Abstract base class for Layer of given dimension (D=2 or 3). More...

#include <connection_creator.h>

Inheritance diagram for nest::Layer< D >:

Public Member Functions
	Layer ()
	Creates an empty layer. More...

	Layer (const Layer &l)
	Copy constructor. More...

	~Layer ()
	Virtual destructor. More...

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

void	get_status (DictionaryDatum &) const
	Export properties of the layer by setting entries in the status dictionary. More...

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

virtual Position< D >	get_position (index sind) const =0
	Get position of node. More...

std::vector< double_t >	get_position_vector (const index sind) const

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

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

std::vector< double_t >	compute_displacement (const std::vector< double_t > &from_pos, const index to) const
	Returns displacement of node from given position. More...

double_t	compute_distance (const Position< D > &from_pos, const index to) const
	Returns distance to node from given position. More...

double_t	compute_distance (const std::vector< double_t > &from_pos, const index to) const
	Returns distance to node from given position. More...

lockPTR< Ntree< D, index > >	get_local_positions_ntree (Selector filter=Selector())
	Get positions for local nodes in layer. More...

lockPTR< Ntree< D, index > >	get_global_positions_ntree (Selector filter=Selector())
	Get positions for all nodes in layer, including nodes on other MPI processes. More...

lockPTR< Ntree< D, index > >	get_global_positions_ntree (Selector filter, std::bitset< D > periodic, Position< D > lower_left, Position< D > extent)
	Get positions globally, overriding the dimensions of the layer and the periodic flags. More...

std::vector< std::pair < Position< D >, index > > *	get_global_positions_vector (Selector filter=Selector())

virtual std::vector< std::pair < Position< D >, index > >	get_global_positions_vector (Selector filter, const MaskDatum &mask, const Position< D > &anchor, bool allow_oversized)

std::vector< index >	get_global_nodes (const MaskDatum &mask, const std::vector< double_t > &anchor, bool allow_oversized)
	Return a vector with the GIDs of the nodes inside the mask. More...

void	connect (AbstractLayer &target, ConnectionCreator &connector)
	Connect this layer to the given target layer. More...

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

void	dump_connections (std::ostream &out, const Token &syn_model)
	Dumps information about all connections of the given type having their source in the given layer to the given output stream. More...

bool	is_subnet () const
	Layers do not allow entry to the ChangeSubnet command, nodes can not be added by the user. More...

Public Member Functions inherited from nest::AbstractLayer
	AbstractLayer ()
	Constructor. More...

virtual	~AbstractLayer ()
	Virtual destructor. More...

std::vector< Node * >::iterator	local_begin (int_t depth)
	Start of local children at given depth. More...

std::vector< Node * >::iterator	local_end (int_t depth)
	End of local children at given depth. More...

std::vector< Node * > ::const_iterator	local_begin (int_t depth) const
	Start of local children at given depth. More...

std::vector< Node * > ::const_iterator	local_end (int_t depth) const
	End of local children at given depth. More...

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

	Subnet (const Subnet &)

virtual	~Subnet ()

void	set_status (const DictionaryDatum &)

void	get_status (DictionaryDatum &) const

bool	has_proxies () const
	Returns true if the node has proxies on remote threads. More...

size_t	global_size () const
	Returns total number of children. More...

size_t	local_size () const
	Returns number of childern in local process. More...

bool	global_empty () const
	returns true if subnet is empty globally More...

bool	local_empty () const
	returns true if subnet has no local nodes More...

void	reserve (size_t)

index	add_node (Node *)
	Add a local node to the subnet. More...

index	add_remote_node (index gid, index mid)
	Add a remote node to the subnet. More...

vector< Node * >::iterator	local_begin ()
	Return iterator to the first local child node. More...

vector< Node * >::iterator	local_end ()
	Return iterator to the end of the local child-list. More...

vector< Node * >::const_iterator	local_begin () const
	Return const iterator to the first local child node. More...

vector< Node * >::const_iterator	local_end () const
	Return const iterator to the end of the local child-list. More...

Node *	at_lid (index) const
	Return pointer to Node at given LID if it is local. More...

std::string	get_label () const
	Return the subnets's user label. More...

void	set_label (std::string const)
	Set the subnet's user label. More...

DictionaryDatum	get_customdict () const
	Set the subnet's custom dictionary. More...

void	set_customdict (DictionaryDatum const dict)
	Return pointer to the subnet's custom dictionary. More...

std::string	print_network (int, int, std::string="")
	Prints out one line of the tree view of the network. More...

bool	is_homogeneous () const

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

	Node (Node const &)

virtual	~Node ()

virtual Node *	clone () const
	Virtual copy constructor. More...

virtual bool	potential_global_receiver () const
	Returns true for potential global receivers (e.g. More...

virtual void	set_has_proxies (const bool)
	Sets has_proxies_ member variable (to switch to global spike detection mode) More...

virtual void	set_local_receiver (const bool)
	Sets local_receiver_ member variable (to switch to global spike detection mode) More...

virtual bool	local_receiver () const
	Returns true if the node only receives events from nodes/devices on the same thread. More...

virtual bool	one_node_per_process () const
	Returns true if the node exists only once per process, but does not have proxies on remote threads. More...

virtual bool	is_off_grid () const
	Returns true if the node if it sends/receives -grid events This is used to discriminate between different types of nodes, when adding new nodes to the network. More...

virtual bool	is_proxy () const
	Returns true if the node is a proxy node. More...

std::string	get_name () const
	Return class name. More...

index	get_gid () const
	Return global Network ID. More...

index	get_lid () const
	Return local node ID. More...

index	get_subnet_index () const
	Return the index to the node in the node array of the parent subnet. More...

int	get_model_id () const
	Return model ID of the node. More...

Subnet *	get_parent () const
	Return pointer to parent subnet. More...

bool	is_frozen () const
	Returns true if node is frozen, i.e., shall not be updated. More...

bool	is_local () const
	Returns true if the node is allocated in the local process. More...

void	init_state ()
	Set state variables to the default values for the model. More...

void	init_buffers ()
	Initialize buffers of a node. More...

virtual void	finalize ()
	Finalize node. More...

virtual void	set_status (const DictionaryDatum &)=0
	Change properties of the node according to the entries in the dictionary. More...

virtual void	get_status (DictionaryDatum &) const =0
	Export properties of the node by setting entries in the status dictionary. More...

virtual port	send_test_event (Node &receiving_node, rport receptor_type, synindex syn_id, bool dummy_target)
	Send an event to the receiving_node passed as an argument. More...

virtual port	handles_test_event (SpikeEvent &, rport receptor_type)
	Check if the node can handle a particular event and receptor type. More...

virtual port	handles_test_event (RateEvent &, rport receptor_type)

virtual port	handles_test_event (DataLoggingRequest &, rport receptor_type)

virtual port	handles_test_event (CurrentEvent &, rport receptor_type)

virtual port	handles_test_event (ConductanceEvent &, rport receptor_type)

virtual port	handles_test_event (DoubleDataEvent &, rport receptor_type)

virtual port	handles_test_event (DSSpikeEvent &, rport receptor_type)

virtual port	handles_test_event (DSCurrentEvent &, rport receptor_type)

virtual void	register_stdp_connection (double_t)
	Register a STDP connection. More...

virtual void	unregister_stdp_connection (double_t)
	Unregister a STDP connection. More...

virtual void	handle (SpikeEvent &e)
	Handle incoming spike events. More...

virtual void	handle (RateEvent &e)
	Handler for rate events. More...

virtual void	handle (DataLoggingRequest &e)
	Handler for universal data logging request. More...

virtual void	handle (DataLoggingReply &e)
	Handler for universal data logging request. More...

virtual void	handle (CurrentEvent &e)
	Handler for current events. More...

virtual void	handle (ConductanceEvent &e)
	Handler for conductance events. More...

virtual void	handle (DoubleDataEvent &e)
	Handler for DoubleData events. More...

virtual double_t	get_K_value (double_t t)
	return the Kminus value at t (in ms). More...

virtual void	get_K_values (double_t t, double_t &Kminus, double_t &triplet_Kminus)
	write the Kminus and triplet_Kminus values at t (in ms) to the provided locations. More...

virtual void	get_history (double_t t1, double_t t2, std::deque< histentry >::iterator start, std::deque< histentry >::iterator finish)
	return the spike history for (t1,t2]. More...

virtual void	event_hook (DSSpikeEvent &)
	Modify Event object parameters during event delivery. More...

virtual void	event_hook (DSCurrentEvent &)

void	set_thread (thread)
	Store the number of the thread to which the node is assigned. More...

thread	get_thread () const
	Retrieve the number of the thread to which the node is assigned. More...

void	set_vp (thread)
	Store the number of the virtual process to which the node is assigned. More...

thread	get_vp () const
	Retrieve the number of the virtual process to which the node is assigned. More...

void	set_model_id (int)
	Set the model id. More...

DictionaryDatum	get_status_base ()
	Return a dictionary with the node's properties. More...

void	set_status_base (const DictionaryDatum &)
	Set status dictionary of a node. More...

bool	is_model_prototype () const
	Returns true if node is model prototype. More...

void	set_thread_lid (const index)
	set thread local index More...

index	get_thread_lid () const
	get thread local index More...

bool	buffers_initialized () const
	True if buffers have been initialized. More...

void	set_buffers_initialized (bool initialized)

Protected Member Functions
void	clear_ntree_cache_ () const
	Clear the cache for global position information. More...

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

lockPTR< Ntree< D, index > >	do_get_global_positions_ntree_ (const Selector &filter)

virtual void	insert_global_positions_ntree_ (Ntree< D, index > &tree, const Selector &filter)=0
	Insert global position info into ntree. More...

virtual void	insert_global_positions_vector_ (std::vector< std::pair< Position< D >, index > > &, const Selector &filter)=0
	Insert global position info into vector. More...

virtual void	insert_local_positions_ntree_ (Ntree< D, index > &tree, const Selector &filter)=0
	Insert local position info into ntree. More...

Protected Member Functions inherited from nest::Subnet
void	init_node_ (const Node &)

void	init_state_ (const Node &)
	Private function to initialize the state of a node to model defaults. More...

void	init_buffers_ ()
	Private function to initialize the buffers of a node. More...

void	calibrate ()
	Re-calculate dependent parameters of the node. More...

void	update (Time const &, const long_t, const long_t)
	Bring the node from state $t$ to $t+n*dt$. More...

Protected Member Functions inherited from nest::Node
virtual size_t	num_thread_siblings_ () const
	Return the number of thread siblings in SiblingContainer. More...

virtual Node *	get_thread_sibling_ (index) const
	Return the specified member of a SiblingContainer. More...

virtual Node *	get_thread_sibling_safe_ (index) const
	Return specified member of a SiblingContainer, with access control. More...

Model &	get_model_ () const

void	set_frozen_ (bool frozen)
	Mark node as frozen. More...

template<typename ConcreteNode >
const ConcreteNode &	downcast (const Node &)
	Auxiliary function to downcast a Node to a concrete class derived from Node. More...

Protected Attributes
Position< D >	lower_left_
	lower left corner (minimum coordinates) of layer More...

Position< D >	extent_
	size of layer More...

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

Protected Attributes inherited from nest::AbstractLayer
int_t	depth_
	number of neurons at each position More...

Protected Attributes inherited from nest::Subnet
vector< Node * >	nodes_
	Pointer to child nodes. More...

Multirange	gids_
	GIDs of global child nodes. More...

Static Protected Attributes
static lockPTR< Ntree< D, index > >	cached_ntree_
	Global position information for a single layer. More...

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

static Selector	cached_selector_

Static Protected Attributes inherited from nest::AbstractLayer
static index	cached_ntree_layer_ = -1
	GID for the single layer for which we cache global position information. More...

static index	cached_vector_layer_ = -1
	GID for the single layer for which we cache global position information. More...

Static Protected Attributes inherited from nest::Node
static Network *	net_ =NULL
	Pointer to global network driver. More...

Friends
class	MaskedLayer< D >

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

Static Public Member Functions inherited from nest::Node
static Network *	network ()
	Return pointer to network driver class. More...

Detailed Description

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

Abstract base class for Layer of given dimension (D=2 or 3).

Constructor & Destructor Documentation

template<int D>

nest::Layer< D >::Layer ( )

inline

Creates an empty layer.

template<int D>

nest::Layer< D >::Layer ( const Layer< D > & l )

inline

Copy constructor.

template<int D>

nest::Layer< D >::~Layer ( )

inline

Virtual destructor.

Member Function Documentation

template<int D>

void nest::Layer< D >::clear_ntree_cache_ ( ) const

inlineprotectedvirtual

Clear the cache for global position information.

Implements nest::AbstractLayer.

template<int D>

void nest::Layer< D >::clear_vector_cache_ ( ) const

inlineprotectedvirtual

Clear the cache for global position information.

Implements nest::AbstractLayer.

template<int D>

Position< D > nest::Layer< D >::compute_displacement	(	const Position< D > &	from_pos,
		const Position< D > &	to_pos
	)		const

virtual

Returns displacement of a position from another position.

When using periodic boundary conditions, will return minimum displacement.

Parameters

from_pos	position vector in layer
to_pos	position to which displacement is to be computed

Returns: vector pointing from from_pos to to_pos

Referenced by nest::ConnectionCreator::connect_to_target_(), nest::ConnectionCreator::convergent_connect_(), nest::ConnectionCreator::divergent_connect_(), nest::Layer< D >::dump_connections(), and nest::ConnectionCreator::source_driven_connect_().

template<int D>

Position< D > nest::Layer< D >::compute_displacement	(	const Position< D > &	from_pos,
		const index	to
	)		const

inline

Returns displacement of node from given position.

When using periodic boundary conditions, will return minimum displacement.

Parameters

from_pos	position vector in layer
to	node in layer to which displacement is to be computed

Returns: vector pointing from from_pos to node to's position

template<int D>

std::vector< double_t > nest::Layer< D >::compute_displacement	(	const std::vector< double_t > &	from_pos,
		const index	to
	)		const

inlinevirtual

Returns displacement of node from given position.

When using periodic boundary conditions, will return minimum displacement.

Parameters

from_pos	position vector in layer
to	node in layer to which displacement is to be computed

Returns: vector pointing from from_pos to node to's position

Implements nest::AbstractLayer.

template<int D>

double_t nest::Layer< D >::compute_distance	(	const Position< D > &	from_pos,
		const index	to
	)		const

inline

Returns distance to node from given position.

When using periodic boundary conditions, will return minimum distance.

Parameters

from_pos	position vector in layer
to	node in layer to which displacement is to be computed

Returns: length of vector pointing from from_pos to node to's position

template<int D>

double_t nest::Layer< D >::compute_distance	(	const std::vector< double_t > &	from_pos,
		const index	to
	)		const

inlinevirtual

Returns distance to node from given position.

When using periodic boundary conditions, will return minimum distance.

Parameters

from_pos	position vector in layer
to	node in layer to which displacement is to be computed

Returns: length of vector pointing from from_pos to node to's position

Implements nest::AbstractLayer.

template<int D>

void nest::Layer< D >::connect	(	AbstractLayer< D > &	target,
		ConnectionCreator &	connector
	)

virtual

Connect this layer to the given target layer.

The actual connections are made in class ConnectionCreator.

Parameters

target	target layer to connect to. Must have same dimension as this layer.
connector	connection properties

Implements nest::AbstractLayer.

References nest::ConnectionCreator::connect(), and numerics::e.

template<int D>

lockPTR< Ntree< D, index > > nest::Layer< D >::do_get_global_positions_ntree_ ( const Selector & filter )

protected

template<int D>

void nest::Layer< D >::dump_connections	(	std::ostream &	out,
		const Token &	syn_model
	)

virtual

Dumps information about all connections of the given type having their source in the given layer to the given output stream.

For distributed simulations this function will dump the connections with local targets only.

Parameters

out	output stream
synapse_id	type of connection

Implements nest::AbstractLayer.

References assert(), nest::Layer< D >::compute_displacement(), def(), nest::names::delay, TokenArray::get(), nest::names::n, TokenArray::size(), nest::names::source, nest::names::synapse_model, nest::names::target, and nest::names::weight.

template<int D>

void nest::Layer< D >::dump_nodes ( std::ostream & os ) const

virtual

Write layer data to stream.

For each node in layer, write one line to stream containing: GID x-position y-position [z-position]

Parameters

os	output stream

Implements nest::AbstractLayer.

template<int D>

Position<D> nest::Layer< D >::get_center ( ) const

inline

Returns: center of layer.

References nest::Layer< D >::extent_, and nest::Layer< D >::lower_left_.

template<int D>

const Position<D>& nest::Layer< D >::get_extent ( ) const

inline

Returns: extent of layer.

References nest::Layer< D >::extent_.

Referenced by nest::MaskedLayer< D >::check_mask_(), and nest::MaskedLayer< D >::MaskedLayer().

template<int D>

std::vector< index > nest::Layer< D >::get_global_nodes	(	const MaskDatum &	mask,
		const std::vector< double_t > &	anchor,
		bool	allow_oversized
	)

virtual

Return a vector with the GIDs of the nodes inside the mask.

Implements nest::AbstractLayer.

References nest::MaskedLayer< D >::begin(), and nest::MaskedLayer< D >::end().

template<int D>

lockPTR< Ntree< D, index > > nest::Layer< D >::get_global_positions_ntree ( Selector filter = Selector() )

Get positions for all nodes in layer, including nodes on other MPI processes.

The positions will be cached so that subsequent calls for the same layer are fast. One one layer is cached at the time, so the user should group together all ConnectLayers calls using the same pool layer.

References assert().

Referenced by nest::MaskedLayer< D >::MaskedLayer().

template<int D>

lockPTR< Ntree< D, index > > nest::Layer< D >::get_global_positions_ntree	(	Selector	filter,
		std::bitset< D >	periodic,
		Position< D >	lower_left,
		Position< D >	extent
	)

Get positions globally, overriding the dimensions of the layer and the periodic flags.

The supplied lower left corner and extent coordinates are only used for the dimensions where the supplied periodic flag is set.

References nest::names::extent.

template<int D>

std::vector< std::pair< Position< D >, index > > * nest::Layer< D >::get_global_positions_vector ( Selector filter = Selector() )

References assert().

Referenced by nest::ConnectionCreator::convergent_connect_(), nest::ConnectionCreator::divergent_connect_(), nest::ConnectionCreator::source_driven_connect_(), and nest::ConnectionCreator::target_driven_connect_().

template<int D>

std::vector< std::pair< Position< D >, index > > nest::Layer< D >::get_global_positions_vector	(	Selector	filter,
		const MaskDatum &	mask,
		const Position< D > &	anchor,
		bool	allow_oversized
	)