def test_nrntest_test_2():
h = hoc.HocObject()
h('''
create axon, soma, dend[3]
connect axon(0), soma(0)
for i=0, 2 connect dend[i](0), soma(1)
axon { nseg = 5 L=100 diam = 1 insert hh }
forsec "dend" { nseg = 3 L=50 diam = 2 insert pas e_pas = -65 }
soma { L=10 diam=10 insert hh }
''')
assert h.axon.name() == "axon"
assert str(h.dend) == "dend[?]"
assert str(h.dend[1]) == "dend[1]"
assert str(h.dend[1].name()) == "dend[1]"
def e(stmt):
try:
exec(stmt)
except Exception:
assert (str(sys.exc_info()[0]) + ': ' + str(
sys.exc_info()[1]) == "<class 'TypeError'>: not assignable")
e('h.axon = 1')
e('h.dend[1] = 1')
assert str(h) == "<TopLevelHocInterpreter>"
assert str(h.axon) == "axon"
assert str(h.axon.name()) == "axon"
assert str(h.axon(0.5)) == "axon(0.5)"
assert str(h.axon(0.5).hh) == "hh"
assert str(h.axon(0.5).hh.name()) == "hh"
assert h.axon(0.5).hh.gnabar == 0.12
def test_nrntest_test_2():
h = hoc.HocObject()
h(
'''
create axon, soma, dend[3]
connect axon(0), soma(0)
for i=0, 2 connect dend[i](0), soma(1)
axon { nseg = 5 L=100 diam = 1 insert hh }
forsec "dend" { nseg = 3 L=50 diam = 2 insert pas e_pas = -65 }
soma { L=10 diam=10 insert hh }
'''
)
assert h.axon.name() == "axon"
assert str(h.dend) == "dend[?]"
assert str(h.dend[1]) == "dend[1]"
assert str(h.dend[1].name()) == "dend[1]"
def e(stmt):
err = 0
try:
exec(stmt, globals(), locals())
except Exception:
assert ('not assignable' in str(sys.exc_info()[1]))
err = 1
assert(err == 1)
e('h.axon = 1')
e('h.dend[1] = 1')
assert str(h) == "<TopLevelHocInterpreter>"
assert str(h.axon) == "axon"
assert str(h.axon.name()) == "axon"
assert str(h.axon(0.5)) == "axon(0.5)"
assert str(h.axon(0.5).hh) == "hh"
assert str(h.axon(0.5).hh.name()) == "hh"
assert h.axon(0.5).hh.gnabar == 0.12
assert h.axon(0.5) in h.axon
assert h.axon(0.5) not in h.soma
from neuron import h, gui
h('create axon')
import __main__
import sys
def e(stmt) :
try:
print stmt
exec stmt in __main__.__dict__
except:
print sys.exc_info()[0], ': ', sys.exc_info()[1]
e('print h.axon.i_membrane_')
e('print h.axon(.5).i_membrane_')
h.delete_section()
h.load_file("imemaxon2.hoc")
for seg in h.axon:
print seg.x, seg.i_membrane*seg.area()*(0.01), seg.i_membrane_
for seg in h.axon.allseg():
print seg.x, seg._ref_i_membrane_[0], seg.i_membrane_
print h.axon.i_membrane, h.axon(.5).i_membrane
print h.axon.i_membrane_
def get_trace(file_name,
synapse_type=0,
synapse_numbers=(10, 10),
hz=None,
space_plot=False,
vm=-65.0,
cli=5.0,
ldend_diam=0.5):
"""
Get the voltage trace and cli trace from running a hoc file.
Optionally, specify space_plot to get the cli along the entire neuron (nseg dependent).
`vm` and `cli` should be specified by running `get_base_vm_cli` beforehand and passing in those values.
:param file_name: hoc-specified neuron to load (from hoc_files/cells)
:type file_name: str
:param synapse_type: 0 if 'f-in' NETSTIM synapses. 1 if 'persistetnt' fluctuating conductance synapses.
:type synapse_type: int
:param synapse_numbers: Number of (E,I) synapses.
:type synapse_numbers: tuple of int
:param hz: Input to the synapses. Keys used are 'in' and 'ex'.
Either frequency-based (`synapse_type` is `0`) or relative conductance (`synapse_type` is `1`).
:type hz: dict of str
:param space_plot: Compute cli at every location.
:type space_plot: bool
:param vm: Initial membrane potential
:type vm: float
:param cli: Initial chloride ion concentration
:type cli: float
:param ldend_diam: Diameter of distal dendrite.
:type ldend_diam: float
:return: Time array, voltage array, chloride array,
space plot dict data of form `{distance from soma: chloride array}`
:rtype: tuple[h.Vector, h.Vector, h.Vector, dict of float:h.Vector]
"""
if hz is None:
hz = {'in': 5, 'ex': 5}
load_file(file_name)
h.changeSynapseType(synapse_type)
h.newSynapses(synapse_numbers[0], synapse_numbers[1])
if synapse_type == 0:
h.inPy(hz['in'], 1, 1)
h.ex(hz['ex'], 1, 1)
else:
h.inPy(hz['in'])
h.ex(hz['ex'])
if "distal" in file_name:
compartment = h.ldend
elif "proximal" in file_name:
compartment = h.bdend
else:
compartment = h.soma
h("forall {" + "cli={} ".format(cli) + "cli0_KCC2={}".format(cli) + "}")
for sec in h.allsec:
for seg in sec:
seg.cli = cli
h.cli0_cl_ion = cli
h.ldend.diam = ldend_diam
# sort on key
data = {}
if space_plot:
h.distance(0, 1, sec=h.soma)
for sec in h.allsec:
for seg in sec:
# label = f"{sec.name()}({seg.x:.5f})"
label = h.distance(seg.x, sec=sec)
if 'dend' in sec.name():
label *= -1
data[label] = h.Vector()
data[label].record(sec(seg.x)._ref_cli)
h.tstop = 1000.0
time_past = current_time('ms')
logger.info("running {}...".format(file_name))
h.v_init = vm
h.finitialize(vm)
t_vec = h.Vector()
t_vec.record(h._ref_t)
v_vec = h.Vector()
v_vec.record(h.axon(0.5)._ref_v)
cli_vec = h.Vector()
cli_vec.record(compartment(0.5)._ref_cli)
h.run()
logger.info("time taken: {}ms".format(current_time('ms') - time_past))
logger.info("no. spikes = {}".format(h.apc.n))
return t_vec, v_vec, cli_vec, data