Rewritten graph generation routine.

It is now much simpler, and works better.

src/graph/generation/Makefile.am

+## Process this file with automake to produce Makefile.in
+
+AM_CPPFLAGS =\
+    -I. -I.. \
+    -I $(pythondir)/numpy/core/include/numpy/ \
+    -I../boost-workaround \
+    -DHAVE_CONFIG_H
+
+AM_CXXFLAGS =\
+    -Wall \
+    $(PYTHON_CPPFLAGS) \
+    $(BOOST_CPPFLAGS)
+
+AM_CFLAGS=$(AM_CXXFLAGS)
+
+libgraph_tool_generationdir = $(pythondir)/graph_tool/generation
+
+libgraph_tool_generation_LTLIBRARIES = libgraph_tool_generation.la
+
+libgraph_tool_generation_la_includedir = $(pythondir)/graph_tool/include
+
+libgraph_tool_generation_la_SOURCES = \
+    graph_generation.cc
+
+libgraph_tool_generation_la_include_HEADERS = \
+    graph_generation.hh
+
+libgraph_tool_generation_la_LIBADD = \
+    $(PYTHON_LDFLAGS) \
+    $(BOOST_LDFLAGS) \
+    $(OPENMP_LDFLAGS) \
+    -lboost_python \
+    -lboost_iostreams \
+    -lexpat
+
+# needed for typeinfo objects to work across DSO boundaries.
+# see http://gcc.gnu.org/faq.html#dso
+libgraph_tool_generation_la_LDFLAGS = \
+    -module \
+    -avoid-version \
+    -export-dynamic \
+    -no-undefined \
+    -Wl,-E

src/graph/generation/graph_generation.hh

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2007  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 3
+// 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, see <http://www.gnu.org/licenses/>.
+
+#ifndef GRAPH_GENERATION_HH
+#define GRAPH_GENERATION_HH
+
+#include <tr1/unordered_set>
+#include <tr1/unordered_map>
+#include <boost/array.hpp>
+#define BOOST_DISABLE_ASSERTS
+#include <boost/multi_array.hpp>
+#include <boost/random.hpp>
+#include <boost/functional/hash.hpp>
+
+namespace graph_tool
+{
+using namespace std;
+using namespace boost;
+
+typedef boost::mt19937 rng_t;
+
+// Graph Generation
+// ================
+//
+// this graph generation routine is based on two inputs, the in-out degree
+// probability matrix deg_matrix:
+//
+//   deg_matrix(j,k) = P(j,k)
+//
+// and the 4-dimensional in-out degree correlation matrix deg_corr:
+//
+//   deg_corr(j, k, j', k') = P((j,k) -> (j',k')), i.e. the probability that a
+//   directed edge exists between two _specific_ vertices of degrees (j,k) and
+//   (j',k')
+//
+// Both these structures are expensive to store, and having them would still
+// mean that rejection sampling would have to be used to generate the graph,
+// which can be quite slow, and unnecessary when the samples are easy to
+// obtain. Therefore what is actually used are two functions, deg_sample() and
+// deg_corr_sample(j,k) which should return a (j,k) degree sample which obeys
+// the above probabilities.
+//
+// Furthermore we want also to generate _undirected_ graphs, which have the
+// above probabilities changed to P(k) and deg_corr(k) respectively.
+
+// Utilities
+// =========
+
+// desired vertex type, with desired j,k values and the index in the real graph
+struct dvertex_t
+{
+    dvertex_t() {}
+    dvertex_t(size_t in, size_t out): in_degree(in), out_degree(out) {}
+    dvertex_t(const pair<size_t,size_t>& deg): in_degree(deg.first),
+                                               out_degree(deg.second) {}
+    size_t index, in_degree, out_degree;
+    bool operator==(const dvertex_t& other) const {return other.index == index;}
+};
+
+// utility class to sample uniformly from a collection of values
+template <class ValueType>
+class Sampler
+{
+public:
+    Sampler() {}
+
+    template <class Iterator>
+    Sampler(Iterator iter, Iterator end)
+    {
+        for(; iter != end; ++iter)
+            _candidates.push_back(*iter);
+    }
+
+    void Insert(const ValueType& v) { _candidates.push_back(v); }
+
+    void Remove(size_t index)
+    {
+        swap(_candidates[index], _candidates.back());
+        _candidates.pop_back();
+    }
+
+    void RemoveLast()
+    {
+        if (_last != _candidates.size())
+        {
+            swap(_candidates[_last], _candidates.back());
+            _candidates.pop_back();
+        }
+    }
+
+    ValueType operator()(rng_t& rng, bool remove = true)
+    {
+        uniform_int<> sample(0, _candidates.size() - 1);
+        int i = sample(rng);
+        if (remove)
+        {
+            swap(_candidates[i], _candidates.back());
+            ValueType ret = _candidates.back();
+            _candidates.pop_back();
+            _last = numeric_limits<size_t>::max();
+            return ret;
+        }
+        else
+        {
+            _last = i;
+            return _candidates[i];
+        }
+    }
+
+private:
+    vector<ValueType> _candidates;
+    size_t _last;
+};
+
+// used for verbose display
+void print_progress(size_t current, size_t total, stringstream& str)
+{
+    size_t atom = max(total/100, 1);
+    if ( (current % atom == 0) || current == total)
+    {
+        for (size_t j = 0; j < str.str().length(); ++j)
+            cout << "\b";
+        str.str("");
+        str << current+1 << " of " << total << " (" <<
+            (current+1)*100/total << "%)";
+        cout << str.str() << flush;
+    }
+}
+
+void print_update(size_t current, stringstream& str)
+{
+    for (size_t j = 0; j < str.str().length(); ++j)
+        cout << "\b";
+    for (size_t j = 0; j < str.str().length(); ++j)
+        cout << " ";
+    for (size_t j = 0; j < str.str().length(); ++j)
+        cout << "\b";
+    str.str("");
+    str << current;
+    cout << str.str() << flush;
+}
+
+//
+// Generation strategies
+// =====================
+//
+// Directed and undirected graphs have different generation strategies, which
+// are defined in the classes below.
+
+//
+// Directed graph generation strategy
+//
+
+class DirectedStrat
+{
+public:
+    typedef pair<size_t, size_t> deg_t; // degree type
+
+    DirectedStrat(size_t N, bool no_parallel, bool no_self_loops)
+        : _N(N), _no_parallel(no_parallel), _no_self_loops(no_self_loops)
+    {
+        if (_no_parallel)
+            _max_deg = (_no_self_loops) ? _N - 1 : N;
+        else
+            _max_deg = numeric_limits<size_t>::max();
+    }
+
+    // sample the degrees of all the vertices
+    template <class Graph, class DegSample, class VertexIndex>
+    size_t SampleDegrees(Graph& g, vector<dvertex_t>& vertices,
+                         VertexIndex vertex_index, DegSample& deg_sample,
+                         rng_t& rng, bool verbose)
+    {
+        stringstream str;
+        size_t sum_j=0, sum_k=0;
+        for(size_t i = 0; i < _N; ++i)
+        {
+            if (verbose)
+                print_progress(i, _N, str);
+            dvertex_t& v = vertices[i];
+            v.index = vertex_index[add_vertex(g)];
+            do
+            {
+                tie(v.in_degree, v.out_degree) = deg_sample();
+            }
+            while (_no_parallel &&
+                   (v.in_degree > _max_deg || v.out_degree > _max_deg));
+            sum_j += v.in_degree;
+            sum_k += v.out_degree;
+        }
+
+        if (verbose)
+        {
+            cout << "\nfixing average degrees. Total degree difference: "
+                 << flush;
+            str.str("");
+        }
+
+        // <j> and <k> must be the same. Re-sample random pairs until this holds
+        uniform_int<size_t> vertex_sample(0, _N-1);
+        size_t count = 0;
+        while (sum_j != sum_k)
+        {
+            dvertex_t& v = vertices[vertex_sample(rng)];
+            sum_j -= v.in_degree;
+            sum_k -= v.out_degree;
+            do
+            {
+                tie(v.in_degree, v.out_degree) = deg_sample();
+            }
+            while (_no_parallel &&
+                   (v.in_degree > _max_deg || v.out_degree > _max_deg));
+            sum_j += v.in_degree;
+            sum_k += v.out_degree;
+            if (verbose && (count % 100 == 0 || sum_j == sum_k))
+                print_update(min(sum_j-sum_k, sum_k-sum_j), str);
+            count++;
+        }
+        return sum_k;
+    }
+
+    deg_t GetDegree(const dvertex_t& v) { return make_pair(v.out_degree,
+                                                           v.out_degree); }
+    bool IsTarget(const dvertex_t& v) { return v.in_degree > 0; }
+
+    template <class Graph>
+    bool IsStillTarget(Graph& g, const dvertex_t& v)
+    {
+        return (in_degree(vertex(v.index, g), g) != v.in_degree);
+    }
+
+private:
+    size_t _N;
+    bool _no_parallel;
+    bool _no_self_loops;
+    size_t _max_deg;
+};
+
+//
+// Undirected graph generation strategy
+//
+
+class UndirectedStrat
+{
+public:
+    typedef size_t deg_t;
+
+    UndirectedStrat(size_t N, bool no_parallel, bool no_self_loops)
+        : _N(N), _no_parallel(no_parallel), _no_self_loops(no_self_loops)
+    {
+        if (_no_parallel)
+            _max_deg = (_no_self_loops) ? _N - 1 : N;
+        else
+            _max_deg = numeric_limits<size_t>::max();
+    }
+
+    // samples the degress of all vertices
+    template <class Graph, class DegSample, class VertexIndex>
+    size_t SampleDegrees(Graph& g, vector<dvertex_t>& vertices,
+                         VertexIndex vertex_index, DegSample& deg_sample,
+                         rng_t& rng, bool verbose)
+    {
+        stringstream str;
+        size_t sum_k=0;
+        for(size_t i = 0; i < _N; ++i)
+        {
+            if (verbose)
+                print_progress(i, _N, str);
+            dvertex_t& v = vertices[i];
+            v.index = vertex_index[add_vertex(g)];
+            do
+            {
+                v.out_degree = deg_sample(true);
+            }
+            while (_no_parallel && v.out_degree > _max_deg);
+            sum_k += v.out_degree;
+        }
+
+        if (verbose)
+        {
+            cout << "\nFixing degree sum (must be even): "
+                 << flush;
+            str.str("");
+        }
+
+        // sum_k must be an even number (2*num_edges). Re-sample degrees until
+        // this holds
+        uniform_int<size_t> vertex_sample(0, _N-1);
+        size_t count = 0;
+        while (sum_k % 2 != 0)
+        {
+            dvertex_t& v = vertices[vertex_sample(rng)];
+            sum_k -= v.out_degree;
+            do
+            {
+                v.out_degree = deg_sample(true);
+            }
+            while (_no_parallel && (v.out_degree > _max_deg));
+            sum_k +=  v.out_degree;
+            if (verbose && (count % 100 || sum_k % 2 == 0))
+                print_update(sum_k, str);
+            count++;
+        }
+        return sum_k;
+    }
+
+    deg_t GetDegree(const dvertex_t& v) { return v.out_degree; }
+    bool IsTarget(const dvertex_t& v) { return v.out_degree > 0; }
+
+    template <class Graph>
+    bool IsStillTarget(Graph& g, const dvertex_t& v)
+    {
+        return (out_degree(vertex(v.index, g), g) != v.out_degree);
+    }
+
+private:
+    size_t _N;
+    bool _no_parallel;
+    bool _no_self_loops;
+    size_t _max_deg;
+};
+
+//
+// Correlation strategies
+// ======================
+//
+// Graphs can be uncorrelated or two-point correlated. The first is a special
+// case of the second, but it happens quite often and it can be optimized. Below
+// are two classes which implement both strategies.
+
+//
+// Correlated graph strategy
+//
+
+template <class Deg>
+class CorrelatedStrat
+{
+public:
+    void InsertTarget(const dvertex_t& v, const Deg& deg)
+    {
+        _targets.insert(make_pair(deg, v));
+    }
+
+    template <class CorrSample>
+    dvertex_t GetRandomTarget(const Deg& source_deg, CorrSample& corr_sample,
+                              rng_t& rng)
+    {
+        // keep sampling until we find a vertex
+        typename targets_t::iterator iter,end;
+        Deg target_deg;
+        do
+        {
+            //choose the target vertex according to correlation
+            target_deg = corr_sample(source_deg);
+            tie(iter, end) = _targets.equal_range(target_deg);
+        }
+        while (iter == end);
+        // sample random target on the same class
+        Sampler<typename targets_t::iterator> sampler;
+        for(; iter != end; ++iter)
+            sampler.Insert(iter);
+        _last = sampler(rng);
+        return _last->second;
+    }
+
+    void RemoveLast() { _targets.erase(_last); }
+
+private:
+    typedef tr1::unordered_multimap<Deg, dvertex_t, hash<Deg> > targets_t;
+    targets_t _targets;
+    typename targets_t::iterator _last;
+};
+
+//
+// Uncorrelated graph strategy
+//
+
+template <class Deg>
+class UncorrelatedStrat
+{
+public:
+    void InsertTarget(const dvertex_t& v, const Deg& deg)
+    {
+        _targets.Insert(v);
+    }
+
+    template <class CorrSample>
+    dvertex_t GetRandomTarget(const Deg& source_deg, CorrSample& corr_sample,
+                              rng_t& rng)
+    {
+        return _targets(rng, false);
+    }
+
+    void RemoveLast() { _targets.RemoveLast(); }
+
+private:
+    Sampler<dvertex_t> _targets;
+};
+
+//
+// Main Algorithm
+// ==============
+//
+// generates a directed or undirected graph with given degree distribution and
+// correlation as defined above
+
+template <class IsCorrelated>
+struct gen_random_graph
+{
+    gen_random_graph(size_t N): _N(N) {}
+
+    template <class Graph, class DegSample, class CorrDegSample>
+    void operator()(Graph* gp, DegSample& deg_sample,
+                    CorrDegSample& deg_corr_sample, bool no_parallel,
+                    bool no_self_loops, bool undirected,
+                    size_t seed, bool verbose)
+        const
+    {
+        Graph& g = *gp;
+        size_t N = _N;
+        typename property_map<Graph,vertex_index_t>::type vertex_index =
+            get(vertex_index_t(), g);
+        rng_t rng(static_cast<rng_t::result_type>(seed));
+
+        // figure out the necessary strategies
+        typedef typename is_convertible
+            <typename graph_traits<Graph>::directed_category,
+            directed_tag>::type is_directed;
+        typedef typename mpl::if_<is_directed, DirectedStrat,
+                                  UndirectedStrat>::type gen_strat_t;
+        typedef typename gen_strat_t::deg_t deg_t;
+        typedef typename mpl::if_<IsCorrelated, CorrelatedStrat<deg_t>,
+                                  UncorrelatedStrat<deg_t> >::type corr_strat_t;
+
+        gen_strat_t gen_strat(N, no_parallel, no_self_loops);
+        corr_strat_t corr_strat;
+
+        stringstream str; // used for verbose status
+
+        if (verbose)
+            cout << "adding vertices: " << flush;
+
+        // sample the N (j,k) pairs
+        vector<dvertex_t> vertices(N);
+        size_t E = gen_strat.SampleDegrees(g, vertices, vertex_index,
+                                           deg_sample, rng, verbose);
+
+        vector<dvertex_t> sources; // edge sources
+
+        // fill up sources, targets and target_degrees
+        sources.reserve(E);
+        for(size_t i = 0; i < N; ++i)
+        {
+            for(size_t k = 0; k < vertices[i].out_degree; ++k)
+                sources.push_back(vertices[i]);
+            if (gen_strat.IsTarget(vertices[i]))
+                corr_strat.InsertTarget(vertices[i],
+                                        gen_strat.GetDegree(vertices[i]));
+        }
+
+        // shuffle sources
+        for (size_t i = 0; i < sources.size(); ++i)
+        {
+            uniform_int<size_t> source_sample(i, sources.size()-1);
+            swap(sources[i], sources[source_sample(rng)]);
+        }
+
+        if (verbose)
+        {
+            cout << "\nadding edges: " << flush;
+            str.str("");
+        }
+
+        // connect the sources to targets
+        for (int i = 0; i < int(sources.size()); ++i)
+        {
+            dvertex_t source = sources[i], target;
+            deg_t source_deg = gen_strat.GetDegree(source);
+
+            // in undirected graphs, there's no difference between source and
+            // target
+            if (!is_directed::value && !gen_strat.IsStillTarget(g, source))
+                continue;
+
+            tr1::unordered_set<size_t> old_targets;
+            if (no_parallel)
+            {
+                typename graph_traits<Graph>::out_edge_iterator e, e_end;
+                for (tie(e, e_end) = out_edges(vertex(source.index, g), g);
+                     e != e_end; ++e)
+                    old_targets.insert(boost::target(*e,g));
+            }
+
+            // get target
+            target = corr_strat.GetRandomTarget(source_deg, deg_corr_sample,
+                                                rng);
+
+            // if unacceptable (because parallel and/or self_loop), throw it
+            // back and disconnect a random previous (different) source
+            if ((no_parallel && (old_targets.find(target.index)
+                                 != old_targets.end())) ||
+                (no_self_loops && (source.index == target.index)))
+            {
+                if (i == 0) // just try again
+                {
+                    i--;
+                    continue;
+                }
+
+                uniform_int<size_t> source_sample(0, i-1);
+                size_t s_index;
+                // keep trying: we don't want the same source again, and no
+                // sources with zero out-degree (which can happen when the graph
+                // is undirected, when they're orphaned after a removed edge)
+                do
+                {
+                    s_index = source_sample(rng);
+                }
+                while (sources[s_index] == source ||
+                       out_degree(vertex(sources[s_index].index, g), g) == 0);
+
+                dvertex_t rsource = sources[s_index]; // random source
+
+                // get the random edge
+                typename graph_traits<Graph>::out_edge_iterator e, e_end;
+                tie(e, e_end) = out_edges(vertex(rsource.index, g), g);
+                Sampler<typename graph_traits<Graph>::edge_descriptor>
+                    esampler(e, e_end);
+                typename graph_traits<Graph>::edge_descriptor re =
+                    esampler(rng, false); // random edge
+
+                // if edge's target was already full, put it back in target list
+                dvertex_t rtarget =
+                    vertices[vertex_index[boost::target(re, g)]];
+                if (!gen_strat.IsStillTarget(g, rtarget))
+                    corr_strat.InsertTarget(rtarget,
+                                            gen_strat.GetDegree(rtarget));
+
+                // for undirected graphs, we need also to check the source
+                if (!is_directed::value)
+                {
+                    dvertex_t rsource =
+                        vertices[vertex_index[boost::source(re, g)]];
+                    if (!gen_strat.IsStillTarget(g, rsource))
+                        corr_strat.InsertTarget(rsource,