def run_sim(model, data, simtime=100e-3, simdt=1e-6, plotdt=1e-4, solver='ee'):
"""Reset and run the simulation.
model: model container element
data: data container element
simtime: simulation run time
simdt: simulation timestep
plotdt: plotting time step
solver: neuronal solver to use.
"""
global inited
if not inited:
utils.resetSim([model.path, data.path],
simdt,
plotdt,
simmethod=solver)
inited = True
else:
moose.reinit()
moose.start(simtime)
def runsim(self, simtime, stepsize=0.1, pulsearray=None):
"""Run the simulation for `simtime`. Save the data at the
end."""
mutils.resetSim([self.model_container.path, self.data_container.path], self.simdt, self.plotdt, simmethod=self.solver)
if pulsearray is not None:
self.tweak_stimulus(pulsearray)
moose.reinit()
start = datetime.now()
step_run(simtime, stepsize)
end = datetime.now()
# The sleep is required to get all threads to end
while moose.isRunning():
time.sleep(0.1)
delta = end - start
config.logger.info('Simulation time with solver %s: %g s' % \
(self.solver,
delta.seconds + delta.microseconds * 1e-6))
self.tseries = np.arange(0, simtime+self.plotdt, self.plotdt)
# Now save the data
for table_id in self.data_container.children:
try:
data = np.vstack((self.tseries, table_id[0].vec))
except ValueError as e:
self.tseries = np.linspace(0, simtime, len(table_id[0].vec))
data = np.vstack((self.tseries, table_id[0].vec))
fname = 'data/%s_%s_%s.dat' % (self.celltype,
table_id[0].name,
self.solver)
np.savetxt(fname, np.transpose(data))
print 'Saved', table_id[0].name, 'in', fname
def assignClocks(self,modelpath,modeltype):
if modeltype == MooseHandler.type_kkit:
#self.mooseHandler.updateClocks(MooseHandler.DEFAULT_SIMDT_KKIT, MooseHandler.DEFAULT_PLOTDT_KKIT)
#script auto asigns clocks!
pass
elif modeltype == MooseHandler.type_neuroml:
#self.mooseHandler.updateClocks(MooseHandler.DEFAULT_SIMDT, MooseHandler.DEFAULT_PLOTDT)
#print MooseHandler.DEFAULT_SIMDT, MooseHandler.DEFAULT_PLOTDT
if moose.exists('/cells'):
#use Aditya's method to assign clocks - also reinits!
## Exponential Euler
#mooseUtils.resetSim(['/cells','/elec'], MooseHandler.DEFAULT_SIMDT, MooseHandler.DEFAULT_PLOTDT, simmethod='ee')
## HSolve
mooseUtils.resetSim(['/cells','/elec'], MooseHandler.DEFAULT_SIMDT, MooseHandler.DEFAULT_PLOTDT)
else:
print "This NeuroML model does not have any <population> of cells."
print "You need to load a NetworkML or NeuroML level 3 model."
elif modeltype == MooseHandler.type_python:
#specific for the hopfield tutorial!
#self.mooseHandler.updateClocks(MooseHandler.DEFAULT_SIMDT, MooseHandler.DEFAULT_PLOTDT)
clock = 1e-4
self.simControlSimdtLineEdit.setText(str(clock))
self.simControlPlotdtLineEdit.setText(str(clock))
self.mooseHandler.updateClocks(clock, clock) #simdt,plotdt
moose.useClock(1, '/hopfield/##[TYPE=IntFire]', 'process')
moose.useClock(2, '/hopfield/##[TYPE=PulseGen]', 'process')
moose.useClock(2, '/hopfield/##[TYPE=SpikeGen]', 'process')
moose.useClock(8, '/hopfield/##[TYPE=Table]', 'process')
else:
print 'Clocks have not been assigned! - GUI does not support this format yet'
def test_hhcomp():
"""Create and simulate a single spherical compartment with
Hodgkin-Huxley Na and K channel.
Plots Vm, injected current, channel conductances.
"""
model = moose.Neutral('/model')
data = moose.Neutral('/data')
comp, na, k = create_hhcomp(parent=model.path)
print comp.Rm, comp.Cm, na.Ek, na.Gbar, k.Ek, k.Gbar
pg = moose.PulseGen('%s/pg' % (model.path))
pg.firstDelay = 20e-3
pg.firstWidth = 40e-3
pg.firstLevel = 1e-9
pg.secondDelay = 1e9
moose.connect(pg, 'output', comp, 'injectMsg')
inj = moose.Table('%s/pulse' % (data.path))
moose.connect(inj, 'requestOut', pg, 'getOutputValue')
vm = moose.Table('%s/Vm' % (data.path))
moose.connect(vm, 'requestOut', comp, 'getVm')
gK = moose.Table('%s/gK' % (data.path))
moose.connect(gK, 'requestOut', k, 'getGk')
gNa = moose.Table('%s/gNa' % (data.path))
moose.connect(gNa, 'requestOut', na, 'getGk')
simdt = 1e-6
plotdt = 1e-4
simtime = 100e-3
if (1):
moose.showmsg( '/clock' )
for i in range(8):
moose.setClock( i, simdt )
moose.setClock( 8, plotdt )
moose.reinit()
else:
utils.resetSim([model.path, data.path], simdt, plotdt, simmethod='ee')
moose.showmsg( '/clock' )
moose.start(simtime)
t = np.linspace(0, simtime, len(vm.vector))
plt.subplot(211)
plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
plt.plot(t, inj.vector * 1e9, label='injected (nA)')
plt.legend()
plt.title('Vm')
plt.subplot(212)
plt.title('Conductance (uS)')
plt.plot(t, gK.vector * 1e6, label='K')
plt.plot(t, gNa.vector * 1e6, label='Na')
plt.legend()
plt.show()
plt.close()
def run_sim(model, data, simtime=100e-3, simdt=1e-6, plotdt=1e-4, solver='ee'):
"""Reset and run the simulation.
model: model container element \n
data: data container element \n
simtime: simulation run time \n
simdt: simulation timestep \n
plotdt: plotting time step \n
solver: neuronal solver to use \n
"""
global inited
if not inited:
utils.resetSim([model.path, data.path], simdt, plotdt, simmethod=solver)
inited = True
else:
moose.reinit()
moose.start(simtime)
def vclamptest(compartment,
vclamp,
duration=50e-3,
delay=150e-3,
solver='ee',
vhold=None,
mc=None,
dc=None,
simdt=1e-5,
plotdt=0.25e-3):
"""Do a series of voltage clamp experiemnts on compartment.
parameters:
compartment: Compartment object to be voltage clamped
vclamp: array of clamping voltage values.
duration: duration of each clamp
delay: delay between successive application of clamping voltages
vhold: holding voltage, If None, the Em of the
compartment is used.
mc: model container, the vclamp object will be created inside
mc/electronics. If None, we use compartment.parent.parent
dc: data container, the data recording tables will be created
inside it. If None, we use compartment.parent.parent
"""
if vhold is None:
vhold = compartment.Em
if mc is None:
mc = compartment.parent.parent
if dc is None:
dc = compartment.parent.parent
electronics = moose.Neutral('%s/electronics' % (mc.path))
command = moose.PulseGen('%s/command_source' % (electronics.path))
clamp = moose.VClamp('%s/vclamp' % (electronics.path))
moose.connect(command, 'output', clamp, 'commandIn')
moose.connect(compartment, 'VmOut', clamp, 'sensedIn')
moose.connect(clamp, 'currentOut', compartment, 'injectMsg')
simtime = 0
command.count = len(vclamp)
command.baseLevel = vhold
for ii, clamping_voltage in enumerate(vclamp):
simtime += delay + duration
command.delay[ii] = delay
command.width[ii] = duration
command.level[ii] = clamping_voltage
injected = moose.Table('%s/Iinject' % (dc.path))
moose.connect(injected, 'requestData', clamp, 'getCurrent')
voltage = moose.Table('%s/Vcommand' % (dc.path))
moose.connect(voltage, 'requestData', command, 'getOutputValue')
vm = moose.Table('%s/Vm' % (dc.path))
moose.connect(vm, 'requestData', compartment, 'getVm')
utils.resetSim([mc.path, dc.path], simdt, plotdt, simmethod=solver)
moose.start(simtime)
ivec = np.asarray(injected.vector)
vvec = np.asarray(voltage.vector)
vmvec = np.asarray(vm.vector)
ts = np.linspace(0, simtime, len(vvec))
sidx = np.nonzero(np.diff(vvec) > 0)[0]
eidx = np.nonzero(np.diff(vvec) < 0)[0]
iarrays = []
for ii in range(len(vclamp)):
iarrays.append(ivec[sidx[ii]:eidx[ii]].copy())
return {
"Vm": vmvec,
"commandVoltage": vvec,
"inject": ivec,
"ts": ts,
"injectArrays": iarrays
}
def vclamptest(compartment, vclamp, duration=50e-3, delay=150e-3, solver='ee', vhold=None, mc=None, dc=None, simdt=1e-5, plotdt=0.25e-3):
"""Do a series of voltage clamp experiemnts on compartment.
parameters:
compartment: Compartment object to be voltage clamped
vclamp: array of clamping voltage values.
duration: duration of each clamp
delay: delay between successive application of clamping voltages
vhold: holding voltage, If None, the Em of the
compartment is used.
mc: model container, the vclamp object will be created inside
mc/electronics. If None, we use compartment.parent.parent
dc: data container, the data recording tables will be created
inside it. If None, we use compartment.parent.parent
"""
if vhold is None:
vhold = compartment.Em
if mc is None:
mc = compartment.parent.parent
if dc is None:
dc = compartment.parent.parent
electronics = moose.Neutral('%s/electronics' % (mc.path))
command = moose.PulseGen('%s/command_source' % (electronics.path))
clamp = moose.VClamp('%s/vclamp' % (electronics.path))
moose.connect(command, 'output', clamp, 'commandIn')
moose.connect(compartment, 'VmOut', clamp, 'sensedIn')
moose.connect(clamp, 'currentOut', compartment, 'injectMsg')
simtime = 0
command.count = len(vclamp)
command.baseLevel = vhold
for ii, clamping_voltage in enumerate(vclamp):
simtime += delay + duration
command.delay[ii] = delay
command.width[ii] = duration
command.level[ii] = clamping_voltage
injected = moose.Table('%s/Iinject' % (dc.path))
moose.connect(injected, 'requestOut', clamp, 'getCurrent')
voltage = moose.Table('%s/Vcommand' % (dc.path))
moose.connect(voltage, 'requestOut', command, 'getOutputValue')
vm = moose.Table('%s/Vm' % (dc.path))
moose.connect(vm, 'requestOut', compartment, 'getVm')
utils.resetSim([mc.path, dc.path], simdt, plotdt, simmethod=solver)
moose.start(simtime)
ivec = np.asarray(injected.vector)
vvec = np.asarray(voltage.vector)
vmvec = np.asarray(vm.vector)
ts = np.linspace(0, simtime, len(vvec))
sidx = np.nonzero(np.diff(vvec) > 0)[0]
eidx = np.nonzero(np.diff(vvec) < 0)[0]
iarrays = []
for ii in range(len(vclamp)):
iarrays.append(ivec[sidx[ii]: eidx[ii]].copy())
return {
"Vm": vmvec,
"commandVoltage": vvec,
"inject": ivec,
"ts": ts,
"injectArrays": iarrays}