Human-L2-3-Cortical-Microcircuit/L23Net/mod/TestSyn.py

# Based on https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=2750

from neuron import *
import numpy as np
import sys
import matplotlib.pyplot as plt

duration = 500
dt = 0.01


def get_random_stim(rate):
    stimNc = h.NetStim()
    stimNc.noise = 1
    stimNc.start = 0
    stimNc.number = 1e9
    stimNc.interval = 1000.0 / rate
    return stimNc


def get_timed_stim():
    stimNc = h.NetStim()
    stimNc.noise = 0
    stimNc.start = 100
    stimNc.number = 3
    stimNc.interval = 30
    return stimNc


soma = h.Section()
soma.L = 17.841242
soma.diam = 17.841242
soma.push()
soma.insert("pas")
soma.g_pas = 0.0003

"""

syn = h.ExpSyn(0.5, sec=soma)

stim1 = h.IClamp(0.5, sec=soma)
stim1.delay = 50.0
stim1.dur = 5.0
stim1.amp = 0.4

stim2 = h.IClamp(0.5, sec=soma)
stim2.delay = 140.0
stim2.dur = 5.0
stim2.amp = 0.4
"""

def get_base_syn():
    syn = h.ProbAMPANMDA(0.5, sec=soma)

    return syn

syn = get_base_syn()


def run_sim(rate=10):
    print("Running simulation of %s with %s Hz input" % (duration, rate))

    # stimNc = get_random_stim(rate)
    stimNc = get_timed_stim()

    vec_nc = h.Vector()

    nc = h.NetCon(stimNc, syn)
    nc.weight[0] = 0.001
    nc.delay = 0

    nc.record(vec_nc)

    vec = {}
    all_states = ["A_AMPA", "A_NMDA", "B_AMPA", "B_NMDA"]
    gs = ["g_AMPA", "g_NMDA"]
    other = ["v", "t"]

    for var in (all_states + gs + other):
        vec[var] = h.Vector()
        if var != "v" and var != "t":
            exec("print('Recording:  %s')" % var)
            exec("vec ['%s'].record(syn._ref_%s)" % (var, var))

    # record the membrane potentials and
    # synaptic currents
    vec["v"].record(soma(0.5)._ref_v)
    vec["t"].record(h._ref_t)

    # run the simulation
    h.load_file("stdrun.hoc")
    h.init()
    h.tstop = duration
    h.dt = dt
    h.run()

    spikes = []
    isis = []
    lastSpike = None
    for t in vec_nc:
        spikes.append(t)
        # print(t)
        if lastSpike:
            isis.append(t - lastSpike)
        lastSpike = t

    hz = 1000 / (h.tstop / len(spikes))
    print("nc: Spike times: %s" % ["%.3f" % t for t in vec_nc])
    print(
        "nc: Num spikes: %s; avg rate: %s Hz; avg isi: %s ms; std isi: %s ms"
        % (len(spikes), hz, np.average(isis), np.std(isis))
    )
    # assert abs((hz-rate)/rate)<0.01

    """
    scales = {
        "v": 0.001,
        "g": 1e-6,
    }

    for v in postLTP_vals:
        scales[v] = 1
    for var in scales:
        var_file = open("%s.dat" % var, "w")
        for i in range(len(vec["t"])):
            var_file.write("%s\t%s\n" % (vec["t"][i] / 1000, vec[var][i] * scales[var]))
        var_file.close()
    """
    for var in (all_states + gs + other):
        var_file = open("%s.dat" % var, "w")
        for i in range(len(vec["t"])):
            var_file.write("%s\t%s\n" % (vec["t"][i] / 1000, vec[var][i]))
        var_file.close()

    if not "-nogui" in sys.argv:
        # plot the results
        plt.figure()
        plt.title("Membrane potential")
        plt.plot(vec["t"], vec["v"])

        plt.figure()
        plt.title("Conductance")
        plt.plot(vec["t"], vec["g_AMPA"], label="g_AMPA")
        plt.plot(vec["t"], vec["g_NMDA"], label="g_NMDA")
        plt.legend()

        plt.figure()
        plt.title("States")
        for s in all_states:
            plt.plot(vec["t"], vec[s], label=s)
        plt.legend()


run_sim()

if not "-nogui" in sys.argv:
    plt.show()