* added support for reciprocity

* python_filtering: added n_parallel() function


git-svn-id: https://svn.forked.de/graph-tool/trunk@45 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

@@ -89,7 +89,6 @@ modification.add_option("--remove-vertex-property", action="callback", callback=
 modification.add_option("--remove-edge-property", action="callback", callback=push_option, type="string", metavar="PROPERTY|RANGE", help="remove edge property from graph")
 modification.add_option("--insert-vertex-index-property", action="callback", callback=push_option, type="string", metavar="PROPERTY", help="insert vertex index as property")
 modification.add_option("--insert-edge-index-property", action="callback", callback=push_option, type="string", metavar="PROPERTY", help="insert edge index as property")
-modification.add_option("--remove-parallel-edges", action="callback", callback=push_option, help="remove parallel edges from graph")
 
 statistics =  parser.add_option_group("Basic Statistics")
 statistics.add_option("--number-of-vertices", action="callback", callback=push_option, type="string", metavar="FILE", help="get the number of vertices")
@@ -106,7 +105,7 @@ statistics.add_option("--average-sampled-harmonic-distance", action="callback",
 statistics.add_option("--component-size-histogram", action="callback", callback=push_option, type="string", metavar="FILE", help="get the component size histogram")
 statistics.add_option("--average-vertex-property", action="callback", callback=push_option, type="string", metavar="PROPERTY|FILE", help="get the average of the vertex property")
 statistics.add_option("--average-edge-property", action="callback", callback=push_option, type="string", metavar="PROPERTY|FILE", help="get the average of the edge property")
-
+statistics.add_option("--reciprocity", action="callback", callback=push_option, type="string", metavar="FILE", help="get the edge reciprocity")
 
 correlations =  parser.add_option_group("Correlations")
 correlations.add_option("--average-combined-vertex-correlation", action="callback", callback=push_option, type="string", metavar="DEGREE1|DEGREE2|FILE", help="get the average of DEGREE2 in function of DEGREE1. Scalar properties are also accepted as DEGREE1 or DEGREE2")
@@ -409,6 +408,10 @@ def parse_option(opt, just_file=False):
         if just_file:
             return values[1]
         return (graph.GetEdgeHistogram(values[0]), values[1])
+    elif opt.name == "reciprocity":
+        if just_file:
+            return opt.value
+        return (graph.GetReciprocity(), opt.value)
     elif opt.name == "vertex-correlation-histogram":
         values = parse_values(opt.value)
         if len(values) != 3:
@@ -570,10 +573,6 @@ def parse_option(opt, just_file=False):
         if just_file:
             return None
         graph.SetReversed(not graph.GetReversed())
-    elif opt.name == "remove-parallel-edges":
-        if just_file:
-            return None
-        graph.RemoveParallelEdges()
     elif opt.name == "edit-vertex-property" or opt.name == "edit-edge-property":
         values = parse_values(opt.value)
         if len(values) != 2:
@@ -797,7 +796,7 @@ try:
             count += 1
         del history_files
             
-except (OptionError, HistoryException, IOError), e:
-    print "graph-tool:", e
+except (OptionError, HistoryException, IOError, RuntimeError), e:
+    print "graph-tool error:", e
 except KeyboardInterrupt:
     pass

src/graph/Makefile.am

@@ -34,6 +34,7 @@ libgraph_tool_la_SOURCES = \
     graph_generation.cc\
     graph_distance.cc\
     graph_distance_sampled.cc\
+    graph_reciprocity.cc\
     graph_io.cc\
     graph_bind.cc\
     graphml.hpp\

src/graph/graph.cc

@@ -346,50 +346,6 @@ void GraphInterface::InsertVertexIndexProperty(string property)
     _properties.property(property, _vertex_index);
 }
 
-//==============================================================================
-// RemoveParallelEdges(property)
-//==============================================================================
-struct remove_parallel_edges
-{
-    template <class Graph>
-    void operator()(Graph &g) const
-    {
-	typename graph_traits<Graph>::edge_iterator e, e_end;
-	for (tie(e, e_end) = edges(g); e != e_end; ++e)
-	{
-	    bool finished = false;
-	    while (!finished)
-	    {
-		finished = true;
-		typename graph_traits<Graph>::out_edge_iterator oe, oe_end;
-		typename graph_traits<Graph>::vertex_descriptor s,t;
-		s = source(*e,g);
-		t = target(*e,g);
-		for (tie(oe,oe_end) = out_edges(s,g); oe != oe_end; ++oe)
-		    if (*oe != *e && target(*oe,g) == t) // is a parallel edge
-		    {
-			remove_edge(*oe, g);
-			finished = false;
-			break;
-		    }
-	    }
-	}
-    }
-};
-
-void GraphInterface::RemoveParallelEdges()
-{
-    if (_directed)
-    {
-	remove_parallel_edges()(_mg);
-    }
-    else
-    {
-	UndirectedAdaptor<multigraph_t> ug(_mg);
-	remove_parallel_edges()(ug);
-    }
-}
-
 //==============================================================================
 // ComputeGraphLayoutGursoy(iter, seed)
 //==============================================================================

src/graph/graph.hh

@@ -92,6 +92,7 @@ public:
     hist_t GetComponentSizeHistogram() const;
     hist_t GetDistanceHistogram(std::string weight) const;
     hist_t GetSampledDistanceHistogram(std::string weight, size_t samples, size_t seed) const;
+    double GetReciprocity() const;
 
     // filtering
     void SetDirected(bool directed) {_directed = directed;}
@@ -122,7 +123,6 @@ public:
     void InsertVertexIndexProperty(std::string property);
     void EditVertexProperty(std::string property, boost::python::object op);
     void EditEdgeProperty(std::string property, boost::python::object op);
-    void RemoveParallelEdges();
 
     // layout
     void ComputeGraphLayoutGursoy(size_t iter = 0, size_t seed = 4357);

src/graph/graph_bind.cc

@@ -228,6 +228,7 @@ BOOST_PYTHON_MODULE(libgraph_tool)
 	.def("SetExtendedClusteringToProperty", &GraphInterfaceWrap::SetExtendedClusteringToProperty)
 	.def("GetDistanceHistogram", &GraphInterfaceWrap::GetDistanceHistogram)
 	.def("GetSampledDistanceHistogram", &GraphInterfaceWrap::GetSampledDistanceHistogram)
+	.def("GetReciprocity", &GraphInterfaceWrap::GetReciprocity)
 	.def("SetDirected", &GraphInterfaceWrap::SetDirected)
 	.def("GetDirected", &GraphInterfaceWrap::GetDirected)
 	.def("SetReversed", &GraphInterfaceWrap::SetReversed)
@@ -250,7 +251,6 @@ BOOST_PYTHON_MODULE(libgraph_tool)
 	.def("RemoveVertexProperty",  &GraphInterfaceWrap::RemoveVertexProperty)
 	.def("InsertEdgeIndexProperty",  &GraphInterfaceWrap::InsertEdgeIndexProperty)
 	.def("InsertVertexIndexProperty",  &GraphInterfaceWrap::InsertVertexIndexProperty)
-	.def("RemoveParallelEdges",  &GraphInterfaceWrap::RemoveParallelEdges)
 	.def("ComputeGraphLayoutGursoy", &GraphInterfaceWrap::ComputeGraphLayoutGursoy)
 	.def("ComputeGraphLayoutSpringBlock", &GraphInterfaceWrap::ComputeGraphLayoutSpringBlock)
 	.def("WriteToFile", &GraphInterfaceWrap::WriteToFile)

src/graph/graph_python_filtering.hh

@@ -74,6 +74,7 @@ struct populate_python_funcs
 	typedef typename graph_traits<Graph>::vertex_descriptor vertex_descriptor;
 
 	variables["is_self"] = python::make_function(is_self<Graph>(g, e), python::default_call_policies(), mpl::vector<python::object>::type()); 
+	variables["n_parallel"] = python::make_function(n_parallel<Graph>(g, e), python::default_call_policies(), mpl::vector<python::object>::type()); 
 	
 	for(typeof(dp.begin()) iter = dp.begin(); iter != dp.end(); ++iter)
 	{
@@ -242,6 +243,28 @@ struct populate_python_funcs
 	const Graph& _g;
 	const edge_descriptor& _e;
     };
+
+    template<class Graph>
+    struct n_parallel
+    {
+	typedef typename graph_traits<Graph>::edge_descriptor edge_descriptor;
+
+	n_parallel(const Graph& g, const edge_descriptor& e): _g(g), _e(e) {}
+	python::object operator()()
+	{
+	    size_t n = 0;
+	    typename graph_traits<Graph>::vertex_descriptor s,t;
+	    s = source(_e, _g);
+	    t = target(_e, _g);
+	    typename graph_traits<Graph>::adjacency_iterator a, a_end;
+	    for(tie(a, a_end) = adjacent_vertices(s, _g); a != a_end; ++a)
+		if (*a == t)
+		    n++;
+	    return python::object(n-1);
+	}
+	const Graph& _g;
+	const edge_descriptor& _e;
+    };
     
 
 };

src/graph/graph_reciprocity.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2006  Tiago de Paula Peixoto <tiago@forked.de>
+//
+// This program is free software; you can redistribute it and/or
+// modify it under the terms of the GNU General Public License
+// as published by the Free Software Foundation; either version 2
+// of the License, or (at your option) any later version.
+//
+// This program is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with this program; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+
+#include <boost/lambda/lambda.hpp>
+#include <boost/lambda/bind.hpp>
+
+#include "graph.hh"
+#include "histogram.hh"
+#include "graph_filtering.hh"
+#include "graph_selectors.hh"
+#include "graph_properties.hh"
+
+using namespace std;
+using namespace boost;
+using namespace boost::lambda;
+using namespace graph_tool;
+
+struct get_reciprocity
+{
+    template <class Graph>
+    void operator()(Graph& g, double& reciprocity) const
+    {	
+	size_t L = 0;
+	double Lbd = 0.0;
+
+	typename graph_traits<Graph>::edge_iterator e,e_end;
+	for (tie(e,e_end) = edges(g); e != e_end; ++e)
+	{
+	    typename graph_traits<Graph>::vertex_descriptor s,t;
+	    s = source(*e,g);
+	    t = target(*e,g);
+
+	    size_t o = 0;
+	    typename graph_traits<Graph>::adjacency_iterator a, a_end;
+	    for (tie(a,a_end) = adjacent_vertices(s, g); a != a_end; ++a)
+		if (*a == t)
+		    o++;
+
+	    size_t i = 0;
+	    for (tie(a, a_end) = adjacent_vertices(t, g); a != a_end; ++a)
+		if (*a == s)
+		    i++;
+
+	    Lbd += min(i/double(o),1.0);
+	    L++;
+	}
+
+	size_t N = HardNumVertices()(g);
+	double a = L/double(N*(N-1));
+
+	reciprocity = (Lbd/L - a)/(1-a);
+    }
+};
+
+
+double GraphInterface::GetReciprocity() const
+{
+    double reciprocity;
+    check_filter(*this, bind<void>(get_reciprocity(), _1, var(reciprocity)), reverse_check(), directed_check()); 
+    return reciprocity;
+}