def creaetHHComp(parent='/library', name='hhcomp', diameter=1e-6, length=1e-6):
"""Create a compartment with Hodgkin-Huxley type ion channels (Na and
K).
Returns a 3-tuple: (compartment, nachannel, kchannel)
"""
compPath = '{}/{}'.format(parent, name)
mc = comp.MooseCompartment(compPath, length, diameter, {})
c = mc.mc_
sarea = mc.surfaceArea
if moose.exists('/library/na'):
moose.copy('/library/na', c.path, 'na')
else:
create_na_chan(parent=c.path)
na = moose.element('%s/na' % (c.path))
# Na-conductance 120 mS/cm^2
na.Gbar = 120e-3 * sarea * 1e4
na.Ek = 115e-3 + EREST_ACT
moose.connect(c, 'channel', na, 'channel')
if moose.exists('/library/k'):
moose.copy('/library/k', c.path, 'k')
else:
create_k_chan(parent=c.path)
k = moose.element('%s/k' % (c.path))
# K-conductance 36 mS/cm^2
k.Gbar = 36e-3 * sarea * 1e4
k.Ek = -12e-3 + EREST_ACT
moose.connect(c, 'channel', k, 'channel')
return (c, na, k)
def makeCable(self, args):
''' Make a cable out of n compartments '''
for i in range(self.ncomp):
compPath = '{}/comp{}'.format(self.cablePath, i)
l = self.length / self.ncomp
d = self.diameter
c = comp.MooseCompartment(compPath, l, d, args)
self.cable.append(c)
self.connect()
utils.dump("STEP",
"Passive cable is connected and ready for simulation.")
def buildCable(self, args):
''' Build binary cable '''
self.args = args
self.buildParameterLists()
# Cable is a list of lists.
self.cable = list()
for n, (l, d) in enumerate(zip(self.compLengthList,
self.compDiamList)):
utils.dump(
"STEP",
"Binary tree level {}: length {}, diameter {}".format(n, l, d))
noOfCompartments = pow(2, n)
compartmentList = []
for i in range(noOfCompartments):
compPath = '{}/comp_{}_{}'.format(self.cablePath, n, i)
m = comp.MooseCompartment(compPath, l, d, args)
compartmentList.append(m.mc_)
self.cable.append(compartmentList)
self.connectCable()