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Add support for Parameter objects for indegree and outdegree in syn_specs #2501

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merged 6 commits into from
Oct 31, 2022
Merged

Add support for Parameter objects for indegree and outdegree in syn_specs #2501

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ef5bff9
Added tests of using parameters for indegree and outdegree
hakonsbm Oct 13, 2022
a06444e
Implemented support for parameters for indegree and outdegree
hakonsbm Oct 13, 2022
cf751b6
Merge remote-tracking branch 'nest/master' into indegree_outdegree_pa…
hakonsbm Oct 26, 2022
6d1b073
Added documentation on using parameter as in- or outdegree
hakonsbm Oct 28, 2022
f24d006
Updated static code analysis for python scripts path
hakonsbm Oct 28, 2022
d41aed2
Updated spelling
hakonsbm Oct 28, 2022
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26 changes: 18 additions & 8 deletions nestkernel/connection_creator.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -38,23 +38,33 @@ ConnectionCreator::ConnectionCreator( DictionaryDatum dict )
, delay_()
{
Name connection_type;
long number_of_connections( -1 ); // overwritten by dict entry

updateValue< std::string >( dict, names::connection_type, connection_type );
updateValue< bool >( dict, names::allow_autapses, allow_autapses_ );
updateValue< bool >( dict, names::allow_multapses, allow_multapses_ );
updateValue< bool >( dict, names::allow_oversized_mask, allow_oversized_ );

// Need to store number of connections in a temporary variable to be able to detect negative values.
if ( updateValue< long >( dict, names::number_of_connections, number_of_connections ) )

if ( dict->known( names::number_of_connections ) )
{
if ( number_of_connections < 0 )
ParameterDatum* pd = dynamic_cast< ParameterDatum* >( ( *dict )[ names::number_of_connections ].datum() );
if ( pd )
{
throw BadProperty( "Number of connections cannot be less than zero." );
number_of_connections_ = *pd;
}
else
{
// Assume indegree is a scalar.
const long value = ( *dict )[ names::number_of_connections ];
if ( value < 0 )
{
throw BadProperty( "Number of connections cannot be less than zero." );
}
number_of_connections_ = std::shared_ptr< Parameter >( new ConstantParameter( value ) );
}
// We are sure that number of connections isn't negative, so it is safe to store it in a size_t.
number_of_connections_ = number_of_connections;
}

if ( dict->known( names::mask ) )
{
mask_ = NestModule::create_mask( ( *dict )[ names::mask ] );
Expand Down Expand Up @@ -116,7 +126,7 @@ ConnectionCreator::ConnectionCreator( DictionaryDatum dict )
if ( connection_type == names::pairwise_bernoulli_on_source )
{

if ( number_of_connections >= 0 )
if ( dict->known( names::number_of_connections ) )
{
type_ = Fixed_indegree;
}
Expand All @@ -128,7 +138,7 @@ ConnectionCreator::ConnectionCreator( DictionaryDatum dict )
else if ( connection_type == names::pairwise_bernoulli_on_target )
{

if ( number_of_connections >= 0 )
if ( dict->known( names::number_of_connections ) )
{
type_ = Fixed_outdegree;
}
Expand Down
2 changes: 1 addition & 1 deletion nestkernel/connection_creator.h
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,7 @@ class ConnectionCreator
bool allow_autapses_;
bool allow_multapses_;
bool allow_oversized_;
index number_of_connections_;
std::shared_ptr< Parameter > number_of_connections_;
std::shared_ptr< AbstractMask > mask_;
std::shared_ptr< Parameter > kernel_;
std::vector< index > synapse_model_;
Expand Down
48 changes: 23 additions & 25 deletions nestkernel/connection_creator_impl.h
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Original file line number Diff line number Diff line change
Expand Up @@ -344,11 +344,6 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,
Layer< D >& target,
NodeCollectionPTR target_nc )
{
if ( number_of_connections_ < 1 )
{
return;
}

// fixed_indegree connections (fixed fan in)
//
// For each local target node:
Expand Down Expand Up @@ -398,6 +393,9 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,
std::vector< double > source_pos_vector( D );
const std::vector< double > target_pos_vector = target_pos.get_vector();

const unsigned long target_number_connections =
std::round( number_of_connections_->value( rng, source_pos_vector, target_pos_vector, source, tgt ) );

// Get (position,node ID) pairs for sources inside mask
positions.resize( std::distance( masked_source.begin( target_pos ), masked_source_end ) );
std::copy( masked_source.begin( target_pos ), masked_source_end, positions.begin() );
Expand All @@ -423,7 +421,7 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,

if ( positions.empty()
or ( not allow_autapses_ and ( positions.size() == 1 ) and positions[ 0 ].second == target_id )
or ( not allow_multapses_ and ( positions.size() < number_of_connections_ ) ) )
or ( not allow_multapses_ and ( positions.size() < target_number_connections ) ) )
{
std::string msg = String::compose( "Global target ID %1: Not enough sources found inside mask", target_id );
throw KernelException( msg.c_str() );
Expand All @@ -439,8 +437,8 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,
// sources have been selected already.
std::vector< bool > is_selected( positions.size() );

// Draw `number_of_connections_` sources
for ( int i = 0; i < ( int ) number_of_connections_; ++i )
// Draw `target_number_connections` sources
for ( int i = 0; i < ( int ) target_number_connections; ++i )
{
index random_id = lottery( rng );
if ( not allow_multapses_ and is_selected[ random_id ] )
Expand Down Expand Up @@ -474,7 +472,7 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,

if ( positions.empty()
or ( not allow_autapses_ and ( positions.size() == 1 ) and positions[ 0 ].second == target_id )
or ( not allow_multapses_ and ( positions.size() < number_of_connections_ ) ) )
or ( not allow_multapses_ and ( positions.size() < target_number_connections ) ) )
{
std::string msg = String::compose( "Global target ID %1: Not enough sources found inside mask", target_id );
throw KernelException( msg.c_str() );
Expand All @@ -484,8 +482,8 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,
// sources have been selected already.
std::vector< bool > is_selected( positions.size() );

// Draw `number_of_connections_` sources
for ( int i = 0; i < ( int ) number_of_connections_; ++i )
// Draw `target_number_connections` sources
for ( int i = 0; i < ( int ) target_number_connections; ++i )
{
index random_id = rng->ulrand( positions.size() );
if ( not allow_multapses_ and is_selected[ random_id ] )
Expand Down Expand Up @@ -523,18 +521,20 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,
RngPtr rng = get_vp_specific_rng( target_thread );
Position< D > target_pos = target.get_position( ( *tgt_it ).lid );

const unsigned long target_number_connections = std::round( number_of_connections_->value( rng, tgt ) );

std::vector< double > source_pos_vector( D );
const std::vector< double > target_pos_vector = target_pos.get_vector();

if ( ( positions->size() == 0 )
or ( not allow_autapses_ and ( positions->size() == 1 ) and ( ( *positions )[ 0 ].second == target_id ) )
or ( not allow_multapses_ and ( positions->size() < number_of_connections_ ) ) )
or ( not allow_multapses_ and ( positions->size() < target_number_connections ) ) )
{
std::string msg = String::compose( "Global target ID %1: Not enough sources found", target_id );
throw KernelException( msg.c_str() );
}

// We will select `number_of_connections_` sources within the mask.
// We will select `target_number_connections` sources within the mask.
// If there is no kernel, we can just draw uniform random numbers,
// but with a kernel we have to set up a probability distribution
// function using a discrete_distribution.
Expand Down Expand Up @@ -563,8 +563,8 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,
// sources have been selected already.
std::vector< bool > is_selected( positions->size() );

// Draw `number_of_connections_` sources
for ( int i = 0; i < ( int ) number_of_connections_; ++i )
// Draw `target_number_connections` sources
for ( int i = 0; i < ( int ) target_number_connections; ++i )
{
index random_id = lottery( rng );
if ( not allow_multapses_ and is_selected[ random_id ] )
Expand Down Expand Up @@ -601,8 +601,8 @@ ConnectionCreator::fixed_indegree_( Layer< D >& source,
// sources have been selected already.
std::vector< bool > is_selected( positions->size() );

// Draw `number_of_connections_` sources
for ( int i = 0; i < ( int ) number_of_connections_; ++i )
// Draw `target_number_connections` sources
for ( int i = 0; i < ( int ) target_number_connections; ++i )
{
index random_id = rng->ulrand( positions->size() );
if ( not allow_multapses_ and is_selected[ random_id ] )
Expand Down Expand Up @@ -642,11 +642,6 @@ ConnectionCreator::fixed_outdegree_( Layer< D >& source,
Layer< D >& target,
NodeCollectionPTR target_nc )
{
if ( number_of_connections_ < 1 )
{
return;
}

// protect against connecting to devices without proxies
// we need to do this before creating the first connection to leave
// the network untouched if any target does not have proxies
Expand Down Expand Up @@ -689,6 +684,7 @@ ConnectionCreator::fixed_outdegree_( Layer< D >& source,
{
const Position< D > source_pos = source_pos_node_id_pair.first;
const index source_id = source_pos_node_id_pair.second;
const auto src = kernel().node_manager.get_node_or_proxy( source_id );
const std::vector< double > source_pos_vector = source_pos.get_vector();

// We create a target pos vector here that can be updated with the
Expand Down Expand Up @@ -718,8 +714,10 @@ ConnectionCreator::fixed_outdegree_( Layer< D >& source,
probabilities.resize( target_pos_node_id_pairs.size(), 1.0 );
}

const auto number_of_connections = std::round( number_of_connections_->value( grng, src ) );

if ( target_pos_node_id_pairs.empty()
or ( not allow_multapses_ and ( target_pos_node_id_pairs.size() < number_of_connections_ ) ) )
or ( not allow_multapses_ and ( target_pos_node_id_pairs.size() < number_of_connections ) ) )
{
std::string msg = String::compose( "Global source ID %1: Not enough targets found", source_id );
throw KernelException( msg.c_str() );
Expand All @@ -735,8 +733,8 @@ ConnectionCreator::fixed_outdegree_( Layer< D >& source,
// targets have been selected already.
std::vector< bool > is_selected( target_pos_node_id_pairs.size() );

// Draw `number_of_connections_` targets
for ( long i = 0; i < ( long ) number_of_connections_; ++i )
// Draw `number_of_connections` targets
for ( long i = 0; i < ( long ) number_of_connections; ++i )
{
index random_id = lottery( get_rank_synced_rng() );
if ( not allow_multapses_ and is_selected[ random_id ] )
Expand Down
16 changes: 16 additions & 0 deletions testsuite/pytests/test_spatial/test_connect_layers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -198,6 +198,22 @@ def test_connect_layers_indegree_kernel_mask(self):
}
self._check_connections(conn_spec, 20)

def test_connect_layers_indegree_parameter(self):
"""Connecting layers with fixed_indegree and parameter as indegree."""
# Parameter will give numbers close to 5. With std=0.1 they should all be rounded to an indegree of exactly 5.
mean = 5.
param = nest.random.normal(mean=mean, std=0.1)
conn_spec = {'rule': 'fixed_indegree', 'indegree': param, 'p': 1.0, 'allow_multapses': True}
self._check_connections(conn_spec, int(mean) * 20)

def test_connect_layers_outdegree_parameter(self):
"""Connecting layers with fixed_indegree and parameter as indegree."""
# Parameter will give numbers close to 5. With std=0.1 they should all be rounded to an outdegree of exactly 5.
mean = 5.
param = nest.random.normal(mean=mean, std=0.1)
conn_spec = {'rule': 'fixed_outdegree', 'outdegree': param, 'p': 1.0, 'allow_multapses': True}
self._check_connections(conn_spec, int(mean) * 20)

def test_connect_layers_outdegree_mask(self):
"""Connecting layers with fixed_outdegree and mask"""
conn_spec = {
Expand Down