/***************************************************************************
* TimeDrivenPurkinjeCell.h *
* ------------------- *
* copyright : (C) 2015 by Richard Carrill, Niceto Luque and *
Francisco Naveros *
* email : rcarrillo@ugr.es, nluque@ugr.es and *
fnaveros@atc.ugr.es *
***************************************************************************/
/***************************************************************************
* *
* This program 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 3 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************/
#ifndef TIMEDRIVENPURKINJECELL_H_
#define TIMEDRIVENPURKINJECELL_H_
/*!
* \file TimeDrivenPurkinjeCell.h
*
* \author Richard Carrillo
* \author Niceto Luque
* \author Francisco Naveros
* \date May 2015
*
* This file declares a class which implement a Purkinje cell model.
*/
#include "./TimeDrivenNeuronModel.h"
#include <string>
using namespace std;
class InputSpike;
class VectorNeuronState;
class Interconnection;
/*!
* \class TimeDrivenPurkinjeCell.h
*
* \brief Time driven neuron model with a membrane potential, five currents and two conductances.
*
* \author Richard Carrillo
* \author Niceto Luque
* \author Francisco Naveros
* \date May 2015
*/
class TimeDrivenPurkinjeCell : public TimeDrivenNeuronModel {
protected:
static float * alpha_ca_table;
static float * beta_ca_table;
static float * alpha_M_table;
static float * beta_M_table;
static const float Max_V;
static const float Min_V;
static const int TableSize=1024*1024;
static const float aux;
/*!
* \brief leak current
*/
const float g_L;
/*!
* \brief high-threshold noninactivating calcium current
*/
const float g_Ca;
/*!
* \brief muscarinic receptor suppressed potassium current (or M current)
*/
const float g_M;
/*!
* \brief Cylinder length of the soma (cm)
*/
const float Cylinder_length_of_the_soma;
/*!
* \brief Radius of the soma (cm)
*/
const float Radius_of_the_soma;
/*!
* \brief Cell area (cm^2)
*/
const float Area;
const float inv_Area;
/*!
* \brief Membrane capacitance(uF/cm^2)
*/
const float Membrane_capacitance;
const float inv_Membrane_capacitance;
/*!
* \brief Excitatory reversal potential (mV)
*/
float eexc;
/*!
* \brief Inhibitory reversal potential (mV)
*/
float einh;
/*!
* \brief Firing threshold (mV)
*/
float vthr;
/*!
* \brief Resting potential (mV)
*/
float erest;
/*!
* \brief AMPA receptor time constant (ms)
*/
float texc;
float inv_texc;
/*!
* \brief GABA receptor time constant (ms)
*/
float tinh;
float inv_tinh;
/*!
* \brief Refractory period (ms)
*/
float tref;
float tref_0_5;
float inv_tref_0_5;
/*!
* \brief Peak amplitude (mV)
*/
float spkpeak;
/*!
* \brief It loads the neuron model description.
*
* It loads the neuron type description from the file .cfg.
*
* \param ConfigFile Name of the neuron description file (*.cfg).
*
* \throw EDLUTFileException If something wrong has happened in the file load.
*/
void LoadNeuronModel(string ConfigFile) throw (EDLUTFileException);
/*!
* \brief It abstracts the effect of an input spike in the cell.
*
* It abstracts the effect of an input spike in the cell.
*
* \param index The cell index inside the VectorNeuronState.
* \param State Cell current state.
* \param InputConnection Input connection from which the input spike has got the cell.
*/
void SynapsisEffect(int index, Interconnection * InputConnection);
public:
/*!
* \brief Number of state variables for each cell.
*/
static const int N_NeuronStateVariables=6;
/*!
* \brief Number of state variables witch are calculate with a differential equation for each cell (V, ca and M).
*/
static const int N_DifferentialNeuronState=3;
/*!
* \brief Number of state variables witch are calculate with a time dependent equation for each cell (g_exc and g_inh).
*/
static const int N_TimeDependentNeuronState=3;
/*!
* \brief Default constructor with parameters.
*
* It generates a new neuron model object without being initialized.
*
* \param NeuronTypeID Neuron model identificator.
* \param NeuronModelID Neuron model configuration file.
*/
TimeDrivenPurkinjeCell(string NeuronTypeID, string NeuronModelID);
/*!
* \brief Class destructor.
*
* It destroys an object of this class.
*/
virtual ~TimeDrivenPurkinjeCell();
/*!
* \brief It loads the neuron model description and tables (if necessary).
*
* It loads the neuron model description and tables (if necessary).
*
* \throw EDLUTFileException If something wrong has happened in the file load.
*/
virtual void LoadNeuronModel() throw (EDLUTFileException);
/*!
* \brief It return the Neuron Model VectorNeuronState
*
* It return the Neuron Model VectorNeuronState
*
*/
virtual VectorNeuronState * InitializeState();
/*!
* \brief It processes a propagated spike (input spike in the cell).
*
* It processes a propagated spike (input spike in the cell).
*
* \note This function doesn't generate the next propagated spike. It must be externally done.
*
* \param inter the interconection which propagate the spike
* \param target the neuron which receives the spike
* \param time the time of the spike.
*
* \return A new internal spike if someone is predicted. 0 if none is predicted.
*/
virtual InternalSpike * ProcessInputSpike(Interconnection * inter, Neuron * target, double time);
/*!
* \brief Update the neuron state variables.
*
* It updates the neuron state variables.
*
* \param index The cell index inside the VectorNeuronState. if index=-1, updating all cell.
* \param The current neuron state.
* \param CurrentTime Current time.
*
* \return True if an output spike have been fired. False in other case.
*/
virtual bool UpdateState(int index, VectorNeuronState * State, double CurrentTime);
/*!
* \brief It prints the time-driven model info.
*
* It prints the current time-driven model characteristics.
*
* \param out The stream where it prints the information.
*
* \return The stream after the printer.
*/
virtual ostream & PrintInfo(ostream & out);
/*!
* \brief It initialice VectorNeuronState.
*
* It initialice VectorNeuronState.
*
* \param N_neurons cell number inside the VectorNeuronState.
*/
virtual void InitializeStates(int N_neurons, int OpenMPQueueIndex);
/*!
* \brief It evaluates the differential equation in NeuronState and it stores the results in AuxNeuronState.
*
* It evaluates the differential equation in NeuronState and it stores the results in AuxNeuronState.
*
* \param NeuronState value of the neuron state variables where differential equations are evaluated.
* \param AuxNeuronState results of the differential equations evaluation.
*/
virtual void EvaluateDifferentialEcuation(float * NeuronState, float * AuxNeuronState);
/*!
* \brief It evaluates the time depedendent ecuation in NeuronState for elapsed_time and it stores the results in NeuronState.
*
* It evaluates the time depedendent ecuation in NeuronState for elapsed_time and it stores the results in NeuronState.
*
* \param NeuronState value of the neuron state variables where time dependent equations are evaluated.
* \param elapsed_time integration time step.
*/
virtual void EvaluateTimeDependentEcuation(float * NeuronState, float elapsed_time);
/*!
* \brief It Checks if the neuron model has this connection type.
*
* It Checks if the neuron model has this connection type.
*
* \param Type input connection type.
*
* \return A a valid connection type for this neuron model.
*/
virtual int CheckSynapseTypeNumber(int Type);
static float * Generate_alpha_ca_table(){
float * NewLookUpTable=new float[TableSize];
for(int i=0; i<TableSize; i++){
float V = Min_V + ((Max_V-Min_V)*i)/(TableSize-1);
NewLookUpTable[i]=1.6f/(1+exp(-0.072f*(V-5.0f)));;
}
return NewLookUpTable;
}
static float * Generate_beta_ca_table(){
float * NewLookUpTable=new float[TableSize];
for(int i=0; i<TableSize; i++){
float V = Min_V + ((Max_V-Min_V)*i)/(TableSize-1);
NewLookUpTable[i]=(0.02f*(V+8.9f))/(exp((V+8.9f)*0.2f)-1.0f);
}
return NewLookUpTable;
}
static float * Generate_alpha_M_table(){
float * NewLookUpTable=new float[TableSize];
for(int i=0; i<TableSize; i++){
float V = Min_V + ((Max_V-Min_V)*i)/(TableSize-1);
NewLookUpTable[i]=0.3f/(1+exp((-V-2.0f)*0.2f));
}
return NewLookUpTable;
}
static float * Generate_beta_M_table(){
float * NewLookUpTable=new float[TableSize];
for(int i=0; i<TableSize; i++){
float V = Min_V + ((Max_V-Min_V)*i)/(TableSize-1);
NewLookUpTable[i]=0.001f*exp((-V-60.0f)*0.055555555555555f);
}
return NewLookUpTable;
}
static void Get_alpha_and_beta_values(float value, float * alpha_ca, float * beta_ca, float * alpha_M, float * beta_M){
int position=int((value-Min_V)*aux);
*alpha_ca=alpha_ca_table[position];
*beta_ca=beta_ca_table[position];
*alpha_M=alpha_M_table[position];
*beta_M=beta_M_table[position];
}
};
#endif /* TIMEDRIVENPURKINJECELL_H_ */