def scenario4(sim):
"""
Network with spatial structure
"""
init_logging(logfile=None, debug=True)
sim.setup()
rng = NumpyRNG(seed=76454, parallel_safe=False)
input_layout = RandomStructure(boundary=Cuboid(width=500.0, height=500.0, depth=100.0),
origin=(0, 0, 0), rng=rng)
inputs = sim.Population(100, sim.SpikeSourcePoisson(rate=RandomDistribution('uniform', [3.0, 7.0], rng=rng)),
structure=input_layout, label="inputs")
output_layout = Grid3D(aspect_ratioXY=1.0, aspect_ratioXZ=5.0, dx=10.0, dy=10.0, dz=10.0,
x0=0.0, y0=0.0, z0=200.0)
outputs = sim.Population(200, sim.EIF_cond_exp_isfa_ista(),
initial_values = {'v': RandomDistribution('normal', [-65.0, 5.0], rng=rng),
'w': RandomDistribution('normal', [0.0, 1.0], rng=rng)},
structure=output_layout, # 10x10x2 grid
label="outputs")
logger.debug("Output population positions:\n %s", outputs.positions)
DDPC = sim.DistanceDependentProbabilityConnector
input_connectivity = DDPC("0.5*exp(-d/100.0)", rng=rng)
recurrent_connectivity = DDPC("sin(pi*d/250.0)**2", rng=rng)
depressing = sim.TsodyksMarkramSynapse(weight=RandomDistribution('normal', (0.1, 0.02), rng=rng),
delay="0.5 + d/100.0",
U=0.5, tau_rec=800.0, tau_facil=0.0)
facilitating = sim.TsodyksMarkramSynapse(weight=0.05,
delay="0.2 + d/100.0",
U=0.04, tau_rec=100.0,
tau_facil=1000.0)
input_connections = sim.Projection(inputs, outputs, input_connectivity,
receptor_type='excitatory',
synapse_type=depressing,
space=Space(axes='xy'),
label="input connections")
recurrent_connections = sim.Projection(outputs, outputs, recurrent_connectivity,
receptor_type='inhibitory',
synapse_type=facilitating,
space=Space(periodic_boundaries=((-100.0, 100.0), (-100.0, 100.0), None)), # should add "calculate_boundaries" method to Structure classes
label="recurrent connections")
outputs.record('spikes')
outputs.sample(10, rng=rng).record('v')
sim.run(1000.0)
data = outputs.get_data()
sim.end()
return data
def runNetwork(Be,
Bi,
nn_stim,
show_gui=True,
dt = defaultParams.dt,
N_rec_v = 5,
save=False,
simtime = defaultParams.Tpost+defaultParams.Tstim+defaultParams.Tblank+defaultParams.Ttrans,
extra = {},
kernelseed = 123):
exec("from pyNN.%s import *" % simulator_name) in globals()
timer = Timer()
rec_conn={'EtoE':1, 'EtoI':1, 'ItoE':1, 'ItoI':1}
print('####################')
print('### (Be, Bi, nn_stim): ', Be, Bi, nn_stim)
print('####################')
Bee, Bei = Be, Be
Bie, Bii = Bi, Bi
N = defaultParams.N
NE = defaultParams.NE
NI = defaultParams.NI
print('\n # -----> Num cells: %s, size of pert. inh: %s; base rate %s; pert rate %s'% (N, nn_stim, defaultParams.r_bkg, defaultParams.r_stim))
r_extra = np.zeros(N)
r_extra[NE:NE+nn_stim] = defaultParams.r_stim
rr1 = defaultParams.r_bkg*np.random.uniform(.75,1.25, N)
rr2 = rr1 + r_extra
rank = setup(timestep=dt, max_delay=defaultParams.delay_default, reference='ISN', save_format='hdf5', **extra)
print("rank =", rank)
nump = num_processes()
print("num_processes =", nump)
import socket
host_name = socket.gethostname()
print("Host #%d is on %s" % (rank+1, host_name))
if 'threads' in extra:
print("%d Initialising the simulator with %d threads..." % (rank, extra['threads']))
else:
print("%d Initialising the simulator with single thread..." % rank)
timer.start() # start timer on construction
print("%d Setting up random number generator using seed %s" % (rank, kernelseed))
ks = open('kernelseed','w')
ks.write('%i'%kernelseed)
ks.close()
rng = NumpyRNG(kernelseed, parallel_safe=True)
nesp = defaultParams.neuron_params_default
cell_parameters = {
'cm': nesp['C_m']/1000, # Capacitance of the membrane in nF
'tau_refrac': nesp['t_ref'], # Duration of refractory period in ms.
'v_spike': 0.0 , # Spike detection threshold in mV. https://github.com/nest/nest-simulator/blob/master/models/aeif_cond_alpha.cpp
'v_reset': nesp['V_reset'], # Reset value for V_m after a spike. In mV.
'v_rest': nesp['E_L'], # Resting membrane potential (Leak reversal potential) in mV.
'tau_m': nesp['C_m']/nesp['g_L'], # Membrane time constant in ms = cm/tau_m*1000.0, C_m/g_L
'i_offset': nesp['I_e']/1000, # Offset current in nA
'a': 0, # Subthreshold adaptation conductance in nS.
'b': 0, # Spike-triggered adaptation in nA
'delta_T': 2 , # Slope factor in mV. See https://github.com/nest/nest-simulator/blob/master/models/aeif_cond_alpha.cpp
'tau_w': 144.0, # Adaptation time constant in ms. See https://github.com/nest/nest-simulator/blob/master/models/aeif_cond_alpha.cpp
'v_thresh': nesp['V_th'], # Spike initiation threshold in mV
'e_rev_E': nesp['E_ex'], # Excitatory reversal potential in mV.
'tau_syn_E': nesp['tau_syn_ex'], # Rise time of excitatory synaptic conductance in ms (alpha function).
'e_rev_I': nesp['E_in'], # Inhibitory reversal potential in mV.
'tau_syn_I': nesp['tau_syn_in'], # Rise time of the inhibitory synaptic conductance in ms (alpha function).
}
print("%d Creating population with %d neurons." % (rank, N))
celltype = EIF_cond_alpha_isfa_ista(**cell_parameters)
celltype.default_initial_values['v'] = cell_parameters['v_rest'] # Setting default init v, useful for NML2 export
layer_volume = Cuboid(1000,100,1000)
layer_structure = RandomStructure(layer_volume, origin=(0,0,0))
layer_structure_input = RandomStructure(layer_volume, origin=(0,-150,0))
default_cell_radius = 15
stim_cell_radius = 10
#EI_pop = Population(N, celltype, structure=layer_structure, label="EI")
E_pop = Population(NE, celltype, structure=layer_structure, label='E_pop')
E_pop.annotate(color='1 0 0')
E_pop.annotate(radius=default_cell_radius)
E_pop.annotate(type='E') # temp indicator to use for connection arrowhead
#print("%d Creating pop %s." % (rank, E_pop))
I_pop = Population(NI, celltype, structure=layer_structure, label='I_pop')
I_pop.annotate(color='0 0 .9')
I_pop.annotate(radius=default_cell_radius)
I_pop.annotate(type='I') # temp indicator to use for connection arrowhead
#print("%d Creating pop %s." % (rank, I_pop))
I_pert_pop = PopulationView(I_pop, np.array(range(0,nn_stim)),label='I_pert_pop')
I_nonpert_pop = PopulationView(I_pop, np.array(range(nn_stim,NI)),label='I_nonpert_pop')
p_rate = defaultParams.r_bkg
print("%d Creating excitatory Poisson generator with rate %g spikes/s." % (rank, p_rate))
source_typeA_E = SpikeSourcePoisson(rate=p_rate, start=0,duration=defaultParams.Ttrans+defaultParams.Tblank+defaultParams.Tstim+defaultParams.Tpost)
expoissonA_E = Population(NE, source_typeA_E, structure=layer_structure_input, label="stim_E")
print("%d Creating excitatory Poisson generator with rate %g spikes/s." % (rank, p_rate))
source_typeA_I = SpikeSourcePoisson(rate=p_rate, start=0,duration=defaultParams.Ttrans+defaultParams.Tblank)
expoissonA_I = Population(NI, source_typeA_I, structure=layer_structure_input, label="pre_pert_stim_I")
print("%d Creating excitatory Poisson generator with rate %g spikes/s." % (rank, p_rate))
source_typeB = SpikeSourcePoisson(rate=p_rate, start=defaultParams.Ttrans+defaultParams.Tblank,duration=defaultParams.Tstim+defaultParams.Tpost)
#expoissonB_E = Population(NE, source_typeB, label="non_pert_stim_E")
expoissonB_I = Population(len(I_nonpert_pop), source_typeB, structure=layer_structure_input, label="non_pert_stim_I")
p_rate = defaultParams.r_bkg+defaultParams.r_stim
print("%d Creating excitatory Poisson generator with rate %g spikes/s." % (rank, p_rate))
source_typeC = SpikeSourcePoisson(rate=p_rate, start=defaultParams.Ttrans+defaultParams.Tblank, duration=defaultParams.Tstim)
expoissonC = Population(nn_stim, source_typeC, structure=layer_structure_input, label="pert_stim")
p_rate = defaultParams.r_bkg
print("%d Creating excitatory Poisson generator with rate %g spikes/s." % (rank, p_rate))
source_typeD = SpikeSourcePoisson(rate=p_rate, start=defaultParams.Ttrans+defaultParams.Tblank+defaultParams.Tstim, duration=defaultParams.Tpost)
expoissonD = Population(nn_stim, source_typeD, structure=layer_structure_input, label="pert_poststim")
for p in [expoissonA_E,expoissonA_I,expoissonB_I,expoissonC,expoissonD]:
p.annotate(color='0.8 0.8 0.8')
p.annotate(radius=stim_cell_radius)
progress_bar = ProgressBar(width=20)
connector_E = FixedProbabilityConnector(0.15, rng=rng, callback=progress_bar)
connector_I = FixedProbabilityConnector(1, rng=rng, callback=progress_bar)
EE_syn = StaticSynapse(weight=0.001*Bee, delay=defaultParams.delay_default)
EI_syn = StaticSynapse(weight=0.001*Bei, delay=defaultParams.delay_default)
II_syn = StaticSynapse(weight=0.001*Bii, delay=defaultParams.delay_default)
IE_syn = StaticSynapse(weight=0.001*Bie, delay=defaultParams.delay_default)
#I_syn = StaticSynapse(weight=JI, delay=delay)
ext_Connector = OneToOneConnector(callback=progress_bar)
ext_syn_bkg = StaticSynapse(weight=0.001*defaultParams.Be_bkg, delay=defaultParams.delay_default)
ext_syn_stim = StaticSynapse(weight=0.001*defaultParams.Be_stim, delay=defaultParams.delay_default)
E_to_E = Projection(E_pop, E_pop, connector_E, EE_syn, receptor_type="excitatory")
print("E --> E\t\t", len(E_to_E), "connections")
E_to_I = Projection(E_pop, I_pop, connector_E, EI_syn, receptor_type="excitatory")
print("E --> I\t\t", len(E_to_I), "connections")
I_to_I = Projection(I_pop, I_pop, connector_I, II_syn, receptor_type="inhibitory")
print("I --> I\t\t", len(I_to_I), "connections")
I_to_E = Projection(I_pop, E_pop, connector_I, IE_syn, receptor_type="inhibitory")
print("I --> E\t\t", len(I_to_E), "connections")
input_A_E = Projection(expoissonA_E, E_pop, ext_Connector, ext_syn_bkg, receptor_type="excitatory")
print("input --> %s cells pre pert\t"%len(E_pop), len(input_A_E), "connections")
input_A_I = Projection(expoissonA_I, I_pop, ext_Connector, ext_syn_bkg, receptor_type="excitatory")
print("input --> %s cells pre pert\t"%len(I_pop), len(input_A_I), "connections")
##input_B_E = Projection(expoissonB_E, E_pop, ext_Connector, ext_syn_bkg, receptor_type="excitatory")
##print("input --> %s cells post pert\t"%len(E_pop), len(input_B_E), "connections")
input_B_I = Projection(expoissonB_I, I_nonpert_pop, ext_Connector, ext_syn_bkg, receptor_type="excitatory")
print("input --> %s cells post pert\t"%len(I_nonpert_pop), len(input_B_I), "connections")
input_C = Projection(expoissonC, I_pert_pop, ext_Connector, ext_syn_stim, receptor_type="excitatory")
print("input --> %s cells pre pert\t"%len(I_pert_pop), len(input_C), "connections")
input_D = Projection(expoissonD, I_pert_pop, ext_Connector, ext_syn_stim, receptor_type="excitatory")
print("input --> %s cells pre pert\t"%len(I_pert_pop), len(input_D), "connections")
# Can't be used for connections etc. as NeuroML export not (yet) supported
EI_pop = Assembly(E_pop, I_pop, label='EI')
# Record spikes
print("%d Setting up recording in excitatory population." % rank)
EI_pop.record('spikes')
if N_rec_v>0:
EI_pop[0:min(N,N_rec_v)].record('v')
# read out time used for building
buildCPUTime = timer.elapsedTime()
# === Run simulation ===========================================================
# run, measure computer time
timer.start() # start timer on construction
print("%d Running simulation in %s for %g ms (dt=%sms)." % (rank, simulator_name, simtime, dt))
run(simtime)
print("Done")
simCPUTime = timer.elapsedTime()
# write data to file
if save and not simulator_name=='neuroml':
for pop in [EI_pop]:
filename="ISN-%s-%s-%i.gdf"%(simulator_name, pop.label, rank)
ff = open(filename, 'w')
spikes = pop.get_data('spikes', gather=False)
spiketrains = spikes.segments[0].spiketrains
print('Saving data recorded for %i spiketrains in pop %s, indices: %s, ids: %s to %s'% \
(len(spiketrains),
pop.label,
[s.annotations['source_index'] for s in spiketrains],
[s.annotations['source_id'] for s in spiketrains],
filename))
for spiketrain_i in range(len(spiketrains)):
spiketrain = spiketrains[spiketrain_i]
source_id = spiketrain.annotations['source_id']
source_index = spiketrain.annotations['source_index']
#print("Writing spike data for cell %s[%s] (gid: %i): %i spikes: [%s,...,%s] "%(pop.label,source_index, source_id, len(spiketrain),spiketrain[0],spiketrain[-1]))
for t in spiketrain:
ff.write('%s\t%i\n'%(t.magnitude,spiketrain_i))
ff.close()
vs = pop.get_data('v', gather=False)
for segment in vs.segments:
for i in range(len(segment.analogsignals[0].transpose())):
filename="ISN-%s-%s-cell%i.dat"%(simulator_name, pop.label, i)
print('Saving cell %i in %s to %s'%(i,pop.label,filename))
vm = segment.analogsignals[0].transpose()[i]
tt = np.array([t*dt/1000. for t in range(len(vm))])
times_vm = np.array([tt, vm/1000.]).transpose()
np.savetxt(filename, times_vm , delimiter = '\t', fmt='%s')
spike_data = {}
spike_data['senders'] = []
spike_data['times'] = []
index_offset = 1
for pop in [EI_pop]:
if rank == 0:
spikes = pop.get_data('spikes', gather=False)
#print(spikes.segments[0].all_data)
num_rec = len(spikes.segments[0].spiketrains)
print("Extracting spike info (%i) for %i cells in %s"%(num_rec,pop.size,pop.label))
#assert(num_rec==len(spikes.segments[0].spiketrains))
for i in range(num_rec):
ss = spikes.segments[0].spiketrains[i]
for s in ss:
index = i+index_offset
#print("Adding spike at %s in %s[%i] (cell %i)"%(s,pop.label,i,index))
spike_data['senders'].append(index)
spike_data['times'].append(s)
index_offset+=pop.size
print("Build time : %g s" % buildCPUTime)
print("Simulation time : %g s" % simCPUTime)
# === Clean up and quit ========================================================
end()
def setup(self, sim) :
# Create matrix of synaptic weights
self.w = create_weight_matrix()
model = getattr(sim, 'IF_curr_exp')
script_rng = NumpyRNG(seed=6508015, parallel_safe=parallel_safe)
distr = RandomDistribution('normal', [V0_mean, V0_sd], rng=script_rng)
# Create cortical populations
self.pops = {}
layer_structures = {}
total_cells = 0
x_dim_scaled = x_dimension * math.sqrt(N_scaling)
z_dim_scaled = z_dimension * math.sqrt(N_scaling)
default_cell_radius = 10 # for visualisation
default_input_radius = 5 # for visualisation
for layer in layers:
self.pops[layer] = {}
for pop in pops:
y_offset = 0
if layer == 'L6': y_offset = layer_thicknesses['L6']/2
if layer == 'L5': y_offset = layer_thicknesses['L6']+layer_thicknesses['L5']/2
if layer == 'L4': y_offset = layer_thicknesses['L6']+layer_thicknesses['L5']+layer_thicknesses['L4']/2
if layer == 'L23': y_offset = layer_thicknesses['L6']+layer_thicknesses['L5']+layer_thicknesses['L4']+layer_thicknesses['L23']/2
layer_volume = Cuboid(x_dim_scaled,layer_thicknesses[layer],z_dim_scaled)
layer_structures[layer] = RandomStructure(layer_volume, origin=(0,y_offset,0))
self.pops[layer][pop] = sim.Population(int(N_full[layer][pop] * \
N_scaling), model, cellparams=neuron_params, \
structure=layer_structures[layer], label='%s_%s'%(layer,pop))
self.pops[layer][pop].initialize(v=distr)
# Store whether population is inhibitory or excitatory
self.pops[layer][pop].annotate(type=pop)
self.pops[layer][pop].annotate(radius=default_cell_radius)
self.pops[layer][pop].annotate(structure=str(layer_structures[layer]))
this_pop = self.pops[layer][pop]
color='0 0 0'
radius = 10
try:
import opencortex.utils.color as occ
if layer == 'L23':
if pop=='E': color = occ.L23_PRINCIPAL_CELL
if pop=='I': color = occ.L23_INTERNEURON
if layer == 'L4':
if pop=='E': color = occ.L4_PRINCIPAL_CELL
if pop=='I': color = occ.L4_INTERNEURON
if layer == 'L5':
if pop=='E': color = occ.L5_PRINCIPAL_CELL
if pop=='I': color = occ.L5_INTERNEURON
if layer == 'L6':
if pop=='E': color = occ.L6_PRINCIPAL_CELL
if pop=='I': color = occ.L6_INTERNEURON
self.pops[layer][pop].annotate(color=color)
except:
# Don't worry about it, it's just metadata
pass
print("Created population %s with %i cells (color: %s)"%(this_pop.label,this_pop.size, color))
total_cells += this_pop.size
# Spike recording
if record_fraction:
num_spikes = int(round(this_pop.size * frac_record_spikes))
else:
num_spikes = n_record
this_pop[0:num_spikes].record('spikes')
# Membrane potential recording
if record_v:
if record_fraction:
num_v = int(round(this_pop.size * frac_record_v))
else:
num_v = n_record_v
this_pop[0:num_v].record('v')
print("Finished creating all cell populations (%i cells)"%total_cells)
# Create thalamic population
if thalamic_input:
print("Adding thalamic input")
layer_volume = Cuboid(x_dimension,layer_thicknesses['thalamus'],z_dimension)
layer_structure = RandomStructure(layer_volume, origin=(0,thalamus_offset,0))
self.thalamic_population = sim.Population(
thal_params['n_thal'],
sim.SpikeSourcePoisson,
{'rate': thal_params['rate'],
'start': thal_params['start'],
'duration': thal_params['duration']},
structure=layer_structure,
label='thalamic_input')
# Compute DC input before scaling
if input_type == 'DC':
self.DC_amp = {}
for target_layer in layers:
self.DC_amp[target_layer] = {}
for target_pop in pops:
self.DC_amp[target_layer][target_pop] = bg_rate * \
K_ext[target_layer][target_pop] * w_mean * neuron_params['tau_syn_E'] / 1000.
else:
self.DC_amp = {'L23': {'E': 0., 'I': 0.},
'L4' : {'E': 0., 'I': 0.},
'L5' : {'E': 0., 'I': 0.},
'L6' : {'E': 0., 'I': 0.}}
# Scale and connect
# In-degrees of the full-scale model
K_full = scaling.get_indegrees()
if K_scaling != 1 :
self.w, self.w_ext, self.K_ext, self.DC_amp = scaling.adjust_w_and_ext_to_K(K_full, K_scaling, self.w, self.DC_amp)
else:
self.w_ext = w_ext
self.K_ext = K_ext
if sim.rank() == 0:
print('w: %s' % self.w)
net_generation_rng = NumpyRNG(12345, parallel_safe=True)
for target_layer in layers :
for target_pop in pops :
target_index = structure[target_layer][target_pop]
this_pop = self.pops[target_layer][target_pop]
# External inputs
if input_type == 'DC' or K_scaling != 1 :
this_pop.set(i_offset=self.DC_amp[target_layer][target_pop])
if input_type == 'poisson':
poisson_generator = sim.Population(this_pop.size,
sim.SpikeSourcePoisson,
{'rate': bg_rate * self.K_ext[target_layer][target_pop]},
structure=layer_structures[target_layer],
label='input_%s_%s'%(target_layer,target_pop))
poisson_generator.annotate(color='0.5 0.5 0')
poisson_generator.annotate(radius=default_input_radius)
conn = sim.OneToOneConnector()
syn = sim.StaticSynapse(weight=self.w_ext)
sim.Projection(poisson_generator, this_pop, conn, syn, receptor_type='excitatory')
if thalamic_input:
# Thalamic inputs
if sim.rank() == 0 :
print('Creating thalamic connections to %s%s' % (target_layer, target_pop))
C_thal=thal_params['C'][target_layer][target_pop]
n_target=N_full[target_layer][target_pop]
K_thal=round(np.log(1 - C_thal) / np.log((n_target * thal_params['n_thal'] - 1.) /
(n_target * thal_params['n_thal']))) / n_target
FixedTotalNumberConnect(sim, self.thalamic_population,
this_pop, K_thal, w_ext, w_rel * w_ext,
d_mean['E'], d_sd['E'], rng=net_generation_rng)
# Recurrent inputs
for source_layer in layers :
for source_pop in pops :
source_index=structure[source_layer][source_pop]
if sim.rank() == 0:
print('Creating connections from %s%s to %s%s' % (source_layer, source_pop, target_layer, target_pop))
weight=self.w[target_index][source_index]
if source_pop == 'E' and source_layer == 'L4' and target_layer == 'L23' and target_pop == 'E':
w_sd=weight * w_rel_234
else:
w_sd=abs(weight * w_rel)
FixedTotalNumberConnect(sim, self.pops[source_layer][source_pop],
self.pops[target_layer][target_pop],\
K_full[target_index][source_index] * K_scaling,
weight, w_sd,
d_mean[source_pop], d_sd[source_pop], rng=net_generation_rng)