def do_sim(simulation, sim_control=None):
"""setup a simulation"""
global na, cell
# hide the simulation control panel, if there was one
if sim_control:
sim_control.unmap()
cell = FleidervishNeuron()
# add sodium diffusion everywhere
allsec = rxd.Region(h.allsec(), nrn_region='i')
na = rxd.Species(allsec, d=0.6, name='na', charge=1)
# create a current clamp and add it to the cell
cell.ic = h.IClamp(cell.soma(0.5))
cell.ic.dur = 3 # ms
cell.ic.amp = 1.5 # nA
# setup graphs needed by both simulations
concentration_graph = h.Graph(False)
concentration_graph.size(0, 3000, 4, 4.4)
voltage_graph = h.Graph(False)
voltage_graph.size(0, 3000, -90, 60)
h.graphList[0].append(voltage_graph)
h.graphList[1].append(concentration_graph)
# pop up the run control
h.nrncontrolmenu()
# call the funciton which actually sets up the specific simulation
simulation(cell, voltage_graph, concentration_graph)
def __init__(self, cell):
def show_val():
print("Spacer Ra of the model: {}".format(cell.spacer.Ra))
print(
'The starting point is {}, end point is {} with increasing steps of {}'
.format(min_current_var[0], max_current_var[0],
step_current_var[0]))
#Contorl Panel
sim_control = h.HBox()
sim_control.intercept(1)
h.nrncontrolmenu()
attach_current_clamp(cell)
h.xpanel('TEST')
h.xlabel('Choose a simulation to run')
h.xbutton('Spike Protocol', (spike_fig, cell))
h.xbutton('Rheobase Protocol', (fig_rheobase_check, cell))
h.xbutton('Multiple Rheobase Protocol',
(multiple_rheobase_plots_new, cell))
h.xbutton('Increasing Ra Protocol', (fig_ra_rheobase_spacerL, cell))
h.xbutton('Increasing spacer_gpas Protocol',
(fig_g_rheobase_spacerL, cell))
h.xbutton('Increasing cell c_m Protcol',
(fig_cm_rheobase_spacerL, cell))
h.xbutton('Combined Protocol Run', (Combined_Protocol, cell))
h.xpvalue('Rheobase protocol start', min_current_var, 1)
h.xpvalue('Rheobase protocol end', max_current_var, 1)
h.xpvalue('Rheobase step size', step_current_var, 1)
h.xbutton('show value', show_val)
# h.xvalue('enter value', (this_module, 'val'))
h.xpanel()
#Output panel
g = h.Graph()
g.addvar('soma(0.5).v', cell.soma(0.5)._ref_v)
g.addvar('AIS(0.5).v', cell.AIS(0.5)._ref_v)
g.size(0, 1000, -90, 90)
h.graphList[0].append(g)
h.MenuExplore()
sim_control.intercept(0)
sim_control.map()
input()
import matplotlib as mpl
mpl.use('tkagg')
from neuron import h, gui
from Cereb_GrC_regular import Grc_regular
import multiprocessing
import numpy as np
import matplotlib.pyplot as plt
cell = Grc_regular(1)
h.nrncontrolmenu()
time_step = h.CVode()
time_step.active(0) #0 fixed step, 1 variable time step
cpu = multiprocessing.cpu_count()
h.load_file("parcom.hoc")
p = h.ParallelComputeTool()
if cpu > 8:
p.change_nthread(8, 1)
print('Maximum 8 threads')
else:
p.change_nthread(cpu, 1)
print('N° of treads', cpu)
p.multisplit(1)
h('load_file("vm.ses")')
stimdata = dict()
stimdata['timeglobal'] = 2500
def show_menu():
global is_menu
if is_menu == 0:
h.nrnmainmenu() # create main menu
h.nrncontrolmenu() # crate control menu
is_menu = 1
# File to save: of0
# Column: RS_pop[0]/v
h(' objectvar v_v_of0 ')
h(' { v_v_of0 = new Vector() } ')
h(' v_v_of0.record(&v(0.5)) ')
h.v_v_of0.resize((h.tstop * h.steps_per_ms) + 1)
# Column: RS_pop[0]/u
h(' objectvar v_u_of0 ')
h(' { v_u_of0 = new Vector() } ')
h(' v_u_of0.record(&Izhi2007b[0].u) ')
h.v_u_of0.resize((h.tstop * h.steps_per_ms) + 1)
if plot:
h.nrncontrolmenu()
h.run()
if plot:
display_d1.exec_menu("View = plot")
display_d2.exec_menu("View = plot")
py_v_time = [ t/1000 for t in h.v_time.to_python() ] # Convert to Python list for speed...
# File to save: of0
py_v_v_of0 = [ float(x / 1000.0) for x in h.v_v_of0.to_python() ] # Convert to Python list for speed, variable has dim: voltage
py_v_u_of0 = [ float(x / 1.0E9) for x in h.v_u_of0.to_python() ] # Convert to Python list for speed, variable has dim: current