def importAxialResistance(self, nmlcell, intracellularProperties):
sg_to_segments = self._cell_to_sg[nmlcell]
for r in intracellularProperties.resistivity:
segments = getSegments(nmlcell, r, sg_to_segments)
for seg in segments:
comp = self.nml_to_moose[seg]
setRa(comp, SI(r.value))
def importCapacitances(self, nmlcell, moosecell, specificCapacitances):
sg_to_segments = self._cell_to_sg[nmlcell]
for specific_cm in specificCapacitances:
cm = SI(specific_cm.value)
for seg in sg_to_segments[specific_cm.segmentGroup]:
comp = self.nml_to_moose[seg]
comp.Cm = np.pi * sarea(comp)
def createDecayingPoolConcentrationModel(self, concModel):
"""Create prototype for concentration model"""
if concModel.name is not None:
name = concModel.name
else:
name = concModel.id
ca = moose.CaConc('%s/%s' % (self.lib.path, id))
print('11111', concModel.restingConc)
print('2222', concModel.decayConstant)
print('33333', concModel.shellThickness)
ca.CaBasal = SI(concModel.restingConc)
ca.tau = SI(concModel.decayConstant)
ca.thick = SI(concModel.shellThickness)
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[concModel.id] = ca
self.moose_to_nml[ca] = concModel
logger.debug('Created moose element: %s for nml conc %s' %
(ca.path, concModel.id))
def importChannelsToCell(self, nmlcell, moosecell, membraneProperties):
sg_to_segments = self._cell_to_sg[nmlcell]
for chdens in membraneProperties.channelDensity:
segments = getSegments(nmlcell, chdens, sg_to_segments)
condDensity = SI(chdens.condDensity)
try:
ionChannel = self.id_to_ionChannel[chdens.ionChannel]
except KeyError:
print('No channel with id', chdens.ionChannel)
continue
if ionChannel.type_ == 'ionChannelPassive':
for seg in segments:
self.setRm(self.nml_to_moose[seg], condDensity)
else:
for seg in segments:
self.copyChannel(chdens, self.nml_to_moose[seg],
condDensity)