MatrixXd Covariances::marginal(const list<Node*>& nodes) const {
node_lists_t node_lists;
node_lists.push_back(nodes);
return marginal(node_lists).front();
}
int LU_sim::execute( GsTL_project* ) {
// Initialize the global random number generator
Global_random_number_generator::instance()->seed( seed_ );
// Set up a progress notifier
int total_steps = simul_grid_->size() * (nb_of_realizations_);
int frequency = std::max( total_steps / 20, 1 );
SmartPtr<Progress_notifier> progress_notifier =
utils::create_notifier( "Running LU_sim",
total_steps, frequency );
// In LU simulation, the marginal is a Gaussian cdf,
// with mean 0 and variance 1.
Gaussian_cdf marginal( 0.0, 1.0 );
//typedef Geostat_grid::random_path_iterator iterator;
typedef Gval_iterator< TabularMapIndex > iterator;
std::vector< int > id_unknown;
std::vector< int > id_data;
//harddata_grid_->select_property(harddata_property_->name());
if( harddata_grid_ ) {
for( int i=0; i< harddata_property_->size(); i++ ) {
if(!harddata_property_->is_informed(i) ) continue;
id_data.push_back( i );
}
}
for( int i=0; i< simul_grid_->size(); i++ ) {
if( simul_grid_ == harddata_grid_ && harddata_property_->is_informed(i) ) continue;
id_unknown.push_back( i );
}
iterator begin_d( harddata_grid_, harddata_property_ ,0,
id_data.size(), TabularMapIndex(&id_data) );
iterator end_d( harddata_grid_, harddata_property_ ,id_data.size(),
id_data.size(), TabularMapIndex(&id_data) );
Grid_continuous_property* prop = multireal_property_->new_realization();
iterator begin_u( simul_grid_, prop ,0,
id_unknown.size(), TabularMapIndex(&id_unknown) );
iterator end_u( simul_grid_, prop ,id_unknown.size(),
id_unknown.size(), TabularMapIndex(&id_unknown) );
Random_number_generator gen;
LU_simulator<
Covariance<Location>,
Random_number_generator,
Geostat_grid>
lu_sim( covar_,gen, simul_grid_ );
lu_sim.initialize_matrix(begin_u, end_u, begin_d, end_d);
// loop on all realizations
for( int nreal = 0; nreal < nb_of_realizations_ ; nreal ++ ) {
// update the progress notifier
progress_notifier->message() << "working on realization "
<< nreal+1 << gstlIO::end;
if( !progress_notifier->notify() ) return 1;
// Create a new property to hold the realization and tell the simulation
// grid to use it as the current property
appli_message( "Creating new realization" );
//Grid_continuous_property* prop = multireal_property_->new_realization();
if(nreal>0) prop = multireal_property_->new_realization();
prop->set_parameters(parameters_);
simul_grid_->select_property( prop->name() );
// initialize the new realization with the hard data, if that was requested
if( property_copier_ ) {
property_copier_->copy( harddata_grid_, harddata_property_,
simul_grid_, prop );
}
iterator begin_unk( simul_grid_, prop ,0,
id_unknown.size(), TabularMapIndex(&id_unknown) );
iterator end_unk( simul_grid_, prop ,id_unknown.size(),
id_unknown.size(), TabularMapIndex(&id_unknown) );
int status = lu_sim(begin_unk,end_unk,marginal);
// initialize the new realization with the hard data, if that was requested
// if( property_copier_ ) {
// property_copier_->copy( harddata_grid_, harddata_property_,
// simul_grid_, prop );
//initializer_->assign( prop, harddata_grid_, harddata_property_->name() );
// }
if( status == -1 ) {
clean( prop );
return 1;
}
// back-transform if needed
if( use_target_hist_ ) {
cdf_transform( prop->begin(), prop->end(),
marginal, *target_cdf_.raw_ptr() );
}
}
clean();
return 0;
}
/* figure out if this snp is epistatic */
bool epistatic() const { return !marginal(); }
