def run(nogui):
reader = NML2Reader(verbose=True)
filename = 'test_files/passiveCell.nml'
print('Loading: %s' % filename)
reader.read(filename)
msoma = reader.getComp(reader.doc.networks[0].populations[0].id, 0, 0)
print(msoma)
data = moose.Neutral('/data')
pg = reader.getInput('pulseGen1')
inj = moose.Table('%s/pulse' % (data.path))
moose.connect(inj, 'requestOut', pg, 'getOutputValue')
vm = moose.Table('%s/Vm' % (data.path))
moose.connect(vm, 'requestOut', msoma, 'getVm')
simdt = 1e-6
plotdt = 1e-4
simtime = 150e-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)
print("Finished simulation!")
t = np.linspace(0, simtime, len(vm.vector))
if not nogui:
import matplotlib.pyplot as plt
plt.subplot(211)
plt.plot(t, vm.vector * 1e3, label='Vm (mV)')
plt.legend()
plt.title('Vm')
plt.subplot(212)
plt.title('Input')
plt.plot(t, inj.vector * 1e9, label='injected (nA)')
#plt.plot(t, gK.vector * 1e6, label='K')
#plt.plot(t, gNa.vector * 1e6, label='Na')
plt.legend()
plt.show()
plt.close()
def setUp(self):
self.reader = NML2Reader()
self.lib = moose.Neutral('/library')
self.filename = 'test_files/Granule_98/Granule_98.nml'
self.reader.read(self.filename)
for ncell in self.reader.nml_to_moose:
if isinstance(ncell, nml.Cell):
self.ncell = ncell
break
self.mcell = moose.element(moose.wildcardFind('/##[ISA=Cell]')[0])
def setUp(self):
self.reader = NML2Reader(verbose=True)
self.lib = moose.Neutral('/library')
self.filename = 'test_files/passiveCell.nml'
print('Loading: %s' % self.filename)
self.reader.read(self.filename)
for ncell in self.reader.nml_to_moose:
if isinstance(ncell, nml.Cell):
self.ncell = ncell
break
self.mcell = moose.element('/library/%s' % self.ncell.id)
self.soma = moose.element(self.mcell.path + '/soma')
def setUp(self):
self.reader = NML2Reader()
self.lib = moose.Neutral('/library')
self.filename = 'test_files/NML2_FullCell.nml'
self.reader.read(self.filename)
for ncell in self.reader.nml_to_moose:
if isinstance(ncell, nml.Cell):
self.ncell = ncell
break
self.mcell = moose.element('/library/SpikingCell')
self.soma = moose.element(self.mcell.path + '/Soma')
self.dendrite1 = moose.element(self.mcell.path + '/Dendrite1')
self.dendrite2 = moose.element(self.mcell.path + '/Dendrite2')
self.spine1 = moose.element(self.mcell.path + '/Spine1')