hh_psc_alpha.h

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/*
 *  hh_psc_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 HH_PSC_ALPHA_H
#define HH_PSC_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>
#include <gsl/gsl_sf_exp.h>

namespace nest{

  using std::vector;

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

 /* BeginDocumentation
Name: hh_psc_alpha - Hodgkin Huxley neuron model.

Description:

  hh_psc_alpha is an implementation of a spiking neuron using the Hodkin-Huxley formalism.
  
  (1) Post-syaptic currents 
  Incoming spike events induce a post-synaptic change of current 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 pA. 


  (2) Spike Detection
  Spike detection is done by a combined threshold-and-local-maximum search: if there 
  is a local maximum above a certain threshold of the membrane potential, it is considered a spike.

Parameters: 

  The following parameters can be set in the status dictionary.

  V_m        double - Membrane potential in mV 
  E_L        double - Resting membrane potential in mV. 
  g_L        double - Leak conductance in nS.
  C_m        double - Capacity of the membrane in pF.
  tau_ex     double - Rise time of the excitatory synaptic alpha function in ms.
  tau_in     double - Rise time of the inhibitory synaptic alpha function in ms.
  E_Na       double - Sodium reversal potential in mV.
  g_Na       double - Sodium peak conductance in nS.
  E_K        double - Potassium reversal potential in mV.
  g_K        double - Potassium peak conductance in nS.
  Act_m      double - Activation variable m
  Act_h      double - Activation variable h
  Inact_n    double - Inactivation variable n
  I_e        double - Constant external input current in pA.

Problems/Todo:

  better spike detection
  initial wavelet/spike at simulation onset
  
References:
  
  Spiking Neuron Models: 
  Single Neurons, Populations, Plasticity   
  Wulfram Gerstner, Werner Kistler,  Cambridge University Press 

  Theoretical Neuroscience: 
  Computational and Mathematical Modeling of Neural Systems
  Peter Dayan, L. F. Abbott, MIT Press (parameters taken from here)

  Hodgkin, A. L. and Huxley, A. F., 
  A Quantitative Description of Membrane Current 
  and Its Application to Conduction and Excitation in Nerve, 
  Journal of Physiology, 117, 500-544 (1952)

Sends: SpikeEvent

Receives: SpikeEvent, CurrentEvent, DataLoggingRequest

Authors: Schrader
SeeAlso: hh_cond_exp_traub
*/
  
  class hh_psc_alpha:
    public Archiving_Node
  {
    
  public:        
    
    hh_psc_alpha();
    hh_psc_alpha(const hh_psc_alpha&);
    ~hh_psc_alpha();

    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);

    double_t get_potential(Time const &) const;

    void set_potential(Time const &, double_t);
    
    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 hh_psc_alpha_dynamics(double, const double*, double*, void*);

    // The next two classes need to be friend to access the State_ class/member
    friend class RecordablesMap<hh_psc_alpha>;
    friend class UniversalDataLogger<hh_psc_alpha>;

  private:

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

    struct Parameters_ {
      double_t t_ref_;    
      double_t g_Na;            
      double_t g_K;             
      double_t g_L;       
      double_t C_m;       
      double_t E_Na;            
      double_t E_K;         
      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&);  
    };
      
  public:
    // ---------------------------------------------------------------- 

    struct State_ {
  
      enum StateVecElems
    {
      V_M   = 0,
      HH_M     ,  // 1
      HH_H     ,  // 2
      HH_N     ,  // 3
      DI_EXC   ,  // 4
      I_EXC    ,  // 5
      DI_INH   ,  // 6
      I_INH    ,  // 7
      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&);
    };    

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

  private:
    struct Buffers_ {
      Buffers_(hh_psc_alpha&);                   
      Buffers_(const Buffers_&, hh_psc_alpha&);  

      UniversalDataLogger<hh_psc_alpha> 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_t I_stim_;
    };

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

     struct Variables_ { 
      double_t PSCurrInit_E_; 
   
      double_t PSCurrInit_I_;    

      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<hh_psc_alpha> recordablesMap_;
  };

 
inline
port hh_psc_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 hh_psc_alpha::handles_test_event(SpikeEvent&, rport receptor_type)
{
  if (receptor_type != 0)
    throw UnknownReceptorType(receptor_type, get_name());
  return 0;
}

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

inline
port hh_psc_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 hh_psc_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 hh_psc_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);                 // 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 //HH_PSC_ALPHA_H