Layer with free positioning of neurons, positions specified by user. More...

#include <free_layer.h>

Inheritance diagram for nest::FreeLayer< D >:

Collaboration diagram for nest::FreeLayer< D >:

Classes
class	NodePositionData
	Class to be used when communicating positions across MPI processes. More...

Public Member Functions
Position< D >	get_position (size_t sind) const override
	Get position of node.

void	set_status (const Dictionary &) override
	Change properties of the layer according to the entries in the dictionary.

void	get_status (Dictionary &, NodeCollection const *const) const override
	Export properties of the layer by setting entries in the status dictionary, respects slicing of given NodeCollection.

Public Member Functions inherited from nest::Layer< D >
	Layer ()
	Creates an empty layer.

	Layer (const Layer &other_layer)

	~Layer () override

void	set_status (const Dictionary &) override
	Change properties of the layer according to the entries in the dictionary.

void	get_status (Dictionary &, NodeCollection const *const) const override
	Retrieve status, slice according to node collection if given.

unsigned int	get_num_dimensions () const override

const Position< D > &	get_lower_left () const

const Position< D > &	get_extent () const

Position< D >	get_center () const

std::bitset< D >	get_periodic_mask () const

std::vector< double >	get_position_vector (const size_t sind) const override

Position< D >	compute_displacement (const Position< D > &from_pos, const Position< D > &to_pos) const
	Returns displacement of a position from another position.

double	compute_displacement (const std::vector< double > &from_pos, const std::vector< double > &to_pos, const unsigned int dimension) const override

Position< D >	compute_displacement (const Position< D > &from_pos, const size_t to) const
	Returns displacement of node from given position.

std::vector< double >	compute_displacement (const std::vector< double > &from_pos, const size_t to) const override
	Returns displacement of node from given position.

double	compute_distance (const Position< D > &from_pos, const size_t lid) const
	Returns distance to node from given position.

double	compute_distance (const std::vector< double > &from_pos, const size_t lid) const override
	Returns distance to node from given position.

double	compute_distance (const std::vector< double > &from_pos, const std::vector< double > &to_pos) const override

std::shared_ptr< Ntree< D, size_t > >	get_global_positions_ntree (NodeCollectionPTR node_collection)
	Get positions for all nodes in layer, including nodes on other MPI processes.

std::shared_ptr< Ntree< D, size_t > >	get_global_positions_ntree (std::bitset< D > periodic, Position< D > lower_left, Position< D > extent, NodeCollectionPTR node_collection)
	Get positions globally, overriding the dimensions of the layer and the periodic flags.

std::vector< std::pair< Position< D >, size_t > > *	get_global_positions_vector (NodeCollectionPTR node_collection)

virtual std::vector< std::pair< Position< D >, size_t > >	get_global_positions_vector (const MaskPTR mask, const Position< D > &anchor, bool allow_oversized, NodeCollectionPTR node_collection)

std::vector< size_t >	get_global_nodes (const MaskPTR mask, const std::vector< double > &anchor, bool allow_oversized, NodeCollectionPTR node_collection) override
	Return a vector with the node IDs of the nodes inside the mask.

void	connect (NodeCollectionPTR source_nc, AbstractLayerPTR target, NodeCollectionPTR target_nc, ConnectionCreator &connector) override
	Connect this layer to the given target layer.

void	dump_nodes (std::ostream &os) const override
	Write layer data to stream.

void	dump_connections (std::ostream &out, NodeCollectionPTR node_collection, AbstractLayerPTR target_layer, const std::string &syn_model) override
	Dumps information about all connections of the given type having their source in the given layer to the given output stream.

Public Member Functions inherited from nest::AbstractLayer
	AbstractLayer ()

virtual	~AbstractLayer ()

void	set_node_collection (NodeCollectionPTR)

NodeCollectionPTR	get_node_collection ()

Protected Member Functions
template<class Ins >
void	communicate_positions_ (Ins iter, NodeCollectionPTR node_collection)
	Communicate positions across MPI processes.

void	insert_global_positions_ntree_ (Ntree< D, size_t > &tree, NodeCollectionPTR node_collection) override
	Insert global position info into ntree.

void	insert_global_positions_vector_ (std::vector< std::pair< Position< D >, size_t > > &vec, NodeCollectionPTR node_collection) override
	Insert global position info into vector.

size_t	lid_to_position_id_ (size_t lid) const
	Calculate the index in the position vector on this MPI process based on the local ID.

Protected Member Functions inherited from nest::Layer< D >
void	clear_ntree_cache_ () const override
	Clear the cache for global position information.

void	clear_vector_cache_ () const override
	Clear the cache for global position information.

std::shared_ptr< Ntree< D, size_t > >	do_get_global_positions_ntree_ (NodeCollectionPTR node_collection)

Protected Member Functions inherited from nest::AbstractLayer
NodeCollectionMetadataPTR	get_metadata () const
	Gets metadata of the NodeCollection to which this layer belongs.

Protected Attributes
std::vector< Position< D > >	positions_
	Vector of positions.

size_t	num_local_nodes_ = 0

Protected Attributes inherited from nest::Layer< D >
Position< D >	lower_left_
	lower left corner (minimum coordinates) of layer

Position< D >	extent_
	size of layer

std::bitset< D >	periodic_
	periodic b.c.

Protected Attributes inherited from nest::AbstractLayer
NodeCollectionPTR	node_collection_
	The NodeCollection to which the layer belongs.

Additional Inherited Members
Static Public Member Functions inherited from nest::AbstractLayer
static NodeCollectionPTR	create_layer (const Dictionary &)
	Factory function for layers.

Static Protected Attributes inherited from nest::Layer< D >
static std::shared_ptr< Ntree< D, size_t > >	cached_ntree_
	Global position information for a single layer.

static std::vector< std::pair< Position< D >, size_t > > *	cached_vector_ = 0

Static Protected Attributes inherited from nest::AbstractLayer
static NodeCollectionMetadataPTR	cached_ntree_md_ = NodeCollectionMetadataPTR( nullptr )
	Metadata for the layer for which we cache global position information.

static NodeCollectionMetadataPTR	cached_vector_md_ = NodeCollectionMetadataPTR( nullptr )
	Metadata for the layer for which we cache global position information.

Detailed Description

template<int D>
class nest::FreeLayer< D >

Layer with free positioning of neurons, positions specified by user.

Member Function Documentation

◆ communicate_positions_()

template<int D>

template<class Ins >

void nest::FreeLayer< D >::communicate_positions_	(	Ins	iter,
		NodeCollectionPTR	node_collection
	)

protected

Communicate positions across MPI processes.

Parameters

iter	Insert iterator which will receive pairs of Position,node ID
node_collection	NodeCollection of the layer

References nest::MPIManager::communicate(), nest::FreeLayer< D >::NodePositionData::get_node_id(), nest::FreeLayer< D >::NodePositionData::get_position(), nest::get_position(), nest::kernel(), and nest::KernelManager::mpi_manager.

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◆ get_position()

template<int D>

Position< D > nest::FreeLayer< D >::get_position ( size_t sind ) const

overridevirtual

Get position of node.

Only possible for local nodes.

Parameters

sind	index of node

Returns: position of node.

Implements nest::Layer< D >.

◆ get_status()

template<int D>

void nest::FreeLayer< D >::get_status	(	Dictionary &	,
		NodeCollection const * const
	)		const

overridevirtual

Export properties of the layer by setting entries in the status dictionary, respects slicing of given NodeCollection.

Parameters

d	Dictionary.

Note: If passing nullptr-valued NodeCollectionPTR, full metadata irrespective of any slicing is returned.

Implements nest::AbstractLayer.

References nest::NodeCollection::end(), nest::MPIManager::get_num_processes(), nest::Layer< D >::get_status(), nest::kernel(), nest::KernelManager::mpi_manager, nest::names::positions(), and nest::NodeCollection::rank_local_begin().

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◆ insert_global_positions_ntree_()

template<int D>

void nest::FreeLayer< D >::insert_global_positions_ntree_	(	Ntree< D, size_t > &	tree,
		NodeCollectionPTR	node_collection
	)

overrideprotectedvirtual

Insert global position info into ntree.

Implements nest::Layer< D >.

◆ insert_global_positions_vector_()

template<int D>

void nest::FreeLayer< D >::insert_global_positions_vector_	(	std::vector< std::pair< Position< D >, size_t > > &	,
		NodeCollectionPTR
	)

overrideprotectedvirtual

Insert global position info into vector.

Implements nest::Layer< D >.

◆ lid_to_position_id_()

template<int D>

size_t nest::FreeLayer< D >::lid_to_position_id_ ( size_t lid ) const

protected

Calculate the index in the position vector on this MPI process based on the local ID.

Parameters

lid	global index of node within layer

Returns: index in the local position vector

References nest::MPIManager::get_num_processes(), nest::kernel(), and nest::KernelManager::mpi_manager.

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◆ set_status()

template<int D>

void nest::FreeLayer< D >::set_status ( const Dictionary & )

overridevirtual

Change properties of the layer according to the entries in the dictionary.

Parameters

d	Dictionary with named parameter settings.

Implements nest::AbstractLayer.

References nest::names::extent(), nest::NodeManager::get_mpi_local_node_or_device_head(), nest::get_rank_synced_rng(), nest::kernel(), nest::KernelManager::node_manager, nest::names::positions(), and nest::Layer< D >::set_status().

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Member Data Documentation

◆ num_local_nodes_

template<int D>

size_t nest::FreeLayer< D >::num_local_nodes_ = 0

protected

◆ positions_

template<int D>

std::vector< Position< D > > nest::FreeLayer< D >::positions_

protected

Vector of positions.

The documentation for this class was generated from the following file:

free_layer.h

	NEST main@caf0ae8

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ communicate_positions_()

◆ get_position()

◆ get_status()

◆ insert_global_positions_ntree_()

◆ insert_global_positions_vector_()

◆ lid_to_position_id_()

◆ set_status()

Member Data Documentation

◆ num_local_nodes_

◆ positions_