filtering, when only one is active · 300d6f4a
      Tiago Peixoto authored
          
      When only one of vertex or edge filtering was disabled, the allowed
      range of the disabled filter was set to
      ]numeric_limits<double>::min(), numeric_limits<double>::max()[, and
      the selected filtering property was the respective index. But
      according to the STL documentation from GCC,
      numeric_limits<>::min() returns:
          
         "The minimum finite value, or for floating types with
          denormalization, the minimum positive normalized value."
          
      which is always positive for double (!), thus introducing a weird
      regression, where the first vertex (index 0) is always filtered out if
      only the edge filter is active, and vice-versa.
      300d6f4a
  21. 23 Oct, 2007 2 commits
  22. 12 Oct, 2007 2 commits
    • Ale Abdo's avatar
      Implements extended_clustering for directed graphs, based on the fraction of... · 622cc24e
      Ale Abdo authored
      Implements extended_clustering for directed graphs, based on the fraction of possible directed cycles (out-in edges combination).
      The old behavior is still present since it was equivalent to treating the directed graph as undirected (use --undirected option).
      622cc24e
    • 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
  23. 11 Oct, 2007 1 commit
  24. 10 Oct, 2007 2 commits
  25. 07 Oct, 2007 3 commits
    • 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
    • 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
    • Tiago Peixoto's avatar
      fix edge vs. vertex betweenness mixup, and GetCentralPointDominance · 55028b02
      Tiago Peixoto authored
      for undirected graphs
      55028b02
  26. 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
  27. 12 Sep, 2007 2 commits