def simulate_response_example_clamped_spiking(I_e):
'''
Response when SNR is clamped to a voltage for strong and weak synapse
'''
spike_at = 500. # ms
simTime = 700. # ms
my_nest.ResetKernel()
model_list = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, SYNAPES_MODELS)
SNR = MyGroup(NEURON_MODELS[0],
len(SYNAPES_MODELS) + 1,
mm=True,
mm_dt=0.1,
params={'I_e': I_e})
SG = my_nest.Create('spike_generator', params={'spike_times': [spike_at]})
for i in range(len(SYNAPES_MODELS)):
my_nest.Connect(SG, [SNR[i]], model=SYNAPES_MODELS[i])
my_nest.MySimulate(simTime)
SNR.get_signal('v', 'V_m', stop=simTime) # retrieve signal
SNR.signals['V_m'] = SNR.signals['V_m'].my_time_slice(500, 560)
return SNR
def inspect_network():
model_list, model_dict = models()
layer_list, connect_list = network(model_dict)
# Create neurons and synapses
layer_dic = {}
for name, model, props in layer_list:
my_nest.MyLoadModels(model_dict, [model[1]])
#! Create layer, retrieve neurons ids per elements and p
if model[0] == 'spike_generator':
layer = MyLayerPoissonInput(layer_props=props, sd=False)
else:
layer = MyLayerGroup(layer_props=props,
sd=True,
mm=True,
mm_dt=0.1)
layer_dic[name] = layer
# Connect populations
for conn in connect_list:
my_nest.MyLoadModels(model_dict, [conn[2]['synapse_model']])
name = conn[0] + '_' + conn[1] + '_' + conn[3]
tp.ConnectLayers(layer_dic[conn[0]].layer_id,
layer_dic[conn[1]].layer_id, conn[2])
layer_dic[conn[1]].add_connection(source=layer_dic[conn[0]],
type=conn[3],
props=conn[2])
return layer_dic
def simulate_example(I_e):
simTime = 1000. # ms
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
I_e0 = my_nest.GetDefaults(NEURON_MODELS[0])['I_e']
SNR = MyGroup(NEURON_MODELS[0],
1,
sd=True,
mm=True,
mm_dt=1.,
params={'I_e': I_e + I_e0})
my_nest.MySimulate(simTime)
SNR.get_signal('v', 'V_m', stop=simTime) # retrieve signal
SNR.get_signal('s') # retrieve signal
meanRate = round(SNR.signals['spikes'].mean_rate(0, 1000), 1)
print SNR.signals['spikes'].isi()
SNR.signals['V_m'].my_set_spike_peak(21, spkSignal=SNR.signals['spikes'])
s = '\n'
s = s + 'Example:\n'
s = s + ' %s %5s %3s %s %5s %3s \n' % ('Mean rate:', meanRate, 'Hz', 'I_e',
I_e, 'pA')
infoString = s
return SNR, infoString
def simulate_IF(I_vec):
tStim = 700
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
SNR = MyGroup(NEURON_MODELS[0], 1, mm=True, sd=True, mm_dt=0.1)
I_e0 = my_nest.GetStatus(SNR[:])[0]['I_e']
my_nest.SetStatus(SNR[:], params={'I_e': I_e0 + I_E}) # Set I_e
I_e = my_nest.GetStatus(SNR.ids, 'I_e')[0]
I_vec, fIsi, mIsi, lIsi = SNR.IF(I_vec, tStim=tStim)
speed_f = numpy.diff(1000.0 / fIsi) / numpy.diff(I_vec)
speed_l = numpy.diff(1000.0 / lIsi) / numpy.diff(I_vec)
speed_f = speed_f[speed_f > 0]
speed_l = speed_l[speed_l > 0]
s = '\n'
s = s + 'IF:\n'
s = s + ' %s %5s %3s \n' % ('First to Last ISI:', tStim, 'ms')
s = s + ' %s %5s %3s \n' % ('Added I_e:', I_e, 'pA')
s = s + ' %s %4s %s %4s %s %4s\n' % (
'Speed first ((Hz/pA), min:', str(min(speed_f))[0:4], 'max',
str(max(speed_f))[0:4], 'mean', str(sum(speed_f) / len(speed_f))[0:4])
s = s + ' %s %4s %s %4s %s %4s\n' % (
'Speed last (Hz/pA), min:', str(min(speed_l))[0:4], 'max',
str(max(speed_l))[0:4], 'mean', str(sum(speed_l) / len(speed_l))[0:4])
infoString = s
return I_vec, fIsi, mIsi, lIsi, infoString
def simulate_IV(I_vec):
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
SNR = MyGroup(NEURON_MODELS[0], 1, sd=True, mm=True, mm_dt=0.1)
I_e0 = my_nest.GetStatus(SNR[:])[0]['I_e']
my_nest.SetStatus(SNR[:], params={'I_e': I_e0 + I_E}) # Set I_e
I_e = my_nest.GetStatus(SNR.ids, 'I_e')[0]
I_vec, voltage = SNR.IV_I_clamp(I_vec)
#current=current
speed = numpy.diff(voltage) / numpy.diff(I_vec) * 1000.
speed = speed[speed > 0]
s = '\n'
s = s + 'IV:\n'
s = s + ' %s %5s %3s \n' % ('I_e:', I_e, 'pA')
'''
s = s + ' %s %4s %s %4s %s %4s\n' % ( 'Speed (mV/pA=MOhm), min:',
str(min(speed))[0:4],
'max',str(max(speed))[0:4],
'mean',
str(sum(speed)/len(speed))[0:4])
'''#
infoString = s
I_vec = numpy.array(I_vec)
voltage = numpy.array(voltage)
return I_vec, voltage, infoString
def simulate_voltage_ipsp(I_vec):
v_mat = []
ipsp_mat = []
for receptor, syn_model in zip(['V_m', 'V_m', 'V_m'], SYNAPSE_MODELS):
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, [syn_model])
SNR = MyGroup(NEURON_MODELS[0], 1, mm=True, mm_dt=0.1)
voltage, ipsp = SNR.I_PSE(I_vec,
synapse_model=syn_model,
id=0,
receptor=receptor)
v_mat.append(voltage)
ipsp_mat.append(ipsp)
v_mat = numpy.array(v_mat)
ipsp_mat = numpy.array(ipsp_mat)
return v_mat, ipsp_mat
def inspect_network():
model_list, model_dict = models()
layer_list, connect_list = network(model_dict)
# Create neurons and synapses
layer_dic={}
for name, model, props in layer_list:
my_nest.MyLoadModels( model_dict, [model[1]] )
#! Create layer, retrieve neurons ids per elements and p
if model[0]=='spike_generator':
layer=MyLayerPoissonInput(layer_props=props, sd=False)
else:
layer=MyLayerGroup(layer_props=props, sd=True, mm=True, mm_dt = 0.1 )
layer_dic[name]=layer
# Connect populations
for conn in connect_list:
my_nest.MyLoadModels( model_dict, [conn[2]['synapse_model']] )
name=conn[0] + '_' + conn[1]+'_'+conn[3]
tp.ConnectLayers(layer_dic[conn[0]].layer_id, layer_dic[conn[1]].layer_id, conn[2])
layer_dic[conn[1]].add_connection(source=layer_dic[conn[0]], type=conn[3], props=conn[2])
return layer_dic
def plot_text(ax, info_string=''):
my_nest.ResetKernel()
MODEL_LIST = models()
my_nest.MyLoadModels(MODEL_LIST, NEURON_MODELS)
SNR = MyGroup(NEURON_MODELS[0], 1, mm_dt=0.1)
statusSNR = my_nest.GetStatus(SNR[:])[0]
tb = ''
tb = tb + info_string
tb = tb + '\n'
ax.text(
0.85,
0.5,
tb,
fontsize=font_size_text,
horizontalalignment='right',
verticalalignment='center',
transform=ax.transAxes, # to define coordinates in right scale
**{'fontname': 'monospace'})
ax.my_remove_axis(xaxis=True, yaxis=True)
ax.my_remove_spine(left=True, bottom=True, right=True, top=True)
def simulate_steady_state_freq(frequencies, flag='ss'):
global sname_nb
relativeFacilitation=[]
model_list=models()
data={}
n=len(frequencies)
for syn in synapseModels:
my_nest.ResetKernel()
my_nest.MyLoadModels( model_list, neuronModels )
my_nest.MyLoadModels( model_list, [syn])
ss=my_nest.GetDefaults(syn)
synapticEficacy = ss['weight']*ss['U']
SNR = MyGroup( neuronModels[0], n, mm_dt = .1, params={'I_e':-150.},
record_from=['g_GABAA_2'], spath=spath,
sname_nb=sname_nb )
sname_nb+=1
tSim=3*1000/frequencies[0]
spikeTimes=[]
for f in frequencies :
isi = 1000./f
spikeTimes.append(numpy.arange(1,tSim,isi))
if not LOAD:
for target, st in zip(SNR, spikeTimes ) :
source = my_nest.Create('spike_generator',
params={'spike_times':st} )
my_nest.SetDefaults(syn, params={'delay':1.})
my_nest.Connect(source, [target], model=syn)
my_nest.MySimulate(tSim)
SNR.get_signal( 'g','g_GABAA_2', stop=tSim ) # retrieve signal
SNR.save_signal( 'g','g_GABAA_2', stop=tSim )
elif LOAD:
SNR.load_signal( 'g','g_GABAA_2')
signal=SNR.signals['g_GABAA_2']
tmpSteadyState=[]
for i, st in enumerate(spikeTimes, start=1):
if SNR.mm_dt==0.1: indecies=numpy.int64(numpy.ceil(st*10))+9
elif SNR.mm_dt==1.: indecies=numpy.int64(numpy.ceil(st))
values=signal[i].signal[indecies]-signal[i].signal[indecies-1]
if flag=='ss': tmpSteadyState.append(values[-1]/synapticEficacy)
if flag=='max': tmpSteadyState.append(max(values)/synapticEficacy)
relativeFacilitation.append(tmpSteadyState)
relativeFacilitation=numpy.array(relativeFacilitation)
return frequencies, relativeFacilitation
def plot_text(ax, infoString=''):
my_nest.ResetKernel()
model_list = models()
my_nest.MyLoadModels(model_list, neuronModels)
SNR = MyGroup(neuronModels[0], 1, mm_dt=0.1)
statusSNR = my_nest.GetStatus(SNR[:])[0]
tb = ''
tb = tb + ' %s %10s\n' % ('Neuron model', statusSNR['model'])
tb = tb + infoString
tb = tb + '\n'
ax.text(
0.85,
0.5,
tb,
fontsize=font_size_text,
horizontalalignment='right',
verticalalignment='center',
transform=ax.transAxes, # to define coordinates in right scale
**{'fontname': 'monospace'})
ax.my_remove_axis(xaxis=True, yaxis=True)
ax.my_remove_spine(left=True, bottom=True, right=True, top=True)
def plot_text(ax, infoString=''):
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
SNR = MyGroup(NEURON_MODELS[0], 1, mm_dt=0.1)
statusSNR = my_nest.GetStatus(SNR[:])[0]
tb = ''
tb = tb + infoString
tb = tb + '\n'
for key, val in statusSNR.iteritems():
if not key in [
'vp', 'state', 't_spike', 'local', 'parent', 'Delta_T',
'tau_minus_triplet', 'address', 't_ref', 'thread', 'frozen',
'archiver_length', 'global_id', 'local_id', 'recordables',
'receptor_types'
]:
tb = tb + ' %s %5s %3s \n' % (key + ':', str(val), '--')
ax.text(
0.85,
0.5,
tb,
fontsize=font_size_text,
horizontalalignment='right',
verticalalignment='center',
transform=ax.transAxes, # to define coordinates in right scale
**{'fontname': 'monospace'})
ax.my_remove_axis(xaxis=True, yaxis=True)
ax.my_remove_spine(left=True, bottom=True, right=True, top=True)
def simulate_recovery(revoceryTimes):
global sname_nb
relativeRecovery=[]
model_list=models()
data={}
n=len(revoceryTimes)
for syn in synapseModels:
my_nest.ResetKernel()
my_nest.MyLoadModels( model_list, neuronModels )
my_nest.MyLoadModels( model_list, [syn])
ss=my_nest.GetDefaults(syn)
synapticEficacy = ss['weight']*ss['U']
SNR = MyGroup( neuronModels[0], n, mm_dt = .1, params={'I_e':-150.},
record_from=['g_GABAA_2'], spath=spath,
sname_nb=sname_nb)
sname_nb+=1
tSim=5000
spikeTimes=[]
for rt in revoceryTimes:
spikeTimes.append(numpy.array([1.,11.,21.,31.,41.,41+rt]))
if not LOAD:
for target, st in zip(SNR, spikeTimes ) :
source = my_nest.Create('spike_generator',
params={'spike_times':st} )
my_nest.SetDefaults(syn, params={'delay':1.})
my_nest.Connect(source, [target], model=syn)
my_nest.MySimulate(tSim)
SNR.get_signal( 'g','g_GABAA_2', stop=tSim ) # retrieve signal
SNR.save_signal( 'g','g_GABAA_2', stop=tSim )
elif LOAD:
SNR.load_signal( 'g','g_GABAA_2')
signal=SNR.signals['g_GABAA_2']
tmpSteadyState=[]
for i, st in enumerate(spikeTimes, start=1):
if SNR.mm_dt==0.1: indecies=numpy.int64(numpy.ceil(st*10))+9
elif SNR.mm_dt==1.: indecies=numpy.int64(numpy.ceil(st))
values=signal[i].signal[indecies]-signal[i].signal[indecies-1]
tmpSteadyState.append(values[-1]/synapticEficacy)
#tmpSteadyState.append(max(values)/synapticEficacy)
relativeRecovery.append(tmpSteadyState)
relativeRecovery=numpy.array(relativeRecovery)
return revoceryTimes, relativeRecovery
def plot_steady_state_freq(ax, freq_, relative_fac):
colors = ['b', 'g', 'm']
linestyles = ['--', '--', '-']
labels = [
r'$ref_{init}^{MSN_{D1}}$', r'$ref_{max}^{MSN_{D1}}$',
r'$fac^{MSN_{D1}}$'
]
coords = [[0.1, 0.22], [0.2, 0.74], [0.65, 0.45]]
syn_static = ['MSN_SNR_gaba_s_min', 'MSN_SNR_gaba_s_max']
ax.plot(freq_, relative_fac[0, :], **{'color': colors[2]})
ytext = ax.set_ylabel(r'$p_{ss}$/$p_1$')
#pylab.setp(ytext, fontsize=14.)
ax.set_xlabel('Firing rate (spikes/s)')
ax.my_set_no_ticks(yticks=5, xticks=5)
my_nest.ResetKernel()
model_list, model_dict = models()
syns = [SYNAPSE_MODELS[0]]
syns.extend(syn_static)
my_nest.MyLoadModels(model_list, syns)
xdata = ax.lines[0].get_xdata()
ss = my_nest.GetDefaults(SYNAPSE_MODELS[0])
synapticEficacy = ss['weight'] * ss['U']
for syn, color, ls in zip(syn_static, colors[0:2], linestyles[0:2]):
sw = my_nest.GetDefaults(syn)
ax.plot(
[min(xdata), 48],
[sw['weight'] / synapticEficacy, sw['weight'] / synapticEficacy],
**{
'color': color,
'linestyle': ls
})
for coord, label, color in zip(coords, labels, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['font.size'] + 2,
**{'color': color})
lines = ax.lines
for line in lines:
misc.slice_line(line, xlim=[0, 48])
ax.set_xlim(misc.adjust_limit([0, 50]))
ax.set_ylim(misc.adjust_limit([0, 5]))
ax.my_set_no_ticks(yticks=6, xticks=6)
pylab.setp(ax.lines,
linewidth=2.0) # Need to pu ti before generating legend
def simulate_basa_line_STN(ctx_rate,
gpe_rate,
n_ctx,
n_gpe,
neuron_model,
syn_models,
stn_current,
sim_time=1000,
threads=8,
w_GPE_STN=0):
Params_in = {}
if w_GPE_STN: Params_in['GPE_STN_gaba_s'] = w_GPE_STN
model_list, model_dict = models(Params_in)
my_nest.ResetKernel(threads=threads)
my_nest.MyLoadModels(model_dict, neuron_model)
my_nest.MyLoadModels(model_dict, syn_models)
SNR_list = [] # List with SNR groups for synapse.
if n_ctx > 0: CTX = MyPoissonInput(n=n_ctx, sd=True)
if n_gpe > 0: GPE = MyPoissonInput(n=n_gpe, sd=False)
if n_ctx > 0:
CTX.set_spike_times(rates=[ctx_rate],
times=[1],
t_stop=sim_time,
seed=0)
if n_gpe > 0:
GPE.set_spike_times(rates=[gpe_rate],
times=[1],
t_stop=sim_time,
seed=0)
I_e = my_nest.GetDefaults(neuron_model[0])['I_e'] + stn_current
STN = MyGroup(neuron_model[0],
n=1,
sd=True,
params={'I_e': I_e},
mm_dt=.1,
mm=True)
if n_ctx > 0:
my_nest.Connect(CTX[:], STN[:] * len(CTX[:]), model=syn_models[0])
if n_gpe > 0:
my_nest.Connect(GPE[:], STN[:] * len(GPE[:]), model=syn_models[1])
my_nest.MySimulate(sim_time)
STN.get_signal('s', start=0, stop=sim_time)
STN.get_signal('v', recordable='V_m', start=0, stop=sim_time)
return STN
def simulate_voltage_ipsp(I_vec):
simTime = 700. # ms
spikes_at = numpy.arange(500., len(I_vec) * simTime, simTime) # ms
voltage = [] # mV
ipsp_weak = [] # mV
ipsp_strong = [] # mV
my_nest.ResetKernel()
model_list = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, SYNAPES_MODELS)
SNR = MyGroup(NEURON_MODELS[0], len(SYNAPES_MODELS), mm=True, mm_dt=0.1)
SG = my_nest.Create('spike_generator', params={'spike_times': spikes_at})
for i in range(len(SYNAPES_MODELS)):
my_nest.Connect(SG, [SNR[i]], model=SYNAPES_MODELS[i])
simTimeTot = 0
for I_e in I_vec:
my_nest.SetStatus(SNR[:], params={'I_e': float(I_e)})
my_nest.MySimulate(simTime)
simTimeTot += simTime
SNR.get_signal('v', 'V_m', stop=simTimeTot) # retrieve signal
simTimeAcum = 0
for I_e in I_vec:
signal = SNR.signals['V_m'].my_time_slice(400 + simTimeAcum,
700 + simTimeAcum)
simTimeAcum += simTime
clamped_at = signal[1].signal[-1]
minV = min(signal[1].signal)
maxV = max(signal[1].signal)
if abs(minV - clamped_at) < abs(maxV - clamped_at):
size_weak = max(signal[1].signal) - clamped_at
size_strong = max(signal[2].signal) - clamped_at
else:
size_weak = min(signal[1].signal) - clamped_at
size_strong = min(signal[2].signal) - clamped_at
voltage.append(clamped_at)
ipsp_weak.append(size_weak)
ipsp_strong.append(size_strong)
ipsp = numpy.array([ipsp_weak, ipsp_strong])
return voltage, ipsp
def simulate_example_inh_current(I_vec):
simTime = 1000. # ms
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
df = my_nest.GetDefaults(NEURON_MODELS[0])
n = len(I_vec)
STN = MyGroup(NEURON_MODELS[0],
n,
sd=True,
mm=True,
mm_dt=1.0,
record_from=['V_m', 'u'])
I_e0 = my_nest.GetStatus(STN[:])[0]['I_e']
my_nest.SetStatus(STN[:], params={'I_e': I_e0 + I_E + 50}) # Set I_e
I_e = my_nest.GetStatus(STN.ids, 'I_e')[0]
scg = my_nest.Create('step_current_generator', n=n)
rec = my_nest.GetStatus(STN[:])[0]['receptor_types']
for source, target, I in zip(scg, STN[:], I_vec):
my_nest.SetStatus([source], {
'amplitude_times': [280., 700.],
'amplitude_values': [float(I), 0.]
})
my_nest.Connect([source], [target],
params={'receptor_type': rec['CURR']})
my_nest.MySimulate(simTime)
STN.get_signal('v', 'V_m', stop=simTime) # retrieve signal
STN.get_signal('s') # retrieve signal
STN.signals['V_m'].my_set_spike_peak(21, spkSignal=STN.signals['spikes'])
e = my_nest.GetStatus(STN.mm)[0]['events'] # get events
#pylab.plot(e['u'])
#pylab.show()
meanRate = round(STN.signals['spikes'].mean_rate(0, 500), 1)
s = '\n'
s = s + 'Example inhibitory current:\n'
s = s + ' %s %5s %3s %s %5s %3s \n' % ('Mean rate:', meanRate, 'Hz', 'I_e',
I_e, 'pA')
s = s + 'Steps:\n'
s = s + ' %5s %3s \n' % (I_vec, 'pA')
infoString = s
return STN, infoString
def simulate_basa_line_SNr(msn_rate, gpe_rate, stn_rate, n_msn, n_gpe, n_stn, neuron_model, snr_current, sim_time=1000, threads=8, stn_syn='STN_SNR_ampa_s'):
SNR_INJECTED_CURRENT=snr_current
SYNAPSE_MODEL_BACKROUND_STN=[stn_syn]
model_list, model_dict=models()
my_nest.ResetKernel(threads=threads)
my_nest.MyLoadModels( model_dict, neuron_model )
my_nest.MyLoadModels( model_dict, SYNAPSE_MODEL_BACKROUND_MSN)
my_nest.MyLoadModels( model_dict, SYNAPSE_MODEL_BACKROUND_GPE)
my_nest.MyLoadModels( model_dict, SYNAPSE_MODEL_BACKROUND_STN)
SNR_list=[] # List with SNR groups for synapse.
if n_msn>0: MSN_base=MyPoissonInput(n=n_msn, sd=True)
if n_gpe>0: GPE=MyPoissonInput(n=n_gpe, sd=False)
if n_stn>0: STN=MyPoissonInput(n=n_stn, sd=False)
if n_msn>0: MSN_base.set_spike_times(rates=[ msn_rate], times=[1], t_stop=sim_time, seed=0)
if n_gpe>0: GPE.set_spike_times(rates=[gpe_rate], times=[1], t_stop=sim_time, seed=0)
if n_stn>0: STN.set_spike_times(rates=[stn_rate], times=[1], t_stop=sim_time, seed=0)
I_e=my_nest.GetDefaults(neuron_model[0])['I_e']+SNR_INJECTED_CURRENT
SNR=MyGroup( neuron_model[0], n=1, sd=True, params={'I_e':I_e}, mm_dt=.1, mm=True)
if n_msn>0: my_nest.Connect(MSN_base[:], SNR[:]*len(MSN_base[:]), model=SYNAPSE_MODEL_BACKROUND_MSN[0])
if n_gpe>0: my_nest.Connect(GPE[:],SNR[:]*len(GPE[:]), model=SYNAPSE_MODEL_BACKROUND_GPE[0])
if n_stn>0: my_nest.Connect(STN[:],SNR[:]*len(STN[:]), model=SYNAPSE_MODEL_BACKROUND_STN[0])
my_nest.MySimulate(sim_time)
SNR.get_signal( 's', start=0, stop=sim_time )
meanRate=round(SNR.signals['spikes'].mean_rate(1000,sim_time),1)
spk=SNR.signals['spikes'].time_slice(1000,sim_time).raw_data()
CV=numpy.std(numpy.diff(spk[:,0],axis=0))/numpy.mean(numpy.diff(spk[:,0],axis=0))
SNR.get_signal( 'v',recordable='V_m', start=0, stop=sim_time )
SNR.signals['V_m'].my_set_spike_peak( 15, spkSignal= SNR.signals['spikes'] )
pylab.rcParams.update( {'path.simplify':False} )
SNR.signals['V_m'].plot()
pylab.title(str(meanRate)+ 'Hz, CV='+str(CV))
pylab.show()
return
def simulate_ahp(I_vec):
simTime = 3000. # ms
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
n = len(I_vec)
STN = MyGroup(NEURON_MODELS[0], n, sd=True, mm=True, mm_dt=1.0)
I_e0 = my_nest.GetStatus(STN[:])[0]['I_e']
#my_nest.SetStatus(STN[:], params={'I_e':-10.}) # Set I_e
my_nest.SetStatus(STN[:], params={'I_e': 1.0}) # Set I_e
I_e = my_nest.GetStatus(STN.ids, 'I_e')[0]
scg = my_nest.Create('step_current_generator', n=n)
rec = my_nest.GetStatus(STN[:])[0]['receptor_types']
for source, target, I in zip(scg, STN[:], I_vec):
my_nest.SetStatus([source], {
'amplitude_times': [500., 1000.],
'amplitude_values': [float(I), 0.]
})
my_nest.Connect([source], [target],
params={'receptor_type': rec['CURR']})
my_nest.MySimulate(simTime)
STN.get_signal('s') # retrieve signal
STN.signals['spikes'] = STN.signals['spikes'].time_slice(700, 2000)
delays = []
for i, curr in enumerate(I_vec):
delays.append(
max(
numpy.diff(
STN.signals['spikes'].spiketrains[i + 1.0].spike_times)))
meanRate = round(STN.signals['spikes'].mean_rate(0, 500), 1)
s = '\n'
s = s + 'Example inhibitory current:\n'
s = s + ' %s %5s %3s %s %5s %3s \n' % ('Mean rate:', meanRate, 'Hz', 'I_e',
I_e, 'pA')
s = s + 'Steps:\n'
s = s + ' %5s %3s \n' % (I_vec, 'pA')
infoString = s
return I_vec, delays
def plot_text(ax, infoString=''):
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, SYNAPSE_MODELS)
my_nest.MyLoadModels(model_list,
['GPE_SNR_gaba_s_ref', 'GPE_SNR_gaba_s_max'])
SNR = MyGroup(NEURON_MODELS[0], 2, mm_dt=0.1)
statusSNR = my_nest.GetStatus(SNR[:])[0]
statusSynapes = []
for s in SYNAPSE_MODELS:
statusSynapes.append(my_nest.GetDefaults(s))
tb = ''
tb = tb + infoString
for ss in statusSynapes:
tb = tb + '\n'
tb = tb + ' %s %10s\n' % ('Synapse', ss['synapsemodel'])
tb = tb + ' %s %5s %3s\n' % ('Weight', str(round(ss['weight'],
1)), 'nS')
tb = tb + ' %s %5s %3s \n' % ('U:', str(ss['U']), '--')
tb = tb + ' %s %5s %3s \n' % ('tau_fac:', str(ss['tau_fac']), 'ms')
tb = tb + ' %s %5s %3s \n' % ('tau_rec:', str(ss['tau_rec']), 'ms')
tb = tb + ' %s %5s %3s \n' % ('tau_psc:', str(ss['tau_psc']), 'ms')
synapticEficacy = ss['weight'] * ss['U']
tb = tb + ' %s %5s %3s \n' % ('P1:', synapticEficacy, 'nS')
sw = my_nest.GetDefaults('GPE_SNR_gaba_s_ref')
tb = tb + ' %s %5s %3s \n' % (r'$ref_{32 Hz}^{GPe}$ fraction',
str(sw['weight'] / synapticEficacy), '--')
sw = my_nest.GetDefaults('GPE_SNR_gaba_s_max')
tb = tb + ' %s %5s %3s \n' % (r'$dep^{GPe}$ max', str(sw['weight']), '--')
ax.text(
0.85,
0.5,
tb,
fontsize=font_size_text,
horizontalalignment='right',
verticalalignment='center',
transform=ax.transAxes, # to define coordinates in right scale
**{'fontname': 'monospace'})
ax.my_remove_axis(xaxis=True, yaxis=True)
ax.my_remove_spine(left=True, bottom=True, right=True, top=True)
def simulate_basa_line_GPe(msn_rate, stn_rate, gpe_rate, n_msn, n_stn, n_gpe, neuron_model, syn_models, gpe_current, sim_time=1000, threads=8):
model_list, model_dict=models()
my_nest.ResetKernel(threads=threads)
my_nest.MyLoadModels( model_dict, neuron_model )
my_nest.MyLoadModels( model_dict, syn_models)
SNR_list=[] # List with SNR groups for synapse.
if n_msn>0: MSN=MyPoissonInput(n=n_msn, sd=False)
if n_stn>0: STN=MyPoissonInput(n=n_stn, sd=False)
if n_gpe>0: GPE=MyPoissonInput(n=n_gpe, sd=False)
if n_msn>0: MSN.set_spike_times(rates=[msn_rate], times=[1], t_stop=sim_time, seed=0)
if n_stn>0: STN.set_spike_times(rates=[stn_rate], times=[1], t_stop=sim_time, seed=0)
if n_gpe>0: GPE.set_spike_times(rates=[gpe_rate], times=[1], t_stop=sim_time, seed=0)
I_e=my_nest.GetDefaults(neuron_model[0])['I_e']+gpe_current
GPE_target=MyGroup( neuron_model[0], n=1, sd=True, params={'I_e':I_e},
mm_dt=.1, mm=True)
if n_msn>0: my_nest.Connect(MSN[:], GPE_target[:]*len(MSN[:]), model=syn_models[0])
if n_stn>0: my_nest.Connect(STN[:],GPE_target[:]*len(STN[:]), model=syn_models[1])
if n_gpe>0: my_nest.Connect(GPE[:],GPE_target[:]*len(GPE[:]), model=syn_models[2])
my_nest.MySimulate(sim_time)
GPE_target.get_signal( 's', start=0, stop=sim_time )
meanRate=round(GPE_target.signals['spikes'].mean_rate(1000,sim_time),1)
spk=GPE_target.signals['spikes'].time_slice(1000,sim_time).raw_data()
CV=numpy.std(numpy.diff(spk[:,0],axis=0))/numpy.mean(numpy.diff(spk[:,0],axis=0))
GPE_target.get_signal( 'v',recordable='V_m', start=0, stop=sim_time )
GPE_target.signals['V_m'].my_set_spike_peak( 15, spkSignal= GPE_target.signals['spikes'] )
pylab.rcParams.update( {'path.simplify':False} )
GPE_target.signals['V_m'].plot()
pylab.title(str(meanRate)+ 'Hz, CV='+str(CV))
pylab.show()
return
def plot_text(ax, infoString):
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, SYNAPSE_MODELS)
SNR = MyGroup(NEURON_MODELS[0], 2, mm_dt=0.1)
statusSNR = my_nest.GetStatus(SNR[:])[0]
statusSynapes = []
for s in SYNAPSE_MODELS:
statusSynapes.append(my_nest.GetDefaults(s))
tb = ''
tb = tb + infoString
tb = tb + '\n'
tb = tb + 'Neuron models:\n '
tb = tb + ' %s \n' % (NEURON_MODELS[0])
tb = tb + '\n'
tb = tb + ' %s %5s %3s \n' % ('E rev:', str(
statusSNR['GABAA_1_E_rev']), 'mV')
tb = tb + ' %s %5s %3s \n' % ('Tau_decay:',
str(statusSNR['GABAA_1_Tau_decay']), 'mV')
tb = tb + ' %s %5s %3s \n' % ('E rev:', str(statusSNR['AMPA_E_rev']), 'mV')
tb = tb + ' %s %5s %3s \n' % ('Tau_decay:', str(
statusSNR['AMPA_Tau_decay']), 'mV')
for ss in statusSynapes:
tb = tb + '\n'
tb = tb + ' %s %10s\n' % ('Synapse', ss['synapsemodel'])
tb = tb + ' %s %5s %3s\n' % ('Weight', str(round(ss['weight'],
1)), 'nS')
ax.text(
0.85,
0.5,
tb,
fontsize=font_size_text,
horizontalalignment='right',
verticalalignment='center',
transform=ax.transAxes, # to define coordinates in right scale
**{'fontname': 'monospace'})
ax.my_remove_axis(xaxis=True, yaxis=True)
ax.my_remove_spine(left=True, bottom=True, right=True, top=True)
def plot_steady_state_freq(ax, frequencies, relativeFacilitation):
colors = ['r', 'c']
linestyles = ['--', '-']
labels = [r'$ref_{30 Hz}^{GPe}$', r'$dep^{GPe}$']
coords = [[0.35, 0.2], [0.1, 0.7]]
syn_static = ['GPE_SNR_gaba_s_ref']
#print relativeFacilitation[0, 23:26]
#print frequencies[23:26]
ax.plot(frequencies, relativeFacilitation[0, :], **{'color': colors[1]})
my_nest.ResetKernel()
model_list, model_dict = models()
syns = [SYNAPSE_MODELS[0]]
syns.extend(syn_static)
my_nest.MyLoadModels(model_list, syns)
xdata = ax.lines[0].get_xdata()
ss = my_nest.GetDefaults(SYNAPSE_MODELS[0])
synapticEficacy = ss['weight'] * ss['U']
sw = my_nest.GetDefaults('GPE_SNR_gaba_s_ref')
ax.plot([min(xdata), max(xdata)],
[sw['weight'] / synapticEficacy, sw['weight'] / synapticEficacy],
**{
'color': colors[0],
'linestyle': linestyles[0]
})
t_a = ax.transAxes
for coord, label, color in zip(coords, labels, colors):
ax.text(coord[0],
coord[1],
label,
transform=ax.transAxes,
fontsize=pylab.rcParams['font.size'] + 2,
**{'color': color})
ytext = ax.set_ylabel(r'$p_{ss}$/$p_1$')
pylab.setp(ytext, fontsize=16.)
ax.set_xlabel('Firing rate (spikes/s)')
ax.my_set_no_ticks(yticks=6, xticks=6)
ax.set_xlim(misc.adjust_limit([0, 100]))
ax.set_ylim(misc.adjust_limit([0, 1]))
pylab.setp(ax.lines,
linewidth=2.0) # Need to pu ti before generating legend
def simulate_basa_line_SNr_multiple(msn_rate,
gpe_rate,
stn_rate,
n_msn,
n_gpe,
n_stn,
neuron_model,
syn_models,
snr_current,
sim_time=1000,
threads=8,
w_STN_SNR=0,
seed=0,
record_vm=True,
n_neurons=1):
Params_in = {}
if w_STN_SNR: Params_in['STN_SNR_ampa_s'] = w_STN_SNR
model_list, model_dict = models(Params_in)
my_nest.ResetKernel(threads=threads)
my_nest.MyLoadModels(model_dict, neuron_model)
my_nest.MyLoadModels(model_dict, syn_models)
SNR_list = []
for i in range(int(n_neurons)):
seed = seed + i
SNR_list.append(
simulate_basa_line_SNr(msn_rate, gpe_rate, stn_rate, n_msn, n_gpe,
n_stn, neuron_model, syn_models,
snr_current, sim_time, threads, w_STN_SNR,
seed, record_vm, True))
my_nest.MySimulate(sim_time)
for i in range(int(n_neurons)):
SNR_list[i].get_signal('s', start=0, stop=sim_time)
if record_vm:
SNR_list[i].get_signal('v',
recordable='V_m',
start=0,
stop=sim_time)
return SNR_list
def simulate_response_example_clamped_silent(I_e):
'''
Response when SNR is clamped to a voltage for Ref 2 and Ref 1 synapse
'''
spike_at = 500. # ms
simTime = 700. # ms
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, SYNAPSE_MODELS)
SNR = MyGroup(NEURON_MODELS[0],
len(SYNAPSE_MODELS),
mm=True,
mm_dt=0.1,
params={'I_e': I_e})
SG = my_nest.Create('spike_generator', params={'spike_times': [spike_at]})
for i in range(len(SYNAPSE_MODELS)):
my_nest.Connect(SG, [SNR[i]], model=SYNAPSE_MODELS[i])
my_nest.MySimulate(simTime)
SNR.get_signal('v', 'V_m', stop=simTime) # retrieve signal
SNR.signals['V_m'] = SNR.signals['V_m'].my_time_slice(400, 700)
clamped_at = SNR.signals['V_m'][1].signal[-1]
size_MSN_weak = min(SNR.signals['V_m'][1].signal) - clamped_at
size_MSN_strong = min(SNR.signals['V_m'][2].signal) - clamped_at
size_GPE_ref = min(SNR.signals['V_m'][3].signal) - clamped_at
s = ''
s = s + ' %s %5s %3s \n' % ('Clamped at:', str(round(clamped_at, 1)), 'mV')
s = s + ' %s %5s %3s \n' % (r'$\delta_w^{MSN}$',
str(round(size_MSN_weak, 1)), 'mV')
s = s + ' %s %5s %3s \n' % (r'$\delta_s^{MSN}$',
str(round(size_MSN_strong, 1)), 'mV')
s = s + ' %s %5s %3s \n' % (r'$\delta_s^{MSN}$', str(round(
size_GPE_ref, 1)), 'mV')
infoString = s
return SNR, infoString
def simulate_example_rebound_spike(I_vec):
simTime = 5000. # ms
my_nest.ResetKernel()
model_list, model_dict=models()
my_nest.MyLoadModels( model_list, NEURON_MODELS )
n=len(I_vec)
GPE = MyGroup( NEURON_MODELS[0], n, sd=True, mm=True, mm_dt = 1.0 )
I_e0=my_nest.GetStatus(GPE[:])[0]['I_e']
#my_nest.SetStatus(GPE[:], params={'I_e':-10.}) # Set I_e
my_nest.SetStatus(GPE[:], params={'I_e':-10.}) # Set I_e
I_e = my_nest.GetStatus(GPE.ids,'I_e')[0]
scg = my_nest.Create( 'step_current_generator',n=n )
rec=my_nest.GetStatus(GPE[:])[0]['receptor_types']
for source, target, I in zip(scg, GPE[:], I_vec):
my_nest.SetStatus([source], {'amplitude_times':[500.,700.],
'amplitude_values':[float(I),0.]})
my_nest.Connect( [source], [target],
params = { 'receptor_type' : rec['CURR'] } )
my_nest.MySimulate(simTime)
GPE.get_signal( 'v','V_m', stop=simTime ) # retrieve signal
GPE.get_signal( 's') # retrieve signal
GPE.signals['V_m'].my_set_spike_peak( 21, spkSignal= GPE.signals['spikes'] )
meanRate=round(GPE.signals['spikes'].mean_rate(0,500),1)
s='\n'
s =s + 'Example inhibitory current:\n'
s = s + ' %s %5s %3s %s %5s %3s \n' % ( 'Mean rate:', meanRate, 'Hz',
'I_e', I_e,'pA' )
s = s + 'Steps:\n'
s = s + ' %5s %3s \n' % ( I_vec, 'pA' )
infoString=s
return GPE, infoString
def simulate_example(I_e):
simTime = 3000. # ms
my_nest.ResetKernel()
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
I_e0 = my_nest.GetDefaults(NEURON_MODELS[0])['I_e']
STN = MyGroup(NEURON_MODELS[0],
1,
sd=True,
mm=True,
mm_dt=1.,
params={'I_e': I_e + I_e0})
'''
scg = my_nest.Create( 'step_current_generator',n=1 )
rec=my_nest.GetStatus(STN[:])[0]['receptor_types']
my_nest.SetStatus(scg, {'amplitude_times':[280.,1700.],
'amplitude_values':[100.0,0.]})
my_nest.Connect( scg, STN.ids,
params = { 'receptor_type' : rec['CURR'] } )
'''
my_nest.MySimulate(simTime)
STN.get_signal('v', 'V_m', stop=simTime) # retrieve signal
STN.get_signal('s') # retrieve signal
meanRate = round(STN.signals['spikes'].mean_rate(0, 1000), 1)
print STN.signals['spikes'].isi()
STN.signals['V_m'].my_set_spike_peak(21, spkSignal=STN.signals['spikes'])
s = '\n'
s = s + 'Example:\n'
s = s + ' %s %5s %3s %s %5s %3s \n' % ('Mean rate:', meanRate, 'Hz', 'I_e',
I_e, 'pA')
infoString = s
return STN, infoString
def plot_text(ax, infoString=''):
my_nest.ResetKernel()
model_list = models()
my_nest.MyLoadModels(model_list, neuronModels)
my_nest.MyLoadModels(model_list, synapseModels)
SNR = MyGroup(neuronModels[0], 2, mm_dt=0.1)
statusSNR = my_nest.GetStatus(SNR[:])[0]
statusSynapes = []
for s in synapseModels:
statusSynapes.append(my_nest.GetDefaults(s))
tb = ''
tb = tb + infoString
for ss in statusSynapes:
tb = tb + '\n'
tb = tb + ' %s %10s\n' % ('Synapse', ss['synapsemodel'])
tb = tb + ' %s %5s %3s\n' % ('Weight', str(round(ss['weight'],
1)), 'nS')
if 'U' in ss.keys():
tb = tb + ' %s %5s %3s \n' % ('U:', str(ss['U']), '--')
tb = tb + ' %s %5s %3s \n' % ('tau_fac:', str(ss['tau_fac']), 'ms')
tb = tb + ' %s %5s %3s \n' % ('tau_rec:', str(ss['tau_rec']), 'ms')
tb = tb + ' %s %5s %3s \n' % ('tau_psc:', str(ss['tau_psc']), 'ms')
ax.text(
0.85,
0.5,
tb,
fontsize=font_size_text,
horizontalalignment='right',
verticalalignment='center',
transform=ax.transAxes, # to define coordinates in right scale
**{'fontname': 'monospace'})
ax.my_remove_axis(xaxis=True, yaxis=True)
ax.my_remove_spine(left=True, bottom=True, right=True, top=True)
def plot_steady_state_freq(ax, frequencies, relativeFacilitation ):
colors = ['r','c']
labels=[r'$\delta_{ref}^{STN}$', r'$\delta_{dep}^{STN}$']
coords=[[0.35, 0.2], [0.1, 0.7]]
syn_static=['STN_SNR_ampa_s']
#print relativeFacilitation[0, 23:26]
#print frequencies[23:26]
ax.plot(frequencies,relativeFacilitation[0,:],**{'label':'Data 1+2',
'color':colors[1]})
my_nest.ResetKernel()
model_list, model_dict=models()
syns=[SYNAPSE_MODELS[0]]
syns.extend(syn_static)
my_nest.MyLoadModels( model_list, syns )
xdata=ax.lines[0].get_xdata()
ss=my_nest.GetDefaults(SYNAPSE_MODELS[0])
synapticEficacy = ss['weight']*ss['U']
sw=my_nest.GetDefaults('STN_SNR_ampa_s')
ax.plot([min(xdata), max(xdata)],[sw['weight']/synapticEficacy,
sw['weight']/synapticEficacy],
**{'color':colors[0]})
t_a = ax.transAxes
for coord, label, color in zip(coords, labels, colors):
ax.text( coord[0], coord[1], label , transform=ax.transAxes,
fontsize=pylab.rcParams['text.fontsize']+2,
**{ 'color' : color})
ytext=ax.set_ylabel(r'$p_{ss}$/$p_1$')
pylab.setp(ytext, fontsize=14.)
ax.set_xlabel('Firing rate (spikes/s)')
ax.my_set_no_ticks( yticks=6, xticks = 6 )
ax.set_xlim(misc.adjust_limit([0,20]))
ax.set_ylim(misc.adjust_limit([0,1]))
def simulate_basa_line_SNr(msn_rate,
gpe_rate,
stn_rate,
n_msn,
n_gpe,
n_stn,
neuron_model,
snr_current,
sim_time=1000,
threads=8,
stn_syn='STN_SNR_ampa_s'):
SNR_INJECTED_CURRENT = snr_current
SYNAPSE_MODEL_BACKROUND_STN = [stn_syn]
model_list, model_dict = models()
my_nest.ResetKernel(threads=threads)
my_nest.MyLoadModels(model_dict, neuron_model)
my_nest.MyLoadModels(model_dict, SYNAPSE_MODEL_BACKROUND_MSN)
my_nest.MyLoadModels(model_dict, SYNAPSE_MODEL_BACKROUND_GPE)
my_nest.MyLoadModels(model_dict, SYNAPSE_MODEL_BACKROUND_STN)
SNR_list = [] # List with SNR groups for synapse.
if n_msn > 0: MSN_base = MyPoissonInput(n=n_msn, sd=True)
if n_gpe > 0: GPE = MyPoissonInput(n=n_gpe, sd=False)
if n_stn > 0: STN = MyPoissonInput(n=n_stn, sd=False)
if n_msn > 0:
MSN_base.set_spike_times(rates=[msn_rate],
times=[1],
t_stop=sim_time,
seed=0)
if n_gpe > 0:
GPE.set_spike_times(rates=[gpe_rate],
times=[1],
t_stop=sim_time,
seed=0)
if n_stn > 0:
STN.set_spike_times(rates=[stn_rate],
times=[1],
t_stop=sim_time,
seed=0)
I_e = my_nest.GetDefaults(neuron_model[0])['I_e'] + SNR_INJECTED_CURRENT
SNR = MyGroup(neuron_model[0],
n=1,
sd=True,
params={'I_e': I_e},
mm_dt=.1,
mm=True)
if n_msn > 0:
my_nest.Connect(MSN_base[:],
SNR[:] * len(MSN_base[:]),
model=SYNAPSE_MODEL_BACKROUND_MSN[0])
if n_gpe > 0:
my_nest.Connect(GPE[:],
SNR[:] * len(GPE[:]),
model=SYNAPSE_MODEL_BACKROUND_GPE[0])
if n_stn > 0:
my_nest.Connect(STN[:],
SNR[:] * len(STN[:]),
model=SYNAPSE_MODEL_BACKROUND_STN[0])
my_nest.MySimulate(sim_time)
SNR.get_signal('s', start=0, stop=sim_time)
meanRate = round(SNR.signals['spikes'].mean_rate(1000, sim_time), 1)
spk = SNR.signals['spikes'].time_slice(1000, sim_time).raw_data()
CV = numpy.std(numpy.diff(spk[:, 0], axis=0)) / numpy.mean(
numpy.diff(spk[:, 0], axis=0))
SNR.get_signal('v', recordable='V_m', start=0, stop=sim_time)
SNR.signals['V_m'].my_set_spike_peak(15, spkSignal=SNR.signals['spikes'])
pylab.rcParams.update({'path.simplify': False})
SNR.signals['V_m'].plot()
pylab.title(str(meanRate) + 'Hz, CV=' + str(CV))
pylab.show()
return
def simulate_network(params_msn_d1,
params_msn_d2,
params_stn,
synapse_models,
sim_time,
seed,
I_e_add,
threads=1,
start_rec=0,
model_params={}):
'''
params_msn_d1 - dictionary with timing and burst freq setup for msn
{'base_rates':[0.1, 0.1, ..., 0.1], #Size number of actions
'mod_rates': [[20,0,...,0],
[0,20,...,0],...[0,0,...,20]] #size number of actions times number of events
'mod_times':[[500,1000],[1500,2000],[9500,10000]] # size number of events
'n_neurons':500}
params_msn_d2 - dictionary with timing and burst freq setup for gpe
params_stn - dictionary {'rate':50}
same as params_msn
neuron_model - string, the neuron model to use
synapse_models - dict, {'MSN':'...', 'GPE':,'...', 'STN':'...'}
sim_time - simulation time
seed - seed for random generator
I_e_add - diabled
start_rec - start recording from
model_params - general model paramters
'''
I_e_add = {'SNR': 300, 'STN': 0, 'GPE': 30}
f = 0.01 #0.01#0.5
I_e_variation = {'GPE': 25 * f, 'SNR': 100 * f, 'STN': 10 * f}
my_nest.ResetKernel(threads=8)
numpy.random.seed(seed)
params = {
'conns': {
'MSN_D1_SNR': {
'syn': synapse_models[0]
},
'GPE_SNR': {
'syn': synapse_models[1]
}
}
}
params = misc.dict_merge(model_params, params)
model_list, model_dict = models()
group_list, group_dict, connect_list, connect_params = network(
model_dict, params)
print connect_params
groups = {}
for name, model, setup in group_list:
# Update input current
my_nest.MyLoadModels(model_dict, [model])
if name in I_e_add.keys():
I_e = my_nest.GetDefaults(model)['I_e'] + I_e_add[name]
my_nest.SetDefaults(model, {'I_e': I_e})
groups[name] = []
for action in range(connect_params['misc']['n_actions']):
if model in ['MSN_D1_spk_gen', 'MSN_D2_spk_gen']:
group = MyPoissonInput(params=setup,
sd=True,
sd_params={
'start': start_rec,
'stop': sim_time
})
else:
group = MyGroup(params=setup,
sd=True,
mm=False,
mm_dt=0.1,
sd_params={
'start': start_rec,
'stop': sim_time
})
groups[name].append(group)
for action in range(connect_params['misc']['n_actions']):
groups['MSN_D1'][action].set_spike_times(
list(params_msn_d1['mod_rates'][action]),
list(params_msn_d1['mod_times']),
sim_time,
ids=groups['MSN_D1'][action].ids)
groups['MSN_D2'][action].set_spike_times(
params_msn_d2['mod_rates'][action],
params_msn_d2['mod_times'],
sim_time,
ids=groups['MSN_D2'][action].ids)
# Create neurons and synapses
for source, target, props in connect_list:
my_nest.MyLoadModels(model_dict, [props['model']])
for action in range(connect_params['misc']['n_actions']):
pre = list(groups[source][action].ids)
post = list(groups[target][action].ids)
my_nest.MyRandomConvergentConnect(pre, post, params=props)
STN_CTX_input_base = my_nest.Create('poisson_generator',
params={
'rate': params_stn['rate'],
'start': 0.,
'stop': sim_time
})
my_nest.MyLoadModels(model_dict, ['CTX_STN_ampa_s'])
for action in range(connect_params['misc']['n_actions']):
my_nest.DivergentConnect(STN_CTX_input_base,
groups['STN'][action].ids,
model='CTX_STN_ampa_s')
my_nest.MySimulate(sim_time)
for action in range(connect_params['misc']['n_actions']):
groups['MSN_D1'][action].get_signal('s',
start=start_rec,
stop=sim_time)
groups['MSN_D2'][action].get_signal('s',
start=start_rec,
stop=sim_time)
groups['GPE'][action].get_signal('s', start=start_rec, stop=sim_time)
groups['SNR'][action].get_signal('s', start=start_rec, stop=sim_time)
groups['STN'][action].get_signal('s', start=start_rec, stop=sim_time)
return groups
def simulate_basa_line_GPe(msn_rate,
stn_rate,
gpe_rate,
n_msn,
n_stn,
n_gpe,
neuron_model,
syn_models,
gpe_current,
sim_time=1000,
threads=8):
model_list, model_dict = models()
my_nest.ResetKernel(threads=threads)
my_nest.MyLoadModels(model_dict, neuron_model)
my_nest.MyLoadModels(model_dict, syn_models)
SNR_list = [] # List with SNR groups for synapse.
if n_msn > 0: MSN = MyPoissonInput(n=n_msn, sd=False)
if n_stn > 0: STN = MyPoissonInput(n=n_stn, sd=False)
if n_gpe > 0: GPE = MyPoissonInput(n=n_gpe, sd=False)
if n_msn > 0:
MSN.set_spike_times(rates=[msn_rate],
times=[1],
t_stop=sim_time,
seed=0)
if n_stn > 0:
STN.set_spike_times(rates=[stn_rate],
times=[1],
t_stop=sim_time,
seed=0)
if n_gpe > 0:
GPE.set_spike_times(rates=[gpe_rate],
times=[1],
t_stop=sim_time,
seed=0)
I_e = my_nest.GetDefaults(neuron_model[0])['I_e'] + gpe_current
GPE_target = MyGroup(neuron_model[0],
n=1,
sd=True,
params={'I_e': I_e},
mm_dt=.1,
mm=True)
if n_msn > 0:
my_nest.Connect(MSN[:],
GPE_target[:] * len(MSN[:]),
model=syn_models[0])
if n_stn > 0:
my_nest.Connect(STN[:],
GPE_target[:] * len(STN[:]),
model=syn_models[1])
if n_gpe > 0:
my_nest.Connect(GPE[:],
GPE_target[:] * len(GPE[:]),
model=syn_models[2])
my_nest.MySimulate(sim_time)
GPE_target.get_signal('s', start=0, stop=sim_time)
meanRate = round(GPE_target.signals['spikes'].mean_rate(1000, sim_time), 1)
spk = GPE_target.signals['spikes'].time_slice(1000, sim_time).raw_data()
CV = numpy.std(numpy.diff(spk[:, 0], axis=0)) / numpy.mean(
numpy.diff(spk[:, 0], axis=0))
GPE_target.get_signal('v', recordable='V_m', start=0, stop=sim_time)
GPE_target.signals['V_m'].my_set_spike_peak(
15, spkSignal=GPE_target.signals['spikes'])
pylab.rcParams.update({'path.simplify': False})
GPE_target.signals['V_m'].plot()
pylab.title(str(meanRate) + 'Hz, CV=' + str(CV))
pylab.show()
return
def simulate_selection_vs_neurons(selection_intervals=[0.0, 500.0],
hz=20,
load=True):
global SNR_INJECTED_CURRENT
global NEURON_MODELS
global N_GPE
global N_MSN_BURST
global N_MSN
global GPE_BASE_RATE
global FILE_NAME
global OUTPUT_PATH
global SYNAPSE_MODELS_TESTED
global SEL_ONSET
#n_exp=100
n_exp = 2
if hz > 7:
n_max_sel = 60
if hz > 20:
n_max_sel = 30
else:
n_max_sel = 100
RATE_BASE = 0.1
RATE_SELE = hz
save_result_at = (OUTPUT_PATH + '/' + FILE_NAME +
'-simulate_selection_vs_neurons' + str(hz) + '-hz.pkl')
save_header_at = (OUTPUT_PATH + '/' + FILE_NAME +
'-simulate_selection_vs_neurons' + str(hz) +
'-hz_header')
burst_time = 500.
sim_time = burst_time + SEL_ONSET + 500.
EXPERIMENTS = range(n_exp)
MODEL_LIST = models()
my_nest.ResetKernel()
my_nest.MyLoadModels(MODEL_LIST, NEURON_MODELS)
my_nest.MyLoadModels(MODEL_LIST, SYNAPSE_MODELS_TESTED)
my_nest.MyLoadModels(MODEL_LIST, SYNAPSE_MODELS_BACKGROUND)
MSN_list = [] # MSN input for each experiment
for i_exp in EXPERIMENTS:
MSN = MyPoissonInput(n=N_MSN + n_max_sel, sd=True)
MSN_list.append(MSN)
GPE_list = [] # GPE input for each experiment
for i_exp in EXPERIMENTS:
GPE = MyPoissonInput(n=N_GPE, sd=True)
GPE_list.append(GPE)
SNR_list = [] # SNR groups for each synapse and number of selected MSN
SNR_list_experiments = []
for i_syn, syn in enumerate(SYNAPSE_MODELS_TESTED):
SNR = []
for i_sel in range(n_max_sel + 1): # Plus one to get no burst point
I_e = my_nest.GetDefaults(
NEURON_MODELS[0])['I_e'] + SNR_INJECTED_CURRENT
SNR.append(
MyGroup(NEURON_MODELS[0],
n=n_exp,
sd=True,
params={'I_e': I_e}))
SNR_list.append(SNR)
if not load:
for i_exp in EXPERIMENTS:
MSN = MSN_list[i_exp]
GPE = GPE_list[i_exp]
# Set spike times
# Base rate
for id in MSN[1:N_MSN]:
MSN.set_spike_times(id=id,
rates=[RATE_BASE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Selection
for id in MSN[N_MSN:N_MSN + n_max_sel]:
rates = [RATE_BASE, RATE_SELE, RATE_BASE]
times = [1, SEL_ONSET, burst_time + SEL_ONSET]
t_stop = sim_time
MSN.set_spike_times(id=id,
rates=rates,
times=times,
t_stop=t_stop,
seed=int(numpy.random.random() * 10000.0))
# Base rate GPE
for id in GPE[:]:
GPE.set_spike_times(id=id,
rates=[GPE_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Connect
for i_syn, syn in enumerate(SYNAPSE_MODELS_TESTED):
# i_sel goes over 0,..., n_max_sel
for i_sel in range(0, n_max_sel + 1):
target = SNR_list[i_syn][i_sel][i_exp]
my_nest.ConvergentConnect(MSN[0:N_MSN - i_sel], [target],
model=syn)
my_nest.ConvergentConnect(MSN[N_MSN:N_MSN + i_sel],
[target],
model=syn)
my_nest.ConvergentConnect(
GPE[:], [target], model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.MySimulate(sim_time)
for SNR_sel in SNR_list:
for SNR in SNR_sel:
SNR.get_signal('s')
sel_interval_mean_rates = []
sel_interval_mean_rates_std = []
for i_interval, interval in enumerate(selection_intervals):
t1 = selection_intervals[i_interval][0]
t2 = selection_intervals[i_interval][1]
mean_rates = []
mean_rates_std = []
# Time until arrival of spikes in SNr
delay = my_nest.GetDefaults(SYNAPSE_MODELS_BACKGROUND[0])['delay']
for SNR_sel in SNR_list:
m_r = []
m_r_std = []
for SNR in SNR_sel:
m_r.append(SNR.signals['spikes'].mean_rate(
SEL_ONSET + t1 + delay, SEL_ONSET + t2 + delay))
m_r_std.append(SNR.signals['spikes'].mean_rate_std(
SEL_ONSET + t1 + delay, SEL_ONSET + t2 + delay))
mean_rates.append(m_r)
mean_rates_std.append(m_r_std)
mean_rates = numpy.array(mean_rates)
mean_rates_std = numpy.array(mean_rates_std)
sel_interval_mean_rates.append(mean_rates)
sel_interval_mean_rates_std.append(mean_rates_std)
nb_neurons = numpy.arange(0, n_max_sel + 1, 1)
s = '\n'
s = s + ' %s %5s %3s \n' % ('N MSNs:', str(N_MSN), '#')
s = s + ' %s %5s %3s \n' % ('N experiments:', str(n_exp), '#')
s = s + ' %s %5s %3s \n' % ('MSN base rate:', str(MSN_BASE_RATE), 'Hz')
s = s + ' %s %5s %3s \n' % ('MSN burst rate:', str(MSN_BURST_RATE),
'Hz')
s = s + ' %s %5s %3s \n' % ('GPe rate:', str(GPE_BASE_RATE), 'Hz')
s = s + ' %s %5s %3s \n' % ('Burst time:', str(burst_time), 'ms')
s = s + ' %s %5s %3s \n' % ('SNR_INJECTED_CURRENT:',
str(SNR_INJECTED_CURRENT), 'pA')
for i_interval, interval in enumerate(selection_intervals):
s = s + ' %s %5s %3s \n' % ('Sel interval ' + str(i_interval) +
':', str(selection_intervals), 'ms')
info_string = s
header = HEADER_SIMULATION_SETUP + s
misc.text_save(header, save_header_at)
misc.pickle_save([
nb_neurons, sel_interval_mean_rates, sel_interval_mean_rates_std,
info_string
], save_result_at)
elif load:
nb_neurons, sel_interval_mean_rates, sel_interval_mean_rates_std, info_string = misc.pickle_load(
save_result_at)
return nb_neurons, sel_interval_mean_rates, sel_interval_mean_rates_std, info_string
def simulate_example(load=True):
global SNR_INJECTED_CURRENT
global NEURON_MODELS
global N_GPE
global N_MSN_BURST
global N_MSN
global GPE_BASE_RATE
global FILE_NAME
global OUTPUT_PATH
global SYNAPSE_MODELS_TESTED
global SEL_ONSET
#n_exp =200 # number of experiments
n_exp = 20 # number of experiments
# Path were raw data is saved. For example the spike trains.
save_result_at = OUTPUT_PATH + '/' + FILE_NAME + '-simulate_example.pkl'
save_header_at = OUTPUT_PATH + '/' + FILE_NAME + '-simulate_example_header'
burst_time = 500.
sim_time = burst_time + SEL_ONSET + 1000.
MODEL_LIST = models()
my_nest.ResetKernel()
my_nest.MyLoadModels(MODEL_LIST, NEURON_MODELS)
my_nest.MyLoadModels(MODEL_LIST, SYNAPSE_MODELS_TESTED)
my_nest.MyLoadModels(MODEL_LIST, SYNAPSE_MODELS_BACKGROUND)
SNR_list = [] # List with SNR groups for synapse.
if not load:
MSN_base = MyPoissonInput(n=N_MSN_BASE * n_exp, sd=True)
MSN_burst = MyPoissonInput(n=N_MSN_BURST * n_exp, sd=True)
GPE = MyPoissonInput(n=N_GPE * n_exp, sd=True)
# Set spike times MSN and GPe
# Non bursting MSNs
for id in MSN_base[:]:
seed = numpy.random.random_integers(0, 1000000.0)
MSN_base.set_spike_times(id=id,
rates=[MSN_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=seed)
# Background GPe
for id in GPE[:]:
seed = numpy.random.random_integers(0, 1000000.0)
GPE.set_spike_times(id=id,
rates=[GPE_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=seed)
# Bursting MSNs
for id in MSN_burst[:]:
rates = [MSN_BASE_RATE, MSN_BURST_RATE, MSN_BASE_RATE]
times = [1, SEL_ONSET, burst_time + SEL_ONSET]
t_stop = sim_time
seed = numpy.random.random_integers(0, 1000000.0)
MSN_burst.set_spike_times(id=id,
rates=rates,
times=times,
t_stop=t_stop,
seed=seed)
for i_syn in range(len(SYNAPSE_MODELS_TESTED)):
params = []
I_e = my_nest.GetDefaults(
NEURON_MODELS[0])['I_e'] + SNR_INJECTED_CURRENT
for i in range(n_exp):
#params.append({'I_e':numpy.random.normal(I_e,
# 0.1*I_e)})
params.append({'I_e': I_e})
#{'I_e':SNR_INJECTED_CURRENT}
SNR = MyGroup(NEURON_MODELS[0],
n=n_exp,
sd=True,
params=params,
mm_dt=.1,
record_from=[''])
SNR_list.append(SNR)
# Connect, experiment specific
sources_MSN_SNR_base = numpy.arange(0, n_exp * N_MSN_BASE)
sources_MSN_SNR_burst = numpy.arange(0, n_exp * N_MSN_BURST)
targets_MSN_SNR_base = numpy.mgrid[0:n_exp, 0:N_MSN_BASE][0].reshape(
1, N_MSN_BASE * n_exp)[0]
targets_MSN_SNR_burst = numpy.mgrid[0:n_exp, 0:N_MSN_BURST][0].reshape(
1, N_MSN_BURST * n_exp)[0]
sources_GPE_SNR = numpy.arange(0, n_exp * N_GPE)
targets_GPE_SNR = numpy.mgrid[0:n_exp,
0:N_GPE][0].reshape(1, N_GPE * n_exp)[0]
for i_syn, syn in enumerate(SYNAPSE_MODELS_TESTED):
syn = SYNAPSE_MODELS_TESTED[i_syn]
SNR = SNR_list[i_syn]
my_nest.Connect(MSN_base[sources_MSN_SNR_base],
SNR[targets_MSN_SNR_base],
model=syn)
my_nest.Connect(MSN_burst[sources_MSN_SNR_burst],
SNR[targets_MSN_SNR_burst],
model=syn)
my_nest.Connect(GPE[sources_GPE_SNR],
SNR[targets_GPE_SNR],
model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.MySimulate(sim_time)
MSN_base.get_signal('s', start=0, stop=sim_time)
MSN_burst.get_signal('s', start=0, stop=sim_time)
for SNR in SNR_list:
SNR.get_signal('s', start=0, stop=sim_time)
# Get firing rates of MSNs
MSN_firing_rates = []
MSN_all = copy.deepcopy(MSN_base)
MSN_all.merge(MSN_burst)
time_bin = 20.
groups = [MSN_base, MSN_burst, MSN_all]
for group in groups:
timeAxis, firingRates = group.signals['spikes'].my_firing_rate(
bin=time_bin, display=False)
MSN_firing_rates.append([timeAxis, firingRates])
# Pick out spikes for burst, base and all to use in scatter plot
MSN_spikes_and_ids = []
g1 = MSN_burst.slice(MSN_burst[0:N_MSN_BURST])
g2 = MSN_base.slice(MSN_base[0:N_MSN_BASE])
ids_MSN_burst = range(450, 450 + N_MSN_BURST)
ids_MSN_base = [id for id in range(N_MSN) if id not in IDS_MSN_BURST]
# Rename ids for plotting purpose
g1_dict = dict([[id1, id2] for id1, id2 in zip(g1.ids, ids_MSN_burst)])
g2_dict = dict([[id1, id2] for id1, id2 in zip(g2.ids, ids_MSN_base)])
groups = [g1, g2]
dics = [g1_dict, g2_dict]
for group, dic in zip(groups, dics):
raw_data = group.signals['spikes'].raw_data()
for i in range(raw_data.shape[0]):
raw_data[i, 1] = dic[raw_data[i, 1]]
MSN_spikes_and_ids.append(raw_data)
#times, binned_data=MSN_base.signals['spikes'].binned_raw_data(0, sim_time, res=1, clip=0)
#filtered_binned_data=misc.time_resolved_rate(binned_data, 100, kernel_type='triangle', res=1)
pre_ref_1 = str(SNR_list[0].signals['spikes'].mean_rate(
SEL_ONSET - 500, SEL_ONSET))
pre_ref_2 = str(SNR_list[1].signals['spikes'].mean_rate(
SEL_ONSET - 500, SEL_ONSET))
pre_dyn = str(SNR_list[2].signals['spikes'].mean_rate(
SEL_ONSET - 500, SEL_ONSET))
s = '\n'
s = s + 'Simulate example:\n'
s = s + '%s %5s %3s \n' % ('N experiments:', str(n_exp), '#')
s = s + '%s %5s %3s \n' % ('Bin size MSN hz:', str(time_bin), 'ms')
s = s + '%s %5s %3s \n' % ('MSN base rate:', str(MSN_BASE_RATE), 'Hz')
s = s + '%s %5s %3s \n' % ('MSN burst rate:', str(MSN_BURST_RATE),
'Hz')
s = s + '%s %5s %3s \n' % ('GPe rate:', str(GPE_BASE_RATE), 'Hz')
s = s + '%s %5s %3s \n' % ('Burst time:', str(burst_time), 'ms')
s = s + '%s %5s %3s \n' % ('Pre sel rate Ref:', pre_ref_1[0:4], 'Hz')
s = s + '%s %5s %3s \n' % ('Pre sel rate Ref:', pre_ref_2[0:4], 'Hz')
s = s + '%s %5s %3s \n' % ('Pre sel rate Dyn:', pre_dyn[0:4], 'Hz')
header = HEADER_SIMULATION_SETUP + s
misc.pickle_save([MSN_firing_rates, MSN_spikes_and_ids, SNR_list, s],
save_result_at)
misc.text_save(header, save_header_at)
else:
MSN_firing_rates, MSN_spikes_and_ids, SNR_list, s = misc.pickle_load(
save_result_at)
return MSN_firing_rates, MSN_spikes_and_ids, SNR_list, s
def simulate_network(params_msn_d1, params_msn_d2, params_stn,
synapse_models, sim_time, seed, I_e_add, threads=1,
start_rec=0, model_params={}):
'''
params_msn_d1 - dictionary with timing and burst freq setup for msn
{'base_rates':[0.1, 0.1, ..., 0.1], #Size number of actions
'mod_rates': [[20,0,...,0],
[0,20,...,0],...[0,0,...,20]] #size number of actions times number of events
'mod_times':[[500,1000],[1500,2000],[9500,10000]] # size number of events
'n_neurons':500}
params_msn_d2 - dictionary with timing and burst freq setup for gpe
params_stn - dictionary {'rate':50}
same as params_msn
neuron_model - string, the neuron model to use
synapse_models - dict, {'MSN':'...', 'GPE':,'...', 'STN':'...'}
sim_time - simulation time
seed - seed for random generator
I_e_add - diabled
start_rec - start recording from
model_params - general model paramters
'''
I_e_add={'SNR':300, 'STN':0,'GPE':30}
f=0.01#0.01#0.5
I_e_variation={'GPE':25*f,'SNR':100*f,'STN':10*f}
my_nest.ResetKernel(threads=8)
numpy.random.seed(seed)
params = {'conns':{'MSN_D1_SNR':{'syn':synapse_models[0]},
'GPE_SNR':{'syn':synapse_models[1]}}}
params=misc.dict_merge(model_params, params)
model_list, model_dict = models()
group_list, group_dict, connect_list, connect_params = network(model_dict, params)
print connect_params
groups={}
for name, model, setup in group_list:
# Update input current
my_nest.MyLoadModels( model_dict, [model] )
if name in I_e_add.keys():
I_e=my_nest.GetDefaults(model)['I_e']+I_e_add[name]
my_nest.SetDefaults(model,{'I_e':I_e})
groups[name]=[]
for action in range(connect_params['misc']['n_actions']):
if model in ['MSN_D1_spk_gen','MSN_D2_spk_gen']:
group=MyPoissonInput(params=setup, sd=True, sd_params={'start':start_rec, 'stop':sim_time})
else:
group=MyGroup(params=setup, sd=True, mm=False, mm_dt = 0.1,
sd_params={'start':start_rec, 'stop':sim_time} )
groups[name].append(group)
for action in range(connect_params['misc']['n_actions']):
groups['MSN_D1'][action].set_spike_times(list(params_msn_d1['mod_rates'][action]),
list(params_msn_d1['mod_times']), sim_time,
ids=groups['MSN_D1'][action].ids)
groups['MSN_D2'][action].set_spike_times(params_msn_d2['mod_rates'][action],
params_msn_d2['mod_times'], sim_time,
ids=groups['MSN_D2'][action].ids)
# Create neurons and synapses
for source, target, props in connect_list:
my_nest.MyLoadModels( model_dict, [props['model']] )
for action in range(connect_params['misc']['n_actions']):
pre=list(groups[source][action].ids)
post=list(groups[target][action].ids)
my_nest.MyRandomConvergentConnect(pre, post, params=props)
STN_CTX_input_base=my_nest.Create('poisson_generator',params={'rate':params_stn['rate'], 'start':0., 'stop':sim_time})
my_nest.MyLoadModels( model_dict, ['CTX_STN_ampa_s'] )
for action in range(connect_params['misc']['n_actions']):
my_nest.DivergentConnect(STN_CTX_input_base, groups['STN'][action].ids,
model='CTX_STN_ampa_s')
my_nest.MySimulate(sim_time)
for action in range(connect_params['misc']['n_actions']):
groups['MSN_D1'][action].get_signal( 's', start=start_rec, stop=sim_time )
groups['MSN_D2'][action].get_signal( 's', start=start_rec, stop=sim_time )
groups['GPE'][action].get_signal( 's', start=start_rec, stop=sim_time )
groups['SNR'][action].get_signal( 's', start=start_rec, stop=sim_time )
groups['STN'][action].get_signal( 's', start=start_rec, stop=sim_time )
return groups
