Implement layout module ('draw' from python) and arf layout

This implements a layout module (called 'draw' from python) with an
implementation of the arf spring-block layout.

configure.ac

@@ -294,6 +294,7 @@ src/graph/community/Makefile
 src/graph/util/Makefile
 src/graph/topology/Makefile
 src/graph/flow/Makefile
+src/graph/layout/Makefile
 src/graph_tool/Makefile
 ])
 

src/graph/Makefile.am

 ## Process this file with automake to produce Makefile.in
 
-SUBDIRS = generation stats clustering community util topology centrality correlations flow
+SUBDIRS = generation stats clustering community util topology centrality correlations flow layout
 
 AM_CPPFLAGS =\
     -I$(srcdir)/.. \
@@ -24,6 +24,8 @@ libgraph_tool_core_la_SOURCES = \
     graph_filtering.cc \
     graph_io.cc \
     graph_properties.cc \
+    graph_properties_group.cc \
+    graph_properties_ungroup.cc \
     graph_python_interface.cc \
     graph_python_interface_export.cc \
     graph_selectors.cc \
@@ -39,6 +41,7 @@ libgraph_tool_core_la_include_HEADERS = \
     graph_filtering.hh \
     graph.hh \
     graph_properties.hh \
+    graph_properties_group.hh \
     graph_python_interface.hh \
     graph_selectors.hh \
     graph_util.hh \

src/graph/layout/Makefile.am

+## Process this file with automake to produce Makefile.in
+
+AM_CPPFLAGS = $(MOD_CPPFLAGS)
+
+AM_CFLAGS = $(AM_CXXFLAGS)
+
+libgraph_tool_layoutdir = $(pythondir)/graph_tool/draw
+
+libgraph_tool_layout_LTLIBRARIES = libgraph_tool_layout.la
+
+libgraph_tool_layout_la_includedir = $(pythondir)/graph_tool/include
+
+libgraph_tool_layout_la_LIBADD = $(MOD_LIBADD)
+
+libgraph_tool_layout_la_LDFLAGS = $(MOD_LDFLAGS)
+
+libgraph_tool_layout_la_SOURCES = \
+    graph_arf.cc \
+    graph_bind_layout.cc
+
+libgraph_tool_layout_la_include_HEADERS = \
+    graph_arf.hh

src/graph/layout/graph_arf.cc

+// 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/>.
+
+#include "graph_filtering.hh"
+#include "graph.hh"
+#include "graph_properties.hh"
+
+#include <boost/lambda/bind.hpp>
+
+#include "graph_arf.hh"
+
+using namespace std;
+using namespace boost;
+using namespace graph_tool;
+
+void arf_layout(GraphInterface& g, boost::any pos, boost::any weight, double d,
+                double a, double dt, size_t max_iter, double epsilon,
+                size_t dim)
+{
+    typedef ConstantPropertyMap<int32_t,GraphInterface::edge_t> weight_map_t;
+    typedef mpl::push_back<edge_scalar_properties, weight_map_t>::type
+        edge_props_t;
+
+    if(weight.empty())
+        weight = weight_map_t(1);
+
+    run_action<graph_tool::detail::never_directed>()
+        (g,
+         lambda::bind<void>(get_arf_layout(), lambda::_1, lambda::_2,
+                            lambda::_3, a, d, dt, epsilon, max_iter, dim),
+         vertex_floating_vector_properties(), edge_props_t())(pos, weight);
+}
+
+#include <boost/python.hpp>
+
+void export_arf()
+{
+    python::def("arf_layout", &arf_layout);
+}
+
+

src/graph/layout/graph_arf.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_ARF_HH
+#define GRAPH_ARF_HH
+
+#include <tr1/random>
+#include <limits>
+#include <iostream>
+
+namespace graph_tool
+{
+using namespace std;
+using namespace boost;
+
+struct get_arf_layout
+{
+    template <class Graph, class PosMap, class WeightMap>
+    void operator()(Graph& g, PosMap pos, WeightMap weight, double a, double d,
+                    double dt, double epsilon, size_t max_iter, size_t dim)
+        const
+    {
+        typedef typename property_traits<PosMap>::value_type::value_type pos_t;
+
+        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(dim);
+        }
+
+        pos_t delta = epsilon + 1;
+        size_t n_iter = 0;
+        pos_t r = d*sqrt(pos_t(HardNumVertices()(g)));
+        while (delta > epsilon && (max_iter == 0 || n_iter < max_iter))
+        {
+            delta = 0;
+            #pragma omp parallel for default(shared) private(i) \
+                reduction(+:delta)
+            for (i = 0; i < N; ++i)
+            {
+                typename graph_traits<Graph>::vertex_descriptor v =
+                    vertex(i, g);
+                if (v == graph_traits<Graph>::null_vertex())
+                    continue;
+
+                vector<pos_t> delta_pos(dim,0);
+
+                typename graph_traits<Graph>::vertex_iterator w, w_end;
+                for (tie(w, w_end) = vertices(g); w != w_end; ++w)
+                {
+                    if (*w == v)
+                        continue;
+                    pos_t diff = 0;
+                    for (size_t j = 0; j < dim; ++j)
+                    {
+                        pos_t dx = pos[*w][j] - pos[v][j];
+                        diff += dx*dx;
+                        delta_pos[j] += dx;
+                    }
+                    diff = sqrt(diff);
+                    if (diff < 1e-6)
+                        diff = 1e-6;
+                    pos_t m = r/diff;
+                    for (size_t j = 0; j < dim; ++j)
+                    {
+                        pos_t dx = pos[*w][j] - pos[v][j];
+                        delta_pos[j] -= m*dx;
+                    }
+                }
+
+                typename graph_traits<Graph>::out_edge_iterator e, e_end;
+                for (tie(e,e_end) = out_edges(v, g); e != e_end; ++e)
+                {
+                    typename graph_traits<Graph>::vertex_descriptor u =
+                        target(*e, g);
+                    if (u == v)
+                        continue;
+                    pos_t m = a*get(weight, *e) - 1;
+                    for (size_t j = 0; j < dim; ++j)
+                    {
+                        pos_t dx = pos[u][j] - pos[v][j];
+                        delta_pos[j] += m*dx;
+                    }
+                }
+
+                for (size_t j = 0; j < dim; ++j)
+                {
+                    pos[v][j] += dt*delta_pos[j];
+                    delta += abs(delta_pos[j]);
+                }
+            }
+            n_iter++;
+        }
+    }
+};
+
+} // namespace graph_tool
+
+
+#endif // GRAPH_ARF_HH

src/graph/layout/graph_bind_layout.cc

+// 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/>.
+
+#include <boost/python.hpp>
+
+using namespace boost::python;
+void export_arf();
+
+BOOST_PYTHON_MODULE(libgraph_tool_layout)
+{
+    export_arf();
+}
+

src/graph/layout/graph_layout.cc

-// 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/>.
-
-#include "graph_filtering.hh"
-#include "graph.hh"
-#include "graph_properties.hh"
-
-#include <boost/graph/gursoy_atun_layout.hpp>
-#include <boost/graph/kamada_kawai_spring_layout.hpp>
-#include <boost/graph/fruchterman_reingold.hpp>
-#include <boost/graph/random_layout.hpp>
-#include <boost/random.hpp>
-#include <boost/lambda/lambda.hpp>
-
-using namespace std;
-using namespace boost;
-using namespace boost::lambda;
-using namespace graph_tool;
-
-struct compute_gursoy
-{
-    template <class Graph, class PosMap, class WeightMap, class IndexMap>
-    void operator()(const Graph* gp, size_t iter, size_t seed, PosMap pos,
-                    WeightMap weight, string topology, IndexMap index_map) const
-    {
-        const Graph& g = *gp;
-        mt19937 rng(static_cast<mt19937::result_type>(seed));
-        size_t n = HardNumVertices()(&g);
-
-        typename get_weight_map<WeightMap>::type weight_map(weight);
-
-        if (iter == 0)
-            iter = n;
-        if (topology == "square")
-        {
-            square_topology<mt19937> top(rng, sqrt(n));
-            gursoy_atun_layout(g, top,  pos, iter, sqrt(double(n)),
-                               1.0, 0.8, 0.2, index_map, weight_map);
-        }
-        else if (topology == "circle")
-        {
-            circle_topology<mt19937> top(rng, n/2);
-            gursoy_atun_layout(g, top,  pos, iter, sqrt(double(n)),
-                               1.0, 0.8, 0.2, index_map, weight_map);
-        }
-        else if (topology == "heart")
-        {
-            heart_topology<mt19937> top(rng);
-            vector_property_map<heart_topology<mt19937>::point_type,
-                                IndexMap> pos_map (index_map);
-            gursoy_atun_layout(g, top, pos_map, iter, sqrt(double(n)),
-                              1.0, 0.8, 0.2, index_map, weight_map);
-            typename graph_traits<Graph>::vertex_iterator v, v_end;
-            for (tie(v, v_end) = vertices(g); v != v_end; ++v)
-            {
-                pos[*v][0] = pos_map[*v][0];
-                pos[*v][1] = pos_map[*v][1];
-            }
-        }
-        else
-        {
-            throw GraphException("invalid topology for graph layout: " +
-                                 topology);
-        }
-    }
-
-    template <class PropertyMap>
-    struct get_weight_map
-    {
-        typedef typename property_traits<PropertyMap>::value_type
-            value_type;
-        typedef typename mpl::if_<
-            typename mpl::or_<is_floating_point<value_type>,
-                              is_same<PropertyMap,dummy_property_map> >::type,
-            PropertyMap,
-            ConvertedPropertyMap<PropertyMap,double> >::type type;
-    };
-};
-
-struct copy_points
-{
-    template <class Graph, class VectorProperty, class PointsMap>
-    void operator()(const Graph* g, VectorProperty vec_prop, PointsMap pos_map)
-        const
-    {
-        typename graph_traits<Graph>::vertex_iterator v, v_end;
-        for (tie(v, v_end) = vertices(*g); v != v_end; ++v)
-        {
-            vec_prop[*v].resize(2);
-            vec_prop[*v][0] = pos_map[*v][0];
-            vec_prop[*v][1] = pos_map[*v][1];
-        }
-    }
-};
-
-struct copy_weights
-{
-    template <class Graph, class WeightSrcMap, class WeightTgtMap>
-    void operator()(const Graph* g, WeightSrcMap src_map, WeightTgtMap tgt_map)
-        const
-    {
-        do_copy(g, src_map, tgt_map, is_same<WeightSrcMap, WeightTgtMap>());
-    }
-
-    template <class Graph, class WeightSrcMap, class WeightTgtMap>
-    void do_copy(const Graph* g, WeightSrcMap src_map, WeightTgtMap tgt_map,
-                 true_type) const
-    {
-        tgt_map = src_map;
-    }
-
-    template <class Graph, class WeightSrcMap, class WeightTgtMap>
-    void do_copy(const Graph* g, WeightSrcMap src_map, WeightTgtMap tgt_map,
-                 false_type) const
-    {
-        typename graph_traits<Graph>::edge_iterator e, e_end;
-        for (tie(e, e_end) = edges(*g); e != e_end; ++e)
-        {
-            tgt_map[*e] = src_map[*e];
-        }
-    }
-};
-
-
-struct compute_spring_block
-{
-    template <class Graph, class PosMap, class IndexMap, class WeightMap>
-    void operator()(const Graph* gp, string type, size_t iter, size_t seed,
-                    PosMap pos, bool progressive, WeightMap weight,
-                    IndexMap index_map)
-        const
-    {
-        const Graph& g = *gp;
-        mt19937 rng(static_cast<mt19937::result_type>(seed));
-        size_t n = HardNumVertices()(&g);
-
-        if (iter == 0)
-            iter = 100;
-        double radius = n;
-        if (!progressive)
-            random_graph_layout(g, pos, -radius/2, radius/2,
-                                -radius/2, radius/2, rng);
-        if (type == "fg-grid")
-        {
-            fruchterman_reingold_force_directed_layout
-                (g, pos, radius, radius,
-                 cooling(linear_cooling<double>(iter)).
-                 vertex_index_map(index_map));
-        }
-        else if (type == "fg-all-pairs")
-        {
-            fruchterman_reingold_force_directed_layout
-                (g, pos, radius, radius,
-                 cooling(linear_cooling<double>(iter)).
-                 vertex_index_map(index_map).force_pairs(all_force_pairs()));
-        }
-        else if (type == "kw")
-        {
-            typedef typename graph_traits<Graph>::directed_category
-                directed_category;
-            bool retval;
-            retval = compute_kamada_kawai(g, iter, n, pos, weight,
-                                          typename is_convertible
-                                                      <directed_category,
-                                                       undirected_tag>::type());
-            if (!retval)
-                throw GraphException("the Kamada-Kawai layout algorithm only "
-                                     "works for connected graphs!");
-        }
-        else
-        {
-            throw GraphException("invalid type of spring-block graph layout: " +
-                                 type);
-        }
-    }
-
-    template <class Graph, class PosMap, class WeightMap>
-    bool compute_kamada_kawai(Graph &g, size_t iter, size_t n, PosMap pos,
-                              WeightMap weight, boost::true_type) const
-    {
-        return kamada_kawai_spring_layout(g, pos, weight, side_length(n));
-    }
-
-    template <class Graph, class PosMap, class WeightMap>
-    bool compute_kamada_kawai(Graph &g,  size_t iter, size_t n, PosMap pos,
-                              WeightMap weight, boost::false_type) const
-    {
-        UndirectedAdaptor<Graph> ug(g);
-        return kamada_kawai_spring_layout(ug, pos, weight, side_length(n));
-    }
-};
-
-
-struct copy_positions
-{
-    template <class Graph, class VectorProperty, class PosMap>
-    void operator()(const Graph* g, VectorProperty vec_prop, PosMap pos_map)
-        const
-    {
-        typename graph_traits<Graph>::vertex_iterator v, v_end;
-        for (tie(v, v_end) = vertices(*g); v != v_end; ++v)
-        {
-            vec_prop[*v].resize(2);
-            vec_prop[*v][0] = pos_map[*v].x;
-            vec_prop[*v][1] = pos_map[*v].y;
-        }
-    }
-};
-
-void GraphInterface::ComputeGraphLayoutGursoy(string pos_prop, string weight,
-                                              string topology, size_t iter,
-                                              size_t seed)
-{
-    typedef vector_property_map<double, edge_index_map_t> temp_weight_t;
-    boost::any pos_map, weight_map;
-    try
-    {
-        pos_map = prop(pos_prop, _vertex_index, _properties);
-        if (!belongs<vertex_floating_vector_properties>()(pos_map))
-            throw GraphException("property " + pos_prop +
-                                 "is not of floating point vector type");
-        if (weight == "")
-        {
-            weight_map = dummy_property_map();
-        }
-        else
-        {
-            temp_weight_t temp_weight(_edge_index);
-            run_action<>()(*this, bind<void>(copy_weights(), _1, _2,
-                                             temp_weight),
-                           edge_scalar_properties())
-                (prop(weight, _edge_index, _properties));
-            weight_map = temp_weight;
-        }
-    }
-    catch (property_not_found& e)
-    {
-        throw GraphException("error getting property: " + string(e.what()));
-    }
-
-    vector_property_map<convex_topology<2>::point_type, vertex_index_map_t>
-        pos(_vertex_index);
-    run_action<>()(*this, bind<void>(compute_gursoy(), _1, iter, seed, pos,
-                                     _2, topology, _vertex_index),
-                   mpl::vector<temp_weight_t,dummy_property_map>())
-        (weight_map);
-    run_action<>()(*this, bind<void>(copy_points(), _1, _2, pos),
-                   vertex_floating_vector_properties())(pos_map);
-}
-
-struct pos_t
-{
-    double x;
-    double y;
-};
-
-void GraphInterface::ComputeGraphLayoutSpringBlock(string pos_prop,
-                                                   string weight, string type,
-                                                   size_t iter,
-                                                   bool progressive,
-                                                   size_t seed)
-{
-    typedef vector_property_map<double, edge_index_map_t> temp_weight_t;
-    boost::any pos_map, weight_map;
-    try
-    {
-        pos_map = prop(pos_prop, _vertex_index, _properties);
-        if (!belongs<vertex_floating_vector_properties>()(pos_map))
-            throw GraphException("property " + pos_prop +
-                                 "is not of floating point vector type");
-
-        if (weight == "")
-        {
-            weight_map = ConstantPropertyMap<double,edge_t>(1.0);
-        }
-        else
-        {
-            temp_weight_t temp_weight(_edge_index);
-            run_action<>()(*this, bind<void>(copy_weights(), _1, _2,
-                                             temp_weight),
-                           edge_scalar_properties())
-                (prop(weight, _edge_index, _properties));
-            weight_map = temp_weight;
-        }
-    }
-    catch (property_not_found& e)
-    {
-        throw GraphException("error getting property: " + string(e.what()));
-    }
-
-    typedef mpl::vector<temp_weight_t, ConstantPropertyMap<double,edge_t> >
-        weight_maps;
-
-    vector_property_map<pos_t, vertex_index_map_t> pos(_vertex_index);
-    run_action<>()(*this, bind<void>(compute_spring_block(), _1, type, iter,
-                                     seed, pos, progressive, _2, _vertex_index),
-                   weight_maps())
-        (weight_map);
-    run_action<>()(*this, bind<void>(copy_positions(), _1, _2, pos),
-                   vertex_floating_vector_properties())(pos_map);
-}

src/graph_tool/draw/__init__.py

@@ -22,9 +22,15 @@
 """
 
 import sys, os, os.path, time, warnings
-from .. core import _degree, _prop, PropertyMap
+from .. core import _degree, _prop, PropertyMap, _check_prop_vector,\
+     _check_prop_scalar, _check_prop_writable, group_vector_property,\
+     ungroup_vector_property
 from .. decorators import _limit_args
 import numpy.random
+from numpy import *
+
+from .. dl_import import dl_import
+dl_import("import libgraph_tool_layout")
 
 try:
     import gv
@@ -38,6 +44,8 @@ except ImportError:
     warnings.warn("error importing matplotlib module... " + \
                   "graph_draw() will not work.", ImportWarning)
 
+__all__ = ["graph_draw", "arf_layout", "random_layout"]
+
 def graph_draw(g, pos=None, size=(15, 15), pin=False, layout= "neato",
                maxiter=None, ratio= "fill", overlap="prism", sep=None,
                splines=False, vsize=0.1, penwidth=1.0, elen=None, gprops={},
@@ -59,7 +67,7 @@ def graph_draw(g, pos=None, size=(15, 15), pin=False, layout= "neato",
         If True, the vertices are not moved from their initial position.
     layout : string (default: "neato")
         Layout engine to be used. Possible values are "neato", "fdp", "dot",
-        "circo" and "twopi".
+        "circo", "twopi" and "arf".
     maxiter : int (default: None)
         If specified, limits the maximum number of iterations.
     ratio : string or float (default: "fill")
@@ -241,9 +249,17 @@ def graph_draw(g, pos=None, size=(15, 15), pin=False, layout= "neato",