* fix clustering and add jackknife variance

* fix history temp file handling buglet


git-svn-id: https://svn.forked.de/graph-tool/trunk@10 d4600afd-f417-0410-95de-beed9576f240

src/graph-tool

@@ -333,7 +333,9 @@ def parse_option(opt, just_file=False):
     elif opt.name == "global-clustering-coefficient":
         if just_file:
             return opt.value
-        return (graph.GetGlobalClustering(), opt.value)
+        (avg, dev) = graph.GetGlobalClustering()
+        ret = "%f\t%f" % (avg, dev)
+        return (ret, opt.value)
     elif opt.name == "set-local-clustering-to-property":
         if just_file:
             return None
@@ -499,7 +501,7 @@ class HistoryFile:
         self.file_name = os.path.expanduser(file_name)
         self.prefixes = set()
         self.file = None
-        self.time = time.clock()
+        self.time = clock()
         self.temp = self.file_name + "___temp"
         if self.file_name.endswith(".bz2"):
             self.temp = self.file_name.rstrip(".bz2") + "___temp.bz2"
@@ -561,10 +563,10 @@ class HistoryFile:
             
     def write(self, data, prefix):
         write_data(data, self.file, prefix)
-        if time.clock() - self.time > self.rate:
+        if clock() - self.time > self.rate:
             self.file.close()
             self.refresh()
-            self.time = time.clock()
+            self.time = clock()
 
 # signal handling
 graph.InitSignalHandling()
@@ -596,7 +598,7 @@ try:
         history_files = dict() # open history files
         variables = dict() # template variables
         exec values[0] in variables #init
-        exec "___continue = %s" % values[2] in variables # condition
+        exec "___continue = %s" % values[1] in variables # condition
         count = 0
         while variables["___continue"]:
             for opt in histories:
@@ -620,9 +622,10 @@ try:
                 else:
                     parse_option(new_opt)
 
-            exec values[1] in variables # step
-            exec "___continue = %s" % values[2] in variables # condition
+            exec values[2] in variables # step
+            exec "___continue = %s" % values[1] in variables # condition
             count += 1
+        del history_files
             
 except (OptionError, HistoryException), e:
     print "graph-tool:", e

src/graph/graph.hh

@@ -82,7 +82,7 @@ public:
 
     //clustering
     void   SetLocalClusteringToProperty(std::string property);
-    double GetGlobalClustering() const;
+    std::pair<double,double> GetGlobalClustering();
 
     // other
     hist_t GetComponentSizeHistogram() const;

src/graph/graph_clustering.cc

@@ -99,7 +99,7 @@ pair<int,int> get_triangles(typename graph_traits<Graph>::vertex_descriptor v, c
 struct get_global_clustering
 {
     template <class Graph>
-    void operator()(const Graph &g, double &c) const
+    void operator()(const Graph &g, double &c, double &c_err) const
     {
 	size_t triangles = 0, n = 0;
 	pair<size_t, size_t> temp;
@@ -111,17 +111,30 @@ struct get_global_clustering
 	    triangles += temp.first; 
 	    n += temp.second;
 	}
-	c = double(triangles)/(3*n);
+	c = double(triangles)/n;
+
+	// "jackknife" variance
+	c_err = 0.0;
+	for(v = v_begin; v != v_end; ++v)
+	{
+	    temp = get_triangles(*v, g);
+	    double cl = double(triangles - temp.first)/(n - temp.second);
+	    c_err = (c - cl)*(c - cl);
+	}
+	c_err = sqrt(c_err);
     }
 };
 
 
-double
-GraphInterface::GetGlobalClustering() const
+pair<double,double>
+GraphInterface::GetGlobalClustering()
 {
-    double c;
-    check_filter(*this, bind<void>(get_global_clustering(), _1, var(c)), reverse_check(), directed_check()); 
-    return c;
+    double c, c_err;
+    bool directed = _directed;
+    _directed = false;
+    check_filter(*this, bind<void>(get_global_clustering(), _1, var(c), var(c_err)), reverse_check(), always_undirected()); 
+    _directed = directed;
+    return make_pair(c,c_err);
 }
 
 //==============================================================================
@@ -166,7 +179,10 @@ void GraphInterface::SetLocalClusteringToProperty(string property)
     typedef associative_property_map<map_t> clust_map_t;
     clust_map_t clust_map(vertex_to_clust);
 
-    check_filter(*this, bind<void>(set_clustering_to_property(), _1, var(clust_map)), reverse_check(), directed_check()); 
+    bool directed = _directed;
+    _directed = false;
+    check_filter(*this, bind<void>(set_clustering_to_property(), _1, var(clust_map)), reverse_check(), always_undirected()); 
+    _directed = directed;
 
     try
     {