ArrayDatum
ConnectionManager::get_connections( DictionaryDatum params ) const
{
ArrayDatum connectome;
const Token& source_t = params->lookup( names::source );
const Token& target_t = params->lookup( names::target );
const Token& syn_model_t = params->lookup( names::synapse_model );
const TokenArray* source_a = 0;
const TokenArray* target_a = 0;
if ( not source_t.empty() )
source_a = dynamic_cast< TokenArray const* >( source_t.datum() );
if ( not target_t.empty() )
target_a = dynamic_cast< TokenArray const* >( target_t.datum() );
size_t syn_id = 0;
#ifdef _OPENMP
std::string msg;
msg = String::compose( "Setting OpenMP num_threads to %1.", net_.get_num_threads() );
net_.message( SLIInterpreter::M_DEBUG, "ConnectionManager::get_connections", msg );
omp_set_num_threads( net_.get_num_threads() );
#endif
// First we check, whether a synapse model is given.
// If not, we will iterate all.
if ( not syn_model_t.empty() )
{
Name synmodel_name = getValue< Name >( syn_model_t );
const Token synmodel = synapsedict_->lookup( synmodel_name );
if ( !synmodel.empty() )
syn_id = static_cast< size_t >( synmodel );
else
throw UnknownModelName( synmodel_name.toString() );
get_connections( connectome, source_a, target_a, syn_id );
}
else
{
for ( syn_id = 0; syn_id < prototypes_[ 0 ].size(); ++syn_id )
{
ArrayDatum conn;
get_connections( conn, source_a, target_a, syn_id );
if ( conn.size() > 0 )
connectome.push_back( new ArrayDatum( conn ) );
}
}
return connectome;
}
void
nest::weight_recorder::Parameters_::set( const DictionaryDatum& d )
{
if ( d->known( names::senders ) )
{
senders_ = getValue< std::vector< long > >( d->lookup( names::senders ) );
std::sort( senders_.begin(), senders_.end() );
}
if ( d->known( names::targets ) )
{
targets_ = getValue< std::vector< long > >( d->lookup( names::targets ) );
std::sort( targets_.begin(), targets_.end() );
}
}
void
aeif_cond_alpha_multisynapse::State_::set( const DictionaryDatum& d )
{
updateValue< double >( d, names::V_m, y_[ V_M ] );
if ( ( d->known( names::g_ex ) ) && ( d->known( names::dg_ex ) ) && ( d->known( names::g_in ) )
&& ( d->known( names::dg_in ) ) )
{
const std::vector< double_t > g_exc =
getValue< std::vector< double_t > >( d->lookup( names::g_ex ) );
const std::vector< double_t > dg_exc =
getValue< std::vector< double_t > >( d->lookup( names::dg_ex ) );
const std::vector< double_t > g_inh =
getValue< std::vector< double_t > >( d->lookup( names::g_in ) );
const std::vector< double_t > dg_inh =
getValue< std::vector< double_t > >( d->lookup( names::dg_in ) );
if ( ( g_exc.size() != dg_exc.size() ) || ( g_exc.size() != g_inh.size() )
|| ( g_exc.size() != dg_inh.size() ) )
{
throw BadProperty( "Conductances must have the same sizes." );
}
for ( size_t i = 0; i < g_exc.size(); ++i )
{
if ( ( g_exc[ i ] < 0 ) || ( dg_exc[ i ] < 0 ) || ( g_inh[ i ] < 0 ) || ( dg_inh[ i ] < 0 ) )
{
throw BadProperty( "Conductances must not be negative." );
}
y_[ State_::G_EXC + ( State_::NUMBER_OF_STATES_ELEMENTS_PER_RECEPTOR * i ) ] = g_exc[ i ];
y_[ State_::DG_EXC + ( State_::NUMBER_OF_STATES_ELEMENTS_PER_RECEPTOR * i ) ] = dg_exc[ i ];
y_[ State_::G_INH + ( State_::NUMBER_OF_STATES_ELEMENTS_PER_RECEPTOR * i ) ] = g_inh[ i ];
y_[ State_::DG_INH + ( State_::NUMBER_OF_STATES_ELEMENTS_PER_RECEPTOR * i ) ] = dg_inh[ i ];
}
}
updateValue< double >( d, names::w, y_[ W ] );
}
void nest::spike_generator::Parameters_::set(const DictionaryDatum& d, State_& s,
const Time& origin, const Time& now)
{
const bool flags_changed = updateValue<bool>(d, names::precise_times, precise_times_)
|| updateValue<bool>(d, "allow_offgrid_spikes", allow_offgrid_spikes_)
|| updateValue<bool>(d, "shift_now_spikes", shift_now_spikes_);
if ( precise_times_ && ( allow_offgrid_spikes_ || shift_now_spikes_ ) )
throw BadProperty("Option precise_times cannot be set to true when either allow_offgrid_spikes "
"or shift_now_spikes is set to true.");
const bool updated_spike_times = d->known(names::spike_times);
if ( flags_changed && !(updated_spike_times || spike_stamps_.empty()) )
throw BadProperty("Options can only be set together with spike times or if no "
"spike times have been set.");
if ( updated_spike_times )
{
const std::vector<double_t> d_times = getValue<std::vector<double> >(d->lookup(names::spike_times));
const size_t n_spikes = d_times.size();
spike_stamps_.clear();
spike_stamps_.reserve(n_spikes);
spike_offsets_.clear();
if ( precise_times_ )
spike_offsets_.reserve(n_spikes);
// Check spike times for ordering and grid compatibility and insert them
if ( !d_times.empty() )
{
// handle first spike time, no predecessor to compare with
std::vector<double_t>::const_iterator prev = d_times.begin();
assert_valid_spike_time_and_insert_(*prev, origin, now);
// handle all remaining spike times, compare to predecessor
for ( std::vector<double_t>::const_iterator next = prev + 1;
next != d_times.end() ; ++next, ++prev )
if ( *prev > *next )
throw BadProperty("Spike times must be sorted in non-descending order.");
else
assert_valid_spike_time_and_insert_(*next, origin, now);
}
}
// spike_weights can be the same size as spike_times, or can be of size 0 to
// only use the spike_times array
bool updated_spike_weights = d->known("spike_weights");
if (updated_spike_weights)
{
std::vector<double> spike_weights = getValue<std::vector<double> >(d->lookup("spike_weights"));
if (spike_weights.empty())
spike_weights_.clear();
else
{
if (spike_weights.size() != spike_stamps_.size())
throw BadProperty("spike_weights must have the same number of elements as spike_times,"
" or 0 elements to clear the property.");
spike_weights_.swap(spike_weights);
}
}
// Set position to start if something changed
if ( updated_spike_times || updated_spike_weights || d->known(names::origin) )
s.position_ = 0;
}
index AbstractLayer::create_layer(const DictionaryDatum & layer_dict)
{
index length = 0;
const char *layer_model_name = 0;
std::vector<long_t> element_ids;
std::string element_name;
Token element_model;
const Token& t = layer_dict->lookup(names::elements);
ArrayDatum* ad = dynamic_cast<ArrayDatum *>(t.datum());
if (ad) {
for (Token* tp = ad->begin(); tp != ad->end(); ++tp) {
element_name = std::string(*tp);
element_model = net_->get_modeldict().lookup(element_name);
if ( element_model.empty() )
throw UnknownModelName(element_name);
// Creates several nodes if the next element in
// the elements variable is a number.
if ((tp+1 != ad->end()) && dynamic_cast<IntegerDatum*>((tp+1)->datum())) {
// Select how many nodes that should be created.
const long_t number = getValue<long_t>(*(++tp));
for(long_t i=0;i<number;++i)
element_ids.push_back(static_cast<long>(element_model));
} else {
element_ids.push_back(static_cast<long>(element_model));
}
}
} else {
element_name = getValue<std::string>(layer_dict, names::elements);
element_model = net_->get_modeldict().lookup(element_name);
if ( element_model.empty() )
throw UnknownModelName(element_name);
element_ids.push_back(static_cast<long>(element_model));
}
if (layer_dict->known(names::positions)) {
if (layer_dict->known(names::rows) or layer_dict->known(names::columns) or layer_dict->known(names::layers))
throw BadProperty("Can not specify both positions and rows or columns.");
TokenArray positions = getValue<TokenArray>(layer_dict, names::positions);
if (positions.size() == 0) {
throw BadProperty("Empty positions array.");
}
std::vector<double_t> pos = getValue<std::vector<double_t> >(positions[0]);
if (pos.size() == 2)
layer_model_name = "topology_layer_free";
else if (pos.size() == 3)
layer_model_name = "topology_layer_free_3d";
else
throw BadProperty("Positions must have 2 or 3 coordinates.");
length = positions.size();
} else if (layer_dict->known(names::columns)) {
if (not layer_dict->known(names::rows)) {
throw BadProperty("Both columns and rows must be given.");
}
length=getValue<long_t>(layer_dict, names::columns) * getValue<long_t>(layer_dict, names::rows);
if (layer_dict->known(names::layers)) {
layer_model_name = "topology_layer_grid_3d";
length *= getValue<long_t>(layer_dict, names::layers);
} else {
layer_model_name = "topology_layer_grid";
}
} else {
throw BadProperty("Unknown layer type.");
}
assert(layer_model_name != 0);
Token layer_model = net_->get_modeldict().lookup(layer_model_name);
if ( layer_model.empty() )
throw UnknownModelName(layer_model_name);
index layer_node = net_->add_node(layer_model);
// Remember original subnet
const index cwnode = net_->get_cwn()->get_gid();
net_->go_to(layer_node);
// Create layer nodes.
for ( size_t i = 0 ; i < element_ids.size() ; ++i )
{
for ( index n = 0 ; n < length ; ++n )
{
net_->add_node(element_ids[i]);
}
}
// Return to original subnet
net_->go_to(cwnode);
//Set layer parameters according to input dictionary.
AbstractLayer *layer = dynamic_cast<AbstractLayer *>(net_->get_node(layer_node));
layer->depth_ = element_ids.size();
layer->set_status(layer_dict);
return layer_node;
}