Base class for common properties of StimulationDevices. More...

#include <stimulation_device.h>

Inheritance diagram for nest::StimulationDevice:

Collaboration diagram for nest::StimulationDevice:

Classes
struct	Parameters_

Public Types
enum	Type { CURRENT_GENERATOR , SPIKE_GENERATOR , DOUBLE_DATA_GENERATOR , DELAYED_RATE_CONNECTION_GENERATOR }
	Device type. More...

Public Member Functions
	StimulationDevice ()

	StimulationDevice (StimulationDevice const &)

	~StimulationDevice () override=default

bool	is_active (const Time &) const override
	Determine whether device is active.

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

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

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

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

void	pre_run_hook () override
	Re-calculate dependent parameters of the node.

void	enforce_single_syn_type (synindex)
	Throws IllegalConnection if synapse id differs from initial synapse id.

virtual Type	get_type () const

const std::string &	get_label () const

virtual void	set_data_from_stimulation_backend (std::vector< double > &)

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

virtual void	init_buffers ()
	Reset buffers.

virtual void	init_state ()
	Reset dynamic state to that of model.

virtual void	pre_run_hook ()
	Set internal variables before calls to SimulationManager::run()

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

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

	DeviceNode (DeviceNode const &dn)

void	set_local_device_id (const size_t ldid) override
	Sets the local device id.

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

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	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.

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	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 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_stdp_connection (double, double)
	Register a STDP connection.

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 double	get_Ca_minus () const
	Return the Ca_minus value at time Ca_t which corresponds to the time of the last update in Calcium concentration which is performed each time a Node spikes.

virtual double	get_synaptic_elements (std::string) const
	Get the number of synaptic element for the current Node at Ca_t which corresponds to the time of the last spike.

virtual int	get_synaptic_elements_vacant (std::string) const
	Get the number of vacant synaptic element for the current Node Return 0 if not overridden.

virtual int	get_synaptic_elements_connected (std::string) const
	Get the number of connected synaptic element for the current Node.

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

virtual void	update_synaptic_elements (double)
	Triggers the update of all SynapticElements stored in the synaptic_element_map_.

virtual void	decay_synaptic_elements_vacant ()
	Is used to reduce the number of synaptic elements in the node through time.

virtual void	connect_synaptic_element (std::string, int)
	Is used to update the number of connected synaptic elements (SynapticElement::z_connected_) when a synapse is formed or deleted.

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

virtual double	get_LTD_value (double t)

virtual void	get_K_values (double t, double &Kminus, double &nearest_neighbor_Kminus, double &Kminus_triplet)
	write the Kminus, nearest_neighbor_Kminus, and Kminus_triplet values at t (in ms) to the provided locations.

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

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

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

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::Device
	Device ()

	Device (const Device &n)

virtual	~Device ()

long	get_t_min_ () const
	Return lower limit in steps.

long	get_t_max_ () const
	Return upper limit in steps.

Time const &	get_origin () const

Time const &	get_start () const

Time const &	get_stop () const

Protected Member Functions
void	set_initialized_ () final

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.

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.

Protected Attributes
struct nest::StimulationDevice::Parameters_	P_

Protected Attributes inherited from nest::DeviceNode
size_t	local_device_id_

Private Attributes
synindex	first_syn_id_
	Synapse type of the first outgoing connection made by the Device.

Dictionary	backend_params_

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.

Detailed Description

Base class for common properties of StimulationDevices.

Stimulation devices are all devices injecting currents, spike trains or other signals into a network. They provide only output and do not receive any input.

Stimulation devices come in (at least) two varieties: those providing analog signals (CurrentEvent) and thos providing spike trains (SpikeEvent). Device activation needs to be handled differently in both cases. The general principle is that of the left-open, right-closed interval (start, stop]. For devices emitting spikes, spikes with times in that interval will be emitted.

For analog stimuli, e.g., currents, a stimulus is present in the interval (t, t+h], where h is the simulation resolution, if the effect of the stimulus can be observed at t+h. Thus, if a stimulus is to be active from time a, its effect will first be observable at a+h. This requires that the Event communicating the stimulus must be delivered at time a, i.e., by the deliver_events() call prior to the update for (a, a+h].

Since stimulation devices are connected to their targets with a delay of one time step, this means that analog stimulation devices need to emit the event during the update step for the interval (a-h, a]. Thus, the device needs to be PRO-ACTIVE.

Further, activity of stimulation devices is determined on the basis of simulation time, not event time stamps. This means that the first simulation time step during which the device must emit events is the step for which the global clock has time a-h. If stimulation is to end by time b, this means that the last event should be emitted during the time step for which the global clock has time b-2h.

Note: Any stimulation devices transmitting analog signals must NOT HAVE PROXIES.; The distinction between analog and spike emitting devices is implemented by making StimulationDevice a template class with the type of the Event sent as template parameter. Member is_active() is not implemented in general and is available only for those cases for which it is explicitly specialized.; StimulationDevice inherits protected from Device, so that implementations of is_active() can access t_min and t_max.

Todo:: The timing of analog devices is correct only if they are transmitted using Network::send_local(), but we cannot enforce this currently.

Member Enumeration Documentation

◆ Type

enum nest::StimulationDevice::Type

Device type.

Enumerator
CURRENT_GENERATOR
SPIKE_GENERATOR
DOUBLE_DATA_GENERATOR
DELAYED_RATE_CONNECTION_GENERATOR

Constructor & Destructor Documentation

◆ StimulationDevice() [1/2]

nest::StimulationDevice::StimulationDevice ( )

◆ StimulationDevice() [2/2]

nest::StimulationDevice::StimulationDevice ( StimulationDevice const & sd )

◆ ~StimulationDevice()

nest::StimulationDevice::~StimulationDevice ( )

overridedefault

Member Function Documentation

◆ enforce_single_syn_type()

void nest::StimulationDevice::enforce_single_syn_type ( synindex syn_id )

Throws IllegalConnection if synapse id differs from initial synapse id.

References first_syn_id_, and nest::invalid_synindex.

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◆ get_element_type()

std::string nest::StimulationDevice::get_element_type ( ) const

inlineoverridevirtual

Return the element type of the node.

The returned string is a free label describing the class of network elements a node belongs to. Currently used values are "neuron", "recorder", "stimulator", and "other", which are all defined as static string objects in the names namespace. This function is overwritten with a corresponding value in the derived classes

Reimplemented from nest::Node.

References nest::names::stimulator().

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◆ get_label()

const std::string & nest::StimulationDevice::get_label ( ) const

References nest::StimulationDevice::Parameters_::label_, and P_.

Referenced by nest::StimulationBackendMPI::get_port().

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◆ get_status()

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

overridevirtual

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

Parameters

d	Dictionary.

Implements nest::Node.

References backend_params_, nest::names::element_type(), nest::StimulationDevice::Parameters_::get(), nest::Node::get_node_id(), nest::Device::get_status(), P_, nest::names::stimulator(), and Dictionary::update_dictionary().

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◆ get_type()

virtual Type nest::StimulationDevice::get_type ( ) const

inlinevirtual

Reimplemented in nest::ac_generator, nest::dc_generator, nest::gamma_sup_generator, nest::inhomogeneous_poisson_generator, nest::mip_generator, nest::noise_generator, nest::poisson_generator, nest::poisson_generator_ps, nest::ppd_sup_generator, nest::pulsepacket_generator, nest::sinusoidal_poisson_generator, nest::spike_dilutor::DilutorStimulationDevice, nest::spike_generator, nest::step_current_generator, and nest::step_rate_generator.

Referenced by is_active().

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◆ has_proxies()

bool nest::StimulationDevice::has_proxies ( ) const

inlineoverridevirtual

Returns true if the node has proxies on remote threads.

This is used to discriminate between different types of nodes, when adding new nodes to the network.

Reimplemented from nest::Node.

◆ init_buffers()

virtual void nest::Device::init_buffers ( )

inlinevirtual

Reset buffers.

Reimplemented from nest::Device.

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◆ init_state()

virtual void nest::Device::init_state ( )

inlinevirtual

Reset dynamic state to that of model.

Reimplemented from nest::Device.

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◆ is_active()

bool nest::StimulationDevice::is_active ( const Time & T ) const

overridevirtual

Determine whether device is active.

The argument is the value of the simulation time.

See also: class comment for details.

Implements nest::Device.

References CURRENT_GENERATOR, DELAYED_RATE_CONNECTION_GENERATOR, DOUBLE_DATA_GENERATOR, nest::Time::get_steps(), nest::Device::get_t_max_(), nest::Device::get_t_min_(), and get_type().

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◆ pre_run_hook() [1/3]

void nest::Device::pre_run_hook ( )

virtual

Set internal variables before calls to SimulationManager::run()

Implements nest::Node.

◆ pre_run_hook() [2/3]

void nest::StimulationDevice::pre_run_hook ( )

overridevirtual

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 nest::Device::pre_run_hook().

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◆ pre_run_hook() [3/3]

virtual void nest::Node::pre_run_hook ( )

virtual

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.

◆ set_data_from_stimulation_backend()

virtual void nest::StimulationDevice::set_data_from_stimulation_backend ( std::vector< double > & )

inlinevirtual

Reimplemented in nest::ac_generator, nest::dc_generator, nest::gamma_sup_generator, nest::inhomogeneous_poisson_generator, nest::mip_generator, nest::noise_generator, nest::poisson_generator, nest::poisson_generator_ps, nest::ppd_sup_generator, nest::pulsepacket_generator, nest::sinusoidal_poisson_generator, nest::step_rate_generator, nest::spike_generator, and nest::step_current_generator.

◆ set_initialized_()

void nest::StimulationDevice::set_initialized_ ( )

finalprotectedvirtual

Reimplemented from nest::Node.

References backend_params_, nest::IOManager::enroll_stimulator(), nest::KernelManager::io_manager, nest::kernel(), P_, and nest::StimulationDevice::Parameters_::stimulus_source_.

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◆ set_status()

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

overridevirtual

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

Parameters

d	Dictionary with named parameter settings.

Implements nest::Node.

References backend_params_, Dictionary::clear(), nest::IOManager::enroll_stimulator(), nest::Node::get_node_id(), Dictionary::has_been_accessed(), nest::KernelManager::io_manager, nest::kernel(), P_, nest::StimulationDevice::Parameters_::set(), nest::Device::set_status(), and nest::StimulationDevice::Parameters_::stimulus_source_.

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◆ update()

void nest::StimulationDevice::update	(	Time const &	,
		const long	,
		const long
	)

inlineoverridevirtual

Advance the state of the node in time through the given interval.

This method advances the state of the node through the interval (origin+from, origin+to], which is at most min_delay long.

Precondition: State of the node corresponds to the time origin+from.
Postcondition: State of the node corresponds to the time origin+to.

Each step between from and to corresponds to one simulation timestep (nest.resolution).

If events are emitted, they have time stamps in the interval T+from+1 .. T+to.

Parameters

origin	network time at beginning of time slice
from	initial step inside time slice
to	post-final step inside time slice

Implements nest::Node.

Member Data Documentation

◆ backend_params_

Dictionary nest::StimulationDevice::backend_params_

private

Referenced by get_status(), set_initialized_(), and set_status().

◆ first_syn_id_

synindex nest::StimulationDevice::first_syn_id_

private

Synapse type of the first outgoing connection made by the Device.

Used to check that devices connect using only a single synapse type, see #481 and #737. Since this value must survive resets, it is stored here, even though it is an implementation detail.

Referenced by enforce_single_syn_type().

◆ P_

struct nest::StimulationDevice::Parameters_ nest::StimulationDevice::P_

protected

Referenced by get_label(), get_status(), set_initialized_(), and set_status().

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

	NEST main@caf0ae8

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ Type

Constructor & Destructor Documentation

◆ StimulationDevice() [1/2]

◆ StimulationDevice() [2/2]

◆ ~StimulationDevice()

Member Function Documentation

◆ enforce_single_syn_type()

◆ get_element_type()

◆ get_label()

◆ get_status()

◆ get_type()

◆ has_proxies()

◆ init_buffers()

◆ init_state()

◆ is_active()

◆ pre_run_hook() [1/3]

◆ pre_run_hook() [2/3]

◆ pre_run_hook() [3/3]

◆ set_data_from_stimulation_backend()

◆ set_initialized_()

◆ set_status()

◆ update()

Member Data Documentation

◆ backend_params_

◆ first_syn_id_

◆ P_