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_basa_line_STN(ctx_rate, gpe_rate, n_ctx, n_gpe, neuron_model, syn_models, stn_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_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 )
meanRate=round(STN.signals['spikes'].mean_rate(1000,sim_time),1)
spk=STN.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))
STN.get_signal( 'v',recordable='V_m', start=0, stop=sim_time )
STN.signals['V_m'].my_set_spike_peak( 15, spkSignal= STN.signals['spikes'] )
pylab.rcParams.update( {'path.simplify':False} )
STN.signals['V_m'].plot()
pylab.title(str(meanRate)+ 'Hz, CV='+str(CV))
pylab.show()
return
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_basa_line_SNr(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,
multiple=False):
if not multiple:
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 = [] # List with SNR groups for synapse.
if n_msn > 0: MSN = 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.set_spike_times(rates=[msn_rate],
times=[1],
t_stop=sim_time,
seed=seed)
if n_gpe > 0:
GPE.set_spike_times(rates=[gpe_rate],
times=[1],
t_stop=sim_time,
seed=seed)
if n_stn > 0:
STN.set_spike_times(rates=[stn_rate],
times=[1],
t_stop=sim_time,
seed=seed)
I_e = my_nest.GetDefaults(neuron_model[0])['I_e'] + snr_current
SNR = MyGroup(neuron_model[0],
n=1,
sd=True,
params={'I_e': I_e},
mm_dt=.1,
mm=record_vm)
if n_msn > 0:
my_nest.Connect(MSN[:], SNR[:] * len(MSN[:]), model=syn_models[0])
if n_gpe > 0:
my_nest.Connect(GPE[:], SNR[:] * len(GPE[:]), model=syn_models[1])
if n_stn > 0:
my_nest.Connect(STN[:], SNR[:] * len(STN[:]), model=syn_models[2])
return SNR
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,
w_GPE_GPE=False,
w_STN_GPE=False):
Params_in = {}
if w_GPE_GPE: Params_in['GPE_GPE_gaba_s'] = w_GPE_GPE
if w_STN_GPE: Params_in['STN_GPE_ampa_s'] = w_STN_GPE
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_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)
GPE_target.get_signal('v', recordable='V_m', start=0, stop=sim_time)
return GPE_target
def simulate_selection_vs_neurons(selRateInterval=[0.0, 500.0],
hz=0,
load=True):
global SEL_ONSET
global SNR_INJECTED_CURRENT
global N_GPE
global N_STN
global MSN_RATE_BASE
global GPE_BASE_RATE
global STN_BASE_RATE
SNAME_NB = hz
#n_exp=200
n_exp = 20
N_MAX_SEL = N_GPE + 1 # Plus one to account for the case when all GPe have stopped
RATE_SELE = hz
save_at = (SPATH + '/' + NEURON_MODELS[0] + '-' + str(SNAME_NB) +
'-hz.pkl')
#SEL_TIME = 1000.
sim_time = SEL_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)
GPE_list = [] # GPE input for each experiment
for i_exp in experiments:
GPE = MyPoissonInput(n=N_GPE + N_MAX_SEL)
GPE_list.append(GPE)
MSN_list = [] # MSN input for each experiment
for i_exp in experiments:
MSN = MyPoissonInput(n=N_MSN, sd=True)
MSN_list.append(MSN)
STN_list = [] # STN input for each experiment
for i_exp in experiments:
STN = MyPoissonInput(n=N_STN, sd=True)
STN_list.append(STN)
SNR_list = [] # SNR groups for each synapse and number of selected GPE
I_e = my_nest.GetDefaults(NEURON_MODELS[0])['I_e'] + SNR_INJECTED_CURRENT
for i, i_syn in enumerate(SYNAPSE_MODELS_TESTED):
SNR = []
for i_sel in range(N_MAX_SEL):
SNR.append(
MyGroup(NEURON_MODELS[0],
n=n_exp,
params={'I_e': I_e},
sd=True,
sd_params={
'start': 0.,
'stop': sim_time
}))
SNR_list.append(SNR)
if not load:
for i_exp in experiments:
GPE = GPE_list[i_exp]
MSN = MSN_list[i_exp]
STN = STN_list[i_exp]
# Set spike times
# Base rate
for id in MSN[:]:
MSN.set_spike_times(id=id,
rates=[MSN_RATE_BASE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Base rate STN
for id in STN[:]:
STN.set_spike_times(id=id,
rates=[STN_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Set spike times
# Base rate
for id in GPE[0:N_GPE]:
GPE.set_spike_times(id=id,
rates=[GPE_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Selection
for id in GPE[N_GPE:N_GPE + N_MAX_SEL]:
rates = [GPE_BASE_RATE, RATE_SELE, GPE_BASE_RATE]
times = [1, SEL_ONSET, SEL_TIME + SEL_ONSET]
t_stop = sim_time
GPE.set_spike_times(id=id,
rates=rates,
times=times,
t_stop=t_stop,
seed=int(numpy.random.random() * 10000.0))
# Connect
for i, syn in enumerate(SYNAPSE_MODELS_TESTED):
for i_sel in range(N_MAX_SEL):
target = SNR_list[i][i_sel][i_exp]
my_nest.ConvergentConnect(GPE[0:N_GPE - i_sel], [target],
model=syn)
my_nest.ConvergentConnect(GPE[N_GPE:N_GPE + i_sel],
[target],
model=syn)
my_nest.ConvergentConnect(
MSN[:], [target], model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.ConvergentConnect(
STN[:], [target], model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate(sim_time)
for SNR_sel in SNR_list:
for SNR in SNR_sel:
SNR.get_signal('s')
misc.pickle_save_groups(SNR_list, save_at)
elif load:
SNR_list = misc.pickle_load_groups(save_at)
t1 = selRateInterval[0]
t2 = selRateInterval[1]
mean_rates = []
delay = my_nest.GetDefaults(SYNAPSE_MODELS_TESTED[0])['delay']
for SNR_sel in SNR_list:
m_r = []
for SNR in SNR_sel:
m_r_pre = SNR.signals['spikes'].mean_rate(SEL_ONSET - (t2 - t1),
SEL_ONSET)
m_r_post = SNR.signals['spikes'].mean_rate(SEL_ONSET + t1 + delay,
SEL_ONSET + t2 + delay)
m_r.append(m_r_post)
mean_rates.append(m_r)
mean_rates = numpy.array(mean_rates)
nb_neurons = numpy.arange(0, N_MAX_SEL, 1)
s = '\n'
s = s + ' %s %5s %3s \n' % ('N GPEs:', str(N_GPE), '#')
s = s + ' %s %5s %3s \n' % ('N experiments:', str(n_exp), '#')
s = s + ' %s %5s %3s \n' % ('Base rate:', str(GPE_BASE_RATE), 'spikes/s')
s = s + ' %s %5s %3s \n' % ('Selection rate:', str(RATE_SELE), 'spikes/s')
s = s + ' %s %5s %3s \n' % ('Selection time:', str(SEL_TIME), 'ms')
s = s + ' %s %5s %3s \n' % ('SNR_INJECTED_CURRENT:',
str(SNR_INJECTED_CURRENT), 'pA')
info_string = s
return nb_neurons, mean_rates, info_string
def simulate_example(hz=0, load=True):
global SNR_INJECTED_CURRENT
global NEURON_MODELS
global N_GPE
global N_SEL
global N_MSN
global N_STN
global MSN_RATE_BASE
global STN_BASE_RATE
global SNAME
global SPATH
global SYNAPSE_MODELS
global SEL_ONSET
global GPE_BASE_RATE
#n_exp = 20
n_exp = 200
RATE_SELE = hz # Selection rate
save_at = SPATH + '/' + NEURON_MODELS[0] + '-example.pkl'
sim_time = SEL_TIME + SEL_ONSET + 500.
SNAME_NB = hz + 1000
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)
GPE_list = [] # GPE input for each experiment
for i_exp in experiments:
GPE = MyPoissonInput(n=N_GPE,
sd=True,
spath=SPATH,
sname_nb=SNAME_NB + i_exp)
GPE_list.append(GPE)
MSN_list = [] # MSN input for each experiment
for i_exp in experiments:
MSN = MyPoissonInput(n=N_MSN, sd=False)
MSN_list.append(MSN)
STN_list = [] # MSN input for each experiment
for i_exp in experiments:
STN = MyPoissonInput(n=N_STN, sd=False)
STN_list.append(STN)
SNR_list = [] # SNR groups for each synapse
I_e = my_nest.GetDefaults(NEURON_MODELS[0])['I_e'] + SNR_INJECTED_CURRENT
for i_syn in range(len(SYNAPSE_MODELS_TESTED)):
SNR = MyGroup(NEURON_MODELS[0], n=n_exp, params={'I_e': I_e}, sd=True)
SNR_list.append(SNR)
if not load:
for i_exp in experiments:
GPE = GPE_list[i_exp]
MSN = MSN_list[i_exp]
STN = STN_list[i_exp]
# Set spike times
# Base rate MSN
for id in MSN[:]:
MSN.set_spike_times(id=id,
rates=[MSN_RATE_BASE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Base rate STN
for id in STN[:]:
STN.set_spike_times(id=id,
rates=[STN_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Set spike times
# Base rate
for id in GPE[0:N_GPE - N_SEL]:
GPE.set_spike_times(id=id,
rates=[GPE_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Selection
for id in GPE[N_GPE - N_SEL:N_GPE]:
rates = [GPE_BASE_RATE, RATE_SELE, GPE_BASE_RATE]
times = [1, SEL_ONSET, SEL_TIME + SEL_ONSET]
t_stop = sim_time
GPE.set_spike_times(id=id,
rates=rates,
times=times,
t_stop=t_stop,
seed=int(numpy.random.random() * 10000.0))
# Connect
for i_syn, syn in enumerate(SYNAPSE_MODELS_TESTED):
target = SNR_list[i_syn][i_exp]
my_nest.ConvergentConnect(GPE[:], [target], model=syn)
my_nest.ConvergentConnect(MSN[:], [target],
model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.ConvergentConnect(STN[:], [target],
model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate(sim_time)
for GPE in GPE_list:
GPE.get_signal('s')
for SNR in SNR_list:
SNR.get_signal('s')
misc.pickle_save([GPE_list, SNR_list], save_at)
elif load:
GPE_list, SNR_list = misc.pickle_load(save_at)
pre_ref = str(SNR_list[0].signals['spikes'].mean_rate(
SEL_ONSET - 5000, SEL_ONSET))
pre_dyn = str(SNR_list[1].signals['spikes'].mean_rate(
SEL_ONSET - 500, SEL_ONSET))
statusSynapes = []
for syn in SYNAPSE_MODELS_TESTED:
statusSynapes.append(my_nest.GetDefaults(syn))
s = '\n'
s = s + 'Example:\n'
s = s + ' %s %5s %3s \n' % ('N experiments:', str(len(experiments)), '#')
s = s + ' %s %5s %3s \n' % ('N GPEs:', str(N_GPE), '#')
s = s + ' %s %5s %3s \n' % ('Base rate:', str(GPE_BASE_RATE), 'spikes/s')
s = s + ' %s %5s %3s \n' % ('Selection rate:', str(RATE_SELE), 'spikes/s')
s = s + ' %s %5s %3s \n' % ('Selection time:', str(SEL_TIME), 'ms')
s = s + ' %s %5s %3s \n' % ('Pre sel rate Ref:', pre_ref[0:4], 'spikes/s')
s = s + ' %s %5s %3s \n' % ('Pre sel rate Dyn:', pre_dyn[0:4], 'spikes/s')
for ss in statusSynapes:
s = s + '\n'
s = s + ' %s %10s\n' % ('Synapse', ss['synapsemodel'])
s = s + ' %s %5s %3s\n' % ('Weight', str(round(ss['weight'], 1)), 'nS')
return GPE_list, SNR_list, s
def simulate_GPE_vs_SNR_const_syn_events(load=True):
global N_GPE
global N_MSN
global MSN_BASE_RATE
global SNR_INJECTED_CURRENT
save_at = (SPATH+'/'+NEURON_MODELS[0]+'-' + '-GPE_vs_SNR_const_syn_events.pkl')
nGPE_range=numpy.arange(N_GPE,4,-1)
# To maintain CONSTANT_SYN_EVENTS in to SNr while changing number of pausing
# GPe we have to increase the mean rate of the non-pausing GPe's
GPEmeanRates=CONSTANT_SYN_EVENTS/nGPE_range
SNRmeanRates=[]
sim_time=10000.
I_e=0.
if not load:
for r, n_gpe in zip(GPEmeanRates,nGPE_range):
my_nest.ResetKernel()
model_list=models()
my_nest.MyLoadModels( model_list, NEURON_MODELS )
my_nest.MyLoadModels( model_list, SYNAPSE_MODELS_TESTED )
my_nest.MyLoadModels( model_list, SYNAPSE_MODELS_BACKGROUND )
GPE = MyPoissonInput( n=n_gpe)
MSN = MyPoissonInput( n=N_MSN)
STN = MyPoissonInput( n=N_STN)
I_e=my_nest.GetDefaults(NEURON_MODELS[0])['I_e']+SNR_INJECTED_CURRENT
SNR = MyGroup( NEURON_MODELS[0], n=len(SYNAPSE_MODELS_TESTED),
sd=True,params={'I_e':I_e})
for id in GPE[:]:
GPE.set_spike_times(id=id, rates=[r], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
for id in MSN[:]:
MSN.set_spike_times(id=id, rates=[MSN_BASE_RATE], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
for id in STN[:]:
STN.set_spike_times(id=id, rates=[STN_BASE_RATE], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
for i, syn in enumerate(SYNAPSE_MODELS_TESTED):
my_nest.ConvergentConnect(GPE[:],[SNR[i]], model=syn)
my_nest.ConvergentConnect(MSN[:],[SNR[i]], model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.ConvergentConnect(STN[:],[SNR[i]], model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate( sim_time )
SNR.get_signal( 's') # retrieve signal
SNRmeanRates.append(SNR.signals['spikes'].mean_rates(5000,sim_time))
SNRmeanRates=numpy.array(SNRmeanRates).transpose()
GPEmeanRates=numpy.array(GPEmeanRates)
rateAtThr=''
for SNRr in SNRmeanRates:
tmp=str(GPEmeanRates[SNRr>=SELECTION_THR][-1])
rateAtThr+=' '+tmp[0:4]
s='\n'
s =s + 'GPE vs SNr rate:\n'
s = s + ' %s %5s %3s \n' % ( 'N GPEs:', str ( N_GPE ), '#' )
s = s + ' \n%s %5s %3s \n' % ( 'GPE rates:', str ( GPEmeanRates[0] ) + '-'+
str ( GPEmeanRates[-1] ), 'spikes/s' )
s = s + ' %s %5s %3s \n' % ( 'Threshold SNr:', str ( SELECTION_THR ), 'spikes/s' )
s = s + ' \n%s %5s %3s \n' % ( 'GPE rate at threshold SNr:', str ( rateAtThr ), 'spikes/s' )
s = s + ' \n%s %5s %3s \n' % ( 'Simulation time:', str ( sim_time), 'ms' )
s = s + ' %s %5s %3s \n' % ( 'I_e:', str ( I_e ), 'pA' )
s = s + ' %s %5s %3s \n' % ( 'Steady state rate ref:', str ( round(SNRmeanRates[0][0],1) ), 'pA' )
s = s + ' %s %5s %3s \n' % ( 'Steady state rate dyn:', str ( round(SNRmeanRates[1][0],1) ), 'pA' )
statusSynapse=[]
for syn in SYNAPSE_MODELS_TESTED:
statusSynapse.append( my_nest.GetDefaults(syn) )
for ss in statusSynapse:
s = s + '\n'
s = s + ' %s %10s\n' % ( 'Synapse', ss['synapsemodel'])
s = s + ' %s %5s %3s\n' % ( 'Weight',
str( round( ss['weight'], 1) ), 'nS')
infoString=s
misc.pickle_save([GPEmeanRates, SNRmeanRates, infoString],
save_at)
elif load:
GPEmeanRates, SNRmeanRates, infoString = misc.pickle_load(save_at)
return nGPE_range, GPEmeanRates, SNRmeanRates, infoString
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_example(MSN_hz=20, GPE_hz=0, load=True, n_gpe_sel=3, sel_time_GPE=500):
global GPE_BASE_RATE
global STN_BASE_RATE
global MSN_BASE_RATE
global MSN_BURST_TIME
global NEURON_MODELS
global N_GPE
global N_STN
global N_MSN
global N_MSN_BURST
global SNAME
global SPATH
global SYNAPSE_MODELS
global SEL_ONSET
global SNR_INJECTED_CURRENT
n_exp = 200
msn_rate_sel = MSN_hz # Selection rate
gpe_sel_rate = GPE_hz # Selection rate
sel_time_MSN = MSN_BURST_TIME
sim_time = sel_time_MSN+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)
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_MSN_BURST, sd=True)
MSN_list.append(MSN)
GPE_list=[] # GPE input for each experiment
for i_exp in EXPERIMENTS:
GPE = MyPoissonInput( n=N_GPE+n_gpe_sel, sd=True)
GPE_list.append(GPE)
STN_list=[] # GPE input for each experiment
for i_exp in EXPERIMENTS:
STN = MyPoissonInput( n=N_STN, sd=True)
STN_list.append(GPE)
SNR_list=[] # SNR groups for each synapse
for i, SNR_i_c in enumerate(SNR_INJECTED_CURRENT):
I_e=my_nest.GetDefaults(NEURON_MODELS[0])['I_e']+SNR_i_c
SNR = MyGroup( NEURON_MODELS[0], n=n_exp, params={'I_e':I_e},
sd=True, mm=False,
mm_dt=.1, record_from=[''])
SNR_list.append(SNR)
if not load:
for i_exp in EXPERIMENTS:
# MSN
MSN = MSN_list[i_exp]
# Set spike times
# Base rate
for id in MSN[0:N_MSN]:
MSN.set_spike_times(id=id, rates=[MSN_BASE_RATE], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
# Selection MSN
for id in MSN[N_MSN:N_MSN+N_MSN_BURST]:
rates = [MSN_BASE_RATE, msn_rate_sel, MSN_BASE_RATE]
times = [1, SEL_ONSET, sel_time_MSN + 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))
# GPE
GPE = GPE_list[i_exp]
# Set spike times
# Base rate
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))
# Selection GPE
for id in GPE[N_GPE:N_GPE+n_gpe_sel]:
rates = [GPE_BASE_RATE, gpe_sel_rate, GPE_BASE_RATE]
# If GPe excited smaller selection time
times = [1, SEL_ONSET, sel_time_GPE + SEL_ONSET]
t_stop = sim_time
GPE.set_spike_times(id=id, rates=rates, times=times,
t_stop=t_stop, seed=int(numpy.random.random()*100000.0))
# Base rate STN
for id in STN[:]:
STN.set_spike_times(id=id, rates=[STN_BASE_RATE], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
idx_MSN_s=range(0,N_MSN-N_MSN_BURST)
idx_MSN_s.extend(range(N_MSN,N_MSN+N_MSN_BURST))
idx_GPE_s=range(0,N_GPE-n_gpe_sel)
idx_GPE_s.extend(range(N_GPE,N_GPE+n_gpe_sel))
# Connect with MSN burst
target=SNR_list[0][i_exp]
my_nest.ConvergentConnect(MSN[idx_MSN_s], [target], model=SYNAPSE_MODELS[0])
my_nest.ConvergentConnect(GPE[0:N_GPE], [target], model=SYNAPSE_MODELS[1])
my_nest.ConvergentConnect(STN[:], [target], model=SYNAPSE_MODELS_BACKGROUND[0])
# With GPe pause
target=SNR_list[1][i_exp]
my_nest.ConvergentConnect(MSN[0:N_MSN], [target], model=SYNAPSE_MODELS[0])
my_nest.ConvergentConnect(GPE[idx_GPE_s], [target], model=SYNAPSE_MODELS[1])
my_nest.ConvergentConnect(STN[:], [target], model=SYNAPSE_MODELS_BACKGROUND[0])
# With MSN burst and GPe pause
target=SNR_list[2][i_exp]
my_nest.ConvergentConnect(MSN[idx_MSN_s], [target], model=SYNAPSE_MODELS[0])
my_nest.ConvergentConnect(GPE[idx_GPE_s], [target], model=SYNAPSE_MODELS[1])
my_nest.ConvergentConnect(STN[:], [target], model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.MySimulate( sim_time )
for MSN in MSN_list:
MSN.get_signal( 's' )
for GPE in GPE_list:
GPE.get_signal( 's' )
for SNR in SNR_list:
SNR.get_signal( 's' )
misc.pickle_save([MSN_list, GPE_list,SNR_list] , save_at)
if load:
MSN_list, GPE_list, SNR_list=misc.pickle_load(save_at)
pre_dyn_MSN=str(SNR_list[0].signals['spikes'].mean_rate(SEL_ONSET-500,
SEL_ONSET))
pre_dyn_GPE=str(SNR_list[1].signals['spikes'].mean_rate(SEL_ONSET-500,
SEL_ONSET))
s='\n'
s=s+'Example:\n'
s = s + ' %s %5s %3s \n' % ( 'N experiments:', str ( len(EXPERIMENTS) ), '#' )
s = s + ' %s %5s %3s \n' % ( 'N MSN:', str ( N_MSN ), '#' )
s = s + ' %s %5s %3s \n' % ( 'N GPE:', str ( N_GPE ), '#' )
s='\n'
s = s + ' %s %5s %3s \n' % ( 'Base rate MSN:', str ( MSN_BASE_RATE),'spikes/s' )
s = s + ' %s %5s %3s \n' % ( 'Sel rate MSN:', str ( msn_rate_sel ), 'spikes/s' )
s = s + ' %s %5s %3s \n' % ( 'Sel time MSN:', str ( sel_time_MSN ), 'ms' )
s='\n'
s = s + ' %s %5s %3s \n' % ( 'Base rate GPe:', str ( GPE_BASE_RATE),'spikes/s' )
s = s + ' %s %5s %3s \n' % ( 'Sel rate GPe:', str ( gpe_sel_rate ), 'spikes/s' )
s = s + ' %s %5s %3s \n' % ( 'Sel time GPe:', str ( sel_time_GPE ), 'ms' )
s = s + ' %s %5s %3s \n' % ( 'Pre sel rate Dyn MSN:', pre_dyn_MSN[0:4], 'spikes/s' )
s = s + ' %s %5s %3s \n' % ( 'Pre sel rate Dyn GPe:', pre_dyn_GPE[0:4], 'spikes/s' )
return MSN_list, GPE_list, SNR_list, s
info_string=s
return MSN_hzs, GPE_hzs, data, info_string
def simulate_rate_first_and_second_bursts(
selection_intervals=[0.0, 500.0, 1000., 1500.], load=True):
global SNR_INJECTED_CURRENT
global NEURON_MODELS
global N_GPE
global N_MSN_BURST
global N_MSN
global N_STN
global MSN_BASE_RATE
global GPE_BASE_RATE
global STN_BASE_RATE
global FILE_NAME
global OUTPUT_PATH
global SYNAPSE_MODELS_TESTED
global SEL_ONSET
#n_exp=20
n_exp = 200
msn_burst_rate = 20
n_msn_burst = N_MSN_BURST
transient_stop = selection_intervals[2] - selection_intervals[1]
save_result_at = (OUTPUT_PATH + '/simulate_rate_first_and_second_bursts_' +
str(transient_stop) + 'ms.pkl')
save_header_at = (OUTPUT_PATH + '/simulate_rate_first_and_second_bursts_' +
str(transient_stop) + 'ms_header')
burst_time = 500.
sim_time = SEL_ONSET + selection_intervals[3] + 500.
EXPERIMENTS = range(n_exp)
model_list = models()
my_nest.ResetKernel(threads=1)
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, SYNAPSE_MODELS_TESTED)
my_nest.MyLoadModels(model_list, SYNAPSE_MODELS_BACKGROUND)
if not load:
MSN_list = [] # MSN input for each experiment
for i_exp in EXPERIMENTS:
MSN = MyPoissonInput(n=N_MSN + n_msn_burst, 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)
STN_list = [] # GPE input for each experiment
for i_exp in EXPERIMENTS:
STN = MyPoissonInput(n=N_STN, sd=True)
STN_list.append(STN)
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(1):
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)
for i_exp in EXPERIMENTS:
MSN = MSN_list[i_exp]
GPE = GPE_list[i_exp]
STN = STN_list[i_exp]
# Set spike times
# Base rate
for id in MSN[1:N_MSN]:
MSN.set_spike_times(id=id,
rates=[MSN_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Selection
for id in MSN[N_MSN:N_MSN + n_msn_burst]:
rates = [
MSN_BASE_RATE, msn_burst_rate, MSN_BASE_RATE,
msn_burst_rate, MSN_BASE_RATE
]
t1 = selection_intervals[0]
t2 = selection_intervals[1]
t3 = selection_intervals[2]
t4 = selection_intervals[3]
times = [
1, SEL_ONSET + t1, SEL_ONSET + t2, SEL_ONSET + t3,
SEL_ONSET + t4
]
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))
# Base rate GPE
for id in STN[:]:
STN.set_spike_times(id=id,
rates=[STN_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, n_sel in enumerate(
range(n_msn_burst, n_msn_burst + 1)):
target = SNR_list[i_syn][i_sel][i_exp]
my_nest.ConvergentConnect(MSN[0:N_MSN - n_sel], [target],
model=syn)
my_nest.ConvergentConnect(MSN[N_MSN:N_MSN + n_sel],
[target],
model=syn)
my_nest.ConvergentConnect(
GPE[:], [target], model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.ConvergentConnect(
STN[:], [target], model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate(sim_time)
for SNR_sel in SNR_list:
for SNR in SNR_sel:
SNR.get_signal('s')
t1 = selection_intervals[0]
t3 = selection_intervals[2]
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:
# Mean rate during first 200 ms
m_r.append(SNR.signals['spikes'].mean_rate(
SEL_ONSET + t1 + delay, SEL_ONSET + t1 + 200 + delay))
m_r.append(SNR.signals['spikes'].mean_rate(
SEL_ONSET + t3 + delay, SEL_ONSET + t3 + 200 + delay))
m_r_std.append(SNR.signals['spikes'].mean_rate_std(
SEL_ONSET + t1 + delay, SEL_ONSET + t1 + 200 + delay))
m_r_std.append(SNR.signals['spikes'].mean_rate_std(
SEL_ONSET + t3 + delay, SEL_ONSET + t3 + 200 + 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)
s = '\n'
s = s + 'simulate_rate_first_and_second_bursts\n'
s = s + '%s %5s %3s \n' % ('Simulation time', str(sim_time), '#')
s = s + '%s %5s %3s \n' % ('N MSNs:', str(N_MSN), '#')
s = s + '%s %5s %3s \n' % ('N MSN_bursts:', str(n_msn_burst), '#')
s = s + '%s %5s %3s \n' % ('N experiments:', str(n_exp), '#')
s = s + '%s %5s %3s \n' % ('MSN base rate:', str(MSN_BASE_RATE),
'spikes/s')
s = s + '%s %5s %3s \n' % ('MSN burst rate:', str(MSN_BURST_RATE),
'spikes/s')
s = s + '%s %5s %3s \n' % ('MSN burst time:', str(burst_time), 'ms')
s = s + '%s %5s %3s \n' % ('GPe base rate:', str(GPE_BASE_RATE),
'spikes/s')
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 = s
misc.text_save(header, save_header_at)
misc.pickle_save([mean_rates, mean_rates_std, info_string],
save_result_at)
elif load:
mean_rates, mean_rates_std, info_string = misc.pickle_load(
save_result_at)
return mean_rates, mean_rates_std, info_string
def simulate_example(load=True):
global GPE_BASE_RATE
global FILE_NAME
global N_GPE
global N_STN
global N_MSN_BURST
global N_MSN
global NEURON_MODELS
global OUTPUT_PATH
global SEL_ONSET
global SNR_INJECTED_CURRENT
global SYNAPSE_MODELS_TESTED
#n_exp =200 # number of experiments
n_exp = 200 # number of experiments
# Path were raw data is saved. For example the spike trains.
save_result_at = OUTPUT_PATH + '/simulate_example.pkl'
save_header_at = OUTPUT_PATH + '/simulate_example_header'
burst_time = 500.
sim_time = SEL_INTERVAL_2[1] + 500
model_list = models()
my_nest.ResetKernel(threads=8)
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)
MSN_burst = MyPoissonInput(n=N_MSN_BURST * n_exp)
GPE = MyPoissonInput(n=N_GPE * n_exp, sd=True)
STN = MyPoissonInput(n=N_STN * 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)
# Background STN
for id in STN[:]:
seed = numpy.random.random_integers(0, 1000000.0)
STN.set_spike_times(id=id,
rates=[STN_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, MSN_BURST_RATE,
MSN_BASE_RATE
]
times = [
1, SEL_INTERVAL_1[0], SEL_INTERVAL_1[1], SEL_INTERVAL_2[0],
SEL_INTERVAL_2[1]
]
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)):
I_e = my_nest.GetDefaults(
NEURON_MODELS[0])['I_e'] + SNR_INJECTED_CURRENT
SNR = MyGroup(NEURON_MODELS[0],
n=n_exp,
sd=True,
params={'I_e': I_e},
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]
sources_STN_SNR = numpy.arange(0, n_exp * N_STN)
targets_STN_SNR = numpy.mgrid[0:n_exp,
0:N_STN][0].reshape(1, N_STN * 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.Connect(STN[sources_STN_SNR],
SNR[targets_STN_SNR],
model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate(sim_time)
for SNR in SNR_list:
SNR.get_signal('s', start=0, stop=sim_time)
pre_ref_1 = str(SNR_list[0].signals['spikes'].mean_rate(
SEL_ONSET - 500, SEL_ONSET))
burst_1 = str(SNR_list[0].signals['spikes'].mean_rate(
SEL_ONSET, SEL_ONSET + 200))
burst_2 = str(SNR_list[0].signals['spikes'].mean_rate(
SEL_ONSET + 1000, SEL_ONSET + 1200))
s = '\n'
s = s + 'Simulate example:\n'
s = s + '%s %5s %3s \n' % ('Simulation time', str(sim_time), '#')
s = s + '%s %5s %3s \n' % ('N experiments:', str(n_exp), '#')
s = s + '%s %5s %3s \n' % ('MSN base rate:', str(MSN_BASE_RATE),
'spikes/s')
s = s + '%s %5s %3s \n' % ('MSN burst rate:', str(MSN_BURST_RATE),
'spikes/s')
s = s + '%s %5s %3s \n' % ('GPe rate:', str(GPE_BASE_RATE), 'spikes/s')
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],
'spikes/s')
s = s + '%s %5s %3s \n' % ('Burst 1:', burst_1[0:4], 'spikes/s')
s = s + '%s %5s %3s \n' % ('Burst 2:', burst_2[0:4], 'spikes/s')
header = s
misc.text_save(header, save_header_at)
misc.pickle_save([SNR_list, s], save_result_at)
else:
SNR_list, s = misc.pickle_load(save_result_at)
return SNR_list, s
def simulate_MSN_vs_SNR_rate(load=True):
global SNR_INJECTED_CURRENT
global N_MSN
global N_GPE
global N_STN
global GPE_BASE_RATE
# Path were raw data is saved. For example the spike trains.
save_result_at = OUTPUT_PATH + '/simulate_MSN_vs_SNR_rate.pkl'
save_header_at = OUTPUT_PATH + '/simulate_MSN_vs_SNR_rate_header'
MSNmeanRates = numpy.arange(0.1, 3.1, 0.1)
SNRmeanRates = []
sim_time = 100000.
if not load:
for r in MSNmeanRates:
my_nest.ResetKernel(threads=3)
model_list, model_dict = models()
my_nest.MyLoadModels(model_list, NEURON_MODELS)
my_nest.MyLoadModels(model_list, SYNAPSE_MODELS_TESTED)
my_nest.MyLoadModels(model_list, SYNAPSE_MODELS_BACKGROUND)
MSN = MyPoissonInput(n=N_MSN)
GPE = MyPoissonInput(n=N_GPE)
STN = MyPoissonInput(n=N_STN)
I_e = my_nest.GetDefaults(
NEURON_MODELS[0])['I_e'] + SNR_INJECTED_CURRENT
SNR = MyGroup(NEURON_MODELS[0],
n=len(SYNAPSE_MODELS_TESTED),
params={'I_e': I_e},
sd=True)
for id in MSN[:]:
MSN.set_spike_times(id=id,
rates=numpy.array([r]),
times=numpy.array([1]),
t_stop=sim_time,
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))
# Base rate STN
for id in STN[:]:
STN.set_spike_times(id=id,
rates=[STN_BASE_RATE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
for i, syn in enumerate(SYNAPSE_MODELS_TESTED):
my_nest.ConvergentConnect(MSN[:], [SNR[i]], model=syn)
my_nest.ConvergentConnect(GPE[:], [SNR[i]],
model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.ConvergentConnect(STN[:], [SNR[i]],
model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate(sim_time)
SNR.get_signal('s') # retrieve signal
SNRmeanRates.append(SNR.signals['spikes'].mean_rates(
1000.0, sim_time))
SNRmeanRates = numpy.array(SNRmeanRates).transpose()
MSNmeanRates = numpy.array(MSNmeanRates)
rateAtThr = ''
for SNRr in SNRmeanRates:
tmp = str(MSNmeanRates[SNRr >= SELECTION_THR][-1])
rateAtThr += ' ' + tmp[0:4]
s = '\n'
s = s + 'simulate_MSN_vs_SNR_rate:\n'
s = s + ' %s %5s %3s \n' % ('N MSNs:', str(N_MSN), '#')
s = s + ' \n%s \n%5s %3s \n' % ('MSN rates:', str(
MSNmeanRates[0]) + '-' + str(MSNmeanRates[-1]), 'spikes/s')
s = s + ' %s %5s %3s \n' % ('N GPes:', str(N_GPE), '#')
s = s + ' %s %5s %3s \n' % ('Threshold SNr:', str(SELECTION_THR),
'spikes/s')
s = s + ' \n%s \n%5s %3s \n' % ('MSN rate right before threshold SNr:',
str(rateAtThr), 'spikes/s')
s = s + ' \n%s %5s %3s \n' % ('Simulation time:', str(sim_time), 'ms')
s = s + ' %s %5s %3s \n' % ('Injected current:',
str(SNR_INJECTED_CURRENT), 'pA')
infoString = s
header = HEADER_SIMULATION_SETUP + s
misc.text_save(header, save_header_at)
misc.pickle_save([MSNmeanRates, SNRmeanRates, infoString],
save_result_at)
elif load:
MSNmeanRates, SNRmeanRates, infoString = misc.pickle_load(
save_result_at)
return MSNmeanRates, SNRmeanRates, infoString
def simulate_example(hz=0, load=True):
global NEURON_MODELS
global SNAME
global SPATH
global SYNAPSE_MODELS
global SEL_ONSET
global I_E
N_EXP = 200
N_GPE = 50
N_SEL = 30 # Number of selected GPE
N_INH = 0 # Number of inhibited GPE
RATE_BASE = 15 # Base rate
RATE_SELE = hz # Selection rate
RATE_INHI = 0
SAVE_AT = SPATH + '/' + NEURON_MODELS[0] + '-example.pkl'
SEL_TIME = 20.
sim_time = SEL_TIME + SEL_ONSET + 800.
SNAME_NB = hz + 1000
EXPERIMENTS = range(N_EXP)
MODEL_LIST = models()
my_nest.ResetKernel()
my_nest.MyLoadModels(MODEL_LIST, NEURON_MODELS)
my_nest.MyLoadModels(MODEL_LIST, SYNAPSE_MODELS)
GPE_list = [] # GPE input for each experiment
for i_exp in EXPERIMENTS:
GPE = MyPoissonInput(n=N_GPE,
sd=True,
spath=SPATH,
sname_nb=SNAME_NB + i_exp)
GPE_list.append(GPE)
SNR_list = [] # SNR groups for each synapse
for i_syn, syn in enumerate(SYNAPSE_MODELS):
SNR = MyGroup(NEURON_MODELS[0],
n=N_EXP,
params={'I_e': I_E},
sd=True,
mm=False,
mm_dt=.1,
record_from=[''],
spath=SPATH,
sname_nb=SNAME_NB + i_syn)
SNR_list.append(SNR)
if not load:
for i_exp in EXPERIMENTS:
GPE = GPE_list[i_exp]
# Set spike times
# Base rate
for id in GPE[:]:
GPE.set_spike_times(id=id,
rates=[RATE_BASE],
times=[1],
t_stop=sim_time)
# Selection
for id in GPE[N_GPE - N_SEL:N_GPE + 1]:
rates = [RATE_BASE, RATE_SELE, RATE_BASE]
times = [1, SEL_ONSET, SEL_TIME + SEL_ONSET]
t_stop = sim_time
GPE.set_spike_times(id=id,
rates=rates,
times=times,
t_stop=t_stop)
# Inhibition
for id in GPE[N_GPE - N_SEL - N_INH:N_GPE + 1 - N_SEL]:
rates = [RATE_BASE, RATE_INHI, RATE_BASE]
times = [1, SEL_ONSET, SEL_TIME + SEL_ONSET]
t_stop = sim_time
GPE.set_spike_times(id=id,
rates=rates,
times=times,
t_stop=t_stop)
# Connect
for i_syn, syn in enumerate(SYNAPSE_MODELS):
target = SNR_list[i_syn][i_exp]
my_nest.ConvergentConnect(GPE[:], [target], model=syn)
my_nest.MySimulate(sim_time)
for GPE in GPE_list:
GPE.get_signal('s')
for SNR in SNR_list:
SNR.get_signal('s')
misc.pickle_save([GPE_list, SNR_list], SAVE_AT)
if load:
GPE_list, SNR_list = misc.pickle_load(SAVE_AT)
pre_ref = str(SNR_list[0].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 + 'Example:\n'
s = s + ' %s %5s %3s \n' % ('N experiments:', str(len(EXPERIMENTS)), '#')
s = s + ' %s %5s %3s \n' % ('Base rate:', str(RATE_BASE), 'Hz')
s = s + ' %s %5s %3s \n' % ('Selection rate:', str(RATE_SELE), 'Hz')
s = s + ' %s %5s %3s \n' % ('Selection time:', str(SEL_TIME), 'ms')
s = s + ' %s %5s %3s \n' % ('Pre sel rate Ref:', pre_ref[0:4], 'Hz')
s = s + ' %s %5s %3s \n' % ('Pre sel rate Dyn:', pre_dyn[0:4], 'Hz')
return GPE_list, SNR_list, s
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_get_rates(msn_burst_rate=20, load=True, len_ms=500.):
n_exp = 50
sim_time = DP['SEL_TIME'] + DP['SEL_ONSET'] + 1000.
experiments = range(n_exp)
model_list = models()
my_nest.ResetKernel()
my_nest.MyLoadModels(model_list, DP['NEURON_MODELS'])
my_nest.MyLoadModels(model_list, DP['SYNAPSE_MODELS_TESTED'])
my_nest.MyLoadModels(model_list, DP['SYNAPSE_MODELS_BACKGROUND'])
MSN_list = [] # MSN input for each experiment
for i_exp in experiments:
MSN = MyPoissonInput(n=DP['N_MSN'], sd=True)
MSN_list.append(MSN)
GPE_list = [] # GPE input for each experiment
for i_exp in experiments:
GPE = MyPoissonInput(n=DP['N_GPE'], sd=True)
GPE_list.append(GPE)
SNR_list = [] # SNR groups for each synapse
for i_syn, syn in enumerate(DP['SYNAPSE_MODELS_TESTED']):
I_e = my_nest.GetDefaults(
DP['NEURON_MODELS'][0])['I_e'] + DP['SNR_INJECTED_CURRENT'][i_syn]
SNR = MyGroup(DP['NEURON_MODELS'][0],
n=n_exp,
sd=True,
params={'I_e': I_e})
SNR_list.append(SNR)
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:DP['N_MSN']]:
MSN.set_spike_times(id=id,
rates=[DP['MSN_BASE_RATE']],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Set spike times
# Base rate
for id in GPE[:]:
GPE.set_spike_times(id=id,
rates=[DP['GPE_BASE_RATE']],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Selection
for id in MSN[DP['N_MSN'] - DP['N_MSN_BURST'] - 50:DP['N_MSN'] - 50]:
rates = [DP['MSN_BASE_RATE'], msn_burst_rate, DP['MSN_BASE_RATE']]
times = [1, DP['SEL_ONSET'], DP['SEL_TIME'] + DP['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))
# Connect
for i_syn, syn in enumerate(DP['SYNAPSE_MODELS_TESTED']):
target = SNR_list[i_syn][i_exp]
my_nest.ConvergentConnect(MSN[:], [target], model=syn)
my_nest.ConvergentConnect(GPE[:], [target],
model=DP['SYNAPSE_MODELS_BACKGROUND'][0])
my_nest.MySimulate(sim_time)
for SNR in SNR_list:
SNR.get_signal('s')
rate_ref_1 = str(SNR_list[0].signals['spikes'].mean_rate(
DP['SEL_ONSET'], DP['SEL_ONSET'] + len_ms))
rate_ref_2 = str(SNR_list[1].signals['spikes'].mean_rate(
DP['SEL_ONSET'], DP['SEL_ONSET'] + len_ms))
rate_dyn = str(SNR_list[2].signals['spikes'].mean_rate(
DP['SEL_ONSET'], DP['SEL_ONSET'] + len_ms))
return [rate_ref_1, rate_ref_2, rate_dyn]
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(hz_1=0., hz_2=100., load=True):
global I_E
global NEURON_MODELS
global N_GPE
global N_SEL
global N_MSN
global N_STN
global MSN_RATE_BASE
global STN_RATE_BASE
global SNAME
global SPATH
global SYNAPSE_MODELS
global SEL_ONSET
N_EXP = 200
RATE_BASE = 25 # Base rate
RATE_SELE_1 = hz_1
RATE_SELE_2 = hz_2 # Selection rate
SAVE_AT = SPATH + '/' + NEURON_MODELS[0] + '-example.pkl'
SEL_TIME_1 = 500.
SEL_TIME_2 = 200.
sim_time = SEL_TIME_1 + SEL_TIME_2 + SEL_ONSET + 500.
SNAME_NB = hz_1 + hz_2 + 1000
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)
GPE_list = [] # GPE input for each experiment
for i_exp in EXPERIMENTS:
GPE = MyPoissonInput(n=N_GPE, sd=True)
GPE_list.append(GPE)
MSN_list = [] # MSN input for each experiment
for i_exp in EXPERIMENTS:
MSN = MyPoissonInput(n=N_MSN, sd=True)
MSN_list.append(MSN)
STN_list = [] # MSN input for each experiment
for i_exp in EXPERIMENTS:
STN = MyPoissonInput(n=N_STN, sd=True)
STN_list.append(STN)
SNR_list = [] # SNR groups for each synapse
for i_syn in SYNAPSE_MODELS_TESTED:
I_e = my_nest.GetDefaults(NEURON_MODELS[0])['I_e'] + I_E
SNR = MyGroup(NEURON_MODELS[0],
n=N_EXP,
params={'I_e': I_e},
sd=True,
mm=False,
mm_dt=.1,
record_from=[''])
SNR_list.append(SNR)
if not load:
for i_exp in EXPERIMENTS:
GPE = GPE_list[i_exp]
MSN = MSN_list[i_exp]
STN = STN_list[i_exp]
# Set spike times
# Base rate MSN
for id in MSN[:]:
MSN.set_spike_times(id=id,
rates=[MSN_RATE_BASE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Base rate
for id in GPE[0:N_GPE - N_SEL]:
GPE.set_spike_times(id=id,
rates=[RATE_BASE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Base rate STN
for id in STN[:]:
STN.set_spike_times(id=id,
rates=[STN_RATE_BASE],
times=[1],
t_stop=sim_time,
seed=int(numpy.random.random() * 10000.0))
# Selection
for id in GPE[N_GPE - N_SEL:N_GPE]:
rates = [RATE_BASE, RATE_SELE_1, RATE_SELE_2, RATE_BASE]
times = [
1, SEL_ONSET, SEL_ONSET + SEL_TIME_1,
SEL_ONSET + SEL_TIME_1 + SEL_TIME_2
]
t_stop = sim_time
GPE.set_spike_times(id=id,
rates=rates,
times=times,
t_stop=t_stop,
seed=int(numpy.random.random() * 10000.0))
# Connect
for i, syn in enumerate(SYNAPSE_MODELS_TESTED):
target = SNR_list[i][i_exp]
my_nest.ConvergentConnect(GPE[:], [target], model=syn)
my_nest.ConvergentConnect(MSN[:], [target],
model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.ConvergentConnect(STN[:], [target],
model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate(sim_time)
for GPE in GPE_list:
GPE.get_signal('s')
for SNR in SNR_list:
SNR.get_signal('s')
misc.pickle_save([GPE_list, SNR_list], SAVE_AT)
elif load:
GPE_list, SNR_list = misc.pickle_load(SAVE_AT)
pre_ref = str(SNR_list[0].signals['spikes'].mean_rate(
SEL_ONSET - 500, SEL_ONSET))
pre_dyn = str(SNR_list[1].signals['spikes'].mean_rate(
SEL_ONSET - 500, SEL_ONSET))
statusSynapes = []
for syn in SYNAPSE_MODELS_TESTED:
statusSynapes.append(my_nest.GetDefaults(syn))
s = '\n'
s = s + 'Example:\n'
s = s + ' %s %5s %3s \n' % ('N experiments:', str(len(EXPERIMENTS)), '#')
s = s + ' %s %5s %3s \n' % ('N GPEs:', str(N_GPE), '#')
s = s + ' %s %5s %3s \n' % ('Base rate:', str(RATE_BASE), 'spikes/s')
s = s + ' %s %5s %3s \n' % ('Selection rate:', str(RATE_SELE_1),
'spikes/s')
s = s + ' %s %5s %3s \n' % ('Selection time:', str(SEL_TIME_1), 'ms')
s = s + ' %s %5s %3s \n' % ('Selection rate:', str(RATE_SELE_2),
'spikes/s')
s = s + ' %s %5s %3s \n' % ('Selection time:', str(SEL_TIME_2), 'ms')
s = s + ' %s %5s %3s \n' % ('Pre sel rate Ref:', pre_ref[0:4], 'spikes/s')
s = s + ' %s %5s %3s \n' % ('Pre sel rate Dyn:', pre_dyn[0:4], 'spikes/s')
for ss in statusSynapes:
s = s + '\n'
s = s + ' %s %10s\n' % ('Synapse', ss['synapsemodel'])
s = s + ' %s %5s %3s\n' % ('Weight', str(round(ss['weight'], 1)), 'nS')
return GPE_list, SNR_list, s
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_GPE_vs_SNR_rate(load=True):
global N_GPE
global N_MSN
global N_STN
global MSN_BASE_RATE
# Path were data is saved. For example the spike trains.
save_at = (SPATH+'/'+NEURON_MODELS[0]+'-' + '-GPE_vs_SNR_rate.pkl')
GPEmeanRates=numpy.arange(0,150,1)
SNRmeanRates=[]
sim_time=50000.
I_e=0.
if not load:
for r in GPEmeanRates:
my_nest.ResetKernel()
model_list=models()
my_nest.MyLoadModels( model_list, NEURON_MODELS )
my_nest.MyLoadModels( model_list, SYNAPSE_MODELS_TESTED )
my_nest.MyLoadModels( model_list, SYNAPSE_MODELS_BACKGROUND )
MSN = MyPoissonInput( n=N_MSN)
GPE = MyPoissonInput( n=N_GPE)
STN = MyPoissonInput( n=N_STN)
I_e=my_nest.GetDefaults(NEURON_MODELS[0])['I_e']+SNR_INJECTED_CURRENT
SNR = MyGroup( NEURON_MODELS[0], n=len(SYNAPSE_MODELS_TESTED),
sd=True,params={'I_e':I_e})
for id in GPE[:]:
GPE.set_spike_times(id=id, rates=[r], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
for id in MSN[:]:
MSN.set_spike_times(id=id, rates=[MSN_BASE_RATE], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
for id in STN[:]:
STN.set_spike_times(id=id, rates=[STN_BASE_RATE], times=[1],
t_stop=sim_time,
seed=int(numpy.random.random()*10000.0))
for i, syn in enumerate(SYNAPSE_MODELS_TESTED):
my_nest.ConvergentConnect(GPE[:],[SNR[i]], model=syn)
my_nest.ConvergentConnect(MSN[:],[SNR[i]], model=SYNAPSE_MODELS_BACKGROUND[0])
my_nest.ConvergentConnect(STN[:],[SNR[i]], model=SYNAPSE_MODELS_BACKGROUND[1])
my_nest.MySimulate( sim_time )
SNR.get_signal( 's') # retrieve signal
SNRmeanRates.append(SNR.signals['spikes'].mean_rates( 5000, sim_time))
SNRmeanRates=numpy.array(SNRmeanRates).transpose()
GPEmeanRates=numpy.array(GPEmeanRates)
rateAtThr=''
for SNRr in SNRmeanRates:
tmp=str(GPEmeanRates[SNRr>=SELECTION_THR][-1])
rateAtThr+=' '+tmp[0:4]
s='\n'
s =s + 'GPE vs SNr rate:\n'
s = s + ' %s %5s %3s \n' % ( 'N GPEs:', str ( N_GPE ), '#' )
s = s + ' %s %5s %3s \n' % ( 'Max SNr rate:', str ( SNRmeanRates[0] ), '#' )
s = s + ' \n%s \n%5s %3s \n' % ( 'GPE rates:', str ( GPEmeanRates[0] ) + '-'+
str ( GPEmeanRates[-1] ), 'spikes/s' )
s = s + ' %s %5s %3s \n' % ( 'Threshold SNr:', str ( SELECTION_THR ), 'spikes/s' )
s = s + ' \n%s \n%5s %3s \n' % ( 'GPE rate at threshold SNr:', str ( rateAtThr ), 'spikes/s' )
s = s + ' \n%s %5s %3s \n' % ( 'Simulation time:', str ( sim_time), 'ms' )
s = s + ' %s %5s %3s \n' % ( 'I_e:', str ( I_e ), 'pA' )
infoString=s
misc.pickle_save([GPEmeanRates, SNRmeanRates, infoString],
save_at)
elif load:
GPEmeanRates, SNRmeanRates, infoString = misc.pickle_load(save_at)
return GPEmeanRates, SNRmeanRates, infoString