Leaky iaf neuron, alpha PSC synapses, canonical implementation. More...

#include <iaf_psc_alpha_canon.h>

Inheritance diagram for nest::iaf_psc_alpha_canon:

Classes
struct	Buffers_
	Buffers of the model. More...

struct	Parameters_
	Independent parameters of the model. More...

struct	State_
	State variables of the model. More...

struct	Variables_
	Internal variables of the model. More...

Public Member Functions
	iaf_psc_alpha_canon ()
	Basic constructor. More...

	iaf_psc_alpha_canon (const iaf_psc_alpha_canon &)
	Copy constructor. More...

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

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

port	handles_test_event (CurrentEvent &, rport)

port	handles_test_event (DataLoggingRequest &, rport)

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

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

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

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...

void	get_status (DictionaryDatum &) const

void	set_status (const DictionaryDatum &)

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

	Node (Node const &)

virtual	~Node ()

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

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

virtual std::string	print_network (int, int, std::string="")
	Prints out one line of the tree view of the network. 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	handles_test_event (RateEvent &, 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 (RateEvent &e)
	Handler for rate events. More...

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

virtual bool	is_subnet () const

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)

Private Member Functions
void	set_spiketime (Time const &)

void	propagate_ (const double_t dt)
	Propagate neuron state. More...

void	emit_spike_ (Time const &origin, const long_t lag, const double_t t0, const double_t dt)
	Emit a single spike caused by DC current in absence of spike input. More...

void	emit_instant_spike_ (Time const &origin, const long_t lag, const double_t spike_offset)
	Emit a single spike at a precisely given time. More...

double_t	get_V_m_ () const
	Read out the real membrane potential. More...

double_t	get_y1_ () const
	Read out state variable y1. More...

double_t	get_y2_ () const
	Read out state variable y2. More...

Interface functions
Note These functions are private, so that they can be accessed only through a Node*.
void	init_state_ (const Node &proto)
	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 &origin, const long_t from, const long_t to)
	Time Evolution Operator. More...

Private Attributes
Parameters_	P_

State_	S_

Variables_	V_

Buffers_	B_

Static Private Attributes
static RecordablesMap < iaf_psc_alpha_canon >	recordablesMap_
	Mapping of recordables names to access functions. More...

Friends
class	RecordablesMap< iaf_psc_alpha_canon >

class	UniversalDataLogger< iaf_psc_alpha_canon >

Threshold-crossing interpolation
These functions determine the time of threshold crossing using interpolation, one function per interpolation order. thresh_find() is the driver function and the only one to be called directly.
enum	interpOrder { NO_INTERPOL, LINEAR, QUADRATIC, CUBIC, END_INTERP_ORDER }
	Interpolation orders. More...

double_t	thresh_find_ (double_t const) const
	Localize threshold crossing. More...

double_t	thresh_find1_ (double_t const) const

double_t	thresh_find2_ (double_t const) const

double_t	thresh_find3_ (double_t const) const

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

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

Detailed Description

Leaky iaf neuron, alpha PSC synapses, canonical implementation.

Note: Inherit privately from Node, so no classes can be derived from this one.

Todo:: Implement current input in consistent way.

Member Enumeration Documentation

enum nest::iaf_psc_alpha_canon::interpOrder

private

Interpolation orders.

Enumerator
NO_INTERPOL
LINEAR
QUADRATIC
CUBIC
END_INTERP_ORDER

Constructor & Destructor Documentation

nest::iaf_psc_alpha_canon::iaf_psc_alpha_canon ( )

Basic constructor.

This constructor should only be used by GenericModel to create model prototype instances.

References recordablesMap_.

nest::iaf_psc_alpha_canon::iaf_psc_alpha_canon ( const iaf_psc_alpha_canon & n )

Copy constructor.

GenericModel::allocate_() uses the copy constructor to clone actual model instances from the prototype instance.

Note: The copy constructor MUST NOT be used to create nodes based on nodes that have been placed in the network.

Member Function Documentation

void nest::iaf_psc_alpha_canon::calibrate ( )

privatevirtual

Re-calculate dependent parameters of the node.

This function is called each time a simulation is begun/resumed. It must re-calculate all internal Variables of the node required for spike handling or updating the node.

Implements nest::Node.

References assert(), numerics::e, numerics::expm1(), nest::Time::get_ms(), nest::Time::get_resolution(), and nest::Time::get_steps().

void nest::iaf_psc_alpha_canon::emit_instant_spike_	(	Time const &	origin,
		const long_t	lag,
		const double_t	spike_offset
	)

private

Emit a single spike at a precisely given time.

Parameters

origin	Time stamp at beginning of slice
lag	Time step within slice
spike_offset	Time offset for spike

References assert(), nest::Time::get_steps(), and nest::Event::set_offset().

void nest::iaf_psc_alpha_canon::emit_spike_	(	Time const &	origin,
		const long_t	lag,
		const double_t	t0,
		const double_t	dt
	)

private

Emit a single spike caused by DC current in absence of spike input.

Emits a single spike and reset neuron given that the membrane potential was below threshold at the beginning of a mini-timestep and above afterwards.

Parameters

origin	Time stamp at beginning of slice
lag	Time step within slice
t0	Beginning of mini-timestep
dt	Duration of mini-timestep

References nest::Time::get_steps(), and nest::Event::set_offset().

void nest::iaf_psc_alpha_canon::get_status ( DictionaryDatum & d ) const

inline

References nest::iaf_psc_alpha_canon::Parameters_::get(), nest::iaf_psc_alpha_canon::State_::get(), P_, nest::names::recordables, recordablesMap_, and S_.

double_t nest::iaf_psc_alpha_canon::get_V_m_ ( ) const

inlineprivate

Read out the real membrane potential.

References nest::iaf_psc_alpha_canon::Parameters_::E_L_, P_, S_, and nest::iaf_psc_alpha_canon::State_::y3_.

Referenced by nest::RecordablesMap< HostNode >::create().

double_t nest::iaf_psc_alpha_canon::get_y1_ ( ) const

inlineprivate

Read out state variable y1.

References S_, and nest::iaf_psc_alpha_canon::State_::y1_.

Referenced by nest::RecordablesMap< HostNode >::create().

double_t nest::iaf_psc_alpha_canon::get_y2_ ( ) const

inlineprivate

Read out state variable y2.

References S_, and nest::iaf_psc_alpha_canon::State_::y2_.

Referenced by nest::RecordablesMap< HostNode >::create().

void nest::iaf_psc_alpha_canon::handle ( SpikeEvent & e )

virtual

Handle incoming spike events.

Default implementation of event handlers just throws an UnexpectedEvent exception.

Parameters

thrd	Id of the calling thread.
e	Event object.

This handler has to be implemented if a Node should accept spike events.

See also: class SpikeEvent; class UnexpectedEvent

Exceptions

UnexpectedEvent This is the default event to throw.

Reimplemented from nest::Node.

References assert(), nest::Event::get_delay(), nest::SpikeEvent::get_multiplicity(), nest::Event::get_offset(), nest::Event::get_rel_delivery_steps(), nest::Event::get_stamp(), nest::Time::get_steps(), and nest::Event::get_weight().

void nest::iaf_psc_alpha_canon::handle ( CurrentEvent & e )

virtual

Handler for current events.

See also: handle(thread, SpikeEvent&)

Exceptions

UnexpectedEvent

Reimplemented from nest::Node.

References assert(), nest::names::c, nest::CurrentEvent::get_current(), nest::Event::get_delay(), nest::Event::get_rel_delivery_steps(), nest::Event::get_weight(), and nest::names::w.

void nest::iaf_psc_alpha_canon::handle ( DataLoggingRequest & e )

virtual

Handler for universal data logging request.

See also: handle(SpikeEvent&)

Exceptions

UnexpectedEvent

Reimplemented from nest::Node.

port nest::iaf_psc_alpha_canon::handles_test_event	(	SpikeEvent &	,
		rport	receptor_type
	)

inlinevirtual

Check if the node can handle a particular event and receptor type.

This function is called upon connection setup by send_test_event().

handles_test_event() function is used to verify that the receiver can handle the event. It can also be used by the receiver to return information to the sender in form of the returned port. The default implementation throws an IllegalConnection exception. Any node class should define handles_test_event() functions for all those event types it can handle.

See Kunkel et al, Front Neuroinform 8:78 (2014), Sec 3.

Note: The semantics of all other handles_test_event() functions is identical.

Exceptions

IllegalConnection

Reimplemented from nest::Node.

References nest::Node::get_name().

port nest::iaf_psc_alpha_canon::handles_test_event	(	CurrentEvent &	,
		rport	receptor_type
	)

inlinevirtual

Reimplemented from nest::Node.

References nest::Node::get_name().

port nest::iaf_psc_alpha_canon::handles_test_event	(	DataLoggingRequest &	dlr,
		rport	receptor_type
	)

inlinevirtual

Reimplemented from nest::Node.

References B_, nest::Node::get_name(), nest::iaf_psc_alpha_canon::Buffers_::logger_, and recordablesMap_.

void nest::iaf_psc_alpha_canon::init_buffers_ ( )

privatevirtual

Private function to initialize the buffers of a node.

This function, which must be overloaded by all derived classes, provides the implementation for initializing the buffers of a node.

See also: Node::init_buffers()

Implements nest::Node.

void nest::iaf_psc_alpha_canon::init_state_ ( const Node & )

privatevirtual

Private function to initialize the state of a node to model defaults.

This function, which must be overloaded by all derived classes, provides the implementation for initializing the state of a node to the model defaults; the state is the set of observable dynamic variables.

Parameters

Reference to model prototype object.

See also: Node::init_state()

Note: To provide a reasonable behavior during the transition to the new scheme, init_state_() has a default implementation calling init_dynamic_state_().

Implements nest::Node.

References S_.

bool nest::iaf_psc_alpha_canon::is_off_grid ( ) const

inlinevirtual

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.

Reimplemented from nest::Node.

void nest::iaf_psc_alpha_canon::propagate_ ( const double_t dt )

private

Propagate neuron state.

Propagate the neuron's state by dt.

Parameters

dt	Interval over which to propagate

References numerics::expm1().

port nest::iaf_psc_alpha_canon::send_test_event	(	Node &	receiving_node,
		rport	receptor_type,
		synindex	syn_id,
		bool	dummy_target
	)

inlinevirtual

Send an event to the receiving_node passed as an argument.

Default implementation of check_connection just throws UnexpectedEvent.

This is required during the connection handshaking to test, if the receiving_node can handle the event type and receptor_type sent by the source node.

If dummy_target is true, this indicates that receiving_node is derived from ConnTestDummyNodeBase and used in the first call to send_test_event(). This can be ignored in most cases, but Nodes sending DS*Events to their own event hooks and then *Events to their proper targets must send DS*Events when called with the dummy target, and *Events when called with the real target, see #478.

Reimplemented from nest::Node.

References numerics::e, nest::Node::handles_test_event(), and nest::Event::set_sender().

void nest::iaf_psc_alpha_canon::set_spiketime ( Time const & now )

inlineprivate

References nest::Time::get_steps().

void nest::iaf_psc_alpha_canon::set_status ( const DictionaryDatum & d )

inline

References P_, S_, nest::iaf_psc_alpha_canon::Parameters_::set(), and nest::iaf_psc_alpha_canon::State_::set().

nest::double_t nest::iaf_psc_alpha_canon::thresh_find1_ ( double_t const dt ) const

private

References nest::names::tau.

nest::double_t nest::iaf_psc_alpha_canon::thresh_find2_ ( double_t const dt ) const

private

References nest::names::a, nest::names::b, nest::names::c, and nest::names::dt.

nest::double_t nest::iaf_psc_alpha_canon::thresh_find3_ ( double_t const dt ) const

private

References nest::names::a, nest::names::dt, nest::names::p, nest::names::phi, numerics::pi, nest::names::tau, and nest::names::u.

nest::double_t nest::iaf_psc_alpha_canon::thresh_find_ ( double_t const dt ) const

inlineprivate

Localize threshold crossing.

Driver function to invoke the correct interpolation function for the chosen interpolation order.

Parameters

double_t length of interval since previous event

Returns: time from previous event to threshold crossing

References nest::names::dt.

void nest::iaf_psc_alpha_canon::update	(	Time const &	origin,
		const long_t	from,
		const long_t	to
	)

privatevirtual

Time Evolution Operator.

update() promotes the state of the neuron from origin+from to origin+to. It does so in steps of the resolution h. Within each step, time is advanced from event to event, as retrieved from the spike queue.

Return from refractoriness is handled as a special event in the queue, which is marked by a weight that is GSL_NAN. This greatly simplifies the code.

For steps, during which no events occur, the precomputed propagator matrix is used. For other steps, the propagator matrix is computed as needed.

While the neuron is refractory, membrane potential (y3_) is clamped to U_reset_.

Implements nest::Node.

References assert(), nest::Scheduler::get_min_delay(), and nest::Time::get_steps().

Friends And Related Function Documentation

friend class RecordablesMap< iaf_psc_alpha_canon >

friend

friend class UniversalDataLogger< iaf_psc_alpha_canon >

friend

Member Data Documentation

nest::RecordablesMap< nest::iaf_psc_alpha_canon > nest::iaf_psc_alpha_canon::recordablesMap_

staticprivate

Mapping of recordables names to access functions.

Referenced by get_status(), handles_test_event(), and iaf_psc_alpha_canon().

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

Classes

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Friends

Threshold-crossing interpolation

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation