Commit ae2fe620 authored by Ale Abdo's avatar Ale Abdo
Browse files

Revert "Remove graph rewiring"

It's still buggy (of course), but now we'll try to fix it in it's own
 branch.

This reverts commit 1cdbdeef.
parent 32ae550d
......@@ -41,6 +41,7 @@ libgraph_tool_la_SOURCES = \
graph_community_network.cc\
graph_line_graph.cc\
graph_betweenness.cc\
graph_rewiring.cc\
graph_layout.cc\
graph_io.cc\
graph_bind.cc\
......
......@@ -113,6 +113,15 @@ public:
double GetModularity(std::string weight, std::string property);
void GetCommunityNetwork(std::string property, std::string size_property, std::string out_file, std::string format) const;
// graph random rewiring (shuffling)
enum rewire_strat_t
{
UNCORRELATED_STRAT,
CORRELATED_STRAT
};
void RandomRewire(rewire_strat_t strat, bool self_loops, bool parallel_edges, size_t seed);
// filtering
void SetDirected(bool directed) {_directed = directed;}
bool GetDirected() const {return _directed;}
......
......@@ -285,6 +285,7 @@ BOOST_PYTHON_MODULE(libgraph_tool)
.def("GetCommunityStructure", &GraphInterfaceWrap::GetCommunityStructure)
.def("GetCommunityNetwork", &GraphInterfaceWrap::GetCommunityNetwork)
.def("GetModularity", &GraphInterfaceWrap::GetModularity)
.def("RandomRewire", &GraphInterfaceWrap::RandomRewire)
.def("SetDirected", &GraphInterfaceWrap::SetDirected)
.def("GetDirected", &GraphInterfaceWrap::GetDirected)
.def("SetReversed", &GraphInterfaceWrap::SetReversed)
......@@ -324,6 +325,10 @@ BOOST_PYTHON_MODULE(libgraph_tool)
.value("Uncorrelated", GraphInterfaceWrap::UNCORRELATED)
.value("Correlated", GraphInterfaceWrap::CORRELATED);
enum_<GraphInterfaceWrap::rewire_strat_t>("RewireStrat")
.value("Uncorrelated", GraphInterfaceWrap::UNCORRELATED_STRAT)
.value("Correlated", GraphInterfaceWrap::CORRELATED_STRAT);
variant_from_python<string>();
variant_from_python<GraphInterfaceWrap::degree_t>();
to_python_converter<pair<double,double>, pair_to_tuple<double,double> >();
......
// 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, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
#include <algorithm>
#include <tr1/unordered_set>
#include <boost/lambda/lambda.hpp>
#include <boost/lambda/bind.hpp>
#include <boost/random.hpp>
#include <boost/functional/hash.hpp>
#include "graph.hh"
#include "graph_filtering.hh"
#include "shared_map.hh"
using namespace std;
using namespace boost;
using namespace boost::lambda;
using namespace graph_tool;
typedef boost::mt19937 rng_t;
struct get_in_degree
{
template <class Graph>
size_t operator()(typename graph_traits<Graph>::vertex_descriptor v, const Graph& g)
{
return get_degree(v, g, typename is_convertible<typename graph_traits<Graph>::directed_category,directed_tag>::type());
}
template <class Graph>
size_t get_degree(typename graph_traits<Graph>::vertex_descriptor v, const Graph& g, true_type)
{
return in_degree(v,g);
}
template <class Graph>
size_t get_degree(typename graph_traits<Graph>::vertex_descriptor v, const Graph& g, false_type)
{
return out_degree(v,g);
}
};
template <class Graph>
struct get_in_edges
{
typedef typename mpl::if_<typename is_convertible<typename graph_traits<Graph>::directed_category,directed_tag>::type,
typename graph_traits<Graph>::in_edge_iterator,
typename graph_traits<Graph>::out_edge_iterator>::type iterator;
pair<iterator,iterator> operator()(typename graph_traits<Graph>::vertex_descriptor v, const Graph& g)
{
return get_edges(v, g, typename is_convertible<typename graph_traits<Graph>::directed_category,directed_tag>::type());
}
pair<iterator,iterator> get_edges(typename graph_traits<Graph>::vertex_descriptor v, const Graph& g, true_type)
{
return in_edges(v,g);
}
pair<iterator,iterator> get_edges(typename graph_traits<Graph>::vertex_descriptor v, const Graph& g, false_type)
{
return out_edges(v,g);
}
};
template <class Graph>
bool is_adjacent(typename graph_traits<Graph>::vertex_descriptor u, typename graph_traits<Graph>::vertex_descriptor v, Graph& g )
{
typename graph_traits<Graph>::out_edge_iterator e, e_end;
for (tie(e, e_end) = out_edges(u, g); e != e_end; ++e)
{
if (target(*e,g) == v)
return true;
}
return false;
}
template <template <class Graph> class RewireStrategy>
struct graph_rewire
{
template <class Graph, class EdgeIndexMap>
void operator()(const Graph& g, EdgeIndexMap edge_index, size_t seed, bool self_loops, bool parallel_edges) const
{
rng_t rng(static_cast<rng_t::result_type>(seed));
RewireStrategy<Graph> rewire(g, rng);
if (!self_loops)
{
// check the existence of self-loops
bool has_self_loops = false;
int i, N = num_vertices(g);
#pragma omp parallel for default(shared) private(i) schedule(dynamic)
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 (is_adjacent(v, v, g))
self_loops = true;
}
if (has_self_loops)
throw GraphException("Self-loop detected. Can't rewire graph without self-loops if it already contains self-loops!");
}
if (!parallel_edges)
{
// check the existence of parallel edges
bool has_parallel_edges = false;
int i, N = num_vertices(g);
#pragma omp parallel for default(shared) private(i) schedule(dynamic)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
if (v == graph_traits<Graph>::null_vertex())
continue;
tr1::unordered_set<typename graph_traits<Graph>::vertex_descriptor> targets;
typename graph_traits<Graph>::out_edge_iterator e, e_end;
for (tie(e, e_end) = out_edges(v, g); e != e_end; ++e)
{
if (targets.find(target(*e, g)) != targets.end())
has_parallel_edges = true;
else
targets.insert(target(*e, g));
}
}
if (has_parallel_edges)
throw GraphException("Parallel edge detected. Can't rewire graph without parallel edges if it already contains parallel edges!");
}
vector<typename graph_traits<Graph>::edge_descriptor> edges(num_edges(g));
int i, N = num_vertices(g);
#pragma omp parallel for default(shared) private(i) schedule(dynamic)
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>::out_edge_iterator e, e_end;
for (tie(e, e_end) = out_edges(v, g); e != e_end; ++e)
edges[edge_index[*e]] = *e;
}
vector<pair<size_t, size_t> > swap_list;
swap_list.reserve(num_edges(g));
// for each vertex, rewire the targets of its out edges
N = num_vertices(g);
#pragma omp parallel for default(shared) private(i) schedule(dynamic)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, g);
if (v == graph_traits<Graph>::null_vertex())
continue;
tr1::unordered_set<typename graph_traits<Graph>::vertex_descriptor> target_set;
//rewire out edges
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>::edge_descriptor swap_partner;
//rewire edge
swap_partner = rewire(*e, target_set, self_loops, parallel_edges);
if (swap_partner == *e)
continue;
target_set.insert(target(swap_partner, g));
#pragma omp critical
{
swap_list.push_back(make_pair(edge_index[*e], edge_index[swap_partner]));
}
}
}
// do the actual graph modification
N = swap_list.size();
#pragma omp parallel for default(shared) private(i) schedule(dynamic)
for (i = 0; i < N; ++i)
{
size_t e1, e2;
tie(e1, e2) = swap_list[i];
typename graph_traits<Graph>::vertex_descriptor s1, s2, new_target1, new_target2;
typename graph_traits<Graph>::edge_descriptor new_edge1, new_edge2 ;
s1 = source(edges[e1], g);
new_target1 = target(edges[e2], g);
s2 = source(edges[e2], g);
new_target2 = target(edges[e1], g);
#pragma omp critical
{
new_edge1 = add_edge(s1, new_target1, const_cast<Graph&>(g)).first;
edge_index[new_edge1] = e1;
new_edge2 = add_edge(s2, new_target2, const_cast<Graph&>(g)).first;
edge_index[new_edge2] = e2;
remove_edge(edges[e1], const_cast<Graph&>(g));
edges[e1] = new_edge1;
remove_edge(edges[e2], const_cast<Graph&>(g));
edges[e2] = new_edge2;
}
}
}
};
template <class Graph>
class RandomRewireStrategy
{
public:
RandomRewireStrategy (const Graph& g, rng_t& rng): _g(g), _rng(rng)
{
int i, N = num_vertices(_g);
#pragma omp parallel for default(shared) private(i) schedule(dynamic)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, _g);
if (v == graph_traits<Graph>::null_vertex())
continue;
size_t k = get_in_degree()(v, _g);
if (k == 0)
continue;
#pragma omp critical
{
if (!_vertices.empty())
_vertices[_vertices.rbegin()->first + k] = v;
else
_vertices[k] = v;
}
}
}
typename graph_traits<Graph>::edge_descriptor operator()(const typename graph_traits<Graph>::edge_descriptor& e,
tr1::unordered_set<typename graph_traits<Graph>::vertex_descriptor>& target_set,
bool self_loops, bool parallel_edges)
{
uniform_int<size_t> vertex_sample(0, _vertices.rbegin()->first-1);
size_t v;
typename graph_traits<Graph>::vertex_descriptor vertex;
do
{
#pragma omp critical
{
v = vertex_sample(_rng);
}
vertex = _vertices.upper_bound(v)->second;
}
while ( (!self_loops && (vertex == source(e, _g)) ) ||
(!parallel_edges && (target_set.find(vertex) != target_set.end())));
vector<typename graph_traits<Graph>::edge_descriptor> candidates;
typename get_in_edges<Graph>::iterator w, w_end;
for (tie(w, w_end) = get_in_edges<Graph>()(vertex, _g); w != w_end; ++w)
{
if (parallel_edges || !is_adjacent(source(*w, _g), vertex, _g))
candidates.push_back(*w);
}
if (candidates.empty())
return e;
uniform_int<size_t> edge_sample(0, candidates.size() - 1);
size_t edge;
#pragma omp critical
{
edge = edge_sample(_rng);
}
return candidates[edge];
}
private:
const Graph& _g;
rng_t& _rng;
typedef map<size_t, typename graph_traits<Graph>::vertex_descriptor> vertices_t;
vertices_t _vertices;
};
template <class Graph>
class CorrelatedRewireStrategy
{
public:
CorrelatedRewireStrategy (const Graph& g, rng_t& rng): _g(g), _rng(rng), _deg_sum(0)
{
int i, N = num_vertices(_g);
#pragma omp parallel for default(shared) private(i) schedule(dynamic)
for (i = 0; i < N; ++i)
{
typename graph_traits<Graph>::vertex_descriptor v = vertex(i, _g);
if (v == graph_traits<Graph>::null_vertex())
continue;
size_t j = get_in_degree()(v, _g);
size_t k = out_degree(v, _g);
#pragma omp critical
{
typename deg_vertices_t::value_type::second_type& vertices = _deg_vertices[make_pair(j,k)];
if (!vertices.empty())
vertices[vertices.rbegin()->first + j] = v;
else
vertices[j] = v;
}
}
}
typename graph_traits<Graph>::edge_descriptor operator()(const typename graph_traits<Graph>::edge_descriptor& e,
tr1::unordered_set<typename graph_traits<Graph>::vertex_descriptor>& target_set,
bool self_loops, bool parallel_edges)
{
typename graph_traits<Graph>::vertex_descriptor t = target(e, _g);
typename deg_vertices_t::value_type::second_type& vertices = _deg_vertices[make_pair(get_in_degree()(t, _g), out_degree(t, _g))];
uniform_int<size_t> vertex_sample(0, vertices.rbegin()->first - 1);
size_t v;
typename graph_traits<Graph>::vertex_descriptor vertex;
do
{
#pragma omp critical
{
v = vertex_sample(_rng);
}
vertex = vertices.upper_bound(v)->second;
}
while ( (!self_loops && (vertex == source(e, _g)) ) ||
(!parallel_edges && (target_set.find(vertex) != target_set.end())));
vector<typename graph_traits<Graph>::edge_descriptor> candidates;
typename get_in_edges<Graph>::iterator w, w_end;
for (tie(w, w_end) = get_in_edges<Graph>()(vertex, _g); w != w_end; ++w)
{
if (parallel_edges || !is_adjacent(source(*w, _g), vertex, _g))
candidates.push_back(*w);
}
if (candidates.empty())
return e;
uniform_int<size_t> edge_sample(0, candidates.size() - 1);
size_t edge;
#pragma omp critical
{
edge = edge_sample(_rng);
}
return candidates[edge];
}
private:
const Graph& _g;
rng_t& _rng;
typedef tr1::unordered_map<pair<size_t, size_t>, map<size_t, typename graph_traits<Graph>::vertex_descriptor>, hash<pair<size_t, size_t> > > deg_vertices_t;
deg_vertices_t _deg_vertices;
size_t _deg_sum;
};
//==============================================================================
// RandomRewire
//==============================================================================
void GraphInterface::RandomRewire(rewire_strat_t strat, bool self_loops, bool parallel_edges, size_t seed)
{
bool reversed = GetReversed();
SetReversed(false);
if (strat == UNCORRELATED_STRAT)
check_filter(*this, bind<void>(graph_rewire<RandomRewireStrategy>(), _1, _edge_index, seed, self_loops, parallel_edges),
never_reversed(), directed_check());
else
check_filter(*this, bind<void>(graph_rewire<CorrelatedRewireStrategy>(), _1, _edge_index, seed, self_loops, parallel_edges),
never_reversed(), directed_check());
SetReversed(reversed);
}
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