/*
* iaf_cond_alpha.h
*
* This file is part of NEST.
*
* Copyright (C) 2004 The NEST Initiative
*
* NEST is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 2 of the License, or
* (at your option) any later version.
*
* NEST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with NEST. If not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef IAF_COND_ALPHA_H
#define IAF_COND_ALPHA_H
#include "config.h"
#ifdef HAVE_GSL
#include "nest.h"
#include "event.h"
#include "archiving_node.h"
#include "ring_buffer.h"
#include "connection.h"
#include "universal_data_logger.h"
#include "recordables_map.h"
#include <gsl/gsl_errno.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_odeiv.h>
/* BeginDocumentation
Name: iaf_cond_alpha - Simple conductance based leaky integrate-and-fire neuron model.
Description:
iaf_cond_alpha is an implementation of a spiking neuron using IAF dynamics with
conductance-based synapses. Incoming spike events induce a post-synaptic change
of conductance modelled by an alpha function. The alpha function
is normalised such that an event of weight 1.0 results in a peak current of 1 nS
at t = tau_syn.
Parameters:
The following parameters can be set in the status dictionary.
V_m double - Membrane potential in mV
E_L double - Leak reversal potential in mV.
C_m double - Capacity of the membrane in pF
t_ref double - Duration of refractory period in ms.
V_th double - Spike threshold in mV.
V_reset double - Reset potential of the membrane in mV.
E_ex double - Excitatory reversal potential in mV.
E_in double - Inhibitory reversal potential in mV.
g_L double - Leak conductance in nS;
tau_syn_ex double - Rise time of the excitatory synaptic alpha function in ms.
tau_syn_in double - Rise time of the inhibitory synaptic alpha function in ms.
I_e double - Constant input current in pA.
Sends: SpikeEvent
Receives: SpikeEvent, CurrentEvent, DataLoggingRequest
References:
Meffin, H., Burkitt, A. N., & Grayden, D. B. (2004). An analytical
model for the large, fluctuating synaptic conductance state typical of
neocortical neurons in vivo. J. Comput. Neurosci., 16, 159–175.
Bernander, O ., Douglas, R. J., Martin, K. A. C., & Koch, C. (1991).
Synaptic background activity influences spatiotemporal integration in
single pyramidal cells. Proc. Natl. Acad. Sci. USA, 88(24),
11569–11573.
Kuhn, Aertsen, Rotter (2004) Neuronal Integration of Synaptic Input in
the Fluctuation- Driven Regime. Jneurosci 24(10) 2345-2356
Author: Schrader, Plesser
SeeAlso: iaf_cond_exp, iaf_cond_alpha_mc
*/
namespace nest
{
/**
* Function computing right-hand side of ODE for GSL solver.
* @note Must be declared here so we can befriend it in class.
* @note Must have C-linkage for passing to GSL. Internally, it is
* a first-class C++ function, but cannot be a member function
* because of the C-linkage.
* @note No point in declaring it inline, since it is called
* through a function pointer.
* @param void* Pointer to model neuron instance.
*/
extern "C"
int iaf_cond_alpha_dynamics (double, const double*, double*, void*);
/**
* Integrate-and-fire neuron model with two conductance-based synapses.
*
* @note Per 2009-04-17, this class has been revised to our newest
* insights into class design. Please use THIS CLASS as a reference
* when designing your own models with nonlinear dynamics.
* One weakness of this class is that it distinguishes between
* inputs to the two synapses by the sign of the synaptic weight.
* It would be better to use receptor_types, cf iaf_cond_alpha_mc.
*/
class iaf_cond_alpha : public Archiving_Node
{
// Boilerplate function declarations --------------------------------
public:
iaf_cond_alpha();
iaf_cond_alpha(const iaf_cond_alpha&);
~iaf_cond_alpha();
/*
* Import all overloaded virtual functions that we
* override in this class. For background information,
* see http://www.gotw.ca/gotw/005.htm.
*/
using Node::connect_sender;
using Node::handle;
port check_connection(Connection&, port);
port connect_sender(SpikeEvent &, port);
port connect_sender(CurrentEvent &, port);
port connect_sender(DataLoggingRequest &, port);
void handle(SpikeEvent &);
void handle(CurrentEvent &);
void handle(DataLoggingRequest &);
void get_status(DictionaryDatum &) const;
void set_status(const DictionaryDatum &);
private:
void init_state_(const Node& proto);
void init_buffers_();
void calibrate();
void update(Time const &, const long_t, const long_t);
// END Boilerplate function declarations ----------------------------
// Friends --------------------------------------------------------
// make dynamics function quasi-member
friend int iaf_cond_alpha_dynamics(double, const double*, double*, void*);
// The next two classes need to be friends to access the State_ class/member
friend class RecordablesMap<iaf_cond_alpha>;
friend class UniversalDataLogger<iaf_cond_alpha>;
private:
// Parameters class -------------------------------------------------
//! Model parameters
struct Parameters_ {
double_t V_th; //!< Threshold Potential in mV
double_t V_reset; //!< Reset Potential in mV
double_t t_ref; //!< Refractory period in ms
double_t g_L; //!< Leak Conductance in nS
double_t C_m; //!< Membrane Capacitance in pF
double_t E_ex; //!< Excitatory reversal Potential in mV
double_t E_in; //!< Inhibitory reversal Potential in mV
double_t E_L; //!< Leak reversal Potential (aka resting potential) in mV
double_t tau_synE; //!< Synaptic Time Constant Excitatory Synapse in ms
double_t tau_synI; //!< Synaptic Time Constant for Inhibitory Synapse in ms
double_t I_e; //!< Constant Current in pA
Parameters_(); //!< Set default parameter values
void get(DictionaryDatum&) const; //!< Store current values in dictionary
void set(const DictionaryDatum&); //!< Set values from dicitonary
};
// State variables class --------------------------------------------
/**
* State variables of the model.
*
* State variables consist of the state vector for the subthreshold
* dynamics and the refractory count. The state vector must be a
* C-style array to be compatible with GSL ODE solvers.
*
* @note Copy constructor and assignment operator are required because
* of the C-style array.
*/
public:
struct State_ {
//! Symbolic indices to the elements of the state vector y
enum StateVecElems { V_M = 0,
DG_EXC, G_EXC,
DG_INH, G_INH,
STATE_VEC_SIZE };
//! state vector, must be C-array for GSL solver
double_t y[STATE_VEC_SIZE];
//!< number of refractory steps remaining
int_t r;
State_(const Parameters_&); //!< Default initialization
State_(const State_&);
State_& operator=(const State_&);
void get(DictionaryDatum&) const; //!< Store current values in dictionary
/**
* Set state from values in dictionary.
* Requires Parameters_ as argument to, eg, check bounds.'
*/
void set(const DictionaryDatum&, const Parameters_&);
};
private:
// Buffers class --------------------------------------------------------
/**
* Buffers of the model.
* Buffers are on par with state variables in terms of persistence,
* i.e., initalized only upon first Simulate call after ResetKernel
* or ResetNetwork, but are implementation details hidden from the user.
*/
struct Buffers_ {
Buffers_(iaf_cond_alpha&); //!<Sets buffer pointers to 0
Buffers_(const Buffers_&, iaf_cond_alpha&); //!<Sets buffer pointers to 0
//! Logger for all analog data
UniversalDataLogger<iaf_cond_alpha> logger_;
/** buffers and sums up incoming spikes/currents */
RingBuffer spike_exc_;
RingBuffer spike_inh_;
RingBuffer currents_;
/* GSL ODE stuff */
gsl_odeiv_step* s_; //!< stepping function
gsl_odeiv_control* c_; //!< adaptive stepsize control function
gsl_odeiv_evolve* e_; //!< evolution function
gsl_odeiv_system sys_; //!< struct describing system
// IntergrationStep_ should be reset with the neuron on ResetNetwork,
// but remain unchanged during calibration. Since it is initialized with
// step_, and the resolution cannot change after nodes have been created,
// it is safe to place both here.
double_t step_; //!< step size in ms
double IntegrationStep_;//!< current integration time step, updated by GSL
/**
* Input current injected by CurrentEvent.
* This variable is used to transport the current applied into the
* _dynamics function computing the derivative of the state vector.
* It must be a part of Buffers_, since it is initialized once before
* the first simulation, but not modified before later Simulate calls.
*/
double_t I_stim_;
};
// Variables class -------------------------------------------------------
/**
* Internal variables of the model.
* Variables are re-initialized upon each call to Simulate.
*/
struct Variables_ {
/**
* Impulse to add to DG_EXC on spike arrival to evoke unit-amplitude
* conductance excursion.
*/
double_t PSConInit_E;
/**
* Impulse to add to DG_INH on spike arrival to evoke unit-amplitude
* conductance excursion.
*/
double_t PSConInit_I;
//! refractory time in steps
int_t RefractoryCounts;
};
// Access functions for UniversalDataLogger -------------------------------
//! Read out state vector elements, used by UniversalDataLogger
template <State_::StateVecElems elem>
double_t get_y_elem_() const { return S_.y[elem]; }
//! Read out remaining refractory time, used by UniversalDataLogger
double_t get_r_() const { return Time::get_resolution().get_ms() * S_.r; }
// Data members -----------------------------------------------------------
// keep the order of these lines, seems to give best performance
Parameters_ P_;
State_ S_;
Variables_ V_;
Buffers_ B_;
//! Mapping of recordables names to access functions
static RecordablesMap<iaf_cond_alpha> recordablesMap_;
};
// Boilerplate inline function definitions ----------------------------------
inline
port iaf_cond_alpha::check_connection(Connection& c, port receptor_type)
{
SpikeEvent e;
e.set_sender(*this);
c.check_event(e);
return c.get_target()->connect_sender(e, receptor_type);
}
inline
port iaf_cond_alpha::connect_sender(SpikeEvent&, port receptor_type)
{
if (receptor_type != 0)
throw UnknownReceptorType(receptor_type, get_name());
return 0;
}
inline
port iaf_cond_alpha::connect_sender(CurrentEvent&, port receptor_type)
{
if (receptor_type != 0)
throw UnknownReceptorType(receptor_type, get_name());
return 0;
}
inline
port iaf_cond_alpha::connect_sender(DataLoggingRequest& dlr,
port receptor_type)
{
if (receptor_type != 0)
throw UnknownReceptorType(receptor_type, get_name());
return B_.logger_.connect_logging_device(dlr, recordablesMap_);
}
inline
void iaf_cond_alpha::get_status(DictionaryDatum &d) const
{
P_.get(d);
S_.get(d);
Archiving_Node::get_status(d);
(*d)[names::recordables] = recordablesMap_.get_list();
}
inline
void iaf_cond_alpha::set_status(const DictionaryDatum &d)
{
Parameters_ ptmp = P_; // temporary copy in case of errors
ptmp.set(d); // throws if BadProperty
State_ stmp = S_; // temporary copy in case of errors
stmp.set(d, ptmp); // throws if BadProperty
// We now know that (ptmp, stmp) are consistent. We do not
// write them back to (P_, S_) before we are also sure that
// the properties to be set in the parent class are internally
// consistent.
Archiving_Node::set_status(d);
// if we get here, temporaries contain consistent set of properties
P_ = ptmp;
S_ = stmp;
}
} // namespace
#endif //IAF_COND_ALPHA_H
#endif //HAVE_GSL