def runsim(self, simtime, stepsize=0.1, pulsearray=None):
"""Run the simulation for `simtime`. Save the data at the
end."""
config.logger.info('running: simtime=%g, stepsize=%g, pulsearray=%s' %
(simtime, stepsize, str(pulsearray)))
self.simtime = simtime
if pulsearray is not None:
self.tweak_stimulus(pulsearray)
for ii in range(self.pulsegen.count):
config.logger.info(
'pulse[%d]: delay=%g, width=%g, level=%g' %
(ii, self.pulsegen.delay[ii], self.pulsegen.width[ii],
self.pulsegen.level[ii]))
config.logger.info('Start reinit')
self.schedule(self.simdt, self.plotdt, self.solver)
moose.reinit()
config.logger.info('Finished reinit')
ts = datetime.now()
mutils.stepRun(simtime,
simtime / 10.0,
verbose=True,
logger=config.logger)
# The sleep is required to get all threads to end
while moose.isRunning():
time.sleep(0.1)
te = datetime.now()
td = te - ts
config.logger.info('Simulation time of %g s at simdt=%g with solver %s: %g s' % \
(simtime, self.simdt, self.solver,
td.seconds + td.microseconds * 1e-6))
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 _runSlot(self):
if moose.isRunning():
print("Stopping simulation in progress ...")
moose.stop()
self._runtime = self.getFloatInput(self._runTimeEdit, self._runTimeLabel.text())
self._overlayPlots(self._overlayAction.isChecked())
self._simdt = self.getFloatInput(self._simTimeStepEdit, self._simTimeStepLabel.text())
clampMode = None
singlePulse = True
if self._electronicsTab.currentWidget() == self._vClampCtrlBox:
clampMode = "vclamp"
baseLevel = self.getFloatInput(self._holdingVEdit, self._holdingVLabel.text())
firstDelay = self.getFloatInput(self._holdingTimeEdit, self._holdingTimeLabel.text())
firstWidth = self.getFloatInput(self._prePulseTimeEdit, self._prePulseTimeLabel.text())
firstLevel = self.getFloatInput(self._prePulseVEdit, self._prePulseVLabel.text())
secondDelay = firstWidth
secondWidth = self.getFloatInput(self._clampTimeEdit, self._clampTimeLabel.text())
secondLevel = self.getFloatInput(self._clampVEdit, self._clampVLabel.text())
if not self._autoscaleAction.isChecked():
self._im_axes.set_ylim(-10.0, 10.0)
else:
clampMode = "iclamp"
baseLevel = self.getFloatInput(self._baseCurrentEdit, self._baseCurrentLabel.text())
firstDelay = self.getFloatInput(self._firstDelayEdit, self._firstDelayLabel.text())
firstWidth = self.getFloatInput(self._firstPulseWidthEdit, self._firstPulseWidthLabel.text())
firstLevel = self.getFloatInput(self._firstPulseEdit, self._firstPulseLabel.text())
secondDelay = self.getFloatInput(self._secondDelayEdit, self._secondDelayLabel.text())
secondLevel = self.getFloatInput(self._secondPulseEdit, self._secondPulseLabel.text())
secondWidth = self.getFloatInput(self._secondPulseWidthEdit, self._secondPulseWidthLabel.text())
singlePulse = self._pulseMode.currentIndex() == 0
if not self._autoscaleAction.isChecked():
self._im_axes.set_ylim(-0.4, 0.4)
self.squid_setup.clamp_ckt.configure_pulses(
baseLevel=baseLevel,
firstDelay=firstDelay,
firstWidth=firstWidth,
firstLevel=firstLevel,
secondDelay=secondDelay,
secondWidth=secondWidth,
secondLevel=secondLevel,
singlePulse=singlePulse,
)
if self._kConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gK = 0.0
else:
self.squid_setup.squid_axon.specific_gK = SquidAxon.defaults["specific_gK"]
if self._naConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gNa = 0.0
else:
self.squid_setup.squid_axon.specific_gNa = SquidAxon.defaults["specific_gNa"]
self.squid_setup.squid_axon.celsius = self.getFloatInput(self._temperatureEdit, self._temperatureLabel.text())
self.squid_setup.squid_axon.K_out = self.getFloatInput(self._kOutEdit, self._kOutLabel.text())
self.squid_setup.squid_axon.Na_out = self.getFloatInput(self._naOutEdit, self._naOutLabel.text())
self.squid_setup.squid_axon.K_in = self.getFloatInput(self._kInEdit, self._kInLabel.text())
self.squid_setup.squid_axon.Na_in = self.getFloatInput(self._naInEdit, self._naInLabel.text())
self.squid_setup.squid_axon.updateEk()
self.squid_setup.schedule(self._simdt, self._plotdt, clampMode)
# The following line is for use with Qthread
self.squid_setup.run(self._runtime)
self._updateAllPlots()
def _runSlot(self):
if moose.isRunning():
print('Stopping simulation in progress ...')
moose.stop()
self._runtime = self.getFloatInput(self._runTimeEdit, self._runTimeLabel.text())
self._overlayPlots(self._overlayAction.isChecked())
self._simdt = self.getFloatInput(self._simTimeStepEdit, self._simTimeStepLabel.text())
clampMode = None
singlePulse = True
if self._electronicsTab.currentWidget() == self._vClampCtrlBox:
clampMode = 'vclamp'
baseLevel = self.getFloatInput(self._holdingVEdit, self._holdingVLabel.text())
firstDelay = self.getFloatInput(self._holdingTimeEdit, self._holdingTimeLabel.text())
firstWidth = self.getFloatInput(self._prePulseTimeEdit, self._prePulseTimeLabel.text())
firstLevel = self.getFloatInput(self._prePulseVEdit, self._prePulseVLabel.text())
secondDelay = firstWidth
secondWidth = self.getFloatInput(self._clampTimeEdit, self._clampTimeLabel.text())
secondLevel = self.getFloatInput(self._clampVEdit, self._clampVLabel.text())
if not self._autoscaleAction.isChecked():
self._im_axes.set_ylim(-10.0, 10.0)
else:
clampMode = 'iclamp'
baseLevel = self.getFloatInput(self._baseCurrentEdit, self._baseCurrentLabel.text())
firstDelay = self.getFloatInput(self._firstDelayEdit, self._firstDelayLabel.text())
firstWidth = self.getFloatInput(self._firstPulseWidthEdit, self._firstPulseWidthLabel.text())
firstLevel = self.getFloatInput(self._firstPulseEdit, self._firstPulseLabel.text())
secondDelay = self.getFloatInput(self._secondDelayEdit, self._secondDelayLabel.text())
secondLevel = self.getFloatInput(self._secondPulseEdit, self._secondPulseLabel.text())
secondWidth = self.getFloatInput(self._secondPulseWidthEdit, self._secondPulseWidthLabel.text())
singlePulse = (self._pulseMode.currentIndex() == 0)
if not self._autoscaleAction.isChecked():
self._im_axes.set_ylim(-0.4, 0.4)
self.squid_setup.clamp_ckt.configure_pulses(baseLevel=baseLevel,
firstDelay=firstDelay,
firstWidth=firstWidth,
firstLevel=firstLevel,
secondDelay=secondDelay,
secondWidth=secondWidth,
secondLevel=secondLevel,
singlePulse=singlePulse)
if self._kConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gK = 0.0
else:
self.squid_setup.squid_axon.specific_gK = SquidAxon.defaults['specific_gK']
if self._naConductanceToggle.isChecked():
self.squid_setup.squid_axon.specific_gNa = 0.0
else:
self.squid_setup.squid_axon.specific_gNa = SquidAxon.defaults['specific_gNa']
self.squid_setup.squid_axon.celsius = self.getFloatInput(self._temperatureEdit, self._temperatureLabel.text())
self.squid_setup.squid_axon.K_out = self.getFloatInput(self._kOutEdit, self._kOutLabel.text())
self.squid_setup.squid_axon.Na_out = self.getFloatInput(self._naOutEdit, self._naOutLabel.text())
self.squid_setup.squid_axon.K_in = self.getFloatInput(self._kInEdit, self._kInLabel.text())
self.squid_setup.squid_axon.Na_in = self.getFloatInput(self._naInEdit, self._naInLabel.text())
self.squid_setup.squid_axon.updateEk()
self.squid_setup.schedule(self._simdt, self._plotdt, clampMode)
# The following line is for use with Qthread
self.squid_setup.run(self._runtime)
self._updateAllPlots()
def run(self):
print((self.name, 'Starting run for', self.runtime, ' seconds'))
moose.reinit()
moose.start(self.runtime)
while moose.isRunning():
time.sleep(1.0)
print((self.name, 'Table length', len(moose.Table('/tab').vector)))
print((self.name, 'Finishing simulation'))
worker_queue.put(self.name)
def run(self, key):
try:
Vm = self.Vm_tables[key]
u = self.u_tables[key]
except KeyError as e:
Vm = moose.Table(self.data_container.path + '/' + key + '_Vm')
nrn = self.neurons[key]
moose.connect(Vm, 'requestOut', nrn, 'getVm')
utable = moose.Table(self.data_container.path + '/' + key + '_u')
utable.connect('requestOut', self.neurons[key], 'getU')
self.Vm_tables[key] = Vm
self.u_tables[key] = utable
try:
Im = self.inject_tables[key]
except KeyError as e:
Im = moose.Table(
self.data_container.path + '/' + key +
'_inject') # May be different for non-pulsegen sources.
Im.connect('requestOut', self._get_neuron(key), 'getIm')
self.inject_tables[key] = Im
self.simtime = IzhikevichDemo.parameters[key][7] * 1e-3
for obj in moose.wildcardFind('%s/##' % (self.model_container.path)):
if obj not in self.scheduled:
moose.useClock(0, obj.path, 'process')
self.scheduled[obj] = True
for obj in moose.wildcardFind('%s/##' % (self.data_container.path)):
if obj not in self.scheduled:
moose.useClock(2, obj.path, 'process')
self.scheduled[obj] = True
moose.reinit()
moose.start(self.simtime)
while moose.isRunning():
time.sleep(100)
time = linspace(0, IzhikevichDemo.parameters[key][7], len(Vm.vector))
# DEBUG
nrn = self._get_neuron(key)
print(('a = %g, b = %g, c = %g, d = %g, initVm = %g, initU = %g' %
(nrn.a, nrn.b, nrn.c, nrn.d, nrn.initVm, nrn.initU)))
#! DEBUG
return (time, Vm, Im)
def runsim(self, simtime, stepsize=0.1, pulsearray=None):
"""Run the simulation for `simtime`. Save the data at the
end."""
config.logger.info('running: simtime=%g, stepsize=%g, pulsearray=%s' % (simtime, stepsize, str(pulsearray)))
self.simtime = simtime
if pulsearray is not None:
self.tweak_stimulus(pulsearray)
for ii in range(self.pulsegen.count):
config.logger.info('pulse[%d]: delay=%g, width=%g, level=%g' % (ii, self.pulsegen.delay[ii], self.pulsegen.width[ii], self.pulsegen.level[ii]))
config.logger.info('Start reinit')
self.schedule(self.simdt, self.plotdt, self.solver)
moose.reinit()
config.logger.info('Finished reinit')
ts = datetime.now()
mutils.stepRun(simtime, simtime/10.0, verbose=True, logger=config.logger)
# The sleep is required to get all threads to end
while moose.isRunning():
time.sleep(0.1)
te = datetime.now()
td = te - ts
config.logger.info('Simulation time of %g s at simdt=%g with solver %s: %g s' % \
(simtime, self.simdt, self.solver,
td.seconds + td.microseconds * 1e-6))
def run(self, key):
try:
Vm = self.Vm_tables[key]
u = self.u_tables[key]
except KeyError as e:
Vm = moose.Table(self.data_container.path + '/' + key + '_Vm')
nrn = self.neurons[key]
moose.connect(Vm, 'requestOut', nrn, 'getVm')
utable = moose.Table(self.data_container.path + '/' + key + '_u')
utable.connect('requestOut', self.neurons[key], 'getU')
self.Vm_tables[key] = Vm
self.u_tables[key] = utable
try:
Im = self.inject_tables[key]
except KeyError as e:
Im = moose.Table(self.data_container.path + '/' + key + '_inject') # May be different for non-pulsegen sources.
Im.connect('requestOut', self._get_neuron(key), 'getIm')
self.inject_tables[key] = Im
self.simtime = IzhikevichDemo.parameters[key][7] * 1e-3
for obj in moose.wildcardFind('%s/##' % (self.model_container.path)):
if obj not in self.scheduled:
moose.useClock(0, obj.path, 'process')
self.scheduled[obj] = True
for obj in moose.wildcardFind('%s/##' % (self.data_container.path)):
if obj not in self.scheduled:
moose.useClock(2, obj.path, 'process')
self.scheduled[obj] = True
moose.reinit()
moose.start(self.simtime)
while moose.isRunning():
time.sleep(100)
time = linspace(0, IzhikevichDemo.parameters[key][7], len(Vm.vector))
# DEBUG
nrn = self._get_neuron(key)
print(('a = %g, b = %g, c = %g, d = %g, initVm = %g, initU = %g' % (nrn.a,nrn.b, nrn.c, nrn.d, nrn.initVm, nrn.initU)))
#! DEBUG
return (time, Vm, Im)
self.data_container.path + "/" + key + "_inject"
) # May be different for non-pulsegen sources.
Im.connect("requestOut", self._get_neuron(key), "getIm")
self.inject_tables[key] = Im
self.simtime = IzhikevichDemo.parameters[key][7] * 1e-3
for obj in moose.wildcardFind("%s/##" % (self.model_container.path)):
if obj not in self.scheduled:
moose.useClock(0, obj.path, "process")
self.scheduled[obj] = True
for obj in moose.wildcardFind("%s/##" % (self.data_container.path)):
if obj not in self.scheduled:
moose.useClock(2, obj.path, "process")
self.scheduled[obj] = True
moose.reinit()
moose.start(self.simtime)
while moose.isRunning():
time.sleep(100)
time = linspace(0, IzhikevichDemo.parameters[key][7], len(Vm.vector))
# DEBUG
nrn = self._get_neuron(key)
print "a = %g, b = %g, c = %g, d = %g, initVm = %g, initU = %g" % (
nrn.a,
nrn.b,
nrn.c,
nrn.d,
nrn.initVm,
nrn.initU,
)
#! DEBUG
return (time, Vm, Im)
except KeyError, e:
Im = moose.Table(self.data_container.path + '/' + key + '_inject') # May be different for non-pulsegen sources.
Im.connect('requestOut', self._get_neuron(key), 'getIm')
self.inject_tables[key] = Im
self.simtime = IzhikevichDemo.parameters[key][7] * 1e-3
for obj in moose.wildcardFind('%s/##' % (self.model_container.path)):
if obj not in self.scheduled:
moose.useClock(0, obj.path, 'process')
self.scheduled[obj] = True
for obj in moose.wildcardFind('%s/##' % (self.data_container.path)):
if obj not in self.scheduled:
moose.useClock(2, obj.path, 'process')
self.scheduled[obj] = True
moose.reinit()
moose.start(self.simtime)
while moose.isRunning():
time.sleep(100)
time = linspace(0, IzhikevichDemo.parameters[key][7], len(Vm.vector))
# DEBUG
nrn = self._get_neuron(key)
print 'a = %g, b = %g, c = %g, d = %g, initVm = %g, initU = %g' % (nrn.a,nrn.b, nrn.c, nrn.d, nrn.initVm, nrn.initU)
#! DEBUG
return (time, Vm, Im)
def _get_neuron(self, key):
try:
params = IzhikevichDemo.parameters[key]
except KeyError as e:
print ' %s : Invalid neuron type. The valid types are:' % (key)
for key in IzhikevichDemo.parameters: