def importChannelsToCell(self, nmlcell, moosecell, membrane_properties):
sg_to_segments = self._cell_to_sg[nmlcell.id]
for chdens in membrane_properties.channel_densities + membrane_properties.channel_density_v_shifts:
segments = getSegments(nmlcell, chdens, sg_to_segments)
condDensity = SI(chdens.cond_density)
erev = SI(chdens.erev)
try:
ionChannel = self.id_to_ionChannel[chdens.ion_channel]
except KeyError:
logger_.info('No channel with id: %s' % chdens.ion_channel)
continue
if self.verbose:
logger_.info(
'Setting density of channel %s in %s to %s; erev=%s (passive: %s)'
% (chdens.id, segments, condDensity, erev,
self.isPassiveChan(ionChannel)))
if self.isPassiveChan(ionChannel):
for seg in segments:
# comp = self.nml_to_moose[seg]
setRm(self.nml_to_moose[seg.id], condDensity)
setEk(self.nml_to_moose[seg.id], erev)
else:
for seg in segments:
self.copyChannel(chdens, self.nml_to_moose[seg.id],
condDensity, erev)
'''moose.le(self.nml_to_moose[seg])
def _getTemperature(self):
if self.network is not None:
if self.network.type == "networkWithTemperature":
return SI(self.network.temperature)
else:
# Why not, if there's no temp dependence in nml..?
return 0
return SI('25')
def importInputs(self, doc):
epath = '%s/inputs' % (self.lib.path)
if moose.exists(epath):
minputs = moose.element(epath)
else:
minputs = moose.Neutral(epath)
for pg_nml in doc.pulse_generators:
epath = '%s/%s' % (minputs.path, pg_nml.id)
pg = moose.element(epath) if moose.exists(
epath) else moose.PulseGen(epath)
pg.firstDelay = SI(pg_nml.delay)
pg.firstWidth = SI(pg_nml.duration)
pg.firstLevel = SI(pg_nml.amplitude)
pg.secondDelay = 1e9
def importAxialResistance(self, nmlcell, intracellularProperties):
sg_to_segments = self._cell_to_sg[nmlcell.id]
for r in intracellularProperties.resistivities:
segments = getSegments(nmlcell, r, sg_to_segments)
for seg in segments:
comp = self.nml_to_moose[seg.id]
setRa(comp, SI(r.value))
def importInitMembPotential(self, nmlcell, moosecell, membraneProperties):
sg_to_segments = self._cell_to_sg[nmlcell.id]
for imp in membraneProperties.init_memb_potentials:
initv = SI(imp.value)
for seg in sg_to_segments[imp.segment_groups]:
comp = self.nml_to_moose[seg.id]
comp.initVm = initv
def importCapacitances(self, nmlcell, moosecell, specificCapacitances):
sg_to_segments = self._cell_to_sg[nmlcell.id]
for specific_cm in specificCapacitances:
cm = SI(specific_cm.value)
for seg in sg_to_segments[specific_cm.segment_groups]:
comp = self.nml_to_moose[seg.id]
comp.Cm = sarea(comp) * cm
def createDecayingPoolConcentrationModel(self, concModel):
"""Create prototype for concentration model"""
if hasattr(concModel, 'name') and concModel.name is not None:
name = concModel.name
else:
name = concModel.id
ca = moose.CaConc('%s/%s' % (self.lib.path, name))
ca.CaBasal = SI(concModel.resting_conc)
ca.tau = SI(concModel.decay_constant)
ca.thick = SI(concModel.shell_thickness)
ca.B = 5.2e-6 # B = 5.2e-6/(Ad) where A is the area of the
# shell and d is thickness - must divide by
# shell volume when copying
self.proto_pools[concModel.id] = ca
self.nml_to_moose[name] = ca
self.moose_to_nml[ca] = concModel
logger_.debug('Created moose element: %s for nml conc %s' %
(ca.path, concModel.id))
def createHHChannel(self, chan, vmin=-150e-3, vmax=100e-3, vdivs=5000):
mchan = moose.HHChannel('%s/%s' % (self.lib.path, chan.id))
mgates = [
moose.element(x) for x in [mchan.gateX, mchan.gateY, mchan.gateZ]
]
assert len(chan.gate_hh_rates
) <= 3, "We handle only up to 3 gates in HHCHannel"
if self.verbose:
logger_.info('== Creating channel: %s (%s) -> %s (%s)' %
(chan.id, chan.gate_hh_rates, mchan, mgates))
all_gates = chan.gates + chan.gate_hh_rates
# Sort all_gates such that they come in x, y, z order.
all_gates = _gates_sorted(all_gates)
for ngate, mgate in zip(all_gates, mgates):
if ngate is None:
continue
if mgate.name.endswith('X'):
mchan.Xpower = ngate.instances
elif mgate.name.endswith('Y'):
mchan.Ypower = ngate.instances
elif mgate.name.endswith('Z'):
mchan.Zpower = ngate.instances
mgate.min = vmin
mgate.max = vmax
mgate.divs = vdivs
# I saw only examples of GateHHRates in
# HH-channels, the meaning of forwardRate and
# reverseRate and steadyState are not clear in the
# classes GateHHRatesInf, GateHHRatesTau and in
# FateHHTauInf the meaning of timeCourse and
# steady state is not obvious. Is the last one
# refering to tau_inf and m_inf??
fwd = ngate.forward_rate
rev = ngate.reverse_rate
self.paths_to_chan_elements[
'%s/%s' %
(chan.id, ngate.id)] = '%s/%s' % (chan.id, mgate.name)
q10_scale = 1
if ngate.q10_settings:
if ngate.q10_settings.type == 'q10Fixed':
q10_scale = float(ngate.q10_settings.fixed_q10)
elif ngate.q10_settings.type == 'q10ExpTemp':
q10_scale = math.pow(
float(ngate.q10_settings.q10_factor),
(self._getTemperature() -
SI(ngate.q10_settings.experimental_temp)) / 10)
else:
raise Exception(
'Unknown Q10 scaling type %s: %s' %
(ngate.q10_settings.type, ngate.q10_settings))
logger_.debug(
'+ Gate: %s; %s; %s; %s; %s; scale=%s' %
(ngate.id, mgate.path, mchan.Xpower, fwd, rev, q10_scale))
if (fwd is not None) and (rev is not None):
alpha = self.calculateRateFn(fwd, vmin, vmax, vdivs)
beta = self.calculateRateFn(rev, vmin, vmax, vdivs)
mgate.tableA = q10_scale * (alpha)
mgate.tableB = q10_scale * (alpha + beta)
# Assuming the meaning of the elements in GateHHTauInf ...
if hasattr(ngate,'time_course') and hasattr(ngate,'steady_state') \
and (ngate.time_course is not None) and (ngate.steady_state is not None):
tau = ngate.time_course
inf = ngate.steady_state
tau = self.calculateRateFn(tau, vmin, vmax, vdivs)
inf = self.calculateRateFn(inf, vmin, vmax, vdivs)
mgate.tableA = q10_scale * (inf / tau)
mgate.tableB = q10_scale * (1 / tau)
if hasattr(ngate, 'steady_state') and (
ngate.time_course is None) and (ngate.steady_state
is not None):
inf = ngate.steady_state
tau = 1 / (alpha + beta)
if inf is not None:
inf = self.calculateRateFn(inf, vmin, vmax, vdivs)
if len(inf) > 0:
mgate.tableA = q10_scale * (inf / tau)
mgate.tableB = q10_scale * (1 / tau)
logger_.info('%s: Created %s for %s' %
(self.filename, mchan.path, chan.id))
return mchan