An archiving node which additionally archives parameters and buffers needed for the Clopath plasticity rule. More...

#include <clopath_archiving_node.h>

Inheritance diagram for nest::ClopathArchivingNode:

Collaboration diagram for nest::ClopathArchivingNode:

Public Member Functions
	ClopathArchivingNode ()

	ClopathArchivingNode (const ClopathArchivingNode &)

double	get_LTD_value (double t) override
	Returns value in LTD history at time t.

void	get_LTP_history (double t1, double t2, std::deque< histentry_extended >::iterator start, std::deque< histentry_extended >::iterator finish) override
	Sets pointer start (finish) to the first (last) entry in LTP_history whose time argument is between t1 and t2.

double	get_theta_plus () const
	Returns threshold theta_plus_.

double	get_theta_minus () const
	Returns threshold theta_minus_.

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

	ArchivingNode (const ArchivingNode &)

double	get_K_value (double t) override
	Return the Kminus (synaptic trace) value at time t (given in ms).

void	get_K_values (double t, double &Kminus, double &nearest_neighbor_Kminus, double &Kminus_triplet) override
	Write the different STDP K values at time t (in ms) to the provided locations.

double	get_K_triplet_value (const std::deque< histentry >::iterator &iter)
	Return the triplet Kminus value for the associated iterator.

void	get_history (double t1, double t2, std::deque< histentry >::iterator start, std::deque< histentry >::iterator finish) override
	Return the spike times (in steps) of spikes which occurred in the range [t1,t2].

void	register_stdp_connection (double t_first_read, double delay) override
	Register a new incoming STDP connection.

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

	StructuralPlasticityNode (const StructuralPlasticityNode &)

double	get_Ca_minus () const override
	return the current value of Ca_minus

double	get_synaptic_elements (std::string n) const override
	Get the number of synaptic element for the current Node.

int	get_synaptic_elements_vacant (std::string n) const override
	Get the number of synaptic elements of type n which are available for new synapse creation.

int	get_synaptic_elements_connected (std::string n) const override
	Get the number of synaptic element of type n which are currently connected.

std::map< std::string, double >	get_synaptic_elements () const override
	Get the number of all synaptic elements for the current Node.

void	update_synaptic_elements (double t) override
	Change the number of synaptic elements in the node depending on the dynamics described by the corresponding growth curve.

void	decay_synaptic_elements_vacant () override
	Delete a certain portion of the vacant synaptic elements which are not in use.

void	connect_synaptic_element (std::string name, int n) override
	Change the number of connected synaptic elements by n.

void	get_status (Dictionary &d) const override
	Export properties of the node by setting entries in the status dictionary.

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

double	get_tau_Ca () const
	Retrieve the current value of tau_Ca which defines the exponential decay constant of the intracellular calcium concentration.

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

	Node (Node const &)

virtual	~Node ()

virtual Node *	clone () const
	This function creates a new object by calling the derived class' copy constructor and returning its pointer.

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

virtual bool	supports_urbanczik_archiving () const
	Returns true if the node supports the Urbanczik-Senn plasticity rule.

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

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.

virtual bool	is_off_grid () const
	Returns true if the node sends/receives off-grid events.

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

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

virtual std::string	get_element_type () const
	Return the element type of the node.

size_t	get_node_id () const
	Return global Network ID.

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

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

bool	node_uses_wfr () const
	Returns true if the node uses the waveform relaxation method.

void	set_node_uses_wfr (const bool)
	Sets node_uses_wfr_ member variable (to be able to set it to "true" for any class derived from Node)

void	init ()
	Initialize node prior to first simulation after node has been created.

virtual void	pre_run_hook ()=0
	Re-calculate dependent parameters of the node.

virtual void	calibrate_time (const TimeConverter &)
	Re-calculate time-based properties of the node.

virtual void	post_run_cleanup ()
	Cleanup node after Run.

virtual void	finalize ()
	Finalize node.

virtual void	update (Time const &, const long, const long)=0
	Advance the state of the node in time through the given interval.

virtual bool	wfr_update (Time const &, const long, const long)
	Advance the state of the node in time through the given interval (see Node::update() for more details).

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

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

virtual size_t	handles_test_event (WeightRecorderEvent &, size_t receptor_type)

virtual size_t	handles_test_event (RateEvent &, size_t receptor_type)

virtual size_t	handles_test_event (DataLoggingRequest &, size_t receptor_type)

virtual size_t	handles_test_event (CurrentEvent &, size_t receptor_type)

virtual size_t	handles_test_event (ConductanceEvent &, size_t receptor_type)

virtual size_t	handles_test_event (DoubleDataEvent &, size_t receptor_type)

virtual size_t	handles_test_event (DSSpikeEvent &, size_t receptor_type)

virtual size_t	handles_test_event (DSCurrentEvent &, size_t receptor_type)

virtual size_t	handles_test_event (GapJunctionEvent &, size_t receptor_type)

virtual size_t	handles_test_event (InstantaneousRateConnectionEvent &, size_t receptor_type)

virtual size_t	handles_test_event (DiffusionConnectionEvent &, size_t receptor_type)

virtual size_t	handles_test_event (DelayedRateConnectionEvent &, size_t receptor_type)

virtual size_t	handles_test_event (LearningSignalConnectionEvent &, size_t receptor_type)

virtual size_t	handles_test_event (SICEvent &, size_t receptor_type)

virtual void	sends_secondary_event (GapJunctionEvent &ge)
	Required to check, if source neuron may send a SecondaryEvent.

virtual void	sends_secondary_event (InstantaneousRateConnectionEvent &re)
	Required to check, if source neuron may send a SecondaryEvent.

virtual void	sends_secondary_event (DiffusionConnectionEvent &de)
	Required to check, if source neuron may send a SecondaryEvent.

virtual void	sends_secondary_event (DelayedRateConnectionEvent &re)
	Required to check, if source neuron may send a SecondaryEvent.

virtual void	sends_secondary_event (LearningSignalConnectionEvent &re)
	Required to check if source node may send a LearningSignalConnectionEvent.

virtual void	sends_secondary_event (SICEvent &sic)
	Required to check if source node may send a SICEvent.

virtual void	register_eprop_connection ()
	Registers an eprop connection.

virtual void	initialize_update_history ()
	Initializes the update history.

virtual long	get_shift () const
	Retrieves the temporal shift of the signal.

virtual void	write_update_to_history (const long t_previous_update, const long t_current_update, const bool is_flush_event, const bool previous_was_flush_event)
	Registers the current update in the update history and deregisters the previous update.

virtual void	erase_used_eprop_history ()
	Erases used e-prop history for bsshslm_2020 models.

virtual void	erase_used_eprop_history (const long t_spike, const long t_spike_previous)
	Erases used e-prop history based on inter-spike interval.

virtual bool	is_eprop_recurrent_node () const
	Checks if the node is part of the recurrent network and thus not a readout neuron.

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

virtual void	handle (WeightRecorderEvent &e)
	Handle incoming weight recording events.

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

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

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

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

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

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

virtual void	handle (GapJunctionEvent &e)
	Handler for gap junction events.

virtual void	handle (InstantaneousRateConnectionEvent &e)
	Handler for rate neuron events.

virtual void	handle (DiffusionConnectionEvent &e)
	Handler for rate neuron events.

virtual void	handle (DelayedRateConnectionEvent &e)
	Handler for delay rate neuron events.

virtual void	handle (LearningSignalConnectionEvent &e)
	Handler for learning signal connection events.

virtual void	handle (SICEvent &e)
	Handler for slow inward current events (SICEvents).

virtual void	get_urbanczik_history (double t1, double t2, std::deque< histentry_extended >::iterator start, std::deque< histentry_extended >::iterator finish, int)

virtual double	get_C_m (int comp)

virtual double	get_g_L (int comp)

virtual double	get_tau_L (int comp)

virtual double	get_tau_s (int comp)

virtual double	get_tau_syn_ex (int comp)

virtual double	get_tau_syn_in (int comp)

virtual void	compute_gradient (const long t_spike, const long t_spike_previous, double &z_previous_buffer, double &z_bar, double &e_bar, double &e_bar_reg, double &epsilon, double &weight, const CommonSynapseProperties &cp, WeightOptimizer *optimizer, bool is_flush_event, bool previous_was_flush_event, double &sum_grad, long &remaining_steps_until_cutoff, long &decay_steps)
	Compute gradient change for eprop synapses.

virtual double	compute_gradient (std::vector< long > &presyn_isis, const long t_previous_update, const long t_previous_trigger_spike, const double kappa, const bool average_gradient)
	Compute gradient change for eprop synapses.

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

virtual void	event_hook (DSCurrentEvent &)

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

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

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

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

void	set_model_id (int)
	Set the model id.

void	set_initialized ()
	Execute post-initialization actions in node models.

virtual SignalType	sends_signal () const

virtual SignalType	receives_signal () const

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

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

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

void	set_thread_lid (const size_t)
	set thread local index

size_t	get_thread_lid () const
	get thread local index

virtual void	set_local_device_id (const size_t lsdid)
	Sets the local device id.

virtual size_t	get_local_device_id () const
	Gets the local device id.

void	set_tmp_nc_index (size_t index)
	Set index in node collection; required by ThirdOutBuilder.

size_t	get_tmp_nc_index ()
	Return and invalidate index in node collection; required by ThirdOutBuilder.

Public Member Functions inherited from nest::IgnoreAndSpikeMechanism
	IgnoreAndSpikeMechanism ()
	Default constructor.

	IgnoreAndSpikeMechanism (const IgnoreAndSpikeMechanism &n)
	Copy constructor.

virtual	~IgnoreAndSpikeMechanism ()=default
	Virtual destructor.

bool	spike_event_is_due (bool emit_dynamic_spike)
	Updates spike schedule and returns whether a spike should be emitted.

void	get_status (Dictionary &d) const
	Retrieves parameters and adds them to the status dictionary.

void	set_status (const Dictionary &d, Node *node)
	Sets and validates parameters from the status dictionary.

Protected Member Functions
void	write_LTD_history (const double t_ltd_ms, double u_bar_minus, double u_bar_bar)
	Creates a new entry in the LTD history and deletes old entries that are not needed any more.

void	write_LTP_history (const double t_ltp_ms, double u, double u_bar_plus)
	Creates a new entry in the LTP history and delets old entries that are not needed any more.

void	write_clopath_history (Time const &t_sp, double u, double u_bar_plus, double u_bar_minus, double u_bar_bar)
	Writes and reads the delayed_u_bar_[plus/minus] buffers and calls write_LTD_history and write_LTP_history if the corresponding Heaviside functions yield 1.

void	init_clopath_buffers ()
	Initialization of buffers.

void	get_status (Dictionary &d) const override
	Export properties of the node by setting entries in the status dictionary.

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

Protected Member Functions inherited from nest::ArchivingNode
void	set_spiketime (Time const &t_sp, double offset=0.0)
	Record spike history.

double	get_spiketime_ms () const
	Return most recent spike time in ms.

void	clear_history ()
	Clear spike history.

Protected Member Functions inherited from nest::StructuralPlasticityNode
void	set_spiketime (Time const &t_sp, double offset=0.0)
	Record spike history.

void	clear_history ()
	Clear spike history.

Protected Member Functions inherited from nest::Node
virtual void	init_state_ ()
	Configure state variables depending on runtime information.

virtual void	init_buffers_ ()
	Configure persistent internal data structures.

virtual void	set_initialized_ ()

Model &	get_model_ () const

void	set_frozen_ (bool frozen)
	Mark node as frozen.

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

Private Attributes
std::vector< histentry_extended >	ltd_history_

std::deque< histentry_extended >	ltp_history_

double	A_LTD_

double	A_LTP_

double	u_ref_squared_

double	theta_plus_

double	theta_minus_

bool	A_LTD_const_

double	delay_u_bars_

size_t	delay_u_bars_steps_

std::vector< double >	delayed_u_bar_plus_

std::vector< double >	delayed_u_bar_minus_

size_t	delayed_u_bars_idx_

size_t	ltd_hist_len_

size_t	ltd_hist_current_

Additional Inherited Members
Public Attributes inherited from nest::Node
DeprecationWarning	deprecation_warning
	Member of DeprecationWarning class to be used by models if parameters are deprecated.

Protected Attributes inherited from nest::ArchivingNode
size_t	n_incoming_
	Number of incoming connections from STDP connectors.

Detailed Description

An archiving node which additionally archives parameters and buffers needed for the Clopath plasticity rule.

Constructor & Destructor Documentation

◆ ClopathArchivingNode() [1/2]

nest::ClopathArchivingNode::ClopathArchivingNode ( )

◆ ClopathArchivingNode() [2/2]

nest::ClopathArchivingNode::ClopathArchivingNode ( const ClopathArchivingNode & n )

Member Function Documentation

◆ get_LTD_value()

double nest::ClopathArchivingNode::get_LTD_value ( double t )

overridevirtual

Returns value in LTD history at time t.

Reimplemented from nest::Node.

References nest::kernel(), and ltd_history_.

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◆ get_LTP_history()

void nest::ClopathArchivingNode::get_LTP_history	(	double	t1,
		double	t2,
		std::deque< histentry_extended >::iterator *	start,
		std::deque< histentry_extended >::iterator *	finish
	)

overridevirtual

Sets pointer start (finish) to the first (last) entry in LTP_history whose time argument is between t1 and t2.

Reimplemented from nest::Node.

References ltp_history_.

◆ get_status()

void nest::ClopathArchivingNode::get_status ( Dictionary & ) const

overrideprotectedvirtual

Export properties of the node by setting entries in the status dictionary.

Parameters

d	Dictionary.

Reimplemented from nest::ArchivingNode.

References nest::names::A_LTD(), A_LTD_, nest::names::A_LTD_const(), A_LTD_const_, nest::names::A_LTP(), A_LTP_, nest::names::delay_u_bars(), delay_u_bars_, nest::ArchivingNode::get_status(), nest::names::theta_minus(), theta_minus_, nest::names::theta_plus(), theta_plus_, nest::names::u_ref_squared(), and u_ref_squared_.

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◆ get_theta_minus()

double nest::ClopathArchivingNode::get_theta_minus ( ) const

inline

Returns threshold theta_minus_.

References theta_minus_.

◆ get_theta_plus()

double nest::ClopathArchivingNode::get_theta_plus ( ) const

inline

Returns threshold theta_plus_.

References theta_plus_.

◆ init_clopath_buffers()

void nest::ClopathArchivingNode::init_clopath_buffers ( )

protected

Initialization of buffers.

The implementation of the delay of the convolved membrane potentials as used here is not described in Clopath et al. 2010, but is present in the code on ModelDB (https://senselab.med.yale.edu/ModelDB/showmodel.cshtml?model=144566) which was presumably used to create the figures in the paper. Since we write into the buffer before we read from it, we have to add 1 to the size of the buffers.

References nest::KernelManager::connection_manager, nest::Time::delay_ms_to_steps(), delay_u_bars_, delay_u_bars_steps_, delayed_u_bar_minus_, delayed_u_bar_plus_, delayed_u_bars_idx_, nest::ConnectionManager::get_max_delay(), nest::kernel(), ltd_hist_current_, ltd_hist_len_, and ltd_history_.

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◆ set_status()

void nest::ClopathArchivingNode::set_status ( const Dictionary & )

overrideprotectedvirtual

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

Parameters

d	Dictionary with named parameter settings.

Reimplemented from nest::ArchivingNode.

References nest::names::A_LTD(), A_LTD_, nest::names::A_LTD_const(), A_LTD_const_, nest::names::A_LTP(), A_LTP_, nest::names::delay_u_bars(), delay_u_bars_, nest::ArchivingNode::set_status(), nest::names::theta_minus(), theta_minus_, nest::names::theta_plus(), theta_plus_, nest::names::u_ref_squared(), and u_ref_squared_.

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◆ write_clopath_history()

void nest::ClopathArchivingNode::write_clopath_history	(	Time const &	t_sp,
		double	u,
		double	u_bar_plus,
		double	u_bar_minus,
		double	u_bar_bar
	)

protected

Writes and reads the delayed_u_bar_[plus/minus] buffers and calls write_LTD_history and write_LTP_history if the corresponding Heaviside functions yield 1.

References delay_u_bars_steps_, delayed_u_bar_minus_, delayed_u_bar_plus_, delayed_u_bars_idx_, nest::Time::get_ms(), theta_minus_, theta_plus_, write_LTD_history(), and write_LTP_history().

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