def run_single_channel(channelname, Gbar, simtime, simdt=testutils.SIMDT, plotdt=testutils.PLOTDT):
testId = uuid.uuid4().int
container = moose.Neutral('test%d' % (testId))
model_container = moose.Neutral('%s/model' % (container.path))
data_container = moose.Neutral('%s/data' % (container.path))
params = testutils.setup_single_compartment(
model_container, data_container,
channelbase.prototypes[channelname],
Gbar)
vm_data = params['Vm']
gk_data = params['Gk']
ik_data = params['Ik']
testutils.setup_clocks(simdt, plotdt)
testutils.assign_clocks(model_container, data_container)
moose.reinit()
print 'Starting simulation', testId, 'for', simtime, 's'
moose.start(simtime)
print 'Finished simulation'
vm_file = 'data/%s_Vm.dat' % (channelname)
gk_file = 'data/%s_Gk.dat' % (channelname)
ik_file = 'data/%s_Ik.dat' % (channelname)
tseries = np.array(range(len(vm_data.vec))) * simdt
print 'Vm:', len(vm_data.vec), 'Gk', len(gk_data.vec), 'Ik', len(ik_data.vec)
data = np.c_[tseries, vm_data.vec]
np.savetxt(vm_file, data)
print 'Saved Vm in', vm_file
print len(gk_data.vec), len(vm_data.vec)
data = np.c_[tseries, gk_data.vec]
np.savetxt(gk_file, data)
print 'Saved Gk in', gk_file
data = np.c_[tseries, ik_data.vec]
np.savetxt(ik_file, data)
print 'Saved Gk in', ik_file
return params
def setup_cadep_channel(model_container, data_container, channel_proto, Gbar, ca_start, ca_stop):
"""Setup a test compartment with [Ca2+] dependent channel."""
params = setup_single_compartment(model_container, data_container, channel_proto, Gbar)
ca_table = moose.StimulusTable(model_container.path + '/CaStim')
ca_table.vec = np.linspace(ca_start, ca_stop, 1000)
ca_table.doLoop = True
ca_recorder = moose.Table(data_container.path + '/Ca')
moose.connect(ca_table, 'output', ca_recorder, 'input')
moose.connect(ca_table, 'output', params['channel'], 'concen')
params['Ca'] = ca_recorder
params['CaStim'] = ca_table
testutils.setup_clocks(simdt, plotdt)
testutils.assign_clocks(model_container, data_container)
moose.useClock(1, '%s,%s' % (ca_recorder.path, ca_table.path), 'process')
return params
def setup_cadep_channel(model_container, data_container, channel_proto, Gbar,
ca_start, ca_stop):
"""Setup a test compartment with [Ca2+] dependent channel."""
params = setup_single_compartment(model_container, data_container,
channel_proto, Gbar)
ca_table = moose.StimulusTable(model_container.path + '/CaStim')
ca_table.vector = np.linspace(ca_start, ca_stop, 1000)
ca_table.doLoop = True
ca_recorder = moose.Table(data_container.path + '/Ca')
moose.connect(ca_table, 'output', ca_recorder, 'input')
moose.connect(ca_table, 'output', params['channel'], 'concen')
params['Ca'] = ca_recorder
params['CaStim'] = ca_table
testutils.setup_clocks(simdt, plotdt)
testutils.assign_clocks(model_container, data_container)
moose.useClock(1, '%s,%s' % (ca_recorder.path, ca_table.path), 'process')
return params