def __init__(self):
self.scheduled = False
self.model_container = moose.Neutral('/model')
self.data_container = moose.Neutral('/data')
self.squid_axon = SquidAxon('/model/squid_axon')
self.clamp_ckt = ClampCircuit('/model/electronics', self.squid_axon)
self.simdt = 0.0
self.plotdt = 0.0
self.setup_recording()
def __init__(self):
self.scheduled = False
self.model_container = moose.Neutral('/model')
self.data_container = moose.Neutral('/data')
self.squid_axon = SquidAxon('/model/squid_axon')
self.clamp_ckt = ClampCircuit('/model/electronics', self.squid_axon)
self.simdt = 0.0
self.plotdt = 0.0
self.setup_recording()
class SquidSetup(object):
def __init__(self):
self.scheduled = False
self.model_container = moose.Neutral('/model')
self.data_container = moose.Neutral('/data')
self.squid_axon = SquidAxon('/model/squid_axon')
self.clamp_ckt = ClampCircuit('/model/electronics', self.squid_axon)
self.simdt = 0.0
self.plotdt = 0.0
self.setup_recording()
def setup_recording(self):
# Setup data collection
self.vm_table = moose.Table('/data/Vm')
moose.connect(self.vm_table, 'requestOut', self.squid_axon, 'getVm')
self.cmd_table = moose.Table('/data/command')
moose.connect(self.cmd_table, 'requestOut', self.clamp_ckt.vclamp, 'getOutputValue')
self.iclamp_table = moose.Table('/data/Iclamp')
moose.connect(self.iclamp_table, 'requestOut', self.clamp_ckt.iclamp, 'getOutputValue')
self.vclamp_table = moose.Table('/data/Vclamp')
moose.connect(self.vclamp_table, 'requestOut', self.clamp_ckt.pid, 'getOutputValue')
self.m_table = moose.Table('/data/m')
moose.connect(self.m_table, 'requestOut', self.squid_axon.Na_channel, 'getX')
self.h_table = moose.Table('/data/h')
moose.connect(self.h_table, 'requestOut', self.squid_axon.Na_channel, 'getY')
self.n_table = moose.Table('/data/n')
moose.connect(self.n_table, 'requestOut', self.squid_axon.K_channel, 'getX')
self.ina_table = moose.Table('/data/INa')
moose.connect(self.ina_table, 'requestOut', self.squid_axon.Na_channel, 'getIk')
self.ik_table = moose.Table('/data/IK')
moose.connect(self.ik_table, 'requestOut', self.squid_axon.K_channel, 'getIk')
self.gna_table = moose.Table('/data/GNa')
moose.connect(self.gna_table, 'requestOut', self.squid_axon.Na_channel, 'getGk')
self.gk_table = moose.Table('/data/GK')
moose.connect(self.gk_table, 'requestOut', self.squid_axon.K_channel, 'getGk')
def schedule(self, simdt, plotdt, clampmode):
self.simdt = simdt
self.plotdt = plotdt
if clampmode == 'vclamp':
self.clamp_ckt.do_voltage_clamp()
else:
self.clamp_ckt.do_current_clamp()
moose.setClock(0, simdt)
moose.setClock(1, simdt)
moose.setClock(2, simdt)
moose.setClock(3, plotdt)
# Ensure we do not create multiple scheduling
if not self.scheduled:
moose.useClock(0, '%s/#[TYPE=Compartment]' % (self.model_container.path), 'init')
moose.useClock(0, '%s/##' % (self.clamp_ckt.path), 'process')
moose.useClock(1, '%s/#[TYPE=Compartment]' % (self.model_container.path), 'process')
moose.useClock(2, '%s/#[TYPE=HHChannel]' % (self.squid_axon.path), 'process')
moose.useClock(3, '%s/#[TYPE=Table]' % (self.data_container.path), 'process')
self.scheduled = True
moose.reinit()
def run(self, runtime):
moose.start(runtime)
def save_data(self):
for child in self.data_container.children:
tab = moose.Table(child)
tab.xplot('%s.dat' % (tab.name), tab.name)
class SquidSetup(object):
def __init__(self):
self.scheduled = False
self.model_container = moose.Neutral('/model')
self.data_container = moose.Neutral('/data')
self.squid_axon = SquidAxon('/model/squid_axon')
self.clamp_ckt = ClampCircuit('/model/electronics', self.squid_axon)
self.simdt = 0.0
self.plotdt = 0.0
self.setup_recording()
def setup_recording(self):
# Setup data collection
self.vm_table = moose.Table('/data/Vm')
moose.connect(self.vm_table, 'requestOut', self.squid_axon, 'getVm')
self.cmd_table = moose.Table('/data/command')
moose.connect(self.cmd_table, 'requestOut', self.clamp_ckt.vclamp,
'getOutputValue')
self.iclamp_table = moose.Table('/data/Iclamp')
moose.connect(self.iclamp_table, 'requestOut', self.clamp_ckt.iclamp,
'getOutputValue')
self.vclamp_table = moose.Table('/data/Vclamp')
moose.connect(self.vclamp_table, 'requestOut', self.clamp_ckt.pid,
'getOutputValue')
self.m_table = moose.Table('/data/m')
moose.connect(self.m_table, 'requestOut', self.squid_axon.Na_channel,
'getX')
self.h_table = moose.Table('/data/h')
moose.connect(self.h_table, 'requestOut', self.squid_axon.Na_channel,
'getY')
self.n_table = moose.Table('/data/n')
moose.connect(self.n_table, 'requestOut', self.squid_axon.K_channel,
'getX')
self.ina_table = moose.Table('/data/INa')
moose.connect(self.ina_table, 'requestOut', self.squid_axon.Na_channel,
'getIk')
self.ik_table = moose.Table('/data/IK')
moose.connect(self.ik_table, 'requestOut', self.squid_axon.K_channel,
'getIk')
self.gna_table = moose.Table('/data/GNa')
moose.connect(self.gna_table, 'requestOut', self.squid_axon.Na_channel,
'getGk')
self.gk_table = moose.Table('/data/GK')
moose.connect(self.gk_table, 'requestOut', self.squid_axon.K_channel,
'getGk')
def schedule(self, simdt, plotdt, clampmode):
self.simdt = simdt
self.plotdt = plotdt
if clampmode == 'vclamp':
self.clamp_ckt.do_voltage_clamp()
else:
self.clamp_ckt.do_current_clamp()
moose.setClock(0, simdt)
moose.setClock(1, simdt)
moose.setClock(2, simdt)
moose.setClock(3, plotdt)
# Ensure we do not create multiple scheduling
if not self.scheduled:
moose.useClock(
0, '%s/#[TYPE=Compartment]' % (self.model_container.path),
'init')
moose.useClock(0, '%s/##' % (self.clamp_ckt.path), 'process')
moose.useClock(
1, '%s/#[TYPE=Compartment]' % (self.model_container.path),
'process')
moose.useClock(2, '%s/#[TYPE=HHChannel]' % (self.squid_axon.path),
'process')
moose.useClock(3, '%s/#[TYPE=Table]' % (self.data_container.path),
'process')
self.scheduled = True
moose.reinit()
def run(self, runtime):
moose.start(runtime)
def save_data(self):
for child in self.data_container.children:
tab = moose.Table(child)
tab.xplot('%s.dat' % (tab.name), tab.name)