IzhiNeuron.cpp

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#include "IzhiNeuron.h"

#include <cmath>
#include <iostream>
using std::cout;
using std::endl;


// IzhiNeuronBase

ThreadSpecificRandomDistribution< NormalDistribution > IzhiNeuronBase::white_noise;


IzhiNeuronBase::IzhiNeuronBase(double a, double b, double c, double d, double Vpeak,
                               double Vinit, double Inoise, double Iinject, double factI)
    : Vpeak(Vpeak), Vinit(Vinit), Inoise(Inoise), Iinject(Iinject)
    , a(a), b(b), c(c), d(d), u(0.2*Vinit), Isyn(0.0)
    , factI(factI)
{
}

IzhiNeuronBase::IzhiNeuronBase(string type, double Vinit,
                               double Inoise, double Iinject, double factI)
    : Vinit(Vinit), Inoise(Inoise), Iinject(Iinject), u(0.2*Vinit), Isyn(0.0)
    , factI(factI)
{
    Vpeak = 35.0;

    // regular spiking
    a=0.02; b=0.2; c=-65.0; d=8.0;

    if(type=="IB"){                     // intrinsically bursting
        a=0.02; b=0.2; c=-55.0; d=4.0;
    }
    else if(type=="CH"){                // chattering
        a=0.02; b=0.2; c=-50.0; d=2.0;
    }
    else if(type=="LTS"){               // low threshold spiking
        a=0.02; b=0.25; c=-65.0; d=2.0;
    }
    else if(type=="TC"){                // thalamo-cortical
        a=0.02; b=0.25; c=-65.0; d=0.05;
    }
    else if(type=="RZ"){                // resonator
        a=0.1; b=0.26; c=-65.0; d=2.0;
    }
    else if(type=="FS"){                // fast spiking
        a=0.1; b=0.2; c=-65.0; d=2.0;
    }
}


int IzhiNeuronBase::advance(AdvanceInfo const &ai)
{
    bool register hasFired = false;

    double V=Vm*1000;

    // all synapses have added the contributions to Isyn, we add Iinject    
    double Itot = Isyn + Iinject;

    if (Inoise > 0.0) {
        Itot += (white_noise() * Inoise);
//        else if(noiseType == 1)
//            Itot += (pink_noise() * Inoise);
    }

    Itot *= 1e3;        // mA
    Itot *= factI;      // to be tuned ;-)

    Vm = V + dt_msec*(0.04*V*V + 5*V + 140 - u + Itot);

    // numerical stability
//    Vm = V + 0.5*dt_msec*(0.04*V*V + 5*V + 140 - u + Itot);
//    Vm = Vm + 0.5*dt_msec*(0.04*Vm*Vm + 5*Vm + 140 - u + Itot);

    u = u + dt_msec*a*(b*V - u);

    if (Vm >= Vpeak) {         // Note that the neuron has fired!
        hasFired = true;
        u = u + d;
        Vm = c;
    }
    Vm = Vm/1000.0;

    // clear synaptic input for next time step
    clearSynapticInput();

    if (hasFired) {
        out_port.setSpike(ai);
        return ADVANCEFLAG_HASSPIKED;
    }

    return 0;
}

inline void IzhiNeuronBase::clearSynapticInput(void)
{
    Isyn = 0.0;
}


int IzhiNeuronBase::adjust(double dt)
{
    dt_msec = dt*1000;

//    pink_noise.adjust(dt);

    return 0;
}


int IzhiNeuronBase::reset(double dt)
{
    SingleOutputSpikeSender::reset();

    Vm = Vinit;     // set membrane voltage to its initial value
    u = 0.0;
    clearSynapticInput();
    adjust(dt);

    return 0;
}



// IzhiNeuron

IzhiNeuron::IzhiNeuron(double a, double b, double c, double d, double Vpeak, double Vinit,
                       double Inoise, double Iinject, double factI)
    : IzhiNeuronBase(a, b, c, d, Vpeak, Vinit, Inoise, Iinject, factI)
{
}


IzhiNeuron::IzhiNeuron(string type, double Vinit, double Inoise, double Iinject, double factI)
    : IzhiNeuronBase(type, Vinit, Inoise, Iinject, factI)
{
}


inline void IzhiNeuron::currentInput(double i)
{
    Isyn += i;
}



// CbIzhiNeuron

CbIzhiNeuron::CbIzhiNeuron(double a, double b, double c, double d, double Vpeak, double Vinit,
    double Inoise, double Iinject, double factI)
    : IzhiNeuronBase(a, b, c, d, Vpeak, Vinit, Inoise, Iinject, factI)
{
}


CbIzhiNeuron::CbIzhiNeuron(string type, double Vinit, double Inoise, double Iinject, double factI)
    : IzhiNeuronBase(type, Vinit, Inoise, Iinject, factI)
{
}


inline void CbIzhiNeuron::currentInput(double i)
{
    Isyn += i;
}


inline void CbIzhiNeuron::conductanceInput(double g, double Erev)
{
    Isyn += g*(Erev-Vm);
}


// ExIzhiNeuronBase

ExIzhiNeuronBase::ExIzhiNeuronBase(double a, double b, double c, double d,
                                   double k, double Vt, double Vr, double Cm,
                                   double Vpeak, double Vinit, double Inoise,
                                   double Iinject, double factI)
    : IzhiNeuronBase(a, b, c, d, Vpeak, Vinit, Inoise, Iinject, factI)
    , k(k), Vr(Vr), Vt(Vt), Cm(Cm)
{
}


ExIzhiNeuronBase::ExIzhiNeuronBase(string type, double Vinit, double Inoise, double Iinject, double factI)
    : IzhiNeuronBase(type, Vinit, Inoise, Iinject, factI)
    , k(k), Vr(Vr), Vt(Vt), Cm(Cm)
{
    // Cm in pF

    // RS regular spiking
    Vpeak=35.0;
    k=0.7; Cm=100; Vr=-60.0; Vt=-40.0;
    a=0.03; b=-2.0; c=-50.0; d=100.0;

    if(type=="IB"){               // intrinsically bursting
        Vpeak=50.0;
        k=1.2; Cm=150; Vr=-75.0; Vt=-45.0;
        a=0.01; b=5.0; c=-56.0; d=130.0;
    }
    else if(type=="CH"){          // chattering
        Vpeak=25.0;
        k=1.5; Cm=50; Vr=-60.0; Vt=-40.0;
        a=0.03; b=1.0; c=-40.0; d=150.0;
    }
    else if(type=="LTS"){         // low threshold spiking
        Vpeak=40.0;
        k=1; Cm=100; Vr=-56.0; Vt=-42.0;
        a=0.03; b=8.0; c=-53.0; d=20.67;
    }
    else if(type=="FS"){          // fast spiking
    // problem nonlinear function for u
        Vpeak=50.0;
        k=1.2; Cm=150; Vr=-75.0; Vt=-45.0;
        a=0.01; b=5.0; c=-56.0; d=130.0;
    }
}



int ExIzhiNeuronBase::advance(AdvanceInfo const &ai)
{
    bool register hasFired = false;

    double V=Vm*1000;
    // all synapses have added the contributions to Isyn, we add Iinject    
    double Itot = Isyn + Iinject;

    if (Inoise > 0.0) {
        Itot += (white_noise() * Inoise);
//      else if(noiseType == 1)
//          Itot += (pink_noise() * Inoise);
    }

    Itot *= 1e12;       // pA
    Itot *= factI;      // to be tuned ;-)

    Vm = V + dt_msec*(k*(V-Vr)*(V-Vt) - u + Itot)/Cm;
//    Vm = V + 0.5*dt_msec*(k*(V-Vr)*(V-Vt) - u + Itot)/C;
//    Vm = Vm + 0.5*dt_msec*(k*(Vm-Vr)*(Vm-Vt) - u + Itot)/C;

    u = u + dt_msec*a*(b*(V-Vr) - u);

    if (Vm >= Vpeak) {       // Note that the neuron has fired!
        hasFired = true;
        u = u + d;
        Vm = c;
    }
    Vm = Vm/1000;

    // clear synaptic input for next time step
    clearSynapticInput();

    if (hasFired) {
        out_port.setSpike(ai);
        return ADVANCEFLAG_HASSPIKED;
    }

    return 0;
}



// ExIzhiNeuron

ExIzhiNeuron::ExIzhiNeuron(double a, double b, double c, double d,
                           double k, double Vt, double Vr, double Cm,
                           double Vpeak, double Vinit, double Inoise,
                           double Iinject, double factI)
    : ExIzhiNeuronBase(a, b, c, d, k, Vt, Vr, Cm, Vpeak, Vinit, Inoise, Iinject, factI)
{
}


ExIzhiNeuron::ExIzhiNeuron(string type, double Vinit, double Inoise, double Iinject, double factI)
    : ExIzhiNeuronBase(type, Vinit, Inoise, Iinject, factI)
{
}

inline void ExIzhiNeuron::currentInput(double i)
{
    Isyn += i;
}


// CbExIzhiNeuron

CbExIzhiNeuron::CbExIzhiNeuron(double a, double b, double c, double d,
                               double k, double Vt, double Vr, double Cm,
                               double Vpeak, double Vinit, double Inoise,
                               double Iinject, double factI)
    : ExIzhiNeuronBase(a, b, c, d, k, Vt, Vr, Cm, Vpeak, Vinit, Inoise, Iinject, factI)
{
}


CbExIzhiNeuron::CbExIzhiNeuron(string type, double Vinit, double Inoise, double Iinject, double factI)
    : ExIzhiNeuronBase(type, Vinit, Inoise, Iinject, factI)
{
}


inline void CbExIzhiNeuron::currentInput(double i)
{
    Isyn += i;
}


inline void CbExIzhiNeuron::conductanceInput(double g, double Erev)
{
    Isyn += g*(Erev-Vm);
}

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