def main():
gid = 0
model = 'kr'
cell_size = 120
N = 20
neurons = [KhaliqRaman(gid,
{'diameter':cell_size,'length':cell_size,
'nSynapses':0,'channelNoise':False})
for gid in range(N)]
baseline = []
pulse = []
for n,current in zip(neurons,np.linspace(0.04,0.07,N)):
baseline.append(h.IClamp(n.soma(0.5)))
baseline[-1].amp = -0.17
baseline[-1].dur = 2000
baseline[-1].delay = 0
pulse.append(h.IClamp(n.soma(0.5)))
pulse[-1].amp = current
pulse[-1].dur = 1000
pulse[-1].delay = 500
for i,n in enumerate(neurons):
n.addSomaticVoltageRecorder()
time = h.Vector()
time.record(h._ref_t)
h.load_file('stdrun.hoc')
h.tstop = 2000
h.run()
import pylab as plt
fig = plt.figure()
for i,n in enumerate(neurons):
# fig.add_subplot(len(neurons),1,i)
plt.plot(time,n.somaticVoltage()+(i-1)*5)
plt.show()
ipdb.set_trace()
h.quit()
def makeStimulus(neuron, simTime):
VecAxon = h.Vector()
VecAxon.record(neuron(0.5)._ref_v)
stim = h.IClamp(neuron(0))
stim.dur = simTime
vecCurrent = h.Vector()
vecCurrent.record(stim._ref_i)
time = h.Vector()
time.record(h._ref_t)
listOfSines = []
listOfTimes = []
for i in range(0, simTime):
a = random.randint(1, 100)
if a > 95:
listOfSines.append(15)
else:
listOfSines.append(0)
listOfTimes.append(i)
print listOfSines
VecT = h.Vector(listOfTimes)
VecStim = h.Vector(listOfSines)
VecStim.play(stim._ref_amp, VecT, 1)
return (VecStim, VecT, stim)
# iPID = []
iPulse = []
#estimatedFreq = []
# gaussCurrent = []
for i,n in enumerate(neurons):
n.addSomaticVoltageRecorder()
# iPID.append(h.Vector())
iPulse.append(h.Vector())
# estimatedFreq.append(h.Vector())
# gaussCurrent.append(h.Vector())
# iPID[-1].record(n._prc_sobol._ref_iPI)
iPulse[i].record(n._prc_sobol._ref_iPulse)
# gaussCurrent[-1].record(n._IClampNoise._ref_i)
# estimatedFreq[-1].record(n._prc_sobol._ref_estimatedFreq)
time = h.Vector()
time.record(h._ref_t)
h.load_file('stdrun.hoc')
print('Going to run for %dms'%duration)
h.tstop = duration
h.run()
# print neurons[0].perturbationTimes()
print('Computed prc for frequency %3.0fHz.'%(frequency))
downsampleFactor=4
for ii,n in enumerate(neurons):
saveNeuron(filename, n, saveVoltage=False, simulationName='PRC %s'%(model))
fid = h5.File(filename, 'a')
groupName = '/Neurons/ID_' + str(n.ID)
group = fid[groupName]
ds = group.create_dataset('Perturbation',data= np.array(iPulse[ii])[::downsampleFactor])
dt = np.unique(np.round(np.diff(np.array(time)[::downsampleFactor]),3))[0]