def find_units(variable):
if variable in recording.UNITS_MAP:
return recording.UNITS_MAP[variable]
else:
# works with NEURON 7.3, not with 7.1, 7.2 not tested
nrn_units = h.units(variable.split('.')[-1])
pq_units = nrn_units.replace("2", "**2").replace("3", "**3")
return pq_units
def add_button(name, actions=None, value=None, extraData=None):
if value is not None:
valueUnits = h.units(value)
if valueUnits != '':
name += " (" + valueUnits + ")"
button = GeppettoJupyterGUISync.ButtonSync(widget_id=G.newId(),
widget_name=name,
extraData=extraData)
if actions is not None:
button.on_click(actions)
return button
def guess_units(variable):
# works with NEURON 7.3, not with 7.1, 7.2 not tested
nrn_units = h.units(variable.split('.')[-1])
pq_units = nrn_units.replace("2", "**2").replace("3", "**3")
return pq_units
ax1 = fig.add_subplot(2,1,1)
soma_plot = ax1.plot(t_vec, soma_v_vec, color='black')
dend_plot = ax1.plot(t_vec, dend_v_vec, color='red')
#rev_plot = ax1.plot([t_vec[0], t_vec[-1]], [syn_.e, syn_.e],
# color='blue', linestyle=':')
ax1.legend(soma_plot + dend_plot,
['soma', 'dend(0.5)', 'syn reversal'])
ax1.set_ylabel('mV')
ax1.set_xlim([25,125])
#ax1.set_xticks([]) # Use ax2's tick labels
ax2 = fig.add_subplot(2,1,2, sharex = ax1)
syn_plot = ax2.plot(t_vec, syn_i_vec, color='blue')
ax2.legend(syn_plot,\
['injected current'])
ax2.set_ylabel(h.units('ExpSyn.i'))
ax2.set_xlabel('time (ms)')
ax2.set_xlim([25,125])
pyplot.show()
# Draw
fig2 = pyplot.figure(figsize=(8,4))
ax1 = fig2.add_subplot(3,1,1)
soma_plot = ax1.plot(t_vec, soma_v_vec, color='black')
ax1.legend(soma_plot,'soma')
ax1.set_ylabel('mV')
ax1.set_xlim([25,125])
ax1.set_ylim([-75,-65])
def guess_units(variable):
# works with NEURON 7.3, not with 7.1, 7.2 not tested
nrn_units = h.units(variable.split('.')[-1])
pq_units = nrn_units.replace("2", "**2").replace("3", "**3")
return pq_units
# Insert active Hodgkin-Huxley current in the soma
soma.insert('hh')
for seg in soma:
seg.hh.gnabar = 0.12 # Sodium conductance in S/cm2
seg.hh.gkbar = 0.036 # Potassium conductance in S/cm2
seg.hh.gl = 0.0003 # Leak conductance in S/cm2
seg.hh.el = -54.3 # Reversal potential in mV
# Insert passive current in the dendrite
dend.insert('pas')
for seg in dend:
seg.pas.g = 0.001 # Passive conductance in S/cm2
seg.pas.e = -65 # Leak reversal potential mV
print(h.units('gnabar_hh'))
for sec in h.allsec():
h.psection(sec=sec)
#stimulation
stim = h.IClamp(dend(1))
print("segment = {}".format(stim.get_segment()))
dir(stim)
stim.delay = 5
stim.dur = 1
stim.amp = 0.1
fig = pyplot.figure(figsize=(8, 4))
ax1 = fig.add_subplot(2, 1, 1)
soma_plot = ax1.plot(t_vec, soma_v_vec, color='black')
dend_plot = ax1.plot(t_vec, dend_v_vec, color='red')
rev_plot = ax1.plot([t_vec[0], t_vec[-1]], [syn_.e, syn_.e],
color='blue',
linestyle=':')
ax1.legend(soma_plot + dend_plot + rev_plot,
['soma', 'dend[0](0.5)', 'syn reversal'])
ax1.set_ylabel('mV')
ax1.set_xticks([]) # Use ax2's tick labels
ax2 = fig.add_subplot(2, 1, 2)
syn_plot = ax2.plot(t_vec, syn_i_vec, color='blue')
ax2.legend(syn_plot, ['synaptic current'])
ax2.set_ylabel(h.units('ExpSyn.i'))
ax2.set_xlabel('time (ms)')
pyplot.show()
#connect axons from cell n to a synapse
nclist = []
syns = []
for i in range(N):
src = cells[i]
tgt = cells[(i + 1) % N]
syn = h.ExpSyn(tgt.dend[0](0.5))
syns.append(syn)
nc = h.NetCon(src.soma(0.5)._ref_v, syn, sec=src.soma)
nc.weight[0] = 0.05
nc.delay = 5
nclist.append(nc)
def u(n): print(n, h.units(n))
from neuron import h
def u(n):
print(n, h.units(n))
u('t')
u('dt')
u('celsius')
u('v')
u('Ra')
u('gnabar_hh')
u('ina')
u('nao')
u('nai')
u('ena')
u('ExpSyn.g')
u('ExpSyn.i')
u('ExpSyn.e')
h('a=1')
h.units('a', 'inch')
u('a')
from neuron import h
h('foo = 2')
h.variable_domain('foo', 1, 5)
h.units('foo', 'cm')
h.xpanel("test")
h.xvalue("foo", "foo", 1)
h.xpvalue("foo", h._ref_foo, 1)
h.xpanel()
