iaf_chs_2007.h

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/*
 *  iaf_chs_2007.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_CHS_2007_H
#define IAF_CHS_2007_H
 
// Includes from nestkernel:
#include "archiving_node.h"
#include "connection.h"
#include "event.h"
#include "nest_types.h"
#include "random_generators.h"
#include "recordables_map.h"
#include "ring_buffer.h"
#include "universal_data_logger.h"
 
namespace nest
{
 
/* BeginUserDocs: neuron, integrate-and-fire, hard threshold
 
Short description
+++++++++++++++++
 
Spike-response model used in Carandini et al. 2007
 
Description
+++++++++++
 
The membrane potential is the sum of stereotyped events: the postsynaptic
potentials (``V_syn``), waveforms that include a spike and the subsequent
after-hyperpolarization (``V_spike``) and Gaussian-distributed white noise.
 
The postsynaptic potential is described by alpha function where
``U_epsp`` is the maximal amplitude of the EPSP and ``tau_epsp`` is the time to
peak of the EPSP.
 
The spike waveform is described as a delta peak followed by a membrane
potential reset and exponential decay. ``U_reset`` is the magnitude of the
reset/after-hyperpolarization and ``tau_reset`` is the time constant of
recovery from this hyperpolarization.
 
The linear subthreshold dynamics is integrated by the Exact
Integration scheme :footcite:p:`Carandini2007`. The neuron dynamics is solved on the time
grid given by the computation step size. Incoming as well as emitted
spikes are forced to that grid.
 
.. note::
 
   The way the noise term was implemented in the original model makes
   it unsuitable for simulation in NEST. The workaround was to prepare
   the noise signal externally prior to simulation. The noise signal,
   if present, has to be at least as long as the simulation.
 
See also :footcite:p:`Rotter1999`.
 
Parameters
++++++++++
 
The following parameters can be set in the status dictionary.
 
========== ============== ==================================================
 tau_epsp  ms             Membrane time constant
 tau_reset ms             Refractory time constant
 U_epsp    real           Maximum amplitude of the EPSP, normalized
 U_reset   real           Reset value of the membrane potential, normalized
 U_noise   real           Noise scale, normalized
 noise     list of real   Noise signal
========== ============== ==================================================
 
References
++++++++++
 
.. footbibliography::
 
Sends
+++++
 
SpikeEvent
 
Receives
++++++++
 
SpikeEvent, DataLoggingRequest
 
Examples using this model
+++++++++++++++++++++++++
 
.. listexamples:: iaf_chs_2007
 
EndUserDocs */
 
void register_iaf_chs_2007( const std::string& name );
 
class iaf_chs_2007 : public ArchivingNode
{
 
public:
  iaf_chs_2007();
  iaf_chs_2007( const iaf_chs_2007& );
 
  using Node::handle;
  using Node::handles_test_event;
 
  size_t send_test_event( Node&, size_t, synindex, bool ) override;
 
  void handle( SpikeEvent& ) override;
  void handle( DataLoggingRequest& ) override;
 
  size_t handles_test_event( SpikeEvent&, size_t ) override;
  size_t handles_test_event( DataLoggingRequest&, size_t ) override;
 
  void get_status( Dictionary& ) const override;
  void set_status( const Dictionary& ) override;
 
private:
  void init_buffers_() override;
  void pre_run_hook() override;
 
  void update( const Time&, const long, const long ) override;
 
  // The next two classes need to be friends to access the State_ class/member
  friend class RecordablesMap< iaf_chs_2007 >;
  friend class UniversalDataLogger< iaf_chs_2007 >;
 
  // ----------------------------------------------------------------
 
  struct State_
  {
    // state variables
    double i_syn_ex_;  // postsynaptic current for exc. inputs, variable 1
    double V_syn_;     // psp waveform, variable 2
    double V_spike_;   // post spike reset waveform, variable 3
    double V_m_;       // membrane potential, variable 4
 
    unsigned long position_;
 
    State_();  
 
    void get( Dictionary& ) const;
    void set( Dictionary const&, Node* );
  };
 
  // ----------------------------------------------------------------
 
  struct Parameters_
  {
    double tau_epsp_;
 
    double tau_reset_;
 
    double E_L_;
 
    double U_th_;
 
    double U_epsp_;
 
    double U_reset_;
 
    double C_;
 
    double U_noise_;
 
    std::vector< double > noise_;
 
    Parameters_();  
 
    void get( Dictionary& ) const;  
 
    void set( const Dictionary&, State_& s, Node* node );
  };
 
 
  // ----------------------------------------------------------------
 
  struct Buffers_
  {
    Buffers_( iaf_chs_2007& );
    Buffers_( const Buffers_&, iaf_chs_2007& );
 
    RingBuffer spikes_ex_;
    RingBuffer currents_;
 
    UniversalDataLogger< iaf_chs_2007 > logger_;
  };
 
  // ----------------------------------------------------------------
 
  struct Variables_
  {
    //    double PSCInitialValue_;
 
    // time evolution operator
    double P20_;
    double P11ex_;
    double P21ex_;
    double P22_;
    double P30_;
 
    normal_distribution normal_dist_;  
  };
 
  // Access functions for UniversalDataLogger -------------------------------
 
  double
  get_V_m_() const
  {
    return S_.V_m_ + P_.E_L_;
  }
 
  // ----------------------------------------------------------------
 
  Parameters_ P_;
  State_ S_;
  Variables_ V_;
  Buffers_ B_;
  static RecordablesMap< iaf_chs_2007 > recordablesMap_;
};
 
inline size_t
iaf_chs_2007::send_test_event( Node& target, size_t receptor_type, synindex, bool )
{
  SpikeEvent e;
  e.set_sender( *this );
 
  return target.handles_test_event( e, receptor_type );
}
 
inline size_t
iaf_chs_2007::handles_test_event( SpikeEvent&, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return 0;
}
 
inline size_t
iaf_chs_2007::handles_test_event( DataLoggingRequest& dlr, size_t receptor_type )
{
  if ( receptor_type != 0 )
  {
    throw UnknownReceptorType( receptor_type, get_name() );
  }
  return B_.logger_.connect_logging_device( dlr, recordablesMap_ );
}
 
inline void
iaf_chs_2007::get_status( Dictionary& d ) const
{
  P_.get( d );
  S_.get( d );
  ArchivingNode::get_status( d );
 
  d[ names::recordables ] = recordablesMap_.get_list();
}
 
inline void
iaf_chs_2007::set_status( const Dictionary& d )
{
  Parameters_ ptmp = P_;  // temporary copy in case of errors
  ptmp.set( d, S_, this );
  State_ stmp = S_;     // temporary copy in case of errors
  stmp.set( d, this );  // 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.
  ArchivingNode::set_status( d );
 
  // if we get here, temporaries contain consistent set of properties
  P_ = ptmp;
  S_ = stmp;
}
 
}  // namespace
 
#endif  // IAF_CHS_2007_H