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')