iaf_cond_exp_sfa_rr.h

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/*
 *  iaf_cond_exp_sfa_rr.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_EXP_SFA_RR_H
#define IAF_COND_EXP_SFA_RR_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_exp_sfa_rr - Simple conductance based leaky integrate-and-fire neuron model.

Description:
iaf_cond_exp_sfa_rr is an iaf_cond_exp_sfa_rr i.e. an implementation of a
spiking neuron using IAF dynamics with conductance-based synapses,
with additional spike-frequency adaptation and relative refractory
mechanisms as described in Dayan+Abbott, 2001, page 166.

As for the iaf_cond_exp_sfa_rr, Incoming spike events induce a post-synaptic
change  of  conductance  modelled  by an  exponential  function.  The
exponential function is  normalised such that an event  of weight 1.0
results in a peak current of 1 nS.

Outgoing spike events induce a change of the adaptation and relative
refractory conductances by q_sfa and q_rr, respectively.  Otherwise
these conductances decay exponentially with time constants tau_sfa
and tau_rr, respectively.

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 - Time constant of the excitatory synaptic exponential function in ms.
tau_syn_in double - Time constant of the inhibitory synaptic exponential function in ms.
q_sfa      double - Outgoing spike activated quantal spike-frequency adaptation conductance increase in nS.
q_rr       double - Outgoing spike activated quantal relative refractory conductance increase in nS.
tau_sfa    double - Time constant of spike-frequency adaptation in ms.
tau_rr     double - Time constant of the relative refractory mechanism in ms.
E_sfa      double - spike-frequency adaptation conductance reversal potential in mV.
E_rr       double - relative refractory mechanism conductance reversal potential in mV.
I_e        double - an external stimulus 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.

Dayan, P. and Abbott, L. F. (2001). Theoretical Neuroscience, MIT
Press (p166)

Author: Sven Schrader, Eilif Muller

SeeAlso: iaf_cond_exp_sfa_rr, aeif_cond_alpha, iaf_psc_delta, iaf_psc_exp, iaf_cond_alpha
*/

namespace nest {

  using std::vector;

  extern "C"
  int iaf_cond_exp_sfa_rr_dynamics(double, const double*, double*, void*);

  class iaf_cond_exp_sfa_rr: public Archiving_Node
  {
    
  public:
    
    iaf_cond_exp_sfa_rr();
    iaf_cond_exp_sfa_rr(const iaf_cond_exp_sfa_rr&);
    ~iaf_cond_exp_sfa_rr();

   using Node::handle;
    using Node::handles_test_event;

    port send_test_event(Node&, rport, synindex, bool);
    
    void handle(SpikeEvent &);
    void handle(CurrentEvent &);
    void handle(DataLoggingRequest &); 
    
    port handles_test_event(SpikeEvent&, rport);
    port handles_test_event(CurrentEvent&, rport);
    port handles_test_event(DataLoggingRequest &, rport);
    
    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_exp_sfa_rr_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_exp_sfa_rr>;
    friend class UniversalDataLogger<iaf_cond_exp_sfa_rr>;

  private:

    // ---------------------------------------------------------------- 

    struct Parameters_ {
      double_t V_th_;       
      double_t V_reset_;    
      double_t t_ref_;      
      double_t g_L;         
      double_t C_m;         
      double_t E_ex;        
      double_t E_in;        
      double_t E_L;         
      double_t tau_synE;    
      double_t tau_synI;    
      double_t I_e;         
      double_t tau_sfa;     
      double_t tau_rr;      
      double_t E_sfa;       
      double_t E_rr;        
      double_t q_sfa;       
      double_t q_rr;        
  
      Parameters_();  

      void get(DictionaryDatum&) const;  
      void set(const DictionaryDatum&);  
    };

  public:
    // ---------------------------------------------------------------- 

    struct State_ {

      enum StateVecElems
    {
      V_M  = 0,           
      G_EXC,     
      G_INH,
      G_SFA,
      G_RR,
      STATE_VEC_SIZE
    };

      double_t y_[STATE_VEC_SIZE];  
      int_t    r_;     

      State_(const Parameters_&);  
      State_(const State_&);
      State_& operator=(const State_&);

      void get(DictionaryDatum&) const;
      void set(const DictionaryDatum&, const Parameters_&);
    };    

  private:
    // ---------------------------------------------------------------- 

    struct Buffers_ {
      Buffers_(iaf_cond_exp_sfa_rr&);                   
      Buffers_(const Buffers_&, iaf_cond_exp_sfa_rr&);  

      UniversalDataLogger<iaf_cond_exp_sfa_rr> logger_;

      RingBuffer spike_exc_;
      RingBuffer spike_inh_;
      RingBuffer currents_;

      gsl_odeiv_step*    s_;    
      gsl_odeiv_control* c_;    
      gsl_odeiv_evolve*  e_;    
      gsl_odeiv_system   sys_;  
      
      // 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_;           
      double   IntegrationStep_;

      double I_stim_;
    };

     // ---------------------------------------------------------------- 

     struct Variables_ { 
      int_t    RefractoryCounts_;
     };

    // Access functions for UniversalDataLogger -------------------------------
    
    template <State_::StateVecElems elem>
    double_t get_y_elem_() const { return S_.y_[elem]; }

    // ---------------------------------------------------------------- 

    Parameters_ P_;
    State_      S_;
    Variables_  V_;
    Buffers_    B_;

    static RecordablesMap<iaf_cond_exp_sfa_rr> recordablesMap_;
  };

  
  inline
port nest::iaf_cond_exp_sfa_rr::send_test_event(Node& target, rport receptor_type, synindex, bool)
{
  SpikeEvent e;
  e.set_sender(*this);
  return target.handles_test_event(e, receptor_type);
}
  
inline
port iaf_cond_exp_sfa_rr::handles_test_event(SpikeEvent&, rport receptor_type)
{
  if (receptor_type != 0)
    throw UnknownReceptorType(receptor_type, get_name());
  return 0;
}
 
inline
port iaf_cond_exp_sfa_rr::handles_test_event(CurrentEvent&, rport receptor_type)
{
  if (receptor_type != 0)
    throw UnknownReceptorType(receptor_type, get_name());
  return 0;
}
 
inline
port iaf_cond_exp_sfa_rr::handles_test_event(DataLoggingRequest& dlr, 
                       rport receptor_type)
{
  if (receptor_type != 0)
    throw UnknownReceptorType(receptor_type, get_name());
  return B_.logger_.connect_logging_device(dlr, recordablesMap_);
}

 
  inline
  void iaf_cond_exp_sfa_rr::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_exp_sfa_rr::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 //HAVE_GSL
#endif //IAF_COND_EXP_SFA_RR_H