Unify all random number generators into a single module-wise instance

The object may be globally reset via the seed_rng() function.

src/graph/topology/graph_random_spanning_tree.cc

@@ -19,20 +19,14 @@
 #include "graph.hh"
 #include "graph_properties.hh"
 
-#include <boost/graph/random_spanning_tree.hpp>
+#include "random.hh"
 
-#if (GCC_VERSION >= 40400)
-#   include <tr1/random>
-#else
-#   include <boost/tr1/random.hpp>
-#endif
+#include <boost/graph/random_spanning_tree.hpp>
 
 using namespace std;
 using namespace boost;
 using namespace graph_tool;
 
-typedef tr1::mt19937 rng_t;
-
 struct get_random_span_tree
 {
     template <class Graph, class IndexMap, class WeightMap, class TreeMap,
@@ -89,10 +83,8 @@ typedef property_map_types::apply<mpl::vector<uint8_t>,
 
 void get_random_spanning_tree(GraphInterface& gi, size_t root,
                               boost::any weight_map, boost::any tree_map,
-                              size_t seed)
+                              rng_t& rng)
 {
-    rng_t rng(static_cast<rng_t::result_type>(seed));
-
     typedef ConstantPropertyMap<size_t,GraphInterface::edge_t> cweight_t;
 
     if (weight_map.empty())

src/graph/topology/graph_subgraph_isomorphism.cc

@@ -18,6 +18,8 @@
 #include "graph.hh"
 #include "graph_filtering.hh"
 
+#include "random.hh"
+
 #include <graph_subgraph_isomorphism.hh>
 #include <graph_python_interface.hh>
 
@@ -65,16 +67,15 @@ struct get_subgraphs
                     VertexLabel vertex_label1, boost::any vertex_label2,
                     EdgeLabel edge_label1, boost::any edge_label2,
                     vector<vector<pair<size_t, size_t> > >& F,
-                    vector<size_t>& vlist, pair<size_t,size_t> sn) const
+                    vector<size_t>& vlist, pair<reference_wrapper<rng_t>,size_t> sn) const
     {
         typedef PropLabelling<Graph1,Graph2,VertexLabel,VertexLabel>
             vlabelling_t;
         typedef PropLabelling<Graph1,Graph2,EdgeLabel,EdgeLabel>
             elabelling_t;
-        size_t seed = sn.first;
+        rng_t& rng = sn.first;
         size_t max_n = sn.second;
 
-        rng_t rng(static_cast<rng_t::result_type>(seed));
         vlist.resize(num_vertices(*g));
         int i, N = num_vertices(*g);
         for (i = 0; i < N; ++i)
@@ -166,7 +167,7 @@ void subgraph_isomorphism(GraphInterface& gi1, GraphInterface& gi2,
                           boost::any vertex_label1, boost::any vertex_label2,
                           boost::any edge_label1, boost::any edge_label2,
                           python::list vmapping, python::list emapping,
-                          size_t max_n, size_t seed)
+                          size_t max_n, rng_t& rng)
 {
     if (gi1.GetDirected() != gi2.GetDirected())
         return;
@@ -191,7 +192,7 @@ void subgraph_isomorphism(GraphInterface& gi1, GraphInterface& gi2,
         run_action<graph_tool::detail::always_directed>()
             (gi1, bind<void>(get_subgraphs(),
                              _1, _2, _3, vertex_label2, _4, edge_label2,
-                             ref(F), ref(vlist), make_pair(seed, max_n)),
+                             ref(F), ref(vlist), make_pair(ref(rng), max_n)),
              directed_graph_view_pointers(), vertex_props_t(),
              edge_props_t())
             (gi2.GetGraphView(), vertex_label1,  edge_label1);
@@ -201,7 +202,7 @@ void subgraph_isomorphism(GraphInterface& gi1, GraphInterface& gi2,
         run_action<graph_tool::detail::never_directed>()
             (gi1, bind<void>(get_subgraphs(),
                              _1, _2, _3, vertex_label2, _4, edge_label2,
-                             ref(F), ref(vlist), make_pair(seed, max_n)),
+                             ref(F), ref(vlist), make_pair(ref(rng), max_n)),
              undirected_graph_view_pointers(), vertex_props_t(),
              edge_props_t())
             (gi2.GetGraphView(), vertex_label1, edge_label1);

src/graph/topology/graph_subgraph_isomorphism.hh

@@ -22,17 +22,14 @@
 #include <utility>
 #if (GCC_VERSION >= 40400)
 #   include <tr1/unordered_set>
-#   include <tr1/random>
 #else
 #   include <boost/tr1/unordered_set.hpp>
-#   include <boost/tr1/random.hpp>
 #endif
 
 namespace boost
 {
 using namespace std;
 
-typedef tr1::mt19937 rng_t;
 
 namespace detail {
 

src/graph/topology/graph_topology.cc

@@ -17,6 +17,7 @@
 
 #include <boost/python.hpp>
 #include "graph.hh"
+#include "random.hh"
 
 using namespace boost;
 using namespace boost::python;
@@ -37,14 +38,14 @@ void subgraph_isomorphism(GraphInterface& gi1, GraphInterface& gi2,
                           boost::any vertex_label1, boost::any vertex_label2,
                           boost::any edge_label1, boost::any edge_label2,
                           python::list vmapping, python::list emapping,
-                          size_t n_max, size_t seed);
+                          size_t n_max, rng_t& rng);
 double reciprocity(GraphInterface& gi);
 size_t sequential_coloring(GraphInterface& gi, boost::any order,
                            boost::any color);
 bool is_bipartite(GraphInterface& gi, boost::any part_map);
 void get_random_spanning_tree(GraphInterface& gi, size_t root,
                               boost::any weight_map, boost::any tree_map,
-                              size_t seed);
+                              rng_t& rng);
 vector<int32_t> get_tsp(GraphInterface& gi, size_t src, boost::any weight_map);
 
 void export_components();

src/graph_tool/__init__.py

@@ -112,7 +112,7 @@ __all__ = ["Graph", "GraphView", "Vertex", "Edge", "Vector_bool",
            "Vector_int16_t", "Vector_int32_t", "Vector_int64_t", "Vector_double",
            "Vector_long_double", "Vector_string", "value_types", "load_graph",
            "PropertyMap", "group_vector_property", "ungroup_vector_property",
-           "infect_vertex_property", "edge_difference", "show_config",
+           "infect_vertex_property", "edge_difference", "seed_rng", "show_config",
            "PropertyArray", "__author__", "__copyright__", "__URL__",
            "__version__"]
 
@@ -1964,3 +1964,15 @@ class GraphView(Graph):
         return self.__base
     base = property(__get_base, doc="Base graph.")
 
+
+
+_rng = libcore.get_rng(numpy.random.randint(0, sys.maxsize))
+
+def seed_rng(seed):
+    "Seed the random number generator used by graph-tool's algorithms."
+    import graph_tool
+    graph_tool._rng = libcore.get_rng(int(seed))
+
+def _get_rng():
+    global _rng
+    return _rng

src/graph_tool/clustering/__init__.py

@@ -46,7 +46,7 @@ from __future__ import division, absolute_import, print_function
 from .. dl_import import dl_import
 dl_import("from . import libgraph_tool_clustering as _gt")
 
-from .. import _degree, _prop, Graph, GraphView
+from .. import _degree, _prop, Graph, GraphView, _get_rng
 from .. topology import isomorphism
 from .. generation import random_rewire
 from .. stats import vertex_hist
@@ -337,8 +337,6 @@ def motifs(g, k, p=1.0, motif_list=None):
        :doi:`10.1109/TCBB.2006.51`
     """
 
-    seed = random.randint(0, sys.maxsize)
-
     sub_list = []
     directed_motifs = g.is_directed()
 
@@ -364,7 +362,7 @@ def motifs(g, k, p=1.0, motif_list=None):
     was_directed = g.is_directed()
     _gt.get_motifs(g._Graph__graph, k, sub_list, hist, pd,
                    True, len(sub_list) == 0,
-                   seed)
+                   _get_rng())
 
     # assemble graphs
     temp = []

src/graph_tool/draw/__init__.py

@@ -66,7 +66,7 @@ Contents
 from __future__ import division, absolute_import, print_function
 
 from .. import GraphView, _check_prop_vector, group_vector_property, \
-     ungroup_vector_property, infect_vertex_property, _prop
+     ungroup_vector_property, infect_vertex_property, _prop, _get_rng
 from .. topology import max_cardinality_matching, max_independent_vertex_set, \
     label_components,  pseudo_diameter
 from .. community import condensation_graph
@@ -338,7 +338,6 @@ def _coarse_graph(g, vweight, eweight, mivs=False, groups=None):
 
 
 def _propagate_pos(g, cg, c, cc, cpos, delta, mivs):
-    seed = numpy.random.randint(sys.maxsize)
     pos = g.new_vertex_property(cpos.value_type())
 
     if mivs is not None:
@@ -350,7 +349,7 @@ def _propagate_pos(g, cg, c, cc, cpos, delta, mivs):
                                        _prop("v", g, pos),
                                        _prop("v", cg, cpos),
                                        delta if mivs is None else 0,
-                                       seed)
+                                       _get_rng())
     if mivs is not None:
         g = g.base
         u = GraphView(g, directed=False)
@@ -358,7 +357,7 @@ def _propagate_pos(g, cg, c, cc, cpos, delta, mivs):
             libgraph_tool_layout.propagate_pos_mivs(u._Graph__graph,
                                                     _prop("v", u, mivs),
                                                     _prop("v", u, pos),
-                                                    delta, seed)
+                                                    delta, _get_rng())
         except ValueError:
             graph_draw(u, mivs, vertex_fillcolor=mivs)
     return pos

src/graph_tool/generation/__init__.py

@@ -47,7 +47,7 @@ from __future__ import division, absolute_import, print_function
 from .. dl_import import dl_import
 dl_import("from . import libgraph_tool_generation")
 
-from .. import Graph, GraphView, _check_prop_scalar, _prop, _limit_args, _gt_type
+from .. import Graph, GraphView, _check_prop_scalar, _prop, _limit_args, _gt_type, _get_rng
 from .. stats import label_parallel_edges, label_self_loops
 import inspect
 import types
@@ -338,7 +338,6 @@ def random_graph(N, deg_sampler, deg_corr=None, cache_probs=True, directed=True,
        no. 1: 016107 (2011) :doi:`10.1103/PhysRevE.83.016107` :arxiv:`1008.3926`
     """
 
-    seed = numpy.random.randint(0, sys.maxsize)
     g = Graph()
     if deg_corr == None:
         uncorrelated = True
@@ -370,7 +369,7 @@ def random_graph(N, deg_sampler, deg_corr=None, cache_probs=True, directed=True,
     libgraph_tool_generation.gen_graph(g._Graph__graph, N, sampler,
                                        uncorrelated, not parallel_edges,
                                        not self_loops, not directed,
-                                       seed, verbose, True)
+                                       _get_rng(), verbose, True)
     g.set_directed(directed)
 
     if degree_block:
@@ -670,8 +669,6 @@ def random_rewire(g, strat="uncorrelated", n_iter=1, edge_sweep=True,
        no. 1: 016107 (2011) :doi:`10.1103/PhysRevE.83.016107` :arxiv:`1008.3926`
 
     """
-    seed = numpy.random.randint(0, sys.maxsize)
-
     if not parallel_edges:
         p = label_parallel_edges(g)
         if p.a.max() != 0:
@@ -699,7 +696,7 @@ def random_rewire(g, strat="uncorrelated", n_iter=1, edge_sweep=True,
                                                     self_loops, parallel_edges,
                                                     corr, _prop("v", g, blockmodel),
                                                     cache_probs,
-                                                    seed, verbose)
+                                                    _get_rng(), verbose)
     if ret_fail:
         return pcount
 
@@ -1223,7 +1220,5 @@ def price_network(N, m=1, c=None, gamma=1, directed=True, seed_graph=None):
         N -= g.num_vertices()
     else:
         g = seed_graph
-    seed = numpy.random.randint(0, sys.maxsize)
-    libgraph_tool_generation.price(g._Graph__graph, N, gamma, c, m, seed)
+    libgraph_tool_generation.price(g._Graph__graph, N, gamma, c, m, _get_rng())
     return g
-

src/graph_tool/stats/__init__.py

@@ -49,7 +49,7 @@ from __future__ import division, absolute_import, print_function
 from .. dl_import import dl_import
 dl_import("from . import libgraph_tool_stats")
 
-from .. import _degree, _prop
+from .. import _degree, _prop, _get_rng
 from numpy import *
 import numpy
 import sys
@@ -391,14 +391,12 @@ def distance_histogram(g, weight=None, bins=[0, 1], samples=None,
     """
 
     if samples != None:
-        seed = numpy.random.randint(0, sys.maxsize)
         ret = libgraph_tool_stats.\
               sampled_distance_histogram(g._Graph__graph,
                                          _prop("e", g, weight),
                                          [float(x) for x in bins],
-                                         samples, seed)
+                                         samples, _get_rng())
     else:
         ret = libgraph_tool_stats.\
               distance_histogram(g._Graph__graph, _prop("e", g, weight), bins)
     return [array(ret[0], dtype="float64") if float_count else ret[0], ret[1]]
-

src/graph_tool/topology/__init__.py

@@ -65,7 +65,7 @@ from .. dl_import import dl_import
 dl_import("from . import libgraph_tool_topology")
 
 from .. import _prop, Vector_int32_t, _check_prop_writable, \
-     _check_prop_scalar, _check_prop_vector, Graph, PropertyMap, GraphView
+     _check_prop_scalar, _check_prop_vector, Graph, PropertyMap, GraphView, _get_rng
 import random, sys, numpy
 __all__ = ["isomorphism", "subgraph_isomorphism", "mark_subgraph",
            "max_cardinality_matching", "max_independent_vertex_set",
@@ -1542,11 +1542,10 @@ def max_independent_vertex_set(g, high_deg=False, mivs=None):
     _check_prop_scalar(mivs, "mivs")
     _check_prop_writable(mivs, "mivs")
 
-    seed = numpy.random.randint(0, sys.maxsize)
     u = GraphView(g, directed=False)
     libgraph_tool_topology.\
         maximal_vertex_set(u._Graph__graph, _prop("v", u, mivs), high_deg,
-                           seed)
+                           _get_rng())
     mivs = g.own_property(mivs)
     return mivs