def run_stdp(NE,NI,v_init,C_e,C_ii,C_ie,mon_bin,dt):
from brian.neurongroup import NeuronGroup
from brian.monitor import PopulationRateMonitor
from brian.stdunits import mV, ms, nS, pF, pA, Hz
from brian.units import second
from brian.equations import Equations
from brian.network import Network
from brian.connections import Connection
from brian.stdp import STDP
from brian.clock import Clock
runtime = 10*second
eta = 1e-2 # Learning rate
tau_stdp = 20*ms # STDP time constant
alpha = 3*Hz*tau_stdp*2 # Target rate parameter
gmax = 100 # Maximum inhibitory weight
eqs_neurons='''
dv/dt=(-gl*(v-el)-(g_ampa*w*v+g_gaba*(v-er)*w)+bgcurrent)/memc : volt
dg_ampa/dt = -g_ampa/tau_ampa : 1
dg_gaba/dt = -g_gaba/tau_gaba : 1
'''
namespace = {'tau_ampa':5.0*ms,'tau_gaba':10.0*ms,
'bgcurrent':200*pA,'memc':200.0*pF,
'el':-60*mV,'w':1.*nS,'gl':10.0*nS,'er':-80*mV}
eqs_neurons = Equations(eqs_neurons, ** namespace)
clock = Clock(dt)
neurons=NeuronGroup(NE+NI,model=eqs_neurons,clock=clock,
threshold=-50.*mV,reset=-60*mV,refractory=5*ms)
neurons.v = v_init
Pe=neurons.subgroup(NE)
Pi=neurons.subgroup(NI)
rme = PopulationRateMonitor(Pe,mon_bin)
rmi = PopulationRateMonitor(Pi,mon_bin)
con_e = Connection(Pe,neurons,'g_ampa')
con_ie = Connection(Pi,Pe,'g_gaba')
con_ii = Connection(Pi,Pi,'g_gaba')
con_e.connect_from_sparse(C_e, column_access=True)
con_ie.connect_from_sparse(C_ie, column_access=True)
con_ii.connect_from_sparse(C_ii, column_access=True)
eqs_istdp = '''
dA_pre/dt=-A_pre/tau_stdp : 1
dA_post/dt=-A_post/tau_stdp : 1
'''
stdp_params = {'tau_stdp':tau_stdp, 'eta':eta, 'alpha':alpha}
eqs_istdp = Equations(eqs_istdp, **stdp_params)
stdp_ie = STDP(con_ie, eqs=eqs_istdp,
pre='''A_pre+=1.
w+=(A_post-alpha)*eta''',
post='''A_post+=1.
w+=A_pre*eta''',
wmax=gmax)
net = Network(neurons, con_e, con_ie, con_ii, stdp_ie, rme, rmi)
net.run(runtime,report='text')
return (rme.times,rme.rate), (rmi.times,rmi.rate)
def test_voxel():
voxel_params = default_params
# voxel_params.e_base=.7
# voxel_params.tau_o=2.7*second
# voxel_params.tau_s=0.95
voxel = Voxel(params=voxel_params)
voxel.G_base = 0.01 * nS
voxel_monitor = MultiStateMonitor(
voxel,
vars=['G_total', 's', 'f_in', 'v', 'f_out', 'q', 'y'],
record=True)
@network_operation(when='start')
def get_input():
if 5 * second < defaultclock.t < 5.05 * second:
voxel.G_total = 1 * nS
else:
voxel.G_total = voxel.G_base
net = Network(voxel, get_input, voxel_monitor)
reinit_default_clock()
net.run(15 * second)
voxel_params = zheng_params
#voxel_params.e_base=.7
#voxel_params.tau_o=2.7*second
#voxel_params.tau_s=0.95
new_voxel = ZhengVoxel(params=voxel_params)
new_voxel.G_base = 0.01 * nS
new_voxel_monitor = MultiStateMonitor(new_voxel,
vars=[
'G_total', 's', 'f_in', 'v',
'f_out', 'q', 'y', 'g', 'cmr_o',
'o_e', 'cb'
],
record=True)
@network_operation(when='start')
def get_new_input():
if 5 * second < defaultclock.t < 5.05 * second:
new_voxel.G_total = 1 * nS
else:
new_voxel.G_total = new_voxel.G_base
@network_operation()
def compute_cmro():
#print('phi=%.3f, f_in=%.3f, o_e=%.3f, o_elog=%.3f, c_ab=%.3f, cb=%.3f, cmr_o=%.3f, g=%.3f' %
# (new_voxel.phi, new_voxel.f_in, new_voxel.o_e, new_voxel.oe_log, new_voxel.c_ab, new_voxel.cb, new_voxel.cmr_o, new_voxel.g))
#new_voxel.cmr_o=(new_voxel.cb-new_voxel.g*new_voxel.params.c_ab)/(new_voxel.params.cb_0-new_voxel.params.g_0*new_voxel.params.c_ab)
new_voxel.oe_log = np.log(1.0 - new_voxel.o_e / (1.0 - new_voxel.g))
new_net = Network(new_voxel, get_new_input, compute_cmro,
new_voxel_monitor)
reinit_default_clock()
new_net.run(15 * second)
plot_results(voxel_monitor, new_voxel_monitor)
def test_max_delay():
'''Test that changing delays after compression works. '''
reinit_default_clock()
inp = SpikeGeneratorGroup(1, [(0, 1*ms)])
G = NeuronGroup(1, model='v:1')
mon = StateMonitor(G, 'v', record=True)
# one synapse
syn = Synapses(inp, G, model='w:1', pre='v+=w', max_delay=5*ms)
syn[:, :] = 1
syn.w[:, :] = 1
syn.delay[:, :] = 0 * ms
net = Network(inp, G, syn, mon)
net.run(defaultclock.dt)
syn.delay[:, :] = 5 * ms
net.run(6.5*ms)
# spike should arrive at 5 + 1 ms
assert (mon[0][mon.times >= 6 * ms] == 1).all()
assert (mon[0][mon.times < 6 * ms] == 0).all()
# same as above but with two synapses
reinit_default_clock()
mon.reinit()
G.reinit()
syn = Synapses(inp, G, model='w:1', pre='v+=w', max_delay=5*ms)
syn[:, :] = 2
syn.w[:, :] = 1
syn.delay[:, :] = [0 * ms, 0 * ms]
net = Network(inp, G, syn, mon)
net.run(defaultclock.dt)
syn.delay[:, :] = [5 * ms, 5 * ms]
net.run(6.5*ms)
# spike should arrive at 5 + 1 ms
assert (mon[0][mon.times >= 6 * ms] == 2).all()
assert (mon[0][mon.times < 6 * ms] == 0).all()
def _prepare_brian_net(self, stimulus):
from brian.directcontrol import SpikeGeneratorGroup
from brian.synapses.synapses import Synapses
from brian.network import Network
self.S = []
netobjs, M_EIP, MV_EIP = ibm.create_netobjs(stimulus,
global_sympy_params.cur)
if len(stimulus) > 0:
N = max(stimulus[:, 0]) + 1
In1 = SpikeGeneratorGroup(N, stimulus[stimulus[:, 0] < N])
self.S.append(In1)
#Create connections, if any
if len(global_mappings_list) > 0:
gml = np.array(global_mappings_list).reshape(-1, 3)
for syn_idx in range(4):
gml_dict, pgml_dict = _dlist_to_mappingdict(
_decode_mappings_list(gml, syn_idx))
if len(gml_dict) > 0:
if len(stimulus) == 0:
input_pop = PoissonGroup(max(gml_dict.keys()) + 1, 0)
else:
input_pop = In1
iname, wname = synapse_trans_dict[syn_idx]
EIP = netobjs['EIP']
S = Synapses(input_pop,
EIP,
model="""w : 1
p : 1""",
pre=iname + "+=w*(rand()<p)")
for i in gml_dict:
S[i, gml_dict[i]] = True
S.w[i, gml_dict[i]] = global_sympy_params.cur[
wname] * np.random.normal(1, ibm.sigma_mismatch,
len(gml_dict[i]))
S.p[i, gml_dict[i]] = pgml_dict[i]
self.S.append(S)
net = Network(netobjs.values() + self.S)
return net, M_EIP, MV_EIP
def test_voxel():
voxel_params=default_params
# voxel_params.e_base=.7
# voxel_params.tau_o=2.7*second
# voxel_params.tau_s=0.95
voxel=Voxel(params=voxel_params)
voxel.G_base=0.01*nS
voxel_monitor = MultiStateMonitor(voxel, vars=['G_total','s','f_in','v','f_out','q','y'], record=True)
@network_operation(when='start')
def get_input():
if 5*second < defaultclock.t < 5.05*second:
voxel.G_total=1*nS
else:
voxel.G_total=voxel.G_base
net=Network(voxel, get_input, voxel_monitor)
reinit_default_clock()
net.run(15*second)
voxel_params=zheng_params
#voxel_params.e_base=.7
#voxel_params.tau_o=2.7*second
#voxel_params.tau_s=0.95
new_voxel=ZhengVoxel(params=voxel_params)
new_voxel.G_base=0.01*nS
new_voxel_monitor = MultiStateMonitor(new_voxel, vars=['G_total','s','f_in','v','f_out','q','y','g','cmr_o','o_e','cb'],
record=True)
@network_operation(when='start')
def get_new_input():
if 5*second < defaultclock.t < 5.05*second:
new_voxel.G_total=1*nS
else:
new_voxel.G_total=new_voxel.G_base
@network_operation()
def compute_cmro():
#print('phi=%.3f, f_in=%.3f, o_e=%.3f, o_elog=%.3f, c_ab=%.3f, cb=%.3f, cmr_o=%.3f, g=%.3f' %
# (new_voxel.phi, new_voxel.f_in, new_voxel.o_e, new_voxel.oe_log, new_voxel.c_ab, new_voxel.cb, new_voxel.cmr_o, new_voxel.g))
#new_voxel.cmr_o=(new_voxel.cb-new_voxel.g*new_voxel.params.c_ab)/(new_voxel.params.cb_0-new_voxel.params.g_0*new_voxel.params.c_ab)
new_voxel.oe_log=np.log(1.0-new_voxel.o_e/(1.0-new_voxel.g))
new_net=Network(new_voxel, get_new_input, compute_cmro, new_voxel_monitor)
reinit_default_clock()
new_net.run(15*second)
plot_results(voxel_monitor, new_voxel_monitor)
'M_EIP': M_EIP,
'MV_EIP': MV_EIP
}
return netobjs, M_EIP, MV_EIP
if __name__ == '__main__':
from pylab import *
from brian.plotting import raster_plot
ion()
from paramTranslation import params, loadBiases
from expSetup import *
configurator = pyNCS.ConfAPI.Configurator()
configurator._readCSV('chipfiles/ifslwta.csv')
configurator.set_parameters(loadBiases('biases/defaultBiases_ifslwta'))
p = params(configurator, 'chipfiles/ifslwta_paramtrans.xml')
p.translate('pinj', 2.8)
p.translate('nsynloclat1', 0.55)
p.translate('nsynloclat2', 0.53)
p.translate('nsynexcinh', 0.45)
p.translate('psynlocinhw', 2.75)
p.translate('psynlocinhth', .3)
stim = np.transpose([
np.random.randint(0, 128, 32000),
np.cumsum(np.random.random(32000) / 16)
])
netobjs, M_EIP, MV_EIP = create_netobjs(stim, p.cur)
net = Network(netobjs.values())
net.run(1)
raster_plot(*[M_EIP])
def run_wta(wta_params, input_freq, sim_params, pyr_params=pyr_params(), inh_params=inh_params(),
output_file=None, save_summary_only=False, record_neuron_state=False, record_spikes=True, record_firing_rate=True,
record_inputs=False, plot_output=False, report='text'):
"""
Run WTA network
wta_params = network parameters
input_freq = mean firing rate of each input group
output_file = output file to write to
save_summary_only = whether or not to save all data or just summary data to file
record_lfp = record LFP data if true
record_voxel = record voxel data if true
record_neuron_state = record neuron state data if true
record_spikes = record spike data if true
record_firing_rate = record network firing rates if true
record_inputs = record input firing rates if true
plot_output = plot outputs if true
"""
start_time = time()
simulation_clock=Clock(dt=sim_params.dt)
input_update_clock=Clock(dt=1/(wta_params.refresh_rate/Hz)*second)
background_input=PoissonGroup(wta_params.background_input_size, rates=wta_params.background_freq,
clock=simulation_clock)
task_inputs=[]
for i in range(wta_params.num_groups):
task_inputs.append(PoissonGroup(wta_params.task_input_size, rates=wta_params.task_input_resting_rate,
clock=simulation_clock))
# Create WTA network
wta_network=WTANetworkGroup(params=wta_params, background_input=background_input, task_inputs=task_inputs,
pyr_params=pyr_params, inh_params=inh_params, clock=simulation_clock)
@network_operation(when='start', clock=input_update_clock)
def set_task_inputs():
for idx in range(len(task_inputs)):
rate=wta_params.task_input_resting_rate
if sim_params.stim_start_time<=simulation_clock.t<sim_params.stim_end_time:
rate=input_freq[idx]*Hz+np.random.randn()*wta_params.input_var
if rate<wta_params.task_input_resting_rate:
rate=wta_params.task_input_resting_rate
task_inputs[idx]._S[0, :]=rate
@network_operation(clock=simulation_clock)
def inject_current():
if simulation_clock.t>sim_params.dcs_start_time:
wta_network.group_e.I_dcs=sim_params.p_dcs
wta_network.group_i.I_dcs=sim_params.i_dcs
# Create network monitor
wta_monitor=WTAMonitor(wta_network, sim_params, record_neuron_state=record_neuron_state, record_spikes=record_spikes,
record_firing_rate=record_firing_rate, record_inputs=record_inputs,
save_summary_only=save_summary_only, clock=simulation_clock)
# Create Brian network and reset clock
net=Network(background_input, task_inputs,set_task_inputs, wta_network, wta_network.connections.values(),
wta_monitor.monitors.values(), inject_current)
print "Initialization time: %.2fs" % (time() - start_time)
# Run simulation
start_time = time()
net.run(sim_params.trial_duration, report=report)
print "Simulation time: %.2fs" % (time() - start_time)
# Write output to file
if output_file is not None:
start_time = time()
wta_monitor.write_output(input_freq, output_file)
print 'Wrote output to %s' % output_file
print "Write output time: %.2fs" % (time() - start_time)
# Plot outputs
if plot_output:
wta_monitor.plot()
return wta_monitor
def run_wta(wta_params,
input_freq,
sim_params,
pyr_params=pyr_params(),
inh_params=inh_params(),
plasticity_params=plasticity_params(),
output_file=None,
save_summary_only=False,
record_lfp=True,
record_voxel=True,
record_neuron_state=False,
record_spikes=True,
record_firing_rate=True,
record_inputs=False,
record_connections=None,
plot_output=False,
report='text'):
"""
Run WTA network
wta_params = network parameters
input_freq = mean firing rate of each input group
output_file = output file to write to
save_summary_only = whether or not to save all data or just summary data to file
record_lfp = record LFP data if true
record_voxel = record voxel data if true
record_neuron_state = record neuron state data if true
record_spikes = record spike data if true
record_firing_rate = record network firing rates if true
record_inputs = record input firing rates if true
plot_output = plot outputs if true
"""
start_time = time()
simulation_clock = Clock(dt=sim_params.dt)
input_update_clock = Clock(dt=1 / (wta_params.refresh_rate / Hz) * second)
background_input = PoissonGroup(wta_params.background_input_size,
rates=wta_params.background_freq,
clock=simulation_clock)
task_inputs = []
for i in range(wta_params.num_groups):
task_inputs.append(
PoissonGroup(wta_params.task_input_size,
rates=wta_params.task_input_resting_rate,
clock=simulation_clock))
# Create WTA network
wta_network = WTANetworkGroup(params=wta_params,
background_input=background_input,
task_inputs=task_inputs,
pyr_params=pyr_params,
inh_params=inh_params,
plasticity_params=plasticity_params,
clock=simulation_clock)
@network_operation(when='start', clock=input_update_clock)
def set_task_inputs():
for idx in range(len(task_inputs)):
rate = wta_params.task_input_resting_rate
if sim_params.stim_start_time <= simulation_clock.t < sim_params.stim_end_time:
rate = input_freq[idx] * Hz + np.random.randn(
) * wta_params.input_var
if rate < wta_params.task_input_resting_rate:
rate = wta_params.task_input_resting_rate
task_inputs[idx]._S[0, :] = rate
@network_operation(clock=simulation_clock)
def inject_current():
if simulation_clock.t > sim_params.dcs_start_time:
wta_network.group_e.I_dcs = sim_params.p_dcs
wta_network.group_i.I_dcs = sim_params.i_dcs
# LFP source
lfp_source = LFPSource(wta_network.group_e, clock=simulation_clock)
# Create voxel
voxel = Voxel(simulation_clock, network=wta_network)
# Create network monitor
wta_monitor = WTAMonitor(wta_network,
lfp_source,
voxel,
sim_params,
record_lfp=record_lfp,
record_voxel=record_voxel,
record_neuron_state=record_neuron_state,
record_spikes=record_spikes,
record_firing_rate=record_firing_rate,
record_inputs=record_inputs,
record_connections=record_connections,
save_summary_only=save_summary_only,
clock=simulation_clock)
@network_operation(when='start', clock=simulation_clock)
def inject_muscimol():
if sim_params.muscimol_amount > 0:
wta_network.groups_e[
sim_params.
injection_site].g_muscimol = sim_params.muscimol_amount
# Create Brian network and reset clock
net = Network(background_input, task_inputs, set_task_inputs, wta_network,
lfp_source, voxel, wta_network.connections.values(),
wta_monitor.monitors.values(), inject_muscimol,
inject_current)
if sim_params.plasticity:
net.add(wta_network.stdp.values())
print "Initialization time: %.2fs" % (time() - start_time)
# writer=LaTeXDocumentWriter()
# labels={}
# labels[voxel]=('v',str(voxel))
# labels[background_input]=('bi',str(background_input))
# labels[lfp_source]=('lfp',str(lfp_source))
# labels[wta_network]=('n',str(wta_network))
# labels[wta_network.group_e]=('e',str(wta_network.group_e))
# labels[wta_network.group_i]=('i',str(wta_network.group_i))
# for i,e_group in enumerate(wta_network.groups_e):
# labels[e_group]=('e%d' % i,'%s %d' % (str(e_group),i))
# for i,task_input in enumerate(task_inputs):
# labels[task_input]=('t%d' % i,'%s %d' % (str(task_input),i))
# for name,conn in wta_network.connections.iteritems():
# labels[conn]=(name,str(conn))
# for name,monitor in wta_monitor.monitors.iteritems():
# labels[monitor]=(name,str(monitor))
# writer.document_network(net=net, labels=labels)
# Run simulation
start_time = time()
net.run(sim_params.trial_duration, report=report)
print "Simulation time: %.2fs" % (time() - start_time)
# Compute BOLD signal
if record_voxel:
start_time = time()
wta_monitor.monitors['voxel_exc'] = get_bold_signal(
wta_monitor.monitors['voxel']['G_total_exc'].values[0],
voxel.params, [500, 2500], sim_params.trial_duration)
wta_monitor.monitors['voxel'] = get_bold_signal(
wta_monitor.monitors['voxel']['G_total'].values[0], voxel.params,
[500, 2500], sim_params.trial_duration)
print "BOLD generation time: %.2fs" % (time() - start_time)
# Write output to file
if output_file is not None:
start_time = time()
wta_monitor.write_output(input_freq, output_file)
print 'Wrote output to %s' % output_file
print "Write output time: %.2fs" % (time() - start_time)
# Plot outputs
if plot_output:
wta_monitor.plot()
return wta_monitor
'MV_EIP': MV_EIP}
return netobjs, M_EIP, MV_EIP
if __name__ == '__main__':
from pylab import *
from brian.plotting import raster_plot
ion()
from paramTranslation import params, loadBiases
from expSetup import *
configurator = pyNCS.ConfAPI.Configurator()
configurator._readCSV('chipfiles/ifslwta.csv')
configurator.set_parameters(loadBiases('biases/defaultBiases_ifslwta'))
p=params(configurator, 'chipfiles/ifslwta_paramtrans.xml')
p.translate('pinj',2.8)
p.translate('nsynloclat1',0.55)
p.translate('nsynloclat2',0.53)
p.translate('nsynexcinh',0.45)
p.translate('psynlocinhw',2.75)
p.translate('psynlocinhth',.3)
stim = np.transpose([np.random.randint(0,128,32000), np.cumsum(np.random.random(32000)/16)])
netobjs, M_EIP, MV_EIP = create_netobjs(stim,p.cur)
net = Network(netobjs.values())
net.run(1)
raster_plot(*[M_EIP])
# sys.exit()
lif_group.V = Vrest
lif_conn = Connection(lif_group, lif_group, 'V', delay=10*msecond)
netw_size = len(lif_group)
n_layers = 10
for layer in range(1, n_layers):
prev_start = netw_size/n_layers*(layer-1)
cur_start = netw_size/n_layers*layer
cur_end = netw_size/n_layers*(layer+1)
lif_conn[prev_start:cur_start, cur_start:cur_end] = w_int
print("Setting up monitors ...")
trace_mon = StateMonitor(lif_group, "V", record=True)
input_mon = SpikeMonitor(inp_group)
spike_mon = SpikeMonitor(lif_group)
network = Network(lif_group, inp_group, inp_conn, lif_conn,
trace_mon, spike_mon, input_mon)
print("Running for %f seconds ..." % (duration))
network.run(duration)
print("Simulation run finished.")
if spike_mon.nspikes == 0:
print("No spikes were fired by the network. Aborting!")
sys.exit()
print("Performing Gaussian convolution ...")
t, conv_spikes = sl.tools.spikeconvolve(spike_mon, 5*msecond)
figure("Spike trains")
splt = subplot(311)
title("External inputs")
raster_plot(input_mon)
axis(xmin=0, xmax=duration/msecond)
subplot(312)
title("Network spikes")
def test_construction_single_synapses():
'''
Test the construction of synapses with a single synapse per connection.
'''
G = NeuronGroup(20, model='v:1', threshold=NoThreshold())
# specifying only one group should use it as source and target
syn = Synapses(G, model='w:1')
assert syn.source is syn.target
# specifying source and target with subgroups
subgroup1, subgroup2 = G[:10], G[10:]
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
assert syn.source is subgroup1
assert syn.target is subgroup2
# create all-to-all connections
syn[:, :] = True
assert len(syn) == 10 * 10
# deleting a synapse should not work
def delete_synapse():
syn[0, 0] = False
assert_raises(ValueError, delete_synapse)
# set the weights
syn.w[:, :] = 2
# set the delays
syn.delay[:, :] = 1 * ms
all_weights = np.array([syn.w[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))])
assert (all_weights == 2).all()
all_delays = np.array([syn.delay[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))])
assert (all_delays == 1 * ms).all()
# create one-to-one connections
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[:, :] = 'i == j'
syn.w[:, :] = 2
assert len(syn) == len(subgroup1)
for i in xrange(len(subgroup1)):
for j in xrange(len(subgroup2)):
if i == j:
assert syn.w[i, j] == 2
else:
assert len(syn.w[i, j]) == 0
net = Network(G, syn)
net.run(defaultclock.dt)
# adding synapses should not work after the simulation has already been run
def adding_a_synapse():
syn[0, 1] = True
assert_raises(AttributeError, adding_a_synapse)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one(subgroup1, subgroup2)
syn.w[:, :] = 2
assert len(syn) == len(subgroup1)
for i in xrange(len(subgroup1)):
for j in xrange(len(subgroup2)):
if i == j:
assert syn.w[i, j] == 2
else:
assert len(syn.w[i, j]) == 0
# Calling connect_one_to_one without specifying groups should use the full
# source or target group
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one(subgroup1)
assert len(syn) == len(subgroup1)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one(post=subgroup2)
assert len(syn) == len(subgroup1)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one()
assert len(syn) == len(subgroup1)
# connect_one_to_one should only work with subgroups of the same size
assert_raises(TypeError, lambda : syn.connect_one_to_one(G[:2], G[:1]))
# create random connections
# the only two cases that can be tested exactly are 0 and 100% connection
# probability
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
# floats are interpreted as connection probabilities
syn[:, :] = 0.0
assert len(syn) == 0
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, subgroup2, 0.0)
assert len(syn) == 0
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[:, :] = 1.0
assert len(syn) == 10 * 10
# set the weights
syn.w[:, :] = 2
# set the delays
syn.delay[:, :] = 1 * ms
all_weights = np.array([syn.w[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))])
assert (all_weights == 2).all()
all_delays = np.array([syn.delay[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))])
assert (all_delays == 1 * ms).all()
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, subgroup2, 1.0)
assert len(syn) == 10 * 10
# set the weights
syn.w[:, :] = 2
# set the delays
syn.delay[:, :] = 1 * ms
all_weights = np.array([syn.w[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))])
assert (all_weights == 2).all()
all_delays = np.array([syn.delay[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))])
assert (all_delays == 1 * ms).all()
# Calling connect_random without specifying groups should use the full
# source or target group
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, sparseness=1.0)
assert len(syn) == 10 * 10
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(post=subgroup2, sparseness=1.0)
assert len(syn) == 10 * 10
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(sparseness=1.0)
assert len(syn) == 10 * 10
# Just test that probabilities between zero and one work at all
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, subgroup2, 0.3)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[:, :] = 0.3
# Test that probabilities outside of the legal range raise an error
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
assert_raises(ValueError,
lambda : syn.connect_random(subgroup1, subgroup2, 1.3))
assert_raises(ValueError,
lambda : syn.connect_random(subgroup1, subgroup2, -.3))
def wrong_probability():
syn[:, :] = -0.3
assert_raises(ValueError, wrong_probability)
def wrong_probability(): #@DuplicatedSignature
syn[:, :] = 1.3
assert_raises(ValueError, wrong_probability)
# this test requires python 2.6
if sys.version_info[0] >= 2 and sys.version_info[1] >=6:
# Running a model with a synapses object with 0 synapses should raise a warning
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
syn.compress()
# Verify some things
assert len(w) == 1
# use arrays as neuron indices instead of slices or ints
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[np.arange(5), np.arange(5)] = True
syn.w[np.arange(5), np.arange(5)] = 2
syn.delay[np.arange(5), np.arange(5)] = 5 * ms
assert len(syn) == 5 * 5
assert all([syn.w[i, j] == 2 for i in xrange(5) for j in xrange(5)])
assert all([syn.delay[i, j] == 5 * ms for i in xrange(5) for j in xrange(5)])
assert all([len(syn.w[i, j]) == 0 for i in xrange(5, len(subgroup1))
for j in xrange(5, len(subgroup2))])
assert all([len(syn.delay[i, j]) == 0 for i in xrange(5, len(subgroup1))
for j in xrange(5, len(subgroup2))])
# Create a synapse without a model (e.g. a simple connection with constant
# weights
syn = Synapses(subgroup1, subgroup2, model='', pre='v+=1')
sample_length = 1 / get_samplerate(None)
cf = 1000 * Hz
print 'Testing click response'
duration = 25*ms
levels = [40, 60, 80, 100, 120]
# a click of two samples
tones = Sound([Sound.sequence([click(sample_length*2, peak=level*dB),
silence(duration=duration - sample_length)])
for level in levels])
ihc = TanCarney(MiddleEar(tones), [cf] * len(levels), update_interval=1)
syn = ZhangSynapse(ihc, cf)
s_mon = StateMonitor(syn, 's', record=True, clock=syn.clock)
R_mon = StateMonitor(syn, 'R', record=True, clock=syn.clock)
spike_mon = SpikeMonitor(syn)
net = Network(syn, s_mon, R_mon, spike_mon)
net.run(duration * 1.5)
for idx, level in enumerate(levels):
plt.figure(1)
plt.subplot(len(levels), 1, idx + 1)
plt.plot(s_mon.times / ms, s_mon[idx])
plt.xlim(0, 25)
plt.xlabel('Time (msec)')
plt.ylabel('Sp/sec')
plt.text(15, np.nanmax(s_mon[idx])/2., 'Peak SPL=%s SPL' % str(level*dB));
ymin, ymax = plt.ylim()
if idx == 0:
plt.title('Click responses')
plt.figure(2)
plt.subplot(len(levels), 1, idx + 1)
def test_max_delay():
'''Test that changing delays after compression works. '''
reinit_default_clock()
inp = SpikeGeneratorGroup(1, [(0, 1 * ms)])
G = NeuronGroup(1, model='v:1')
mon = StateMonitor(G, 'v', record=True)
# one synapse
syn = Synapses(inp, G, model='w:1', pre='v+=w', max_delay=5 * ms)
syn[:, :] = 1
syn.w[:, :] = 1
syn.delay[:, :] = 0 * ms
net = Network(inp, G, syn, mon)
net.run(defaultclock.dt)
syn.delay[:, :] = 5 * ms
net.run(6.5 * ms)
# spike should arrive at 5 + 1 ms
assert (mon[0][mon.times >= 6 * ms] == 1).all()
assert (mon[0][mon.times < 6 * ms] == 0).all()
# same as above but with two synapses
reinit_default_clock()
mon.reinit()
G.reinit()
syn = Synapses(inp, G, model='w:1', pre='v+=w', max_delay=5 * ms)
syn[:, :] = 2
syn.w[:, :] = 1
syn.delay[:, :] = [0 * ms, 0 * ms]
net = Network(inp, G, syn, mon)
net.run(defaultclock.dt)
syn.delay[:, :] = [5 * ms, 5 * ms]
net.run(6.5 * ms)
# spike should arrive at 5 + 1 ms
assert (mon[0][mon.times >= 6 * ms] == 2).all()
assert (mon[0][mon.times < 6 * ms] == 0).all()
def test_construction_single_synapses():
'''
Test the construction of synapses with a single synapse per connection.
'''
G = NeuronGroup(20, model='v:1', threshold=NoThreshold())
# specifying only one group should use it as source and target
syn = Synapses(G, model='w:1')
assert syn.source is syn.target
# specifying source and target with subgroups
subgroup1, subgroup2 = G[:10], G[10:]
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
assert syn.source is subgroup1
assert syn.target is subgroup2
# create all-to-all connections
syn[:, :] = True
assert len(syn) == 10 * 10
# deleting a synapse should not work
def delete_synapse():
syn[0, 0] = False
assert_raises(ValueError, delete_synapse)
# set the weights
syn.w[:, :] = 2
# set the delays
syn.delay[:, :] = 1 * ms
all_weights = np.array([
syn.w[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))
])
assert (all_weights == 2).all()
all_delays = np.array([
syn.delay[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))
])
assert (all_delays == 1 * ms).all()
# create one-to-one connections
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[:, :] = 'i == j'
syn.w[:, :] = 2
assert len(syn) == len(subgroup1)
for i in xrange(len(subgroup1)):
for j in xrange(len(subgroup2)):
if i == j:
assert syn.w[i, j] == 2
else:
assert len(syn.w[i, j]) == 0
net = Network(G, syn)
net.run(defaultclock.dt)
# adding synapses should not work after the simulation has already been run
def adding_a_synapse():
syn[0, 1] = True
assert_raises(AttributeError, adding_a_synapse)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one(subgroup1, subgroup2)
syn.w[:, :] = 2
assert len(syn) == len(subgroup1)
for i in xrange(len(subgroup1)):
for j in xrange(len(subgroup2)):
if i == j:
assert syn.w[i, j] == 2
else:
assert len(syn.w[i, j]) == 0
# Calling connect_one_to_one without specifying groups should use the full
# source or target group
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one(subgroup1)
assert len(syn) == len(subgroup1)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one(post=subgroup2)
assert len(syn) == len(subgroup1)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_one_to_one()
assert len(syn) == len(subgroup1)
# connect_one_to_one should only work with subgroups of the same size
assert_raises(TypeError, lambda: syn.connect_one_to_one(G[:2], G[:1]))
# create random connections
# the only two cases that can be tested exactly are 0 and 100% connection
# probability
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
# floats are interpreted as connection probabilities
syn[:, :] = 0.0
assert len(syn) == 0
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, subgroup2, 0.0)
assert len(syn) == 0
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[:, :] = 1.0
assert len(syn) == 10 * 10
# set the weights
syn.w[:, :] = 2
# set the delays
syn.delay[:, :] = 1 * ms
all_weights = np.array([
syn.w[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))
])
assert (all_weights == 2).all()
all_delays = np.array([
syn.delay[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))
])
assert (all_delays == 1 * ms).all()
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, subgroup2, 1.0)
assert len(syn) == 10 * 10
# set the weights
syn.w[:, :] = 2
# set the delays
syn.delay[:, :] = 1 * ms
all_weights = np.array([
syn.w[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))
])
assert (all_weights == 2).all()
all_delays = np.array([
syn.delay[i, j] for i in xrange(len(subgroup1))
for j in xrange(len(subgroup2))
])
assert (all_delays == 1 * ms).all()
# Calling connect_random without specifying groups should use the full
# source or target group
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, sparseness=1.0)
assert len(syn) == 10 * 10
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(post=subgroup2, sparseness=1.0)
assert len(syn) == 10 * 10
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(sparseness=1.0)
assert len(syn) == 10 * 10
# Just test that probabilities between zero and one work at all
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn.connect_random(subgroup1, subgroup2, 0.3)
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[:, :] = 0.3
# Test that probabilities outside of the legal range raise an error
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
assert_raises(ValueError,
lambda: syn.connect_random(subgroup1, subgroup2, 1.3))
assert_raises(ValueError,
lambda: syn.connect_random(subgroup1, subgroup2, -.3))
def wrong_probability():
syn[:, :] = -0.3
assert_raises(ValueError, wrong_probability)
def wrong_probability(): #@DuplicatedSignature
syn[:, :] = 1.3
assert_raises(ValueError, wrong_probability)
# this test requires python 2.6
if sys.version_info[0] >= 2 and sys.version_info[1] >= 6:
# Running a model with a synapses object with 0 synapses should raise a warning
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
with warnings.catch_warnings(record=True) as w:
# Cause all warnings to always be triggered.
warnings.simplefilter("always")
# Trigger a warning.
syn.compress()
# Verify some things
assert len(w) == 1
# use arrays as neuron indices instead of slices or ints
syn = Synapses(subgroup1, subgroup2, model='w:1', pre='v += w')
syn[np.arange(5), np.arange(5)] = True
syn.w[np.arange(5), np.arange(5)] = 2
syn.delay[np.arange(5), np.arange(5)] = 5 * ms
assert len(syn) == 5 * 5
assert all([syn.w[i, j] == 2 for i in xrange(5) for j in xrange(5)])
assert all(
[syn.delay[i, j] == 5 * ms for i in xrange(5) for j in xrange(5)])
assert all([
len(syn.w[i, j]) == 0 for i in xrange(5, len(subgroup1))
for j in xrange(5, len(subgroup2))
])
assert all([
len(syn.delay[i, j]) == 0 for i in xrange(5, len(subgroup1))
for j in xrange(5, len(subgroup2))
])
# Create a synapse without a model (e.g. a simple connection with constant
# weights
syn = Synapses(subgroup1, subgroup2, model='', pre='v+=1')
def run_wta(
wta_params,
input_freq,
sim_params,
pyr_params=pyr_params(),
inh_params=inh_params(),
plasticity_params=plasticity_params(),
output_file=None,
save_summary_only=False,
record_lfp=True,
record_voxel=True,
record_neuron_state=False,
record_spikes=True,
record_firing_rate=True,
record_inputs=False,
record_connections=None,
plot_output=False,
report="text",
):
"""
Run WTA network
wta_params = network parameters
input_freq = mean firing rate of each input group
output_file = output file to write to
save_summary_only = whether or not to save all data or just summary data to file
record_lfp = record LFP data if true
record_voxel = record voxel data if true
record_neuron_state = record neuron state data if true
record_spikes = record spike data if true
record_firing_rate = record network firing rates if true
record_inputs = record input firing rates if true
plot_output = plot outputs if true
"""
start_time = time()
simulation_clock = Clock(dt=sim_params.dt)
input_update_clock = Clock(dt=1 / (wta_params.refresh_rate / Hz) * second)
background_input = PoissonGroup(
wta_params.background_input_size, rates=wta_params.background_freq, clock=simulation_clock
)
task_inputs = []
for i in range(wta_params.num_groups):
task_inputs.append(
PoissonGroup(wta_params.task_input_size, rates=wta_params.task_input_resting_rate, clock=simulation_clock)
)
# Create WTA network
wta_network = WTANetworkGroup(
params=wta_params,
background_input=background_input,
task_inputs=task_inputs,
pyr_params=pyr_params,
inh_params=inh_params,
plasticity_params=plasticity_params,
clock=simulation_clock,
)
@network_operation(when="start", clock=input_update_clock)
def set_task_inputs():
for idx in range(len(task_inputs)):
rate = wta_params.task_input_resting_rate
if sim_params.stim_start_time <= simulation_clock.t < sim_params.stim_end_time:
rate = input_freq[idx] * Hz + np.random.randn() * wta_params.input_var
if rate < wta_params.task_input_resting_rate:
rate = wta_params.task_input_resting_rate
task_inputs[idx]._S[0, :] = rate
@network_operation(clock=simulation_clock)
def inject_current():
if simulation_clock.t > sim_params.dcs_start_time:
wta_network.group_e.I_dcs = sim_params.p_dcs
wta_network.group_i.I_dcs = sim_params.i_dcs
# LFP source
lfp_source = LFPSource(wta_network.group_e, clock=simulation_clock)
# Create voxel
voxel = Voxel(simulation_clock, network=wta_network)
# Create network monitor
wta_monitor = WTAMonitor(
wta_network,
lfp_source,
voxel,
sim_params,
record_lfp=record_lfp,
record_voxel=record_voxel,
record_neuron_state=record_neuron_state,
record_spikes=record_spikes,
record_firing_rate=record_firing_rate,
record_inputs=record_inputs,
record_connections=record_connections,
save_summary_only=save_summary_only,
clock=simulation_clock,
)
@network_operation(when="start", clock=simulation_clock)
def inject_muscimol():
if sim_params.muscimol_amount > 0:
wta_network.groups_e[sim_params.injection_site].g_muscimol = sim_params.muscimol_amount
# Create Brian network and reset clock
net = Network(
background_input,
task_inputs,
set_task_inputs,
wta_network,
lfp_source,
voxel,
wta_network.connections.values(),
wta_monitor.monitors.values(),
inject_muscimol,
inject_current,
)
if sim_params.plasticity:
net.add(wta_network.stdp.values())
print "Initialization time: %.2fs" % (time() - start_time)
# writer=LaTeXDocumentWriter()
# labels={}
# labels[voxel]=('v',str(voxel))
# labels[background_input]=('bi',str(background_input))
# labels[lfp_source]=('lfp',str(lfp_source))
# labels[wta_network]=('n',str(wta_network))
# labels[wta_network.group_e]=('e',str(wta_network.group_e))
# labels[wta_network.group_i]=('i',str(wta_network.group_i))
# for i,e_group in enumerate(wta_network.groups_e):
# labels[e_group]=('e%d' % i,'%s %d' % (str(e_group),i))
# for i,task_input in enumerate(task_inputs):
# labels[task_input]=('t%d' % i,'%s %d' % (str(task_input),i))
# for name,conn in wta_network.connections.iteritems():
# labels[conn]=(name,str(conn))
# for name,monitor in wta_monitor.monitors.iteritems():
# labels[monitor]=(name,str(monitor))
# writer.document_network(net=net, labels=labels)
# Run simulation
start_time = time()
net.run(sim_params.trial_duration, report=report)
print "Simulation time: %.2fs" % (time() - start_time)
# Compute BOLD signal
if record_voxel:
start_time = time()
wta_monitor.monitors["voxel_exc"] = get_bold_signal(
wta_monitor.monitors["voxel"]["G_total_exc"].values[0], voxel.params, [500, 2500], sim_params.trial_duration
)
wta_monitor.monitors["voxel"] = get_bold_signal(
wta_monitor.monitors["voxel"]["G_total"].values[0], voxel.params, [500, 2500], sim_params.trial_duration
)
print "BOLD generation time: %.2fs" % (time() - start_time)
# Write output to file
if output_file is not None:
start_time = time()
wta_monitor.write_output(input_freq, output_file)
print "Wrote output to %s" % output_file
print "Write output time: %.2fs" % (time() - start_time)
# Plot outputs
if plot_output:
wta_monitor.plot()
return wta_monitor
