def SimSpikingStimulus(stim, time = 1000, t_sim = None, with_labels = True):
'''
Times must be sorted. ex: times = [0, 1, 2] ; scale = [1,0]
*poisson*: integer, output is a poisson process with mean
data/poisson, scaled by *poisson*.
'''
from pyNCSre import pyST
n = np.shape(stim)[1]
nc = 10
stim[stim<=0] = 1e-5
SL = pyST.SpikeList(id_list = range(n))
SLd = pyST.SpikeList(id_list = range(n-nc))
SLc = pyST.SpikeList(id_list = range(n-nc,n))
for i in range(n-nc):
SLd[i] = pyST.STCreate.inh_poisson_generator(stim[:,i],
range(0,len(stim)*time,time),
t_stop=t_sim, refractory = 4.)
if with_labels:
for t in range(0,len(stim)):
SLt= pyST.SpikeList(id_list = range(n-nc,n))
for i in range(n-nc,n):
if stim[t,i]>1e-2:
SLt[i] = pyST.STCreate.regular_generator(stim[t,i],
jitter=True,
t_start=t*time,
t_stop=(t+1)*time)
if len(SLt.raw_data())>0: SLc = pyST.merge_spikelists(SLc, SLt)
if len(SLc.raw_data())>0:
SL = pyST.merge_spikelists(SLd,SLc)
else:
SL = SLd
return SL
def SimSpikingStimulus(stim1, stim2, time=1000, t_sim=None):
'''
Times must be sorted. ex: times = [0, 1, 2] ; scale = [1,0] *poisson*:
integer, output is a poisson process with mean data/poisson, scaled by
*poisson*.
'''
n = stim1.shape[1]
SL = pyST.SpikeList(id_list=range(n+n-2))
times = range(0, len(stim1)*time, time)
for i in range(n):
if np.any(stim1[:, i] > 0):
SL[i] = pyST.STCreate.inh_poisson_generator(stim1[:, i],
times,
t_stop=t_sim)
for i in range(n-2):
if np.any(stim2[:, i] > 0):
SL[n+i] = pyST.STCreate.inh_poisson_generator(stim2[:, i-n+2],
times,
t_stop=t_sim)
plus_times1 = np.array([100]*32)+np.arange(0,2*time*32,2*time)
plus_times2 = np.array([2*time]*32)+np.arange(0,2*time*32,2*time)
plus_times = np.concatenate([plus_times1,plus_times2])
minus_times1 = np.array([time]*32)+np.arange(0,2*time*32,2*time)
minus_times2 = np.array([time+100]*32)+np.arange(0,2*time*32,2*time)
minus_times = np.concatenate([minus_times1,minus_times2])
SL[0] = pyST.SpikeTrain(np.sort(plus_times))
SL[1] = pyST.SpikeTrain(np.sort(minus_times))
return SL
def RegularSpikingStimulus(freqs, ticks=1000):
N_NEURONS = np.shape(freqs)[0]
SL = pyST.SpikeList(id_list=list(range(N_NEURONS)))
for i in range(N_NEURONS):
f = freqs[i]
if f > 0:
SL[i] = pyST.STCreate.regular_generator(freqs[i], t_stop=ticks)
return nsat.exportAER(SL)
def SimSpikingStimulus(rates=[5, 10], t_start=1000, t_stop=4000):
n = np.shape(rates)[0]
SL = pyST.SpikeList(id_list=list(range(n)))
for i in range(n):
SL[i] = pyST.STCreate.regular_generator(rates[i],
t_start=t_start,
t_stop=t_stop,
jitter=False)
# SL[i] = pyST.STCreate.poisson_generator(rates[i], t_start, t_stop)
return SL
def SimSpikingStimulus(stim, t=1000, t_sim=None):
'''
Times must be sorted. ex: times = [0, 1, 2] ; scale = [1,0]
*poisson*: integer, output is a poisson process with mean
data/poisson, scaled by *poisson*.
'''
n = np.shape(stim)[0]
SL = pyST.SpikeList(id_list=list(range(n)))
for i in range(n):
SL[i] = pyST.STCreate.regular_generator(stim[i], t_stop=t_sim)
return SL
def SimSpikingStimulus(t_sim=None):
SL = pyST.SpikeList(id_list=[0, 1, 2, 3])
spk_train0 = [60, 110]
spk_train1 = [10, 75, 140]
spk_train2 = [15, 80, 135]
spk_train3 = [20, 130]
SL[0] = pyST.SpikeTrain(spk_train0, t_start=1)
SL[1] = pyST.SpikeTrain(spk_train1, t_start=1)
SL[2] = pyST.SpikeTrain(spk_train2, t_start=1)
SL[3] = pyST.SpikeTrain(spk_train3, t_start=1)
return SL
def PoissonSpikingStimulus(rates, n_inputs=2):
SL = pyST.SpikeList(id_list=list(range(n_inputs)))
for i in range(n_inputs):
# Tracking
# if i > 0 and i < 20:
# t_start = 0
# t_stop = 500
# rate = 50
# elif i > 20 and i < 40:
# t_start = 500
# t_stop = 1000
# rate = 50
# elif i > 40 and i < 60:
# t_start = 1000
# t_stop = 1500
# rate = 50
# elif i > 60 and i < 80:
# t_start = 1500
# t_stop = 2000
# rate = 50
# elif i > 80 and i < 100:
# t_start = 2000
# t_stop = 2500
# rate = 50
# else:
# continue
# SL[i] = pyST.STCreate.poisson_generator(rate,
# t_start,
# t_stop)
t_start = 100
t_stop = 500
rate = 1
if (i > 40 and i < 60):
t_start = 100
t_stop = 500
rate = 35
if (i < 40 or i > 60):
t_start = 100
t_stop = 500
rate = 10
SL[i] = pyST.STCreate.poisson_generator(rate, t_start, t_stop)
# Selection
# if (i > 20 and i < 40) or (i > 70 and i < 90):
# t_start = 100
# t_stop = 500
# rate = 50
# SL[i] = pyST.STCreate.poisson_generator(rate,
# t_start,
# t_stop)
return nsat.exportAER(SL), SL
def PeriodicPrePostSpikingStimulus(freqs, diff, ticks=1000):
SL = pyST.SpikeList(id_list=list(range(2)))
base_phase = 100.0
shift_phase = base_phase + diff
SL[0] = pyST.STCreate.regular_generator(freqs,
t_start=0,
phase=base_phase,
jitter=False,
t_stop=ticks,
array=False)
SL[1] = pyST.STCreate.regular_generator(freqs,
t_start=0,
phase=shift_phase,
jitter=False,
t_stop=ticks,
array=False)
return SL
def RegularSpikingStimulus(freqs, ticks=1000):
pyST.STCreate.seed(100)
m = np.shape(freqs)[0]
SL = pyST.SpikeList(id_list=list(range(m)))
tm = 500
for i in range(m):
# SL[i] = pyST.STCreate.regular_generator(freqs[i],
# t_start=1,
# t_stop=ticks)
if i != (m - 1):
t_start = tm
t_stop = tm + 2000
SL[i] = pyST.STCreate.poisson_generator(freqs[i], t_start, t_stop)
tm += 2000
SL[m - 2] = SL[m - 3]
SL[m - 1] = SL[m - 3]
return SL
def SimSpikingStimulus(rates, t_sim=None):
m = np.shape(rates)[0]
n = int(m / 2)
C1 = (np.ones((n, n)) + np.random.uniform(0, 1, (n, n)) * 2)
np.fill_diagonal(C1, rates[:n])
C1 = np.maximum(C1, C1.T)
cor_spk1 = correlated_spikes(C1, rates, n)
cor_spk1.cox_process(time=t_sim)
spk1 = cor_spk1.extract_pyNCS_list()
tmp1 = nsat.importAER(spk1)
SL = pyST.SpikeList(id_list=list(range(m)))
for i in range(m):
if i < n:
SL[i] = tmp1[i]
if i >= n:
SL[i] = pyST.STCreate.poisson_generator(rates[i], t_stop=t_sim)
return SL
def SimSpikingStimulus(N_INPUTS, **kwargs):
'''
Times must be sorted. ex: times = [0, 1, 2] ; scale = [1,0]
*poisson*: integer, output is a poisson process with mean data/poisson, scaled by *poisson*.
'''
ids, spkt, tp = genCoincidencePattern(N=N_INPUTS,
t=kwargs['t_sim'],
pf=kwargs['pf'],
rate=kwargs['f'],
Nf_co=0.1,
jitter=kwargs['jitter'])
# Input spike pattern
stimSpk = np.concatenate([[ids], [spkt]]).T
stimSpk = stimSpk.astype(int)
SL = nsat.build_SpikeList(spkt, ids)
add = SL.id_list().astype('i')
SL_shuffled = pyST.SpikeList(id_list=range(max(add)))
# g = np.arange(110)
np.random.shuffle(add)
for i, k in enumerate(add):
SL_shuffled[i] = SL[k]
return SL_shuffled, tp
def setup():
global SL
print('Begin %s:setup()' %
(os.path.splitext(os.path.basename(__file__))[0]))
np.random.seed(100) # Numpy RNG seed
pyST.STCreate.seed(130) # PyNCS RNG seed
N_CORES = 1 # Number of cores
N_NEURONS = [100] # Number of neurons per core
N_INPUTS = [101] # Number of inputs per core
N_STATES = [4] # Number of states pare core
N_UNITS = N_INPUTS[0] + N_NEURONS[0] # Total units
# Constants
XMAX = nsat.XMAX
XMIN = nsat.XMIN
OFF = -16
MAX = nsat.MAX
MIN = nsat.XMIN
NLRN_GROUPS = 8
N_GROUPS = 8
# Main class instance
cfg = nsat.ConfigurationNSAT(sim_ticks=sim_ticks,
N_CORES=N_CORES,
N_INPUTS=N_INPUTS,
N_NEURONS=N_NEURONS,
N_STATES=N_STATES,
monitor_states=True,
monitor_spikes=True,
monitor_weights=True,
w_check=False,
plasticity_en=np.array([True], 'bool'),
ben_clock=True)
cfg.core_cfgs[core].sigma[0] = [0, 0, 10, 0]
# Transition matrix group 0
cfg.core_cfgs[core].A[0] = [[-5, OFF, OFF, OFF], [3, -5, OFF, OFF],
[OFF, OFF, -6, OFF], [OFF, OFF, OFF, OFF]]
# Transition matrix group 1
cfg.core_cfgs[core].A[1] = [[OFF, OFF, OFF, OFF], [OFF, OFF, OFF, OFF],
[OFF, OFF, OFF, OFF], [OFF, OFF, OFF, OFF]]
# Sign matrix group 0
cfg.core_cfgs[core].sA[0] = [[-1, 1, 1, 1], [1, -1, 1, 1], [1, 1, -1, 1],
[1, 1, 1, -1]]
# Threshold
cfg.core_cfgs[core].Xth[0] = 25000
# Refractory period
cfg.core_cfgs[core].t_ref[0] = 40
# Bias
cfg.core_cfgs[core].b[0] = [0, 0, 0, 0]
# Initial conditions
cfg.core_cfgs[core].Xinit = np.array([[0, 0, 0, 0]
for _ in range(N_NEURONS[0])])
# Reset value
cfg.core_cfgs[core].Xreset[0] = [0, MAX, MAX, MAX]
# Turn reset on
cfg.core_cfgs[core].XresetOn[0] = [True, False, False, False]
# Turn plasticity per state on
cfg.core_cfgs[core].plastic[0] = True
# Turn stdp per state on
cfg.core_cfgs[core].stdp_en[0] = True
cfg.core_cfgs[core].is_stdp_exp_on[0] = True
# Global modulator state
cfg.core_cfgs[core].modstate[0] = 2
# Parameters groups mapping function
cfg.core_cfgs[core].nmap = np.zeros((N_NEURONS[0], ), dtype='int')
lrnmap = 1 + np.zeros((N_GROUPS, N_STATES[0]), dtype='int')
lrnmap[0, 1] = 0
cfg.core_cfgs[core].lrnmap = lrnmap
# Synaptic weights
W = np.zeros([N_UNITS, N_UNITS, N_STATES[core]], 'int')
W[0:100, N_INPUTS[core]:, 1] = np.eye(N_NEURONS[core]) * 100
W[100, N_INPUTS[core]:, 2] = 100
# Adjacent matrix
CW = np.zeros(W.shape, dtype='int')
CW[0:100, N_INPUTS[core]:, 1] = np.eye(N_NEURONS[core])
CW[100, N_INPUTS[core]:, 2] = 1
wgt_table, ptr_table = gen_ptr_wgt_table_from_W_CW(W, CW, [])
np.set_printoptions(threshold=np.nan)
cfg.core_cfgs[core].wgt_table = wgt_table
cfg.core_cfgs[core].ptr_table = ptr_table
# Learning STDP parameters
cfg.core_cfgs[core].tca = [[24, 48] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].hica = [[-3, -5, -6] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].sica = [[1, 1, 1] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].slca = [[16, 16, 16] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].tac = [[-32, -64] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].hiac = [[-6, -8, -9] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].siac = [[-1, -1, -1] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].slac = [[16, 16, 16] for _ in range(NLRN_GROUPS)]
# Prepare external stimulus (spikes events)
stim = [50] * N_NEURONS[core]
SL = SimSpikingStimulus(stim, t_sim=sim_ticks)
SLr = pyST.SpikeList(id_list=[100])
SLr[100] = pyST.STCreate.inh_poisson_generator(rate=np.array(
[0., 100., 0.]),
t=np.array([0, 400, 600]),
t_stop=sim_ticks)
SL = pyST.merge_spikelists(SL, SLr)
ext_evts_data = nsat.exportAER(SL)
cfg.set_ext_events(ext_evts_data)
# Write C NSAT parameters binary file
c_nsat_writer = nsat.C_NSATWriter(cfg, path='/tmp', prefix='test_rSTDP')
c_nsat_writer.write()
print('End %s:setup()' % (os.path.splitext(os.path.basename(__file__))[0]))
cfg.core_cfgs[core].ptr_table = ptr_table
# Learning STDP parameters
cfg.core_cfgs[core].tca = [[24, 48] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].hica = [[-3, -5, -6] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].sica = [[1, 1, 1] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].slca = [[16, 16, 16] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].tac = [[-32, -64] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].hiac = [[-6, -8, -9] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].siac = [[-1, -1, -1] for _ in range(NLRN_GROUPS)]
cfg.core_cfgs[core].slac = [[16, 16, 16] for _ in range(NLRN_GROUPS)]
# Prepare external stimulus (spikes events)
stim = [50]*N_NEURONS[core]
SL = SimSpikingStimulus(stim, t_sim=sim_ticks)
SLr = pyST.SpikeList(id_list=[100])
SLr[100] = pyST.STCreate.inh_poisson_generator(rate=np.array([0., 100., 0.]),
t=np.array([0, 400, 600]),
t_stop=sim_ticks)
SL = pyST.merge_spikelists(SL, SLr)
ext_evts_data = nsat.exportAER(SL)
cfg.set_ext_events(ext_evts_data)
# Write C NSAT parameters binary file
c_nsat_writer = nsat.C_NSATWriter(cfg, path='/tmp', prefix='test_rSTDP')
c_nsat_writer.write()
# Write Intel FPGA parameters hex files
# intel_fpga_writer = nsat.IntelFPGAWriter(cfg, path='.',
# prefix='test_rSTDP')
# intel_fpga_writer.write()
