iaf_cond_alpha.h

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/*
 *  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
{
  extern "C"
  int iaf_cond_alpha_dynamics (double, const double*, double*, void*);

  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::handle;
    using Node::handles_test_event;

    port send_test_event(Node& tagret, rport receptor_type, synindex, bool);
    
    port handles_test_event(SpikeEvent&, rport);
    port handles_test_event(CurrentEvent&, rport);
    port handles_test_event(DataLoggingRequest &, rport);

    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 ------------------------------------------------- 

    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;         
  
      Parameters_();        

      void get(DictionaryDatum&) const;  
      void set(const DictionaryDatum&);  
    };
    
    // State variables class -------------------------------------------- 

  public:
    struct State_ {
      
      enum StateVecElems { V_M = 0,           
               DG_EXC, G_EXC,     
               DG_INH, G_INH,
               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:

    // Buffers class -------------------------------------------------------- 

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

      UniversalDataLogger<iaf_cond_alpha> logger_;

      RingBuffer spike_exc_;
      RingBuffer spike_inh_;
      RingBuffer currents_;

      /* GSL ODE stuff */
      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_t I_stim_;
    };
    
    // Variables class ------------------------------------------------------- 
    
    struct Variables_ { 
      double_t PSConInit_E; 
      
      double_t PSConInit_I;    
      
      int_t    RefractoryCounts;
    };
    
    // Access functions for UniversalDataLogger -------------------------------
    
    template <State_::StateVecElems elem>
    double_t get_y_elem_() const { return S_.y[elem]; }
    
    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_;

    static RecordablesMap<iaf_cond_alpha> recordablesMap_;
  };
  

  // Boilerplate inline function definitions ----------------------------------

  inline
port iaf_cond_alpha::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_alpha::handles_test_event(SpikeEvent&, rport receptor_type)
{
  if (receptor_type != 0)
    throw UnknownReceptorType(receptor_type, get_name());
  return 0;
}
 
inline
port iaf_cond_alpha::handles_test_event(CurrentEvent&, rport receptor_type)
{
  if (receptor_type != 0)
    throw UnknownReceptorType(receptor_type, get_name());
  return 0;
}
 
inline
port iaf_cond_alpha::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_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