Implement sfdp_layout

src/graph/layout/Makefile.am

@@ -17,7 +17,9 @@ libgraph_tool_layout_la_LDFLAGS = $(MOD_LDFLAGS)
 libgraph_tool_layout_la_SOURCES = \
     graph_arf.cc \
     graph_fruchterman_reingold.cc \
+    graph_sfdp.cc \
     graph_bind_layout.cc
 
 libgraph_tool_layout_la_include_HEADERS = \
-    graph_arf.hh
+    graph_arf.hh \
+    graph_sfdp.hh

src/graph/layout/graph_bind_layout.cc

@@ -20,10 +20,11 @@
 using namespace boost::python;
 void export_arf();
 void export_fruchterman_reingold();
+void export_sfdp();
 
 BOOST_PYTHON_MODULE(libgraph_tool_layout)
 {
     export_arf();
     export_fruchterman_reingold();
+    export_sfdp();
 }
-

src/graph/layout/graph_sfdp.cc

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2007-2011 Tiago de Paula Peixoto <tiago@skewed.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/>.
+
+#include "graph_filtering.hh"
+#include "graph.hh"
+#include "graph_properties.hh"
+#include "graph_exceptions.hh"
+
+#if (GCC_VERSION >= 40400)
+#   include <tr1/random>
+#else
+#   include <boost/tr1/random.hpp>
+#endif
+
+#include <boost/lambda/bind.hpp>
+
+#include "graph_sfdp.hh"
+
+using namespace std;
+using namespace boost;
+using namespace graph_tool;
+
+typedef tr1::mt19937 rng_t;
+
+void sfdp_layout(GraphInterface& g, boost::any pos, boost::any vweight,
+                 boost::any eweight, boost::any pin, python::object spring_parms,
+                 double theta, double init_step, double step_schedule,
+                 size_t max_level, double epsilon, size_t max_iter,
+                 bool adaptive, bool verbose)
+{
+    typedef ConstantPropertyMap<int32_t,GraphInterface::vertex_t> vweight_map_t;
+    typedef ConstantPropertyMap<int32_t,GraphInterface::edge_t> eweight_map_t;
+    typedef mpl::push_back<vertex_scalar_properties, vweight_map_t>::type
+        vertex_props_t;
+    typedef mpl::push_back<edge_scalar_properties, eweight_map_t>::type
+        edge_props_t;
+
+    double C = python::extract<double>(spring_parms[0]);
+    double K = python::extract<double>(spring_parms[1]);
+    double p = python::extract<double>(spring_parms[2]);
+
+    if(vweight.empty())
+        vweight = vweight_map_t(1);
+    if(eweight.empty())
+        eweight = eweight_map_t(1);
+
+    typedef ConstantPropertyMap<bool,GraphInterface::vertex_t> pin_map_t;
+    typedef mpl::vector<typename property_map_type::apply
+                            <uint8_t,
+                             GraphInterface::vertex_index_map_t>::type,
+                        pin_map_t>::type
+        pin_props_t;
+
+    if(pin.empty())
+        pin = pin_map_t(false);
+    run_action<graph_tool::detail::never_directed>()
+        (g,
+         bind<void>(get_sfdp_layout(C, K, p, theta, init_step,
+                                    step_schedule, max_level, epsilon,
+                                    max_iter, adaptive),
+                    _1, g.GetVertexIndex(), _2, _3, _4, _5, verbose),
+         vertex_floating_vector_properties(), vertex_props_t(), edge_props_t(),
+         pin_props_t())(pos, vweight, eweight, pin);
+}
+
+struct do_propagate_pos
+{
+    template <class Graph, class CoarseGraph, class VertexMap, class PosMap,
+              class RNG>
+    void operator()(Graph& g, CoarseGraph* cg, VertexMap& vmap,
+                    boost::any acvmap, PosMap pos, boost::any acpos,
+                    double delta, RNG& rng) const
+    {
+        typename PosMap::checked_t cpos =
+            any_cast<typename PosMap::checked_t>(acpos);
+        typename VertexMap::checked_t cvmap =
+            any_cast<typename VertexMap::checked_t>(acvmap);
+        typedef typename property_traits<VertexMap>::value_type c_t;
+        typedef typename property_traits<PosMap>::value_type pos_t;
+
+        tr1::variate_generator<RNG&, tr1::uniform_real<> >
+            noise(rng, tr1::uniform_real<>(-delta, delta));
+
+        tr1::unordered_map<c_t, pos_t, boost::hash<c_t> >
+            cmap(num_vertices(*cg));
+        int i, N = num_vertices(*cg);
+        #pragma omp parallel for default(shared) private(i)
+        for (i = 0; i < N; ++i)
+        {
+            typename graph_traits<CoarseGraph>::vertex_descriptor v =
+                vertex(i, *cg);
+            if (v == graph_traits<CoarseGraph>::null_vertex())
+                continue;
+            cmap[cvmap[v]] = cpos[v];
+        }
+
+        N = num_vertices(g);
+        #pragma omp parallel for default(shared) private(i)
+        for (i = 0; i < N; ++i)
+        {
+            typename graph_traits<Graph>::vertex_descriptor v =
+                vertex(i, g);
+            if (v == graph_traits<Graph>::null_vertex())
+                continue;
+            pos[v] = cmap[vmap[v]];
+            {
+                #pragma omp critical
+                for (size_t j = 0; j < pos[v].size(); ++j)
+                    pos[v][j] += noise();
+            }
+        }
+    }
+};
+
+struct get_pointers
+{
+    template <class List>
+    struct apply
+    {
+        typedef typename mpl::transform<List,
+                                        mpl::quote1<add_pointer> >::type type;
+    };
+};
+
+void propagate_pos(GraphInterface& gi, GraphInterface& cgi, boost::any vmap,
+                   boost::any cvmap, boost::any pos, boost::any cpos,
+                   double delta, size_t seed)
+{
+    rng_t rng(static_cast<rng_t::result_type>(seed));
+
+    typedef mpl::vector<typename property_map_type::apply
+                            <int32_t,
+                             GraphInterface::vertex_index_map_t>::type>::type
+        vmaps_t;
+
+
+    run_action<>()
+        (gi, bind<void>(do_propagate_pos(),
+                        _1, _2, _3, cvmap, _4, cpos, delta, ref(rng)),
+         get_pointers::apply<graph_tool::detail::all_graph_views>::type(),
+         vmaps_t(), vertex_floating_vector_properties())
+        (cgi.GetGraphView(), vmap, pos);
+}
+
+struct do_propagate_pos_mivs
+{
+    template <class Graph, class MIVSMap, class PosMap,
+              class RNG>
+    void operator()(Graph& g, MIVSMap mivs, PosMap pos, double delta, RNG& rng) const
+    {
+        typedef typename property_traits<PosMap>::value_type pos_t;
+
+        tr1::variate_generator<RNG&, tr1::uniform_real<> >
+            noise(rng, tr1::uniform_real<>(-delta, delta));
+
+        int i, N = num_vertices(g);
+        #pragma omp parallel for default(shared) private(i)
+        for (i = 0; i < N; ++i)
+        {
+            typename graph_traits<Graph>::vertex_descriptor v =
+                vertex(i, g);
+            if (v == graph_traits<Graph>::null_vertex())
+                continue;
+            if (mivs[v])
+                continue;
+            pos[v].resize(2);
+            pos[v][0] = pos[v][1] = 0;
+            size_t count = 0;
+            typename graph_traits<Graph>::adjacency_iterator a, a_end;
+            for(tie(a, a_end) = adjacent_vertices(v, g); a != a_end; ++a)
+            {
+                if (!mivs[*a])
+                    continue;
+                for (size_t j = 0; j < pos[v].size(); ++j)
+                    pos[v][j] += pos[*a][j];
+                ++count;
+            }
+
+            if (count == 0)
+                throw ValueException("invalid MIVS! Vertex has no neighbours "
+                                     "belonging to the set!");
+
+            if (count == 1)
+            {
+                #pragma omp critical
+                for (size_t j = 0; j < pos[v].size(); ++j)
+                    pos[v][j] += noise();
+            }
+            else
+            {
+                for (size_t j = 0; j < pos[v].size(); ++j)
+                    pos[v][j] /= count;
+            }
+        }
+    }
+};
+
+
+void propagate_pos_mivs(GraphInterface& gi, boost::any mivs, boost::any pos,
+                        double delta, size_t seed)
+{
+    rng_t rng(static_cast<rng_t::result_type>(seed));
+
+    run_action<>()
+        (gi, bind<void>(do_propagate_pos_mivs(),
+                        _1, _2, _3, delta, ref(rng)),
+         vertex_scalar_properties(), vertex_floating_vector_properties())
+        (mivs, pos);
+}
+
+
+struct do_avg_dist
+{
+    template <class Graph, class PosMap>
+    void operator()(Graph& g, PosMap pos, double& ad) const
+    {
+        int i, N = num_vertices(g);
+        size_t count = 0;
+        double d = 0;
+        #pragma omp parallel for default(shared) private(i) \
+            reduction(+: d, count)
+        for (i = 0; i < N; ++i)
+        {
+            typename graph_traits<Graph>::vertex_descriptor v =
+                vertex(i, g);
+            if (v == graph_traits<Graph>::null_vertex())
+                continue;
+            typename graph_traits<Graph>::adjacency_iterator a, a_end;
+            for(tie(a, a_end) = adjacent_vertices(v, g); a != a_end; ++a)
+            {
+                d += dist(pos[v], pos[*a]);
+                count++;
+            }
+        }
+        d /= count;
+        ad = d;
+    }
+};
+
+
+double avg_dist(GraphInterface& gi, boost::any pos)
+{
+    double d;
+    run_action<>()
+        (gi, bind<void>(do_avg_dist(), _1, _2, ref(d)),
+         vertex_scalar_vector_properties()) (pos);
+    return d;
+}
+
+#include <boost/python.hpp>
+
+void export_sfdp()
+{
+    python::def("sfdp_layout", &sfdp_layout);
+    python::def("propagate_pos", &propagate_pos);
+    python::def("propagate_pos_mivs", &propagate_pos_mivs);
+    python::def("avg_dist", &avg_dist);
+}

src/graph/layout/graph_sfdp.hh

+// graph-tool -- a general graph modification and manipulation thingy
+//
+// Copyright (C) 2007-2011 Tiago de Paula Peixoto <tiago@skewed.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_FDP_HH
+#define GRAPH_FDP_HH
+
+#if (GCC_VERSION >= 40400)
+#   include <tr1/random>
+#else
+#   include <boost/tr1/random.hpp>
+#endif
+#include <limits>
+#include <iostream>
+
+namespace graph_tool
+{
+using namespace std;
+using namespace boost;
+
+template <class Pos, class Weight>
+class QuadTree
+{
+public:
+    QuadTree(const Pos& ll, const Pos& ur, int max_level)
+        :_ll(ll), _ur(ur), _cm(2, 0), _count(0),
+         _max_level(max_level)
+    {
+    }
+
+    QuadTree& get_leaf(size_t i)
+    {
+        if (_max_level > 0 && _leafs.empty())
+        {
+            _leafs.reserve(4);
+            for (size_t i = 0; i < 4; ++i)
+            {
+                Pos lll = _ll, lur = _ur;
+                if (i % 2)
+                    lll[0] += (_ur[0] - _ll[0]) / 2;
+                else
+                    lur[0] -= (_ur[0] - _ll[0]) / 2;
+                if (i / 2)
+                    lll[1] += (_ur[1] - _ll[1]) / 2;
+                else
+                    lur[1] -= (_ur[1] - _ll[1]) / 2;
+                _leafs.push_back(QuadTree(lll, lur, _max_level - 1));
+            }
+        }
+
+        return _leafs[i];
+    }
+
+    vector<tuple<Pos,Weight> >& get_dense_leafs()
+    {
+        return _dense_leafs;
+    }
+
+    size_t put_pos(Pos& p, Weight w)
+    {
+        _count += w;
+        _cm[0] += p[0] * w;
+        _cm[1] += p[1] * w;
+
+        if (_max_level == 0)
+        {
+            if (_count == w)
+                _dense_leafs.reserve(10);
+            _dense_leafs.push_back(make_tuple(p, w));
+            return 1;
+        }
+        else
+        {
+            int i = p[0] > (_ll[0] + (_ur[0] - _ll[0]) / 2);
+            int j = p[1] > (_ll[1] + (_ur[1] - _ll[1]) / 2);
+            size_t sc = (_max_level > 0 && _leafs.empty()) ? 4 : 0;
+            return sc + get_leaf(i + 2 * j).put_pos(p, w);
+        }
+        return 0;
+    }
+
+    void get_cm(Pos& cm)
+    {
+        for (size_t i = 0; i < 2; ++i)
+            cm[i] = _cm[i] / _count;
+    }
+
+    double get_w()
+    {
+        return max(_ur[0] - _ll[0],
+                   _ur[1] - _ll[1]);
+    }
+
+    Weight get_count()
+    {
+        return _count;
+    }
+
+    int max_level()
+    {
+        return _max_level;
+    }
+
+private:
+    Pos _ll, _ur;
+    vector<QuadTree> _leafs;
+    vector<tuple<Pos,Weight> > _dense_leafs;
+    Pos _cm;
+    Weight _count;
+    int _max_level;
+};
+
+template <class Pos>
+inline double dist(const Pos& p1, const Pos& p2)
+{
+    double r = 0;
+    for (size_t i = 0; i < 2; ++i)
+        r += pow(p1[i] - p2[i], 2);
+    return sqrt(r);
+}
+
+template <class Pos>
+inline double f_r(double C, double K, double p, const Pos& p1, const Pos& p2)
+{
+    double d = dist(p1, p2);
+    if (d == 0)
+        return 0;
+    return -C * pow(K, 1 + p) / pow(d, p);
+}
+
+template <class Pos>
+inline double f_a(double K, const Pos& p1, const Pos& p2)
+{
+    return pow(dist(p1, p2), 2) / K;
+}
+
+template <class Pos>
+inline double get_diff(const Pos& p1, const Pos& p2, Pos& r)
+{
+    double abs = 0;
+    for (size_t i = 0; i < 2; ++i)
+    {
+        r[i] = p1[i] - p2[i];
+        abs += pow(r[i], 2);
+    }
+    if (abs == 0)
+        abs = 1;
+    for (size_t i = 0; i < 2; ++i)
+        r[i] /= sqrt(abs);
+    return sqrt(abs);
+}
+
+template <class Pos>
+inline double norm(Pos& x)
+{
+    double abs = 0;
+    for (size_t i = 0; i < 2; ++i)
+        abs += pow(x[i], 2);
+    for (size_t i = 0; i < 2; ++i)
+        x[i] /= sqrt(abs);
+    return sqrt(abs);
+}
+
+struct get_sfdp_layout
+{
+    get_sfdp_layout(double C, double K, double p, double theta, double init_step,
+                    double step_schedule, size_t max_level, double epsilon,
+                    size_t max_iter, bool simple)
+        : C(C), K(K), p(p), theta(theta), init_step(init_step),
+          step_schedule(step_schedule), epsilon(epsilon),
+          max_level(max_level), max_iter(max_iter), simple(simple) {}
+
+    double C, K, p, theta, init_step, step_schedule, epsilon;
+    size_t max_level, max_iter;
+    bool simple;
+
+    template <class Graph, class VertexIndex, class PosMap, class VertexWeightMap,
+              class EdgeWeightMap, class PinMap>
+    void operator()(Graph& g, VertexIndex vertex_index, PosMap pos,
+                    VertexWeightMap vweight, EdgeWeightMap eweight, PinMap pin,
+                    bool verbose) const
+    {
+        typedef typename property_traits<PosMap>::value_type pos_t;
+        typedef typename property_traits<PosMap>::value_type::value_type val_t;
+
+        typedef typename property_traits<VertexWeightMap>::value_type vweight_t;
+
+        pos_t ll(2, numeric_limits<val_t>::max()),
+            ur(2, -numeric_limits<val_t>::max());
+
+        int i, N = num_vertices(g);
+        #pragma omp parallel for default(shared) private(i)
+        for (i = 0; i < N; ++i)
+        {
+            typename graph_traits<Graph>::vertex_descriptor v =
+                vertex(i, g);
+            if (v == graph_traits<Graph>::null_vertex())
+                continue;
+            pos[v].resize(2);
+
+            for (size_t j = 0; j < 2; ++j)
+            {
+                #pragma omp critical
+                ll[j] = min(pos[v][j], ll[j]);
+                ur[j] = max(pos[v][j], ur[j]);
+            }
+        }
+
+        val_t delta = epsilon * K + 1, E = 0, E0;
+        E0 = numeric_limits<val_t>::max();
+        size_t n_iter = 0;
+        val_t step = init_step;
+        size_t progress = 0;
+
+        vector<reference_wrapper<QuadTree<pos_t, vweight_t> > > Q;
+        Q.reserve(max_level * 2);
+
+        while (delta > epsilon * K && (max_iter == 0 || n_iter < max_iter))
+        {
+            delta = 0;
+            E0 = E;
+            E = 0;
+
+            pos_t nll(2, numeric_limits<val_t>::max()),
+                nur(2, -numeric_limits<val_t>::max());
+
+            QuadTree<pos_t, vweight_t> qt(ll, ur, max_level);
+            for (i = 0; i < N; ++i)
+            {
+                typename graph_traits<Graph>::vertex_descriptor v =
+                    vertex(i, g);
+                if (v == graph_traits<Graph>::null_vertex())
+                    continue;
+                qt.put_pos(pos[v], vweight[v]);
+            }
+
+            pos_t diff(2, 0), pos_u(2, 0), ftot(2, 0), cm(2, 0);
+
+            size_t nmoves = 0;
+            #pragma omp parallel for default(shared) private(i)  \
+                firstprivate(Q, diff, pos_u, ftot, cm) \
+                reduction(+:E, delta, nmoves)
+            for (i = 0; i < N; ++i)
+            {
+                typename graph_traits<Graph>::vertex_descriptor v =
+                    vertex(i, g);
+                if (v == graph_traits<Graph>::null_vertex())
+                    continue;
+
+                if (pin[v])
+                    continue;
+
+                ftot[0] = ftot[1] = 0;
+                Q.clear();
+                Q.push_back(ref(qt));
+                while (!Q.empty())
+                {
+                    QuadTree<pos_t, vweight_t>& q = Q.back();
+                    Q.pop_back();
+
+                    if (q.max_level() == 0)
+                    {
+                        vector<tuple<pos_t,vweight_t> >& dleafs =
+                            q.get_dense_leafs();
+                        for(size_t j = 0; j < dleafs.size(); ++j)
+                        {
+                            val_t d = get_diff(get<0>(dleafs[j]), pos[v],
+                                               diff);
+                            if (d == 0)
+                                continue;
+                            val_t f = f_r(C, K, p, pos[v], get<0>(dleafs[j]));
+                            f *= get<1>(dleafs[j]) * get(vweight, v);
+                            for (size_t l = 0; l < 2; ++l)
+                                ftot[l] += f * diff[l];
+                        }
+                    }
+                    else
+                    {
+                        double w = q.get_w();
+                        q.get_cm(cm);
+                        double d = get_diff(cm, pos[v], diff);
+                        if (w / d > theta)
+                        {
+                            for(size_t j = 0; j < 4; ++j)
+                            {
+                                QuadTree<pos_t, vweight_t>& leaf = q.get_leaf(j);
+                                if (leaf.get_count() > 0)
+                                    Q.push_back(ref(leaf));
+                            }
+                        }
+                        else
+