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Commit 3243afae authored by Tiago Peixoto's avatar Tiago Peixoto
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* graph_community.cc: 

   - added support for saving annealing history to file
   - added support for continuing from an existing community partition


git-svn-id: https://svn.forked.de/graph-tool/trunk@54 d4600afd-f417-0410-95de-beed9576f240
parent fd7e85eb
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src/graph-tool
View file @ 3243afae
......@@ -126,7 +126,7 @@ layout.add_option("--compute-spring-block-layout", action="callback", callback=p
layout.add_option("--compute-gursoy-atun-layout", action="callback", callback=push_option, type="string", metavar="ITERATIONS[|SEED]", help="compute the Gursoy-Atun layout")
community = parser.add_option_group("Community")
community.add_option("--community-structure", action="callback", callback=push_option, type="string", metavar="PROPERTY|OPTIONS", help="calculate the community structure and assign it to PROPERTY. Options are: g (default: 1.0), N (default: 1000), Tmin (default: 0.01), Tmax (default: 1.0), spins (default: number of vertices), corr_type (default: uncorrelated), weight, seed (default: from clock), verbose. The value of corr_type can be 'random', 'uncorrelated' or 'correlated'.")
community.add_option("--community-structure", action="callback", callback=push_option, type="string", metavar="PROPERTY|OPTIONS", help="calculate the community structure and assign it to PROPERTY. Options are: g (default: 1.0), N (default: 1000), Tmin (default: 0.01), Tmax (default: 1.0), spins (default: number of vertices), corr_type (default: uncorrelated), weight, seed (default: from clock), verbose, history. The value of corr_type can be 'random', 'uncorrelated' or 'correlated'.")
community.add_option("--modularity", action="callback", callback=push_option, type="string", metavar="PROPERTY[|WEIGHT]|FILE", help="calculate the modularity, given a community partition specified by PROPERTY")
layout = parser.add_option_group("History")
......@@ -569,9 +569,14 @@ def parse_option(opt, just_file=False):
else:
weight = ""
verbose = get_suboption("verbose", param) != False
if get_suboption("history", param) != False:
history = get_suboption("history", param)
else:
history = ""
except ValueError,e:
raise OptionError(opt.name, "invalid value '%s': %s" % (opt.value, e))
graph.GetCommunityStructure(g, corr, N, Tmin, Tmax, spins, seed, verbose, weight, prop)
graph.GetCommunityStructure(g, corr, N, Tmin, Tmax, spins, seed, verbose, history, weight, prop)
elif opt.name == "modularity":
values = parse_values(opt.value)
if len(values) < 2 or len(values) > 3:
......
src/graph/graph.hh
View file @ 3243afae
......@@ -104,7 +104,7 @@ public:
CORRELATED
};
void GetCommunityStructure(double gamma, comm_corr_t corr, size_t n_iter, double Tmin, double Tmax, size_t Nseeds, size_t seed, bool verbose, std::string weight, std::string property);
void GetCommunityStructure(double gamma, comm_corr_t corr, size_t n_iter, double Tmin, double Tmax, size_t Nseeds, size_t seed, bool verbose, std::string history_file, std::string weight, std::string property);
double GetModularity(std::string weight, std::string property);
// filtering
......@@ -116,14 +116,14 @@ public:
void SetVertexFilterProperty(std::string property);
std::string GetVertexFilterProperty() const {return _vertex_filter_property;}
void SetVertexFilterRange(std::pair<double, double> allowed_range) {_vertex_range = allowed_range;}
void SetVertexFilterRange(std::pair<double,double> allowed_range) {_vertex_range = allowed_range;}
std::pair<double, double> GetVertexFilterRange() const {return _vertex_range;}
bool IsVertexFilterActive() const;
void SetEdgeFilterProperty(std::string property);
std::string GetEdgeFilterProperty() const {return _edge_filter_property;}
void SetEdgeFilterRange(std::pair<double, double> allowed_range) {_edge_range = allowed_range;}
std::pair<double, double> GetEdgeFilterRange() const {return _edge_range;}
void SetEdgeFilterRange(std::pair<double,double> allowed_range) {_edge_range = allowed_range;}
std::pair<double,double> GetEdgeFilterRange() const {return _edge_range;}
bool IsEdgeFilterActive() const;
void SetGenericVertexFilter(boost::python::object filter) {_vertex_python_filter = filter;}
......
src/graph/graph_community.cc
View file @ 3243afae
......@@ -96,27 +96,39 @@ template <template <class G, class CommunityMap> class NNKS>
struct get_communities
{
template <class Graph, class WeightMap, class CommunityMap>
void operator()(Graph& g, WeightMap weights, CommunityMap s, double gamma, size_t n_iter, pair<double,double> Tinterval, size_t Nspins, size_t seed, bool verbose) const
void operator()(Graph& g, WeightMap weights, CommunityMap s, double gamma, size_t n_iter, pair<double,double> Tinterval, pair<size_t,bool> Nspins, size_t seed, pair<bool,string> verbose) const
{
stringstream out_str;
ofstream out_file;
if (verbose.second != "")
{
out_file.open(verbose.second.c_str());
if (!out_file.is_open())
throw GraphException("error opening file " + verbose.second + " for writing");
out_file.exceptions (ifstream::eofbit | ifstream::failbit | ifstream::badbit);
}
double Tmin = Tinterval.first;
double Tmax = Tinterval.second;
rng_t rng(static_cast<rng_t::result_type>(seed));
boost::uniform_real<double> uniform_p(0.0,1.0);
if (Nspins == 0)
Nspins = HardNumVertices()(g);
if (Nspins.first == 0)
Nspins.first = HardNumVertices()(g);
ManagedUnorderedMap<size_t, size_t> Ns; // spin histogram
ManagedUnorderedMap<size_t, map<double, unordered_set<size_t> > > global_term; // global energy term
// init spins from [0,N-1] and global info
uniform_int<size_t> sample_spin(0, Nspins-1);
uniform_int<size_t> sample_spin(0, Nspins.first-1);
unordered_set<size_t> deg_set;
typename graph_traits<Graph>::vertex_iterator v,v_end;
for (tie(v,v_end) = vertices(g); v != v_end; ++v)
{
s[*v] = sample_spin(rng);
if (Nspins.second)
s[*v] = sample_spin(rng);
Ns[s[*v]]++;
deg_set.insert(out_degree_no_loops(*v, g));
}
......@@ -128,7 +140,7 @@ struct get_communities
for (typeof(deg_set.begin()) iter = deg_set.begin(); iter != deg_set.end(); ++iter)
degs.push_back(*iter);
for (size_t i = 0; i < degs.size(); ++i)
for (size_t sp = 0; sp < Nspins; ++sp)
for (size_t sp = 0; sp < Nspins.first; ++sp)
global_term[degs[i]][gamma*Nnnks(degs[i],sp)].insert(sp);
......@@ -153,7 +165,7 @@ struct get_communities
long double prob = 0;
for (typeof(global_term[degs[i]].begin()) iter = global_term[degs[i]].begin(); iter != global_term[degs[i]].end(); ++iter)
{
long double M = log(numeric_limits<long double>::max()/(Nspins*10));
long double M = log(numeric_limits<long double>::max()/(Nspins.first*10));
long double this_prob = exp((long double)(-iter->first - degs[i])/T + M)*iter->second.size();
if (prob + this_prob != prob)
{
......@@ -190,8 +202,8 @@ struct get_communities
size_t k = out_degree_no_loops(*v,g);
map<double, unordered_set<size_t> >& global_term_k = global_term[k];
map<long double, pair<double, bool> >& cumm_prob_k = cumm_prob[k];
map<double,unordered_set<size_t> >& global_term_k = global_term[k];
map<long double,pair<double,bool> >& cumm_prob_k = cumm_prob[k];
// update energy levels with local info
unordered_set<double> modified_energies;
......@@ -216,7 +228,7 @@ struct get_communities
cumm_prob_k[energy_to_prob[k][*iter]].second = false;
if (global_term_k.find(*iter) != global_term_k.end())
{
long double M = log(numeric_limits<long double>::max()/(Nspins*10));
long double M = log(numeric_limits<long double>::max()/(Nspins.first*10));
long double prob = exp((long double)(-*iter - k)/T + M)*global_term_k[*iter].size();
if (cumm_prob_k.empty() || cumm_prob_k.rbegin()->first + prob != cumm_prob_k.rbegin()->first)
{
......@@ -324,24 +336,38 @@ struct get_communities
s[v] = a;
}
if (verbose)
if (verbose.first)
{
static stringstream str;
for (size_t j = 0; j < str.str().length(); ++j)
for (size_t j = 0; j < out_str.str().length(); ++j)
cout << "\b";
str.str("");
str << setw(lexical_cast<string>(n_iter).size()) << temp_count << " of " << n_iter
<< " (" << setw(2) << (temp_count+1)*100/n_iter << "%) " << "temperature: " << setw(14) << setprecision(10) << T << " spins: " << Ns.size() << " energy levels: ";
out_str.str("");
out_str << setw(lexical_cast<string>(n_iter).size()) << temp_count << " of " << n_iter
<< " (" << setw(2) << (temp_count+1)*100/n_iter << "%) " << "temperature: " << setw(14) << setprecision(10) << T << " spins: " << Ns.size() << " energy levels: ";
size_t n_energy = 0;
for (typeof(global_term.begin()) iter = global_term.begin(); iter != global_term.end(); ++iter)
n_energy += iter->second.size();
str << setw(lexical_cast<string>(Nspins*degs.size()).size()) << n_energy;
out_str << setw(lexical_cast<string>(Nspins.first*degs.size()).size()) << n_energy;
if (steepest_descent)
str << " (steepest descent)";
cout << str.str() << flush;
out_str << " (steepest descent)";
cout << out_str.str() << flush;
}
if (verbose.second != "")
{
try
{
size_t n_energy = 0;
for (typeof(global_term.begin()) iter = global_term.begin(); iter != global_term.end(); ++iter)
n_energy += iter->second.size();
out_file << temp_count << "\t" << setprecision(10) << T << "\t" << Ns.size() << "\t" << n_energy << endl;
}
catch (ifstream::failure e)
{
throw GraphException("error writing to file " + verbose.second + ": " + e.what());
}
}
}
if (verbose)
if (verbose.first)
cout << endl;
}
};
......@@ -422,7 +448,7 @@ public:
private:
Graph& _g;
size_t _K;
ManagedUnorderedMap<size_t, size_t> _Ks;
ManagedUnorderedMap<size_t,size_t> _Ks;
};
template <class Graph, class CommunityMap>
......@@ -484,7 +510,6 @@ public:
void Update(size_t k, size_t old_s, size_t s)
{
for (size_t i = 0; i < _degs.size(); ++i)
{
size_t k1 = _degs[i], k2 = k;
......@@ -533,10 +558,10 @@ public:
private:
Graph& _g;
vector<size_t> _degs;
unordered_map<size_t, size_t> _Nk;
unordered_map<size_t, unordered_map<size_t,double> > _Pkk;
unordered_map<size_t, ManagedUnorderedMap<size_t,size_t> > _Nks;
unordered_map<size_t, ManagedUnorderedMap<size_t,double> > _NNks;
unordered_map<size_t,size_t> _Nk;
unordered_map<size_t,unordered_map<size_t,double> > _Pkk;
unordered_map<size_t,ManagedUnorderedMap<size_t,size_t> > _Nks;
unordered_map<size_t,ManagedUnorderedMap<size_t,double> > _NNks;
};
......@@ -546,7 +571,7 @@ struct get_communities_selector
GraphInterface::comm_corr_t _corr;
template <class Graph, class WeightMap, class CommunityMap>
void operator()(Graph& g, WeightMap weights, CommunityMap s, double gamma, size_t n_iter, pair<double,double> Tinterval, size_t Nspins, size_t seed, bool verbose) const
void operator()(Graph& g, WeightMap weights, CommunityMap s, double gamma, size_t n_iter, pair<double,double> Tinterval, pair<size_t,bool> Nspins, size_t seed, pair<bool,string> verbose) const
{
switch (_corr)
{
......@@ -563,11 +588,33 @@ struct get_communities_selector
}
};
void GraphInterface::GetCommunityStructure(double gamma, comm_corr_t corr, size_t n_iter, double Tmin, double Tmax, size_t Nspins, size_t seed, bool verbose, string weight, string property)
struct copy_spins
{
template <class Graph, class CommunityMapOld, class CommunityMapNew >
void operator()(Graph& g, CommunityMapOld old_s, CommunityMapNew new_s) const
{
typename graph_traits<Graph>::vertex_iterator v, v_end;
for (tie(v, v_end) = vertices(g); v != v_end; ++v)
put(new_s, *v, get(old_s, *v));
}
};
void GraphInterface::GetCommunityStructure(double gamma, comm_corr_t corr, size_t n_iter, double Tmin, double Tmax, size_t Nspins, size_t seed, bool verbose, string history_file, string weight, string property)
{
typedef HashedDescriptorMap<vertex_index_map_t,size_t> comm_map_t;
comm_map_t comm_map(_vertex_index);
bool new_spins = true;
try
{
DynamicPropertyMapWrap<size_t,graph_traits<multigraph_t>::vertex_descriptor> old_s(find_property_map(_properties, property, typeid(graph_traits<multigraph_t>::vertex_descriptor)));
check_filter(*this, bind<void>(copy_spins(), _1, var(old_s), var(comm_map)), reverse_check(), always_undirected());
RemoveVertexProperty(property);
new_spins = false;
}
catch (property_not_found) {}
bool directed = _directed;
_directed = false;
......@@ -580,13 +627,15 @@ void GraphInterface::GetCommunityStructure(double gamma, comm_corr_t corr, size_
{
vector_property_map<double,edge_index_map_t> weight_map =
get_static_property_map<vector_property_map<double,edge_index_map_t> >(weight_prop);
check_filter(*this, bind<void>(get_communities_selector(corr), _1, var(weight_map), var(comm_map), gamma, n_iter, make_pair(Tmin, Tmax), Nspins, seed, verbose),
check_filter(*this, bind<void>(get_communities_selector(corr), _1, var(weight_map), var(comm_map), gamma, n_iter, make_pair(Tmin, Tmax),
make_pair(Nspins, new_spins), seed, make_pair(verbose, history_file)),
reverse_check(), always_undirected());
}
else
{
DynamicPropertyMapWrap<double,graph_traits<multigraph_t>::edge_descriptor> weight_map(weight_prop);
check_filter(*this, bind<void>(get_communities_selector(corr), _1, var(weight_map), var(comm_map), gamma, n_iter, make_pair(Tmin, Tmax), Nspins, seed, verbose),
check_filter(*this, bind<void>(get_communities_selector(corr), _1, var(weight_map), var(comm_map), gamma, n_iter, make_pair(Tmin, Tmax),
make_pair(Nspins, new_spins), seed, make_pair(verbose, history_file)),
reverse_check(), always_undirected());
}
}
......@@ -598,18 +647,12 @@ void GraphInterface::GetCommunityStructure(double gamma, comm_corr_t corr, size_
else
{
ConstantPropertyMap<double,graph_traits<multigraph_t>::edge_descriptor> weight_map(1.0);
check_filter(*this, bind<void>(get_communities_selector(corr), _1, var(weight_map), var(comm_map), gamma, n_iter, make_pair(Tmin, Tmax), Nspins, seed, verbose),
check_filter(*this, bind<void>(get_communities_selector(corr), _1, var(weight_map), var(comm_map), gamma, n_iter, make_pair(Tmin, Tmax),
make_pair(Nspins, new_spins), seed, make_pair(verbose, history_file)),
reverse_check(), always_undirected());
}
_directed = directed;
try
{
find_property_map(_properties, property, typeid(graph_traits<multigraph_t>::edge_descriptor));
RemoveVertexProperty(property);
}
catch (property_not_found) {}
_properties.property(property, comm_map);
}
......
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