Some reorganization and change check_filter() to run_action()

src/graph/graph.cc

@@ -389,11 +389,9 @@ size_t GraphInterface::GetNumberOfVertices() const
 {
     size_t n = 0;
     if (IsVertexFilterActive())
-        check_filter(*this,var(n)=bind<size_t>(HardNumVertices(),_1),
-                     reverse_check(),directed_check());
+        run_action(*this,var(n)=bind<size_t>(HardNumVertices(),_1));
     else
-        check_filter(*this,var(n)=bind<size_t>(SoftNumVertices(),_1),
-                     reverse_check(),directed_check());
+        run_action(*this,var(n)=bind<size_t>(SoftNumVertices(),_1));
     return n;
 }
 
@@ -404,11 +402,9 @@ size_t GraphInterface::GetNumberOfEdges() const
 {
     size_t n = 0;
     if (IsEdgeFilterActive() || IsVertexFilterActive())
-        check_filter(*this,var(n)=bind<size_t>(HardNumEdges(),_1),
-                     reverse_check(),directed_check());
+        run_action(*this,var(n)=bind<size_t>(HardNumEdges(),_1));
     else
-        check_filter(*this,var(n)=bind<size_t>(SoftNumEdges(),_1),
-                     reverse_check(),directed_check());
+        run_action(*this,var(n)=bind<size_t>(SoftNumEdges(),_1));
     return n;
 }
 
@@ -441,7 +437,7 @@ struct get_vertex_histogram
 struct choose_vertex_histogram
 {
     choose_vertex_histogram(const GraphInterface& g, GraphInterface::deg_t deg,
-                            GraphInterface::hist_t& hist)
+                            hist_t& hist)
         : _g(g), _hist(hist)
     {
         tie(_deg, _deg_name) = get_degree_type(deg);
@@ -452,20 +448,19 @@ struct choose_vertex_histogram
         if (mpl::at<degree_selector_index,DegreeSelector>::type::value == _deg)
         {
             DegreeSelector selector(_deg_name, _g, true);
-            check_filter(_g, bind<void>(get_vertex_histogram<DegreeSelector>
-                                        (selector), _1, var(_hist)),
-                         reverse_check(),directed_check());
+            run_action(_g, bind<void>(get_vertex_histogram<DegreeSelector>
+                                        (selector), _1, var(_hist)));
         }
     }
     const GraphInterface &_g;
-    GraphInterface::hist_t &_hist;
+    hist_t &_hist;
     GraphInterface::degree_t _deg;
     string _deg_name;
 };
 
 
 // this will return the vertex histogram of degrees or scalar properties
-GraphInterface::hist_t
+hist_t
 GraphInterface::GetVertexHistogram(GraphInterface::deg_t deg) const
 {
     hist_t hist;
@@ -522,14 +517,13 @@ struct get_edge_histogram
 
 
 // returns the histogram of a given edge property
-GraphInterface::hist_t GraphInterface::GetEdgeHistogram(string property) const
+hist_t GraphInterface::GetEdgeHistogram(string property) const
 {
     hist_t hist;
     try
     {
         scalarS prop(property, *this, false);
-        check_filter(*this, bind<void>(get_edge_histogram(prop), _1, var(hist)),
-                     reverse_check(),directed_check());
+        run_action(*this, bind<void>(get_edge_histogram(prop), _1, var(hist)));
     }
     catch (dynamic_get_failure &e)
     {
@@ -576,8 +570,7 @@ void GraphInterface::LabelComponents(string prop)
     typedef vector_property_map<size_t, vertex_index_map_t> comp_map_t;
     comp_map_t comp_map(_vertex_index);
 
-    check_filter(*this, bind<void>(label_components(), _1, comp_map),
-                 reverse_check(), directed_check());
+    run_action(*this, bind<void>(label_components(), _1, comp_map));
 
     try
     {
@@ -634,17 +627,15 @@ void GraphInterface::LabelParallelEdges(string property)
         DynamicPropertyMapWrap<size_t,edge_t>
             parallel_map(find_property_map(_properties, property,
                                            typeid(edge_t)));
-        check_filter(*this, bind<void>(label_parallel_edges(), _1, _edge_index,
-                                       parallel_map),
-                     reverse_check(), directed_check());
+        run_action(*this, bind<void>(label_parallel_edges(), _1, _edge_index,
+                                       parallel_map));
     }
     catch (property_not_found)
     {
         typedef vector_property_map<size_t,edge_index_map_t> parallel_map_t;
         parallel_map_t parallel_map(_edge_index);
-        check_filter(*this, bind<void>(label_parallel_edges(), _1, _edge_index,
-                                       parallel_map),
-                     reverse_check(), directed_check());
+        run_action(*this, bind<void>(label_parallel_edges(), _1, _edge_index,
+                                     parallel_map));
         _properties.property(property, parallel_map);
     }
 }

src/graph/graph.hh

@@ -19,7 +19,6 @@
 #ifndef GRAPH_HH
 #define GRAPH_HH
 
-#include <tr1/unordered_map>
 #include <boost/graph/graph_traits.hpp>
 #include <boost/graph/adjacency_list.hpp>
 #include <boost/vector_property_map.hpp>
@@ -47,39 +46,76 @@ public:
     GraphInterface();
     ~GraphInterface();
 
+    // this enum specifies all the different types of degree
     enum degree_t
     {
         IN_DEGREE,
         OUT_DEGREE,
-        TOTAL_DEGREE,
-        SCALAR
+        TOTAL_DEGREE, // in + out
+        SCALAR        // scalar vertex property
     };
 
-    // histogram types
-    typedef tr1::unordered_map<double,double> hist_t;
-    typedef tr1::unordered_map<pair<double,double>,double,
-                                    hash<pair<double,double> > > hist2d_t;
-    typedef tr1::unordered_map<tuple<double,double,double>,double,
-                               hash<tuple<double,double,double> > > hist3d_t;
-    typedef tr1::unordered_map<double,pair<double,double> > avg_corr_t;
+    typedef variant<degree_t,string> deg_t; // useful when function also expects
+                                            // a scalar vertex property
 
-    typedef variant<degree_t,string> deg_t;
+    //
+    // Basic manipulation
+    //
 
-    //graph generation
-    void GenerateCorrelatedConfigurationalModel
-        (size_t N, python::object ppjk, python::object pceil_pjk,
-         python::object pinv_ceil_pjk, double ceil_pjk_bound,
-         python::object pcorr, python::object pceil_corr,
-         python::object pinv_ceil_corr, double ceil_corr_bound,
-         bool undirected_corr, size_t seed, bool verbose);
-
-    // basic stats
     size_t GetNumberOfVertices() const;
     size_t GetNumberOfEdges() const;
+    void SetDirected(bool directed) {_directed = directed;}
+    bool GetDirected() const {return _directed;}
+    void SetReversed(bool reversed) {_reversed = reversed;}
+    bool GetReversed() const {return _reversed;}
+
+
+    // graph filtering
+    void SetVertexFilterProperty(string property);
+    void SetVertexFilterRange(pair<double,double> allowed_range,
+                              pair<bool,bool> include, bool invert);
+    bool IsVertexFilterActive() const;
+
+    void SetEdgeFilterProperty(string property);
+    void SetEdgeFilterRange(pair<double,double> allowed_range,
+                            pair<bool,bool> include, bool invert);
+    bool IsEdgeFilterActive() const;
+
+
+    // graph modification
+    void RemoveVertexProperty(string property);
+    void RemoveEdgeProperty(string property);
+    void RemoveGraphProperty(string property);
+    void InsertEdgeIndexProperty(string property);
+    void InsertVertexIndexProperty(string property);
+    void EditVertexProperty(string property, string type, python::object op,
+                            python::object g);
+    void EditEdgeProperty(string property, string type, python::object op,
+                          python::object g);
+    void EditGraphProperty(string property, string type, python::object op,
+                           python::object g);
+    void ReIndexEdges();
+    void PurgeVertices(); // removes filtered vertices
+    void PurgeEdges();    // removes filtered edges
+    void RandomRewire(std::string strat, bool self_loops, bool parallel_edges,
+                      size_t seed);
+
+    // i/o
+    void WriteToFile(string s);
+    void WriteToFile(string s, string format);
+    void ReadFromFile(string s);
+    void ReadFromFile(string s, string format);
+
+    //
+    // Algorithms
+    // Below are all the algorithms that operate somehow on the graph
+    //
+
+    // basic statistics
     hist_t GetVertexHistogram(deg_t degree) const;
     hist_t GetEdgeHistogram(string property) const;
 
-    //correlations
+    // correlations
     hist2d_t   GetCombinedVertexHistogram(deg_t degree1, deg_t degree2) const;
     avg_corr_t GetAverageCombinedVertexCorrelation(deg_t degree1,
                                                    deg_t degree2)const;
@@ -91,11 +127,11 @@ public:
                                                       deg_t neighbour_degree,
                                                       string weight) const;
 
-    // mixing
+    // vertex mixing
     pair<double,double> GetAssortativityCoefficient(deg_t deg) const;
     pair<double,double> GetScalarAssortativityCoefficient(deg_t deg) const;
 
-    //clustering
+    // clustering
     void SetLocalClusteringToProperty(string property);
     pair<double,double> GetGlobalClustering();
     void SetExtendedClusteringToProperty(string property_prefix,
@@ -115,7 +151,7 @@ public:
     double GetCentralPointDominance(string vertex_betweenness);
 
     // community structure
-    enum comm_corr_t
+    enum comm_corr_t // null model correlation type
     {
         ERDOS_REYNI,
         UNCORRELATED,
@@ -127,57 +163,24 @@ public:
                                  size_t seed, bool verbose, string history_file,
                                  string weight, string property);
     double GetModularity(string weight, string property);
+    // TODO: this should return a GraphInterface type
     void   GetCommunityNetwork(string property, string size_property,
                                string out_file, string format) const;
 
-    void RandomRewire(std::string strat, bool self_loops, bool parallel_edges,
-                      size_t seed);
-
-    // filtering
-    void SetDirected(bool directed) {_directed = directed;}
-    bool GetDirected() const {return _directed;}
-
-    void SetReversed(bool reversed) {_reversed = reversed;}
-    bool GetReversed() const {return _reversed;}
-
-    void SetVertexFilterProperty(string property);
-    void SetVertexFilterRange(pair<double,double> allowed_range,
-                              pair<bool,bool> include, bool invert);
-    bool IsVertexFilterActive() const;
-
-    void SetEdgeFilterProperty(string property);
-    void SetEdgeFilterRange(pair<double,double> allowed_range,
-                            pair<bool,bool> include, bool invert);
-    bool IsEdgeFilterActive() const;
-
-    // modification
-    void RemoveVertexProperty(string property);
-    void RemoveEdgeProperty(string property);
-    void RemoveGraphProperty(string property);
-    void InsertEdgeIndexProperty(string property);
-    void InsertVertexIndexProperty(string property);
-    void EditVertexProperty(string property, string type, python::object op,
-                            python::object g);
-    void EditEdgeProperty(string property, string type, python::object op,
-                          python::object g);
-    void EditGraphProperty(string property, string type, python::object op,
-                           python::object g);
-    void ReIndexEdges();
-    void PurgeVertices();
-    void PurgeEdges();
+    // Graph generation
+    void GenerateCorrelatedConfigurationalModel
+        (size_t N, python::object ppjk, python::object pceil_pjk,
+         python::object pinv_ceil_pjk, double ceil_pjk_bound,
+         python::object pcorr, python::object pceil_corr,
+         python::object pinv_ceil_corr, double ceil_corr_bound,
+         bool undirected_corr, size_t seed, bool verbose);
 
-    // layout
+    // graph layout
     void ComputeGraphLayoutGursoy(string prop, string weight, string topology,
                                   size_t iter = 0, size_t seed = 4357);
     void ComputeGraphLayoutSpringBlock(string prop, string weight, string type,
                                        size_t iter = 0, size_t seed = 4357);
 
-    // i/o
-    void WriteToFile(string s);
-    void WriteToFile(string s, string format);
-    void ReadFromFile(string s);
-    void ReadFromFile(string s, string format);
-
     // python interface
     python::object Vertices() const;
     python::object Edges() const;
@@ -199,6 +202,10 @@ public:
     // signal handling
     void InitSignalHandling();
 
+    //
+    // Internal types
+    //
+
     // the following defines the edges' internal properties
     typedef property<edge_index_t, size_t> EdgeProperty;
 
@@ -212,15 +219,32 @@ public:
     typedef graph_traits<multigraph_t>::edge_descriptor edge_t;
 
 private:
-    template <class GraphInterfaceType, class Action, class ReverseCheck, 
+
+    // The following function is very central to the implementation of the above
+    // member functions. Most of the algorithms are implemented as template
+    // functors, which must be run on the correct version of the graph, i.e.,
+    // filtered, unfiltered, directed, undirected, etc. The functor in question
+    // must be fed to the function below as the "a" variable, which will take
+    // care of business, selection the correct implementation. The ReverseCheck
+    // and DirectedCheck below are utility types which allow for limiting the
+    // implementation generation when you want it to be confined for only
+    // specific graph types. See graph_filtering.hh for details.
+
+    template <class GraphInterfaceType, class Action, class ReverseCheck,
               class DirectedCheck>
-    friend void check_filter(GraphInterfaceType &g, Action a,
-                             ReverseCheck, DirectedCheck, bool run_all=false);
+    friend void run_action(GraphInterfaceType &g, Action a, 
+                           ReverseCheck, DirectedCheck, bool run_all=false);
+
+    // useful overload for common case where all graph types should be probed
+    template <class GraphInterfaceType, class Action>
+    friend void run_action(GraphInterfaceType &g, Action a); 
+
     friend class scalarS;
 
     // this is the main graph
     multigraph_t _mg;
 
+    // reverse and directed states
     bool _reversed;
     bool _directed;
 
@@ -268,7 +292,6 @@ private:
 pair<GraphInterface::degree_t,string>
 get_degree_type(GraphInterface::deg_t degree);
 
-// GraphException
 // This is the main exception which will be thrown the outside world, when
 // things go wrong
 

src/graph/graph_assortativity.cc

@@ -132,10 +132,9 @@ struct choose_assortativity_coefficient
         if (mpl::at<degree_selector_index, DegreeSelector>::type::value == _deg)
         {
             DegreeSelector deg(_deg_name, _g, true);
-            check_filter(_g, bind<void>(get_assortativity_coefficient
-                                            <DegreeSelector>(deg),
-                                        _1, var(_a), var(_a_err)),
-                         reverse_check(),directed_check());
+            run_action(_g, bind<void>(get_assortativity_coefficient
+                                          <DegreeSelector>(deg),
+                                      _1, var(_a), var(_a_err)));
         }
     }
 
@@ -277,10 +276,9 @@ struct choose_scalar_assortativity_coefficient
         if (mpl::at<degree_selector_index, DegreeSelector>::type::value == _deg)
         {
             DegreeSelector deg(_deg_name, _g, true);
-            check_filter(_g, bind<void>(get_scalar_assortativity_coefficient
+            run_action(_g, bind<void>(get_scalar_assortativity_coefficient
                                             <DegreeSelector>(deg),
-                                        _1, var(_a), var(_a_err)),
-                         reverse_check(),directed_check());
+                                      _1, var(_a), var(_a_err)));
         }
     }
 

src/graph/graph_betweenness.cc

@@ -149,23 +149,22 @@ void GraphInterface::GetBetweenness(string weight, string edge_betweenness,
     if (weight != "")
     {
         bool found = false;
-        check_filter(*this, bind<void>(choose_weight_map(), _1, 
-                                       var(_vertex_index), var(_edge_index), 
-                                       var(weight), var(_properties), 
-                                       var(edge_betweenness_map), 
-                                       var(vertex_betweenness_map),
-                                       var(found)), 
-                     reverse_check(), directed_check());
+        run_action(*this, bind<void>(choose_weight_map(), _1, 
+                                     var(_vertex_index), var(_edge_index), 
+                                     var(weight), var(_properties), 
+                                     var(edge_betweenness_map), 
+                                     var(vertex_betweenness_map),
+                                     var(found)));
         if (!found)
             throw GraphException("error getting scalar property: " + weight);
     }
     else
     {
-        check_filter(*this, bind<void>(get_betweenness(), _1, 
-                                       var(_vertex_index),
-                                       var(edge_betweenness_map), 
-                                       var(vertex_betweenness_map)), 
-                     reverse_check(), directed_check());
+        run_action(*this, bind<void>(get_betweenness(), _1, 
+                                     var(_vertex_index),
+                                     var(edge_betweenness_map), 
+                                     var(vertex_betweenness_map)), 
+                   reverse_check(), directed_check());
     }        
 
     if (vertex_betweenness != "")
@@ -221,8 +220,8 @@ double GraphInterface::GetCentralPointDominance(string vertex_betweenness)
         bool directed = this->GetDirected();
         this->SetReversed(false);
         this->SetDirected(true);
-        check_filter(*this, bind<void>(get_central_point_dominance(), _1, 
-                                       var(betweenness), var(c)), 
+        run_action(*this, bind<void>(get_central_point_dominance(), _1, 
+                                     var(betweenness), var(c)), 
                      never_reversed(), always_directed());
         this->SetReversed(reversed);
         this->SetDirected(directed);

src/graph/graph_bind.cc

@@ -347,14 +347,10 @@ BOOST_PYTHON_MODULE(libgraph_tool)
     to_python_converter<pos_t, pos_t_to_tuple>();
     pos_t_from_tuple();
     pair_from_tuple<bool,bool>();
-    to_python_converter<GraphInterface::hist_t,
-                        hist_to_dict<GraphInterface::hist_t> >();
-    to_python_converter<GraphInterface::hist2d_t,
-                        hist_to_dict<GraphInterface::hist2d_t> >();
-    to_python_converter<GraphInterface::hist3d_t,
-                        hist_to_dict<GraphInterface::hist3d_t> >();
-    to_python_converter<GraphInterface::avg_corr_t,
-                        hist_to_dict<GraphInterface::avg_corr_t> >();
+    to_python_converter<hist_t,hist_to_dict<hist_t> >();
+    to_python_converter<hist2d_t,hist_to_dict<hist2d_t> >();
+    to_python_converter<hist3d_t,hist_to_dict<hist3d_t> >();
+    to_python_converter<avg_corr_t,hist_to_dict<avg_corr_t> >();
 
     class_<LibInfo>("mod_info")
         .add_property("name", &LibInfo::GetName)

src/graph/graph_clustering.cc

@@ -148,9 +148,9 @@ GraphInterface::GetGlobalClustering()
     double c, c_err;
     bool directed = _directed;
     _directed = false;
-    check_filter(*this, bind<void>(get_global_clustering(), _1, var(c), 
+    run_action(*this, bind<void>(get_global_clustering(), _1, var(c), 
                                    var(c_err)), 
-                 reverse_check(), always_undirected()); 
+               reverse_check(), always_undirected()); 
     _directed = directed;
     return make_pair(c,c_err);
 }
@@ -202,9 +202,9 @@ void GraphInterface::SetLocalClusteringToProperty(string property)
 
     bool directed = _directed;
     _directed = false;
-    check_filter(*this, bind<void>(set_clustering_to_property(), _1, 
-                                   var(clust_map)), 
-                 reverse_check(), always_undirected()); 
+    run_action(*this, bind<void>(set_clustering_to_property(), _1, 
+                                 var(clust_map)), 
+               reverse_check(), always_undirected()); 
     _directed = directed;
 
     try

src/graph/graph_community.cc

@@ -20,6 +20,7 @@
 #include <boost/lambda/bind.hpp>
 #include <boost/random.hpp>
 #include <tr1/unordered_set>
+#include <fstream>
 #include <iomanip>
 
 #include "graph.hh"
@@ -698,9 +699,9 @@ void GraphInterface::GetCommunityStructure(double gamma, comm_corr_t corr,
     {
         DynamicPropertyMapWrap<size_t,vertex_t> 
             old_s(find_property_map(_properties, property, typeid(vertex_t)));
-        check_filter(*this, bind<void>(copy_spins(), _1, var(old_s), 
-                                       var(comm_map)),
-                     reverse_check(), always_undirected());
+        run_action(*this, bind<void>(copy_spins(), _1, var(old_s), 
+                                     var(comm_map)),
+                   reverse_check(), always_undirected());
         RemoveVertexProperty(property);
         new_spins = false;
     }
@@ -723,27 +724,26 @@ void GraphInterface::GetCommunityStructure(double gamma, comm_corr_t corr,
                     get_static_property_map
                         <vector_property_map<double,edge_index_map_t> >
                     (weight_prop);
-                check_filter(*this, bind<void>(get_communities_selector(corr),
-                                               _1, var(weight_map), 
-                                               var(comm_map), 
-                                               gamma, n_iter, 
-                                               make_pair(Tmin, Tmax), 
-                                               make_pair(Nspins, new_spins), 
-                                               seed, 
-                                               make_pair(verbose,history_file)),
-                             reverse_check(), always_undirected());
+                run_action(*this, bind<void>(get_communities_selector(corr),
+                                             _1, var(weight_map), 
+                                             var(comm_map), gamma, n_iter, 
+                                             make_pair(Tmin, Tmax), 
+                                             make_pair(Nspins, new_spins), 
+                                             seed, 
+                                             make_pair(verbose,history_file)),
+                           reverse_check(), always_undirected());
             }
             else
             {
                 DynamicPropertyMapWrap<double,edge_t> weight_map(weight_prop);
-                check_filter(*this, bind<void>(get_communities_selector(corr),
-                                               _1, var(weight_map), 
-                                               var(comm_map), gamma, n_iter, 
-                                               make_pair(Tmin, Tmax), 
-                                               make_pair(Nspins, new_spins), 
-                                               seed, 
-                                               make_pair(verbose,history_file)),
-                             reverse_check(), always_undirected());
+                run_action(*this, bind<void>(get_communities_selector(corr),
+                                             _1, var(weight_map), 
+                                             var(comm_map), gamma, n_iter, 
+                                             make_pair(Tmin, Tmax), 
+                                             make_pair(Nspins, new_spins), 
+                                             seed, 
+                                             make_pair(verbose,history_file)),
+                           reverse_check(), always_undirected());
             }
         }
         catch (property_not_found& e)
@@ -755,12 +755,12 @@ void GraphInterface::GetCommunityStructure(double gamma, comm_corr_t corr,
     else
     {
         ConstantPropertyMap<double,edge_t> weight_map(1.0);
-        check_filter(*this, bind<void>(get_communities_selector(corr), _1, 
-                                       var(weight_map), var(comm_map), gamma, 
-                                       n_iter, make_pair(Tmin, Tmax), 
-                                       make_pair(Nspins, new_spins), seed, 
-                                       make_pair(verbose, history_file)),
-                     reverse_check(), always_undirected());
+        run_action(*this, bind<void>(get_communities_selector(corr), _1, 
+                                     var(weight_map), var(comm_map), gamma, 
+                                     n_iter, make_pair(Tmin, Tmax), 
+                                     make_pair(Nspins, new_spins), seed, 
+                                     make_pair(verbose, history_file)),
+                   reverse_check(), always_undirected());
     }
     _directed = directed;
 
@@ -819,17 +819,17 @@ double GraphInterface::GetModularity(string weight, string property)
             dynamic_property_map& weight_prop = 
                 find_property_map(_properties, weight, typeid(edge_t));
             DynamicPropertyMapWrap<double,edge_t> weight_map(weight_prop);
-            check_filter(*this, bind<void>(get_modularity(), _1, 
-                                           var(weight_map), var(comm_map), 
-                                           var(modularity)),
+            run_action(*this, bind<void>(get_modularity(), _1, 
+                                         var(weight_map), var(comm_map), 
+                                         var(modularity)),
             reverse_check(), always_undirected());            
         }
         else
         {
             ConstantPropertyMap<double,edge_t> weight_map(1.0);
-            check_filter(*this, bind<void>(get_modularity(), _1, 
-                                           var(weight_map), var(comm_map), 
-                                           var(modularity)),
+            run_action(*this, bind<void>(get_modularity(), _1, 
+                                         var(weight_map), var(comm_map), 
+                                         var(modularity)),
             reverse_check(), always_undirected());
         }
     }

src/graph/graph_community_network.cc

@@ -29,6 +29,11 @@
 #include "graph_properties.hh"
 #include <boost/graph/graphviz.hpp>
 #include <boost/graph/graphml.hpp>
+#include <boost/algorithm/string.hpp>
+#include <boost/iostreams/filtering_stream.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+#include <boost/iostreams/filter/bzip2.hpp>
+#include <boost/iostreams/device/file.hpp>
 
 using namespace std;
 using namespace boost;
@@ -228,10 +233,9 @@ void GraphInterface::GetCommunityNetwork(string property, string size_property,
                                        auto_ptr<dynamic_property_map>