def brunel_network(eta, g, delay, J_E):
"""
A brunel network, from:
Brunel N, Dynamics of Sparsely Connected Networks of Excitatory and
Inhibitory Spiking Neurons, Journal of Computational Neuroscience 8,
183-208 (2000).
Implementation adapted from:
http://www.nest-simulator.org/py_sample/random-balanced-network-exp-synapses-multiple-time-constants/
Parameters
----------
g : {int, float}, optional
Ratio inhibitory weight/excitatory weight. Default is 5.
eta : {int, float}, optional
External rate relative to threshold rate. Default is 2.
delay : {int, float}, optional
Synaptic delay in ms. Default is 1.5.
J_E : {int, float}, optional
Amplitude of excitatory postsynaptic current. Default is 0.1
"""
# Network parameters
N_rec = 20 # Record from 20 neurons
simulation_end = 1000 # Simulation time
tau_m = 20.0 # Time constant of membrane potential in ms
V_th = 20.0
N_E = 10000 # Number of inhibitory neurons
N_I = 2500 # Number of excitatory neurons
N_neurons = N_E + N_I # Number of neurons in total
C_E = int(N_E / 10) # Number of excitatory synapses per neuron
C_I = int(N_I / 10) # Number of inhibitory synapses per neuron
J_I = -g * J_E # Amplitude of inhibitory postsynaptic current
nu_ex = eta * V_th / (J_E * C_E * tau_m)
p_rate = 1000.0 * nu_ex * C_E
nest.ResetKernel()
# Configure kernel
nest.SetKernelStatus({"grng_seed": 10})
nest.SetDefaults(
'iaf_psc_delta', {
'C_m': 1.0,
'tau_m': tau_m,
't_ref': 2.0,
'E_L': 0.0,
'V_th': V_th,
'V_reset': 10.0
})
# Create neurons
nodes = nest.Create('iaf_psc_delta', N_neurons)
nodes_E = nodes[:N_E]
nodes_I = nodes[N_E:]
noise = nest.Create('poisson_generator', 1, {'rate': p_rate})
spikes = nest.Create('spike_detector', 2, [{
'label': 'brunel-py-ex'
}, {
'label': 'brunel-py-in'
}])
spikes_E = spikes[:1]
spikes_I = spikes[1:]
# Connect neurons to each other
nest.CopyModel('static_synapse_hom_w', 'excitatory', {
'weight': J_E,
'delay': delay
})
nest.Connect(nodes_E, nodes, {
'rule': 'fixed_indegree',
'indegree': C_E
}, 'excitatory')
nest.CopyModel('static_synapse_hom_w', 'inhibitory', {
'weight': J_I,
'delay': delay
})
nest.Connect(nodes_I, nodes, {
'rule': 'fixed_indegree',
'indegree': C_I
}, 'inhibitory')
# Connect poisson generator to all nodes
nest.Connect(noise, nodes, syn_spec='excitatory')
nest.Connect(nodes_E[:N_rec], spikes_E)
nest.Connect(nodes_I[:N_rec], spikes_I)
# Run the simulation
nest.Simulate(simulation_end)
events_E = nest.GetStatus(spikes_E, 'events')[0]
events_I = nest.GetStatus(spikes_I, 'events')[0]
# Excitatory spike trains
# Makes sure the spiketrain is added even if there are no results
# to get a regular result
spiketrains = []
for sender in nodes_E[:N_rec]:
spiketrain = events_E["times"][events_E["senders"] == sender]
spiketrains.append(spiketrain)
return simulation_end, spiketrains
def _test_model(self,
referenceModel,
testant,
gsl_error_tol,
tolerance=0.000001,
nest_ref_model_opts=None,
custom_model_opts=None):
spike_times = [100.0, 200.0]
spike_weights = [1., -1.]
nest.ResetKernel()
neuron1 = nest.Create(referenceModel, params=nest_ref_model_opts)
neuron2 = nest.Create(testant, params=custom_model_opts)
if gsl_error_tol is not None:
neuron2.set({"gsl_error_tol": gsl_error_tol})
spikegenerator = nest.Create('spike_generator',
params={
'spike_times': spike_times,
'spike_weights': spike_weights
})
nest.Connect(spikegenerator, neuron1)
nest.Connect(spikegenerator, neuron2)
multimeter1 = nest.Create('multimeter')
multimeter2 = nest.Create('multimeter')
V_m_specifier = 'V_m' # 'delta_V_m'
multimeter1.set({"record_from": [V_m_specifier]})
multimeter2.set({"record_from": [V_m_specifier]})
nest.Connect(multimeter1, neuron1)
nest.Connect(multimeter2, neuron2)
nest.Simulate(400.0)
Vms1 = multimeter1.get("events")[V_m_specifier]
ts1 = multimeter1.get("events")["times"]
Vms2 = multimeter2.get("events")[V_m_specifier]
ts2 = multimeter2.get("events")["times"]
if TEST_PLOTS:
fig, ax = plt.subplots(2, 1)
ax[0].plot(ts1, Vms1, label="Reference " + referenceModel)
ax[1].plot(ts2, Vms2, label="Testant " + testant)
for _ax in ax:
_ax.legend(loc='upper right')
_ax.grid()
plt.savefig("/tmp/nestml_nest_integration_test_[" +
referenceModel + "]_[" + testant + "].png")
plt.close(fig)
if TEST_PLOTS:
for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]):
fig, ax = plt.subplots(1, 1, figsize=figsize)
ax = [ax]
ax[0].plot(ts2, Vms2, label=testant)
for _ax in ax:
_ax.grid()
ax[0].set_xlabel("Time [ms]")
ax[0].set_ylabel("$V_m$ [mV]")
plt.tight_layout()
plt.savefig("/tmp/nestml_models_library_[" + referenceModel +
"]_synaptic_response" + fname_snip + ".png")
plt.close(fig)
for index in range(0, len(Vms1)):
if abs(Vms1[index] - Vms2[index]) > tolerance \
or np.isnan(Vms1[index]) \
or np.isnan(Vms2[index]):
print(
str(Vms1[index]) + " differs from " + str(Vms2[index]) +
" at iteration: " + str(index) +
" of overall iterations: " + str(len(Vms1)))
raise Exception(testant + ": TEST FAILED")
print(testant + " PASSED")
def setUp(self):
nest.ResetKernel()
nest.set_verbosity('M_ERROR')
def test_SynapseDepressionFacilitation(self):
"""Ensure that depression and facilitation work correctly"""
nest.set_verbosity('M_WARNING')
# This is done using the spike pairing experiment of
# Clopath et al. 2010. First we specify the parameters
resolution = 0.1
init_w = 0.5
spike_times_pre = [[29., 129., 229., 329., 429.],
[29., 62.3, 95.7, 129., 162.3],
[29., 49., 69., 89., 109.],
[129., 229., 329., 429., 529., 629.],
[62.3, 95.6, 129., 162.3, 195.6, 229.],
[49., 69., 89., 109., 129., 149.]]
spike_times_post = [[19., 119., 219., 319., 419.],
[19., 52.3, 85.7, 119., 152.3],
[19., 39., 59., 79., 99.],
[139., 239., 339., 439., 539., 639.],
[72.3, 105.6, 139., 172.3, 205.6, 239.],
[59., 79., 99., 119., 139., 159.]]
tested_models = ["aeif_psc_delta_clopath", "hh_psc_alpha_clopath"]
# Loop over tested neuron models
for nrn_model in tested_models:
if (nrn_model == "aeif_psc_delta_clopath"):
nrn_params = {
'V_m': -70.6,
'E_L': -70.6,
'V_peak': 33.0,
'C_m': 281.0,
'theta_minus': -70.6,
'theta_plus': -45.3,
'A_LTD': 14.0e-5,
'A_LTP': 8.0e-5,
'tau_u_bar_minus': 10.0,
'tau_u_bar_plus': 7.0,
'delay_u_bars': 4.0,
'a': 4.0,
'b': 0.0805,
'V_reset': -70.6 + 21.0,
'V_clamp': 33.0,
't_clamp': 2.0,
't_ref': 0.0,
}
elif (nrn_model == "hh_psc_alpha_clopath"):
nrn_params = {
'V_m': -64.9,
'C_m': 100.0,
'tau_syn_ex': 0.2,
'tau_syn_in': 2.0,
'theta_minus': -64.9,
'theta_plus': -35.0,
'A_LTD': 14.0e-5,
'A_LTP': 8.0e-5,
'tau_u_bar_minus': 10.0,
'tau_u_bar_plus': 114.0,
'delay_u_bars': 5.0,
}
syn_weights = []
# Loop over pairs of spike trains
for (s_t_pre, s_t_post) in zip(spike_times_pre, spike_times_post):
nest.ResetKernel()
nest.resolution = resolution
# Create one neuron
nrn = nest.Create(nrn_model, 1, nrn_params)
prrt_nrn = nest.Create("parrot_neuron", 1)
# Create and connect spike generator
spike_gen_pre = nest.Create("spike_generator", 1,
{"spike_times": s_t_pre})
nest.Connect(spike_gen_pre,
prrt_nrn,
syn_spec={"delay": resolution})
if (nrn_model == "aeif_psc_delta_clopath"):
conn_weight = 80.0
elif (nrn_model == "hh_psc_alpha_clopath"):
conn_weight = 2000.0
spike_gen_params_post = {"spike_times": s_t_post}
spike_gen_post = nest.Create("spike_generator", 1,
{"spike_times": s_t_post})
nest.Connect(spike_gen_post,
nrn,
syn_spec={
"delay": resolution,
"weight": conn_weight
})
# Create weight recorder
wr = nest.Create('weight_recorder', 1)
# Create Clopath synapse with weight recorder
nest.CopyModel("clopath_synapse", "clopath_synapse_rec",
{"weight_recorder": wr})
syn_dict = {
"synapse_model": "clopath_synapse_rec",
"weight": init_w,
"delay": resolution
}
nest.Connect(prrt_nrn, nrn, syn_spec=syn_dict)
# Simulation
simulation_time = (10.0 + max(s_t_pre[-1], s_t_post[-1]))
nest.Simulate(simulation_time)
# Evaluation
w_events = nest.GetStatus(wr)[0]["events"]
weights = w_events["weights"]
syn_weights.append(weights[-1])
# Compare to expected result
syn_weights = np.array(syn_weights)
syn_weights = 100.0 * 15.0 * (syn_weights -
init_w) / init_w + 100.0
if (nrn_model == "aeif_psc_delta_clopath"):
correct_weights = [
57.82638722, 72.16730112, 149.43359357, 103.30408341,
124.03640668, 157.02882555
]
elif (nrn_model == "hh_psc_alpha_clopath"):
correct_weights = [
70.14343863, 99.49206222, 178.1028757, 119.63314118,
167.37750688, 178.83111685
]
self.assertTrue(
np.allclose(syn_weights, correct_weights, rtol=1e-7))
can be found in models/sinusoidal_poisson_generator.h.
The script is structured into two parts and creates one common figure.
In Part 1, two instances of the `sinusoidal_poisson_generator` are
created with different parameters. Part 2 illustrates the effect of
the ``individual_spike_trains`` switch.
'''
'''
We import nest and modules required for analysis and plotting.
'''
import nest
import matplotlib.pyplot as plt
import numpy as np
nest.ResetKernel() # in case we run the script multiple times from iPython
'''
We create two instances of the `sinusoidal_poisson_generator`
with two different parameter sets using `Create`. Moreover, we create
devices to record firing rates (`multimeter`) and spikes
(`spike_detector`) and connect them to the generators using `Connect`.
'''
nest.SetKernelStatus({'resolution': 0.01})
g = nest.Create('sinusoidal_poisson_generator',
n=2,
params=[{
'rate': 10000.0,
'amplitude': 5000.0,
'frequency': 10.0,
def run_synapse_test(
self,
neuron_model_name,
ref_neuron_model_name,
synapse_model_name,
ref_synapse_model_name,
resolution=1., # [ms]
delay=1., # [ms]
sim_time=None, # if None, computed from pre and post spike times
pre_spike_times=None,
post_spike_times=None,
vt_spike_times=None,
fname_snip=""):
if pre_spike_times is None:
pre_spike_times = []
if post_spike_times is None:
post_spike_times = []
if vt_spike_times is None:
vt_spike_times = []
if sim_time is None:
sim_time = max(np.amax(pre_spike_times, initial=0.),
np.amax(post_spike_times, initial=0.),
np.amax(vt_spike_times, initial=0.)) + 5 * delay
nest.ResetKernel()
# nest.set_verbosity("M_ALL")
nest.set_verbosity("M_ERROR")
nest.SetKernelStatus({"resolution": resolution})
nest.Install("nestml_jit_module")
nest.Install("nestml_non_jit_module")
print("Pre spike times: " + str(pre_spike_times))
print("Post spike times: " + str(post_spike_times))
print("VT spike times: " + str(vt_spike_times))
# create spike_generators with these times
pre_sg = nest.Create("spike_generator",
params={"spike_times": pre_spike_times})
post_sg = nest.Create("spike_generator",
params={
"spike_times": post_spike_times,
"allow_offgrid_times": True
})
vt_sg = nest.Create("spike_generator",
params={
"spike_times": vt_spike_times,
"allow_offgrid_times": True
})
# create volume transmitter
vt = nest.Create("volume_transmitter")
vt_parrot = nest.Create("parrot_neuron")
nest.Connect(vt_sg, vt_parrot)
nest.Connect(vt_parrot,
vt,
syn_spec={
"synapse_model": "static_synapse",
"weight": 1.,
"delay": 1.
}) # delay is ignored?!
vt_gid = vt.get("global_id")
# set up custom synapse models
wr = nest.Create("weight_recorder")
wr_ref = nest.Create('weight_recorder')
nest.CopyModel(
synapse_model_name, "stdp_nestml_rec", {
"weight_recorder": wr[0],
"w": 1.,
"the_delay": delay,
"receptor_type": 0,
"vt": vt_gid
})
nest.CopyModel(
ref_synapse_model_name, "stdp_ref_rec", {
"weight_recorder": wr_ref[0],
"weight": 1.,
"delay": delay,
"receptor_type": 0,
"vt": vt_gid
})
# create parrot neurons and connect spike_generators
if sim_mdl:
pre_neuron = nest.Create("parrot_neuron")
post_neuron = nest.Create(neuron_model_name)
if sim_ref:
pre_neuron_ref = nest.Create("parrot_neuron")
post_neuron_ref = nest.Create(ref_neuron_model_name)
if sim_mdl:
spikedet_pre = nest.Create("spike_recorder")
spikedet_post = nest.Create("spike_recorder")
spikedet_vt = nest.Create("spike_recorder")
mm = nest.Create(
"multimeter",
params={
"record_from":
["V_m", "post_tr__for_neuromodulated_stdp_nestml"]
})
if sim_ref:
spikedet_pre_ref = nest.Create("spike_recorder")
spikedet_post_ref = nest.Create("spike_recorder")
mm_ref = nest.Create("multimeter", params={"record_from": ["V_m"]})
if sim_mdl:
nest.Connect(pre_sg,
pre_neuron,
"one_to_one",
syn_spec={"delay": 1.})
nest.Connect(post_sg,
post_neuron,
"one_to_one",
syn_spec={
"delay": 1.,
"weight": 9999.
})
nest.Connect(pre_neuron,
post_neuron,
"all_to_all",
syn_spec={"synapse_model": "stdp_nestml_rec"})
nest.Connect(mm, post_neuron)
nest.Connect(pre_neuron, spikedet_pre)
nest.Connect(post_neuron, spikedet_post)
nest.Connect(vt_parrot, spikedet_vt)
if sim_ref:
nest.Connect(pre_sg,
pre_neuron_ref,
"one_to_one",
syn_spec={"delay": 1.})
nest.Connect(post_sg,
post_neuron_ref,
"one_to_one",
syn_spec={
"delay": 1.,
"weight": 9999.
})
nest.Connect(pre_neuron_ref,
post_neuron_ref,
"all_to_all",
syn_spec={"synapse_model": "stdp_ref_rec"})
nest.Connect(mm_ref, post_neuron_ref)
nest.Connect(pre_neuron_ref, spikedet_pre_ref)
nest.Connect(post_neuron_ref, spikedet_post_ref)
# get STDP synapse and weight before protocol
if sim_mdl:
syn = nest.GetConnections(source=pre_neuron,
synapse_model="stdp_nestml_rec")
if sim_ref:
syn_ref = nest.GetConnections(source=pre_neuron_ref,
synapse_model="stdp_ref_rec")
n_steps = int(np.ceil(sim_time / resolution)) + 1
t = 0.
t_hist = []
if sim_mdl:
w_hist = []
if sim_ref:
w_hist_ref = []
while t <= sim_time:
nest.Simulate(resolution)
t += resolution
t_hist.append(t)
if sim_ref:
w_hist_ref.append(nest.GetStatus(syn_ref)[0]["weight"])
if sim_mdl:
w_hist.append(nest.GetStatus(syn)[0]["w"])
# plot
if TEST_PLOTS:
fig, ax = plt.subplots(nrows=2)
ax1, ax2 = ax
if sim_mdl:
timevec = nest.GetStatus(mm, "events")[0]["times"]
V_m = nest.GetStatus(mm, "events")[0]["V_m"]
ax2.plot(timevec,
nest.GetStatus(mm, "events")[0]
["post_tr__for_neuromodulated_stdp_nestml"],
label="post_tr nestml")
ax1.plot(timevec, V_m, label="nestml", alpha=.7, linestyle=":")
if sim_ref:
pre_ref_spike_times_ = nest.GetStatus(spikedet_pre_ref,
"events")[0]["times"]
timevec = nest.GetStatus(mm_ref, "events")[0]["times"]
V_m = nest.GetStatus(mm_ref, "events")[0]["V_m"]
ax1.plot(timevec, V_m, label="nest ref", alpha=.7)
ax1.set_ylabel("V_m")
for _ax in ax:
_ax.grid(which="major", axis="both")
_ax.grid(which="minor", axis="x", linestyle=":", alpha=.4)
# _ax.minorticks_on()
_ax.set_xlim(0., sim_time)
_ax.legend()
fig.savefig("/tmp/stdp_synapse_test" + fname_snip + "_V_m.png",
dpi=300)
# plot
if TEST_PLOTS:
fig, ax = plt.subplots(nrows=4)
ax1, ax2, ax3, ax4 = ax
if sim_mdl:
pre_spike_times_ = nest.GetStatus(spikedet_pre,
"events")[0]["times"]
print("Actual pre spike times: " + str(pre_spike_times_))
if sim_ref:
pre_ref_spike_times_ = nest.GetStatus(spikedet_pre_ref,
"events")[0]["times"]
print("Actual pre ref spike times: " +
str(pre_ref_spike_times_))
if sim_mdl:
n_spikes = len(pre_spike_times_)
for i in range(n_spikes):
if i == 0:
_lbl = "nestml"
else:
_lbl = None
ax1.plot(2 * [pre_spike_times_[i] + delay], [0, 1],
linewidth=2,
color="blue",
alpha=.4,
label=_lbl)
if sim_mdl:
post_spike_times_ = nest.GetStatus(spikedet_post,
"events")[0]["times"]
print("Actual post spike times: " + str(post_spike_times_))
if sim_ref:
post_ref_spike_times_ = nest.GetStatus(spikedet_post_ref,
"events")[0]["times"]
print("Actual post ref spike times: " +
str(post_ref_spike_times_))
if sim_ref:
n_spikes = len(pre_ref_spike_times_)
for i in range(n_spikes):
if i == 0:
_lbl = "nest ref"
else:
_lbl = None
ax1.plot(2 * [pre_ref_spike_times_[i] + delay], [0, 1],
linewidth=2,
color="cyan",
label=_lbl,
alpha=.4)
ax1.set_ylabel("Pre spikes")
ax2.plot(
timevec,
nest.GetStatus(
mm,
"events")[0]["post_tr__for_neuromodulated_stdp_nestml"],
label="nestml post tr")
if sim_mdl:
n_spikes = len(post_spike_times_)
for i in range(n_spikes):
if i == 0:
_lbl = "nestml"
else:
_lbl = None
ax2.plot(2 * [post_spike_times_[i]], [0, 1],
linewidth=2,
color="black",
alpha=.4,
label=_lbl)
if sim_ref:
n_spikes = len(post_ref_spike_times_)
for i in range(n_spikes):
if i == 0:
_lbl = "nest ref"
else:
_lbl = None
ax2.plot(2 * [post_ref_spike_times_[i]], [0, 1],
linewidth=2,
color="red",
alpha=.4,
label=_lbl)
ax2.set_ylabel("Post spikes")
if sim_mdl:
vt_spike_times_ = nest.GetStatus(spikedet_vt,
"events")[0]["times"]
print("Actual vt spike times: " + str(vt_spike_times_))
if sim_mdl:
n_spikes = len(vt_spike_times_)
for i in range(n_spikes):
ax3.plot(2 * [vt_spike_times_[i]], [0, 1],
linewidth=2,
color="black",
alpha=.4)
ax3.set_ylabel("VT spikes")
if sim_mdl:
ax4.plot(t_hist, w_hist, marker="o", label="nestml")
if sim_ref:
ax4.plot(t_hist,
w_hist_ref,
linestyle="--",
marker="x",
label="ref")
ax4.set_xlabel("Time [ms]")
ax4.set_ylabel("w")
for _ax in ax:
_ax.grid(which="major", axis="both")
_ax.xaxis.set_major_locator(
matplotlib.ticker.FixedLocator(
np.arange(0, np.ceil(sim_time))))
_ax.set_xlim(0., sim_time)
_ax.legend()
fig.savefig("/tmp/stdp_dopa_synapse_test" + fname_snip + ".png",
dpi=300)
# verify
MAX_ABS_ERROR = 1E-6
assert np.all(
np.abs(np.array(w_hist) - np.array(w_hist_ref)) < MAX_ABS_ERROR)
def test_GetTargetNodesPositions(self):
"""Interface check for finding targets."""
ldict = {
'elements': ['iaf_neuron', 'iaf_psc_alpha'],
'rows': 3,
'columns': 3,
'extent': [2., 2.],
'edge_wrap': True
}
cdict = {
'connection_type': 'divergent',
'mask': {
'grid': {
'rows': 2,
'columns': 2
}
}
}
nest.ResetKernel()
l = topo.CreateLayer(ldict)
ian = [
gid for gid in nest.GetLeaves(l)[0]
if nest.GetStatus([gid], 'model')[0] == 'iaf_neuron'
]
ipa = [
gid for gid in nest.GetLeaves(l)[0]
if nest.GetStatus([gid], 'model')[0] == 'iaf_psc_alpha'
]
# connect ian -> all using static_synapse
cdict.update({
'sources': {
'model': 'iaf_neuron'
},
'synapse_model': 'static_synapse'
})
topo.ConnectLayers(l, l, cdict)
for k in ['sources', 'synapse_model']:
cdict.pop(k)
# connect ipa -> ipa using stdp_synapse
cdict.update({
'sources': {
'model': 'iaf_psc_alpha'
},
'targets': {
'model': 'iaf_psc_alpha'
},
'synapse_model': 'stdp_synapse'
})
topo.ConnectLayers(l, l, cdict)
for k in ['sources', 'targets', 'synapse_model']:
cdict.pop(k)
t = topo.GetTargetNodes(ian[:1], l)
self.assertEqual(len(t), 1)
p = topo.GetTargetPositions(ian[:1], l)
self.assertEqual(len(p), 1)
self.assertTrue(all([len(pp) == 2 for pp in p[0]]))
t = topo.GetTargetNodes(ian, l)
self.assertEqual(len(t), len(ian))
self.assertTrue(all(
[len(g) == 8
for g in t])) # 2x2 mask x 2 neurons / element -> eight targets
p = topo.GetTargetPositions(ian, l)
self.assertEqual(len(p), len(ian))
t = topo.GetTargetNodes(ian, l, tgt_model='iaf_neuron')
self.assertEqual(len(t), len(ian))
self.assertTrue(all([len(g) == 4
for g in t])) # 2x2 mask -> four targets
t = topo.GetTargetNodes(ian, l, tgt_model='iaf_psc_alpha')
self.assertEqual(len(t), len(ian))
self.assertTrue(all([len(g) == 4
for g in t])) # 2x2 mask -> four targets
t = topo.GetTargetNodes(ipa, l)
self.assertEqual(len(t), len(ipa))
self.assertTrue(all([len(g) == 4
for g in t])) # 2x2 mask -> four targets
t = topo.GetTargetNodes(ipa, l, syn_model='static_synapse')
self.assertEqual(len(t), len(ipa))
self.assertTrue(all([len(g) == 0 for g in t])) # no static syns
t = topo.GetTargetNodes(ipa, l, syn_model='stdp_synapse')
self.assertEqual(len(t), len(ipa))
self.assertTrue(all([len(g) == 4
for g in t])) # 2x2 mask -> four targets
def test_SynapseDepressionFacilitation(self):
"""Ensure that depression and facilitation work correctly"""
nest.set_verbosity('M_WARNING')
nest.ResetKernel()
resolution = 0.1
nest.resolution = resolution
'''
neuron parameters
'''
nrn_model = 'pp_cond_exp_mc_urbanczik'
nrn_params = {
't_ref': 3.0, # refractory period
'g_sp': 600.0, # somato-dendritic coupling conductance
'soma': {
'V_m': -70.0, # initial value of V_m
'C_m': 300.0, # capacitance of membrane
'E_L': -70.0, # resting potential
'g_L': 30.0, # somatic leak conductance
'E_ex': 0.0, # resting potential for exc input
'E_in': -75.0, # resting potential for inh input
'tau_syn_ex': 3.0, # time constant of exc conductance
'tau_syn_in': 3.0, # time constant of inh conductance
},
'dendritic': {
'V_m': -70.0, # initial value of V_m
'C_m': 300.0, # capacitance of membrane
'E_L': -70.0, # resting potential
'g_L': 30.0, # dendritic leak conductance
'tau_syn_ex': 3.0, # time constant of exc input current
'tau_syn_in': 3.0, # time constant of inh input current
},
# parameters of rate function
'phi_max': 0.15, # max rate
'rate_slope': 0.5, # called 'k' in the paper
'beta': 1.0 / 3.0,
'theta': -55.0,
}
'''
synapse params
'''
syns = nest.GetDefaults(nrn_model)['receptor_types']
init_w = 100.0
syn_params = {
'synapse_model': 'urbanczik_synapse_wr',
'receptor_type': syns['dendritic_exc'],
'tau_Delta': 100.0, # time constant of low pass filtering of the weight change
'eta': 0.75, # learning rate
'weight': init_w,
'Wmax': 4.5*nrn_params['dendritic']['C_m'],
'delay': resolution,
}
'''
neuron and devices
'''
nest.SetDefaults(nrn_model, nrn_params)
nrn = nest.Create(nrn_model)
# spike generator is connected to a parrot neuron which is connected to the mc neuron
prrt_nrn = nest.Create('parrot_neuron')
# excitatory input to the dendrite
pre_syn_spike_times = np.array([1.0, 98.0])
sg_prox = nest.Create('spike_generator', params={
'spike_times': pre_syn_spike_times})
# excitatory input to the soma
spike_times_soma_inp = np.arange(10.0, 50.0, resolution)
spike_weights_soma = 10.0*np.ones_like(spike_times_soma_inp)
sg_soma_exc = nest.Create('spike_generator',
params={'spike_times': spike_times_soma_inp, 'spike_weights': spike_weights_soma})
# for recording all parameters of the Urbanczik neuron
rqs = nest.GetDefaults(nrn_model)['recordables']
mm = nest.Create('multimeter', params={
'record_from': rqs, 'interval': 0.1})
# for recoding the synaptic weights of the Urbanczik synapses
wr = nest.Create('weight_recorder')
# for recording the spiking of the soma
sr_soma = nest.Create('spike_recorder')
'''
create connections
'''
nest.Connect(sg_prox, prrt_nrn, syn_spec={'delay': resolution})
nest.CopyModel('urbanczik_synapse', 'urbanczik_synapse_wr',
{'weight_recorder': wr[0]})
nest.Connect(prrt_nrn, nrn, syn_spec=syn_params)
nest.Connect(sg_soma_exc, nrn,
syn_spec={'receptor_type': syns['soma_exc'], 'weight': 10.0*resolution, 'delay': resolution})
nest.Connect(mm, nrn, syn_spec={'delay': resolution})
nest.Connect(nrn, sr_soma, syn_spec={'delay': resolution})
'''
simulation
'''
nest.Simulate(100.0)
'''
read out devices
'''
# multimeter
rec = nest.GetStatus(mm)[0]['events']
t = rec['times']
V_w = rec['V_m.p']
# compute dendritic prediction of somatic membrane potential
g_D = nrn_params['g_sp']
g_L = nrn_params['soma']['g_L']
E_L = nrn_params['soma']['E_L']
V_w_star = (g_L*E_L + g_D*V_w) / (g_L + g_D)
# weight recorder
data = nest.GetStatus(wr)
senders = data[0]['events']['senders']
targets = data[0]['events']['targets']
weights = data[0]['events']['weights']
times = data[0]['events']['times']
# spike recorder
data = nest.GetStatus(sr_soma)[0]['events']
spike_times_soma = data['times']
# compute predicted rate
phi_max = nrn_params['phi_max']
k = nrn_params['rate_slope']
beta = nrn_params['beta']
theta = nrn_params['theta']
rate = (phi_max / (1.0 + k*np.exp(beta*(theta - V_w_star))))
# compute h(V_w_star)
h = (15.0*beta / (1.0 + np.exp(-beta*(theta - V_w_star)) / k))
# compute alpha response kernel
tau_s = nrn_params['dendritic']['tau_syn_ex']
g_L_prox = nrn_params['dendritic']['g_L']
C_m_prox = nrn_params['dendritic']['C_m']
tau_L = C_m_prox / g_L_prox
E_L_prox = nrn_params['dendritic']['E_L']
t0 = 1.2
alpha_response = (np.heaviside(t - t0, 0.5)*tau_s*(np.exp(-(t - t0) / tau_L) - np.exp(-(t - t0) / tau_s)) /
(g_L_prox*(tau_L - tau_s)))
# compute PI(t)
if len(spike_times_soma) > 0:
t = np.around(t, 4)
spike_times_soma = np.around(spike_times_soma + 0.2, 4)
idx = np.nonzero(np.in1d(t, spike_times_soma))[0]
rate[idx] -= 1.0 / resolution
w_change_raw = -15.0*C_m_prox*rate*h*alpha_response
# compute low pass filtered version of PI
tau_Delta = syn_params['tau_Delta']
eta = syn_params['eta']
w_change_low_pass = eta * np.exp(-t / tau_Delta)*np.cumsum(
np.exp(t / tau_Delta)*w_change_raw)*resolution / tau_Delta
integrated_w_change = np.cumsum(w_change_low_pass)*resolution
syn_weight_comp = init_w + integrated_w_change
'''
comparison between Nest and python implementation
'''
# extract the weight computed in python at the times of the presynaptic spikes
idx = np.nonzero(np.in1d(np.around(t, 4), np.around(pre_syn_spike_times + resolution, 4)))[0]
syn_w_comp_at_spike_times = syn_weight_comp[idx]
realtive_error = (
(weights[-1] - syn_w_comp_at_spike_times[-1]) / (weights[-1] - init_w))
self.assertTrue(abs(realtive_error) < 0.001)
def train(settings, data):
np.random.seed()
rank = nest.Rank()
rng = np.random.randint(500)
num_v_procs = settings['network']['num_threads'] \
* settings['network']['num_procs']
nest.ResetKernel()
nest.SetKernelStatus({
'local_num_threads':
settings['network']['num_threads'],
'total_num_virtual_procs':
num_v_procs,
'resolution':
settings['network']['h'],
'rng_seeds':
range(rng, rng + num_v_procs)
})
layer_out = nest.Create('iaf_psc_exp', settings['topology']['n_layer_out'])
if settings['topology']['two_layers']:
layer_hid = nest.Create('iaf_psc_exp',
settings['topology']['n_layer_hid'])
teacher_1 = nest.Create('step_current_generator',
settings['topology']['n_layer_out'])
spike_generators_1 = nest.Create('spike_generator',
settings['topology']['n_input'])
poisson_layer = nest.Create('poisson_generator',
settings['topology']['n_input'])
parrot_layer = nest.Create('parrot_neuron',
settings['topology']['n_input'])
spike_detector_1 = nest.Create('spike_detector')
spike_detector_2 = nest.Create('spike_detector')
spike_detector_3 = nest.Create('spike_detector')
voltmeter = nest.Create('voltmeter', 1, {
'withgid': True,
'withtime': True
})
if not settings['network']['noise_after_pattern']:
nest.SetStatus(poisson_layer, {
'rate': settings['network']['noise_freq'],
'origin': 0.0
})
nest.Connect(spike_generators_1,
parrot_layer,
'one_to_one',
syn_spec='static_synapse')
nest.Connect(poisson_layer,
parrot_layer,
'one_to_one',
syn_spec='static_synapse')
if settings['learning']['use_teacher']:
nest.Connect(teacher_1,
layer_out,
'one_to_one',
syn_spec='static_synapse')
nest.Connect(layer_out, spike_detector_1, 'all_to_all')
nest.Connect(parrot_layer, spike_detector_2, 'all_to_all')
nest.Connect(voltmeter, layer_out)
nest.SetStatus(layer_out, settings['model']['neuron_out'])
if settings['topology']['two_layers']:
if settings['learning']['use_inhibition']:
interconnect_layer(layer_hid, settings['model']['syn_dict_inh'])
# nest.Connect(layer_out, layer_hid,
# 'all_to_all', syn_spec=settings['syn_dict_inh'])
nest.Connect(parrot_layer, spike_detector_3, 'all_to_all')
nest.Connect(parrot_layer,
layer_hid,
'all_to_all',
syn_spec=settings['model']['syn_dict_stdp_hid'])
nest.Connect(layer_hid,
layer_out,
'all_to_all',
syn_spec=settings['model']['syn_dict_stdp'])
if settings['topology']['use_reciprocal']:
nest.Connect(layer_out,
layer_hid,
'all_to_all',
syn_spec=settings['model']['syn_dict_rec'])
nest.Connect(layer_hid, spike_detector_3, 'all_to_all')
nest.SetStatus(layer_hid, settings['model']['neuron_hid'])
else:
nest.Connect(parrot_layer,
layer_out,
'all_to_all',
syn_spec=settings['model']['syn_dict_stdp'])
if settings['topology']['use_inhibition']:
interconnect_layer(layer_out, settings['model']['syn_dict_inh'])
np.random.seed(500)
i = 0
hi = 1
last_norms = []
norm_history = []
output_latency = []
weights_history = []
early_stop = False
d_time = settings['network']['start_delta']
full_time = settings['learning']['epochs'] \
* len(data['input']) \
* settings['network']['h_time'] \
+ settings['network']['start_delta']
# if settings['two_layers']:
# initial_weights = save_weigths_two_layers(parrot_layer, layer_hid, layer_out, settings)
# else:
# initial_weights = save_weights_one_layer(parrot_layer, layer_out, settings)
nest.Simulate(settings['network']['start_delta'])
while not early_stop:
set_spike_in_generators(data['input'][i], spike_generators_1, d_time,
d_time + settings['network']['h_time'],
settings['network']['h_time'],
settings['network']['h'])
# if True:
# set_spike_in_generators(data['input'][i], spike_generators_1,
# d_time + 1.5, d_time + settings['h_time'] + 1.5,
# settings['h_time'], settings['h'])
# set_spike_in_generators(data['input'][i], spike_generators_1,
# d_time + 3.0, d_time + settings['h_time'] + 3.0,
# settings['h_time'], settings['h'])
spike_times = []
for neuron_number in data['input'][i]:
if data['input'][i][neuron_number]:
spike_times.append(data['input'][i][neuron_number][0])
if settings['learning']['use_teacher']:
if settings['topology']['n_layer_out'] == 1:
set_teacher_input(
np.min(spike_times) \
+ d_time \
+ settings['network']['h'] \
+ settings['learning']['reinforce_delta'],
teacher_1,
settings
)
else:
set_teacher_input(
np.min(spike_times) \
+ d_time \
+ settings['network']['h'] \
+ settings['learning']['reinforce_delta'],
[teacher_1[data['class'][i]]],
settings
)
if settings['network']['noise_after_pattern']:
nest.SetStatus(
poisson_layer, {
'start': d_time + np.max(spike_times),
'stop': float(d_time + settings['network']['h_time']),
'rate': settings['network']['noise_freq']
})
nest.Simulate(settings['network']['h_time'])
ex_class = data['class'][i]
spikes = nest.GetStatus(spike_detector_1, keys="events")[0]['times']
senders = nest.GetStatus(spike_detector_1, keys="events")[0]['senders']
mask = spikes > d_time
spikes = spikes[mask]
senders = senders[mask]
tmp_dict = {
'latency': spikes - d_time,
'senders': senders,
'class': ex_class
}
output_latency.append(tmp_dict)
d_time += settings['network']['h_time']
if i + hi + 1 > len(data['input']):
i = 0
else:
i += hi
if settings['network']['save_history']:
if settings['topology']['two_layers']:
tmp_weights = save_weigths_two_layers(parrot_layer, layer_hid,
layer_out, settings)
tmp_norm_hid = weight_norm(tmp_weights['layer_hid'])
tmp_norm_out = weight_norm(tmp_weights['layer_out'])
tmp_norm = np.linalg.norm([tmp_norm_hid, tmp_norm_out])
norm_history.append(tmp_norm)
else:
tmp_weights = save_weights_one_layer(parrot_layer, layer_out,
settings)
tmp_norm_out = weight_norm(tmp_weights['layer_out'])
norm_history.append(tmp_norm_out)
weights_history.append(tmp_weights)
# if len(norm_history) > 5 * len(data['input']) and settings['early_stop']:
# early_stop = np.std(norm_history[-5 * len(data['input']):]) < 0.025
# else:
early_stop = d_time > full_time
if settings['topology']['two_layers']:
weights = save_weigths_two_layers(parrot_layer, layer_hid, layer_out,
settings)
else:
weights = save_weights_one_layer(parrot_layer, layer_out, settings)
# print(weights['layer_out'].keys())
# with open('weights' + str(weights['layer_out'].keys()) + '.json', 'w') as outfile:
# json.dump(weights, outfile, indent=4)
devices = {
'voltmeter': voltmeter,
'spike_detector_1': spike_detector_1,
'spike_detector_2': spike_detector_2,
'spike_detector_3': spike_detector_3,
}
return weights, output_latency, devices, weights_history, norm_history
def bench(config, order):
simtime = 1000
dt = 1.0
delay = 2.0 # synaptic delay in ms
g = 5.0 # ratio inhibitory weight/excitatory weight
eta = 2.0 # external rate relative to threshold rate
epsilon = 0.1 # connection probability
NE = 4*order # number of excitatory neurons
NI = 1*order # number of inhibitory neurons
N_rec = 50 # record from 50 neurons
CE = int(epsilon*NE) # number of excitatory synapses per neuron
CI = int(epsilon*NI) # number of inhibitory synapses per neuron
tauMem = 20.0 # time constant of membrane potential in ms
theta = 20.0 # membrane threshold potential in mV
neuron_params = {
"C_m": 1.0,
"tau_m": tauMem,
"t_ref": 2.0,
"E_L": 0.0,
"V_reset": 0.0,
"V_m": 0.0,
"V_th": theta,
}
J = 0.1 # postsynaptic amplitude in mV
J_ex = J # amplitude of excitatory postsynaptic potential
J_in = -g*J_ex # amplitude of inhibitory postsynaptic potential
nu_th = theta/(J*CE*tauMem)
nu_ex = eta*nu_th
p_rate = 1000.0*nu_ex*CE
nest.ResetKernel()
nest.SetKernelStatus({"resolution": dt, "print_time": True })
nest.SetDefaults("iaf_psc_delta", neuron_params)
nest.SetDefaults("poisson_generator",{"rate": p_rate})
nodes_ex = nest.Create("iaf_psc_delta",NE)
nodes_in = nest.Create("iaf_psc_delta",NI)
noise = nest.Create("poisson_generator")
espikes = nest.Create("spike_detector")
ispikes = nest.Create("spike_detector")
nest.SetStatus(espikes,[{"label": "brunel-py-ex",
"withtime": True,
"withgid": True}])
nest.SetStatus(ispikes,[{"label": "brunel-py-in",
"withtime": True,
"withgid": True}])
nest.CopyModel("static_synapse","excitatory",{"weight":J_ex, "delay":delay})
nest.CopyModel("static_synapse","inhibitory",{"weight":J_in, "delay":delay})
nest.Connect(noise,nodes_ex, syn_spec="excitatory")
nest.Connect(noise,nodes_in, syn_spec="excitatory")
nest.Connect(nodes_ex[:N_rec], espikes, syn_spec="excitatory")
nest.Connect(nodes_in[:N_rec], ispikes, syn_spec="excitatory")
conn_params_ex = {'rule': 'fixed_indegree', 'indegree': CE}
conn_params_in = {'rule': 'fixed_indegree', 'indegree': CI}
if config == 1:
nest.Connect(nodes_ex, nodes_ex+nodes_in, conn_params_ex, "excitatory")
nest.Connect(nodes_in, nodes_ex+nodes_in, conn_params_in, "inhibitory")
elif config == 2:
stdp_synapse = {
"model": "stdp_triplet_all_in_one_synapse",
"tau_plus": 16.8,
"tau_plus_triplet": 101.0,
"tau_minus": 33.7,
"tau_minus_triplet": 125.0,
"Aplus": 5e-10,
"Aminus": 7e-3,
"Aplus_triplet": 6.2e-3,
"Aminus_triplet": 2.3e-4,
"Kplus": 0.0,
"Kplus_triplet": 0.0,
"Kminus": 0.0,
"Kminus_triplet": 0.0,
"delay": delay,
}
stdp_excitatory = stdp_synapse.copy()
stdp_excitatory.update({
"Wmin": J_ex,
"weight": J_ex,
"Wmax": J_ex,
})
stdp_inhibitory = stdp_synapse.copy()
stdp_inhibitory.update({
"Wmin": J_in,
"weight": J_in,
"Wmax": J_in,
})
nest.Connect(nodes_ex, nodes_ex+nodes_in, conn_params_ex, stdp_excitatory)
nest.Connect(nodes_in, nodes_ex+nodes_in, conn_params_in, stdp_inhibitory)
elif config == 3:
stdp_neuron = {
"tau_plus": 16.8,
"tau_plus_triplet": 101.0,
"tau_minus": 33.7,
"tau_minus_triplet": 125.0,
"Aplus": 5e-10,
"Aminus": 7e-3,
"Aplus_triplet": 6.2e-3,
"Aminus_triplet": 2.3e-4,
"Kplus": 0.0,
"Kplus_triplet": 0.0,
"Kminus": 0.0,
"Kminus_triplet": 0.0,
"nearest_spike": False,
}
stdp_excitatory = stdp_neuron.copy()
stdp_excitatory.update({
"Wmin": J_ex,
"weight": J_ex,
"Wmax": J_ex,
})
stdp_inhibitory = stdp_neuron.copy()
stdp_inhibitory.update({
"Wmin": J_in,
"weight": J_in,
"Wmax": J_in,
})
min_delay = nest.GetKernelStatus('resolution')
pre_syn_spec = { "delay": min_delay }
post_syn_spec = {
"delay": delay - min_delay,
"receptor_type": 1 # differentiate post-synaptic feedback
}
for post in nodes_ex+nodes_in:
syn_post_spec = {
"weight": J_ex,
"delay": delay - min_delay
}
selected_ex = random.sample(filter(lambda n: n != post, nodes_ex), CE)
synapses_ex = nest.Create("stdp_triplet_node", CE, params = stdp_excitatory)
nest.Connect(selected_ex, synapses_ex, 'one_to_one', pre_syn_spec)
nest.Connect(synapses_ex, (post,), 'all_to_all', syn_post_spec)
nest.Connect((post,), synapses_ex, 'all_to_all', post_syn_spec)
for post in nodes_ex+nodes_in:
syn_post_spec = {
"weight": J_in,
"delay": delay - min_delay
}
selected_in = random.sample(filter(lambda n: n != post, nodes_in), CI)
synapses_in = nest.Create("stdp_triplet_node", CI, params = stdp_inhibitory)
nest.Connect(selected_in, synapses_in, 'one_to_one', pre_syn_spec)
nest.Connect(synapses_in, (post,), 'all_to_all', syn_post_spec)
nest.Connect((post,), synapses_in, 'all_to_all', post_syn_spec)
else:
raise Exception('unknown config')
nest.Simulate(simtime)
def run_protocol(self, dt):
"""Set up a network with pre-post spike pairings with t_post - t_pre = dt"""
nest.set_verbosity("M_WARNING")
nest.ResetKernel()
# set pre and postsynaptic spike times
delay = 1. # delay for connections
dspike = 100. # ISI
# set the correct real spike times for generators (correcting for delays)
pre_times = [100., 100. + dspike]
post_times = [k + dt for k in pre_times]
# create spike_generators with these times
pre_spikes = nest.Create("spike_generator",
params={
"spike_times": pre_times,
'precise_times': True
})
post_spikes = nest.Create("spike_generator",
params={
"spike_times": post_times,
'precise_times': True
})
# create parrot neurons and connect spike_generators
pre_parrot = nest.Create("parrot_neuron_ps", 1)
post_parrot = nest.Create("parrot_neuron_ps", 1)
nest.Connect(pre_spikes, pre_parrot, syn_spec={"delay": delay})
nest.Connect(post_spikes, post_parrot, syn_spec={"delay": delay})
# create spike detector
spikes = nest.Create("spike_detector", params={'precise_times': True})
nest.Connect(pre_parrot, spikes)
nest.Connect(post_parrot, spikes)
# connect both parrot neurons with a stdp synapse onto port 1
# thereby spikes transmitted through the stdp connection are
# not repeated postsynaptically.
syn_spec = {
"model": "stdp_synapse",
"receptor_type":
1, # set receptor 1 postsynaptically, to not generate extra spikes
}
conn_spec = {
"rule": "one_to_one",
}
nest.Connect(pre_parrot,
post_parrot,
syn_spec=syn_spec,
conn_spec=conn_spec)
# get STDP synapse and weight before protocol
syn = nest.GetConnections(source=pre_parrot,
synapse_model="stdp_synapse")
syn_status = nest.GetStatus(syn)[0]
w_pre = syn_status['weight']
last_time = max(pre_times[-1], post_times[-1])
nest.Simulate(last_time + 2 * delay)
# get weight post protocol
syn_status = nest.GetStatus(syn)[0]
w_post = syn_status['weight']
return w_pre, w_post
help=
'Length, in milliseconds, of experiment. Must be an integer. Default is 100.'
)
parser.add_argument(
'--no_mc2approx',
action='store_true',
help='If not included, uses mc2 data for a better approximation.')
parser.add_argument(
'--shuffle',
action='store_true',
help='If included, randomly shuffles the mc2 adjacency matrix.')
args = parser.parse_args()
# Set up
#nest.set_verbosity("M_ERROR") # Uncomment this to make NEST quiet
nest.ResetKernel() # Reset nest
nest.SetKernelStatus({"local_num_threads": 8}) # Run on many threads
root = sys.argv[0][:-11] # Current working directory
simulation_id = datetime.now().strftime(
"%s") # Custom ID so files are not overwritten
# Load circuit info
ntnstatus('Loading mc2 structural information')
nnum = 31346 # Number of neurons in circuit
adj = load_npz(root + 'structure/adjmat_mc2.npz').toarray() # Adjacency matrix
exc = np.load(root + 'structure/bbmc2_excitatory.npy'
) # Binary list indicating if neuron is excitatory or not
mc2_delays = np.load(root + 'structure/distances_mc2.npz')[
'data'] # Interpret distances as delays
mc2_layers = np.load(
root + 'structure/layersize_mc2.npy'
def __init__(self,prefix,new_pars=[],pars_file=[]):
'''Creates and simulates a network in NEST'''
#Temporary way to run without the selected pars file
pars_file = []
start_build_net = time.time()
if pars_file==[]: # import generic params_d file
import params_d_psdb
reload(params_d_psdb)
pars = params_d_psdb.Parameters(new_pars)
else: # import specific params_d file
fobj,pathname,description = imp.find_module(pars_file)
params_d_sp = imp.load_module(pars_file,fobj,pathname,description)
pars = params_d_sp.Parameters(new_pars)
self.T_sim = pars.T_sim + pars.T_wup + pars.T_cdown
#self.record_spikes = pars.record_spikes
self.record_vm = pars.record_vm
self.recorders = {}
self.events = {'spikes':[],'vm':[]}
self.pars = pars
self.pars.prefix = prefix
# INITIALIZE NETWORK -----------------------------------------------------------------------
nest_path_tmp = tempfile.mktemp(prefix=pars.nest_path_tmp)
os.mkdir(nest_path_tmp)
nest.ResetKernel()
shutil.rmtree(nest.GetStatus([0],'data_path')[0],ignore_errors=True)
nest.SetStatus([0], {'resolution': pars.dt, 'print_time': pars.print_time,
'overwrite_files':pars.owr_files, 'rng_seeds':[int(pars.rnd_seeds)],
'data_path':nest_path_tmp})
#print '\nBuilding network...'
# CREATE SOURCES ----------------------------------------------------------------------------
self.pg_exc = nest.Create('poisson_generator', 1)
self.pg_inh = nest.Create('poisson_generator', 1)
nest.SetStatus(self.pg_exc, {'rate': pars.pg_rate_exc, 'stop': pars.T_sim+pars.T_wup})
nest.SetStatus(self.pg_inh, {'rate': pars.pg_rate_inh, 'stop': pars.T_sim+pars.T_wup})
self.dc1_exc = nest.Create('dc_generator',1)
nest.SetStatus(self.dc1_exc, pars.dc1_pars)
self.dc2_exc = nest.Create('dc_generator',1)
nest.SetStatus(self.dc2_exc, pars.dc2_pars)
# CREATE POPULATIONS -----------------------------------------------------------------------
#print 'Creating populations...\n'
neurons_exc = []
self.pops_exc = range(len(pars.N_exc))
for ii,nr in enumerate(pars.N_exc):
self.pops_exc[ii] = nest.Create(pars.model_type, abs(nr))
neurons_exc.extend(self.pops_exc[ii])
# set neuron parameters for every population independently
for ntypes in range(len(pars.N_exc)):
nest.SetStatus(self.pops_exc[ntypes], pars.neuron_params_exc[ntypes])
if pars.rnd_dist:
nest.SetStatus(neurons_inh,'tau_m',pars.tau_m_rnd)
neurons_inh = []
self.pops_inh = range(len(pars.N_inh))
for ii,nr in enumerate(pars.N_inh):
self.pops_inh[ii] = nest.Create(pars.model_type, abs(nr))
neurons_inh.extend(self.pops_inh[ii])
# set neuron parameters for every population independently
for ntypes in range(len(pars.N_inh)):
nest.SetStatus(self.pops_inh[ntypes], pars.neuron_params_inh[ntypes])
if pars.rnd_dist:
nest.SetStatus(neurons_inh,'tau_m',pars.tau_m_rnd)
if pars.change_type:
self.time_lis = [pars.chg_time,pars.T_sim]
self.pops = self.pops_exc + self.pops_inh
self.pops_exc = [item for sublist in self.pops_exc for item in sublist]
self.pops_inh = [item for sublist in self.pops_inh for item in sublist]
# Make connections -------------------------------------------------------------------------
#total_neu = [item for sublist in self.pops for item in sublist]
self.pars.neurons_tot = len(self.pops_exc) + len(self.pops_inh)
self.pars.pops_exc = self.pops_exc
self.pars.pops_inh = self.pops_inh
nest.SetStatus(self.pops_exc, params = {'tau_m':pars.tau_m_exc,'C_m':pars.C_m_exc,'tau_syn':pars.tau_syn_ex})
nest.DivergentConnect(self.pg_exc, self.pops_exc, weight = pars.J_ext, delay = pars.min_del)
nest.DivergentConnect(self.pg_inh, self.pops_inh, weight = pars.J_ext, delay = pars.min_del)
#STN connections
num_stn_gpe = int(pars.epsilon_stn_gpe * len(self.pops_inh))
nest.RandomDivergentConnect(self.pops_exc,self.pops_inh, num_stn_gpe, weight = pars.J_stn_gpe, delay = pars.delay_inter)
num_stn_stn = int(pars.epsilon_stn_stn* len(self.pops_exc))
nest.RandomDivergentConnect(self.pops_exc,self.pops_exc, num_stn_stn, weight = pars.J_stn_stn, delay = pars.delay_intra)
#GPE connections
num_gpe_gpe = int(pars.epsilon_gpe_gpe * len(self.pops_inh))
nest.RandomDivergentConnect(self.pops_inh,self.pops_inh, num_gpe_gpe, weight = pars.J_gpe_gpe, delay = pars.delay_intra)
num_gpe_stn = int(pars.epsilon_gpe_stn* len(self.pops_exc))
nest.RandomDivergentConnect(self.pops_inh,self.pops_exc, num_gpe_stn, weight = pars.J_gpe_stn, delay = pars.delay_inter)
if pars.add_spikes == 1:
extra_spike = nest.Create('spike_generator',int(pars.num_gen))
def spike_times():
spt = np.random.uniform(pars.st_val+pars.beg_width,pars.st_val + pars.ex_width,1)
spike_times = (np.sort(np.random.uniform(spt,spt + pars.dur ,pars.num_spk))).tolist()
return spike_times
for ii in extra_spike:
spike_time = spike_times()
spike_time = np.around(spike_time,1)
nest.SetStatus([ii],params = {'spike_times':(np.array(spike_time)).flatten()})
if self.pars.extra_spk == 'exc':
nest.RandomDivergentConnect(extra_spike,self.pops_inh,int(len(self.pops_inh)*pars.epsilon_stn_gpe),weight = pars.J_stn_gpe, delay = pars.delay_inter)
nest.RandomDivergentConnect(extra_spike,self.pops_exc,int(len(self.pops_exc)*pars.epsilon_stn_stn),weight = pars.J_stn_stn, delay = pars.delay_intra)
elif self.pars.extra_spk == 'inh':
nest.RandomDivergentConnect(extra_spike,self.pops_inh,int(len(self.pops_inh)*pars.epsilon_stn_gpe),weight = pars.J_gpe_stn, delay = pars.delay_inter)
nest.RandomDivergentConnect(extra_spike,self.pops_exc,int(len(self.pops_exc)*pars.epsilon_stn_stn),weight = pars.J_gpe_gpe, delay = pars.delay_intra)
# pops_ch = self.pops_exc + self.pops_inh
# pops_ch = self.pops_exc + self.pops_inh
# pops_rd = random.sample(pops_ch,500)
#CREATE RECORDERS----------------------------------------------------------------------------
self.record_spikes = list(np.arange(self.pops_exc[0],self.pops_inh[-1]+1))
#self.record_spikes_new = random.sample(self.record_spikes,1000)
# self.record_spikes = pops_rd
#if self.record_spikes!= []:
sd = nest.Create('spike_detector',1)
nest.SetStatus(sd,{'to_file':True,'to_memory':True})
nest.ConvergentConnect(self.record_spikes,sd)
self.recorders['sd'] = sd
if self.pars.record_vm != []:
vm = nest.Create('voltmeter',1)
#print 'Id of vm recorder: ',vm
nest.SetStatus(vm,{'withtime':True,'withgid':True,'to_file':True,'to_memory':False})
nest.DivergentConnect(vm,self.pars.record_vm)
nest.SetStatus(self.pars.record_vm,{'V_th':1000.}) # record free Vm
self.recorders['vm'] = vm
self.build_net_time = time.time()-start_build_net
def __init__(self):
nest.ResetKernel()
nest.SetKernelStatus({
"resolution": 0.1,
"print_time": True,
"overwrite_files": True,
"local_num_threads": 8
})
nest.CopyModel('iaf_psc_alpha', 'exci')
nest.CopyModel('iaf_psc_alpha', 'inhi')
nest.CopyModel('static_synapse', 'exc', {'weight': 5.0})
nest.CopyModel('static_synapse', 'inh', {'weight': -5.0})
self.l = tp.CreateLayer({
'rows': 90,
'columns': 90,
'elements': ['exci', 5, 'inhi', 5],
'edge_wrap': False
})
cdict = {
'connection_type': 'divergent',
'mask': {
'circular': {
'radius': 0.2
}
},
'kernel': {
'gaussian': {
'p_center': 0.8,
'sigma': 0.075
}
},
'delays': {
'linear': {
'c': 2.0,
'a': 0.02
}
},
'sources': {
'model': 'exci'
},
'targets': {
'model': 'inhi'
},
'synapse_model': 'exc'
}
tp.ConnectLayers(self.l, self.l, cdict)
self.rec_ex = tp.CreateLayer({
'rows': 1,
'columns': 1,
'elements': 'spike_detector'
})
cdict_rec_ex = {
'connection_type': 'convergent',
'sources': {
'model': "exci"
}
}
tp.ConnectLayers(self.l, self.rec_ex, cdict_rec_ex)
# Background stimulation
stim = tp.CreateLayer({
'rows': 1,
'columns': 1,
'elements': 'poisson_generator'
})
stim_i = nest.GetLeaves(stim, local_only=True)[0]
nest.SetStatus(stim_i, {'rate': 30000.})
background_stim_dict = {
'connection_type': 'divergent',
'mask': {
'grid': {
'rows': 90,
'columns': 90
}
},
'synapse_model': 'exc'
}
tp.ConnectLayers(stim, self.l, background_stim_dict)
nest.Simulate(2000.)
rec_ex_true = nest.GetLeaves(self.rec_ex, local_only=True)[0]
self.events_ex = nest.GetStatus(rec_ex_true, "events")[0]
def prepare_simulation(self):
nest.ResetKernel()
nest.set_verbosity('M_ERROR')
'''
We set global kernel parameters. Here we define the resolution
for the simulation, which is also the time resolution for the update
of the synaptic elements.
'''
nest.SetKernelStatus({'resolution': self.dt})
'''
Set Number of virtual processes. Remember SP does not work well with openMP right now, so calls must always be done using mpiexec
'''
nest.SetKernelStatus({'total_num_virtual_procs': self.comm.Get_size()})
print("Total number of virtual processes set to: " +
str(self.comm.Get_size()))
'''
Set Structural Plasticity synaptic update interval which is how often
the connectivity will be updated inside the network. It is important
to notice that synaptic elements and connections change on different
time scales.
'''
nest.SetStructuralPlasticityStatus({
'structural_plasticity_update_interval':
self.update_interval,
'tau_Ca':
10000.0,
'beta_Ca':
0.001,
})
'''
Now we define Structural Plasticity synapses. In this example we create
two synapse models, one for excitatory and one for inhibitory synapses.
Then we define that excitatory synapses can only be created between a
pre synaptic element called 'Axon_ex' and a post synaptic element
called Den_ex. In a similar manner, synaptic elements for inhibitory
synapses are defined.
'''
spsyn_names = ['synapse_in' + str(nam) for nam in range(self.regions)]
spsyn_names_e = [
'synapse_ex' + str(nam) for nam in range(self.regions)
]
sps = {}
for x in range(0, self.regions):
nest.CopyModel('static_synapse', 'synapse_in' + str(x))
nest.SetDefaults('synapse_in' + str(x), {
'weight': self.psc_i,
'delay': 1.0
})
nest.CopyModel('static_synapse', 'synapse_ex' + str(x))
nest.SetDefaults('synapse_ex' + str(x), {
'weight': self.psc_e,
'delay': 1.0
})
sps[spsyn_names[x]] = {
'model': 'synapse_in' + str(x),
'post_synaptic_element': 'Den_in' + str(x),
'pre_synaptic_element': 'Axon_in' + str(x),
}
sps[spsyn_names_e[x]] = {
'model': 'synapse_ex' + str(x),
'post_synaptic_element': 'Den_ex' + str(x),
'pre_synaptic_element': 'Axon_ex' + str(x),
}
nest.SetStructuralPlasticityStatus(
{'structural_plasticity_synapses': sps})
def test(settings, data, weights):
np.random.seed()
rank = nest.Rank()
rng = np.random.randint(500)
num_v_procs = settings['network']['num_threads'] \
* settings['network']['num_procs']
nest.ResetKernel()
nest.SetKernelStatus({
'local_num_threads':
settings['network']['num_threads'],
'total_num_virtual_procs':
num_v_procs,
'resolution':
settings['network']['h'],
'rng_seeds':
range(rng, rng + num_v_procs)
})
layer_out = nest.Create('iaf_psc_exp', settings['topology']['n_layer_out'])
if settings['topology']['two_layers']:
layer_hid = nest.Create('iaf_psc_exp',
settings['topology']['n_layer_hid'])
spike_generators_1 = nest.Create('spike_generator',
settings['topology']['n_input'])
poisson_layer = nest.Create('poisson_generator',
settings['topology']['n_input'])
parrot_layer = nest.Create('parrot_neuron',
settings['topology']['n_input'])
spike_detector_1 = nest.Create('spike_detector')
spike_detector_2 = nest.Create('spike_detector')
spike_detector_3 = nest.Create('spike_detector')
voltmeter = nest.Create('voltmeter', 1, {
'withgid': True,
'withtime': True
})
nest.Connect(spike_generators_1,
parrot_layer,
'one_to_one',
syn_spec='static_synapse')
if settings['network']['test_with_noise']:
nest.SetStatus(poisson_layer,
{'rate': settings['network']['noise_freq']})
nest.Connect(poisson_layer,
parrot_layer,
'one_to_one',
syn_spec='static_synapse')
nest.Connect(layer_out, spike_detector_1, 'all_to_all')
nest.Connect(parrot_layer, spike_detector_2, 'all_to_all')
nest.Connect(voltmeter, layer_out)
nest.SetStatus(layer_out, settings['model']['neuron_out'])
if settings['topology']['two_layers']:
if settings['topology']['use_inhibition']:
interconnect_layer(layer_hid, settings['model']['syn_dict_inh'])
# nest.Connect(layer_out, layer_hid,
# 'all_to_all', syn_spec=settings['syn_dict_inh'])
nest.Connect(parrot_layer,
layer_hid,
'all_to_all',
syn_spec='static_synapse')
nest.Connect(layer_hid,
layer_out,
'all_to_all',
syn_spec='static_synapse')
nest.Connect(layer_hid, spike_detector_3, 'all_to_all')
nest.SetStatus(layer_hid, settings['model']['neuron_hid'])
else:
if settings['topology']['use_inhibition']:
interconnect_layer(layer_out, settings['model']['syn_dict_inh'])
nest.Connect(parrot_layer,
layer_out,
'all_to_all',
syn_spec='static_synapse')
if settings['topology']['two_layers']:
for neuron_id in weights['layer_hid']:
connection = nest.GetConnections(parrot_layer, target=[neuron_id])
nest.SetStatus(connection, 'weight',
weights['layer_hid'][neuron_id])
for neuron_id in weights['layer_out']:
connection = nest.GetConnections(layer_hid, target=[neuron_id])
nest.SetStatus(connection, 'weight',
weights['layer_out'][neuron_id])
else:
for neuron_id in weights['layer_out']:
connection = nest.GetConnections(parrot_layer, target=[neuron_id])
nest.SetStatus(connection, 'weight',
weights['layer_out'][neuron_id])
np.random.seed(500)
output_latency = []
d_time = settings['network']['start_delta']
nest.Simulate(settings['network']['start_delta'])
for example, examples_class in zip(data['input'], data['class']):
set_spike_in_generators(example, spike_generators_1, d_time,
d_time + settings['network']['h_time'],
settings['network']['h_time'],
settings['network']['h'])
# nest.SetStatus(poisson_layer, {'start': 30.})
nest.Simulate(settings['network']['h_time'])
d_time += settings['network']['h_time']
spikes = nest.GetStatus(spike_detector_1,
keys="events")[0]['times'].tolist()
senders = nest.GetStatus(spike_detector_1,
keys="events")[0]['senders'].tolist()
output_latency = {'spikes': spikes, 'senders': senders}
devices = {
'voltmeter': voltmeter,
'spike_detector_1': spike_detector_1,
'spike_detector_2': spike_detector_2,
'spike_detector_3': spike_detector_3,
}
return output_latency, devices
def setUp(self):
nest.ResetKernel()
def reset():
nest.ResetKernel()
def setUp(self):
# test parameter to compare analytic solution to simulation
self.rtol = 1.0
# test parameters
self.N = 100
self.rate_ex = 1.5 * 1e4
self.J = 0.1
# simulation parameters
self.simtime = 500.
self.dt = 0.1
self.start = 200.
nest.set_verbosity('M_WARNING')
nest.ResetKernel()
nest.SetKernelStatus({
'resolution': self.dt,
'use_wfr': False,
'print_time': True
})
# set up driven iaf neuron
self.iaf_neuron = nest.Create('iaf_psc_delta',
self.N) # , params={"C_m": 1.0})
self.poisson_generator = nest.Create('poisson_generator',
params={'rate': self.rate_ex})
nest.Connect(self.poisson_generator,
self.iaf_neuron,
syn_spec={
'weight': self.J,
'delay': self.dt
})
self.spike_detector = nest.Create("spike_detector",
params={'start': self.start})
nest.Connect(self.iaf_neuron, self.spike_detector)
# set up driven siegert neuron
neuron_status = nest.GetStatus(self.iaf_neuron)[0]
siegert_params = {
'tau_m': neuron_status['tau_m'],
't_ref': neuron_status['t_ref'],
'theta': neuron_status['V_th'] - neuron_status['E_L'],
'V_reset': neuron_status['V_reset'] - neuron_status['E_L']
}
self.siegert_neuron = nest.Create('siegert_neuron',
params=siegert_params)
self.siegert_drive = nest.Create('siegert_neuron',
1,
params={'mean': self.rate_ex})
J_mu_ex = neuron_status['tau_m'] * 1e-3 * self.J
J_sigma_ex = neuron_status['tau_m'] * 1e-3 * self.J**2
syn_dict = {
'drift_factor': J_mu_ex,
'diffusion_factor': J_sigma_ex,
'model': 'diffusion_connection'
}
nest.Connect(self.siegert_drive,
self.siegert_neuron,
syn_spec=syn_dict)
self.multimeter = nest.Create("multimeter",
params={
'record_from': ['rate'],
'interval': self.dt
})
nest.Connect(self.multimeter, self.siegert_neuron)
def test_GetKernelStatus(self):
"""GetKernelStatus"""
nest.ResetKernel()
s = nest.GetKernelStatus()
def test(referenceModel, testant, gsl_error_tol, tolerance=0.000001):
nest.ResetKernel()
neuron1 = nest.Create(referenceModel)
neuron2 = nest.Create(testant)
if not (gsl_error_tol is None):
nest.SetStatus(neuron2, {"gsl_error_tol": gsl_error_tol})
spikegenerator = nest.Create('spike_generator',
params={
'spike_times': [100.0, 200.0],
'spike_weights': [20.0, -20.0]
})
nest.Connect(spikegenerator, neuron1)
nest.Connect(spikegenerator, neuron2)
multimeter1 = nest.Create('multimeter')
multimeter2 = nest.Create('multimeter')
V_m_specifier = 'V_m' # 'delta_V_m'
nest.SetStatus(multimeter1, {
"withtime": True,
"record_from": [V_m_specifier]
})
nest.SetStatus(multimeter2, {
"withtime": True,
"record_from": [V_m_specifier]
})
nest.Connect(multimeter1, neuron1)
nest.Connect(multimeter2, neuron2)
nest.Simulate(400.0)
dmm1 = nest.GetStatus(multimeter1)[0]
Vms1 = dmm1["events"][V_m_specifier]
ts1 = dmm1["events"]["times"]
events1 = dmm1["events"]
pylab.figure(1)
dmm2 = nest.GetStatus(multimeter2)[0]
Vms2 = dmm2["events"][V_m_specifier]
ts2 = dmm2["events"]["times"]
pylab.plot(ts1, Vms1, label="Reference " + referenceModel)
pylab.plot(ts2, Vms2, label="Testant " + testant)
pylab.legend(loc='upper right')
pylab.show()
for index in range(0, len(Vms1)):
if abs(Vms1[index] - Vms2[index]) > tolerance:
print('!!!!!!!!!!!!!!!!!!!!')
print(
str(Vms1[index]) + " divers from " + str(Vms2[index]) +
" at iteration: " + str(index) + " of overall iterations: " +
str(len(Vms1)))
print('!!!!!!!!!!!!!!!!!!!!')
raise Exception(testant + ": TEST FAILED")
elif abs(Vms1[index] - Vms2[index]) > 0:
None #print("Greater than 0 difference" + str(abs(Vms1[index]-Vms2[index])) + " at iteration: " + str(index) + " of overall iterations: " + str(len(Vms1)))
print(testant + " PASSED")
def test_rate_instantaneous_and_delayed(self):
# neuron parameters
neuron_params = {'tau': 5., 'sigma': 0.}
drive = 1.5
delay = 2.
weight = 0.5
# simulation parameters
simtime = 100.
dt = 0.001
nest.set_verbosity('M_WARNING')
nest.ResetKernel()
nest.SetKernelStatus({
'resolution': dt,
'use_wfr': True,
'print_time': False
})
# set up rate neuron network
rate_neuron_drive = nest.Create('lin_rate_ipn',
params={
'mu': drive,
'sigma': 0.
})
rate_neuron_1 = nest.Create('lin_rate_ipn', params=neuron_params)
rate_neuron_2 = nest.Create('lin_rate_ipn', params=neuron_params)
multimeter = nest.Create('multimeter',
params={
'record_from': ['rate'],
'precision': 10,
'interval': dt
})
# record rates and connect neurons
neurons = rate_neuron_1 + rate_neuron_2
nest.Connect(multimeter, neurons, 'all_to_all', {'delay': 10.})
nest.Connect(rate_neuron_drive, rate_neuron_1, 'all_to_all', {
'model': 'rate_connection_instantaneous',
'weight': weight
})
nest.Connect(rate_neuron_drive, rate_neuron_2, 'all_to_all', {
'model': 'rate_connection_delayed',
'delay': delay,
'weight': weight
})
# simulate
nest.Simulate(simtime)
# make sure shifted rates are identical
events = nest.GetStatus(multimeter)[0]['events']
senders = events['senders']
rate_1 = np.array(events['rate'][np.where(senders == rate_neuron_1)])
times_2 = np.array(events['times'][np.where(senders == rate_neuron_2)])
rate_2 = np.array(events['rate'][np.where(senders == rate_neuron_2)])
# get shifted rate_2
rate_2 = rate_2[times_2 > delay]
# adjust length of rate_1 to be able to substract
rate_1 = rate_1[:len(rate_2)]
assert (np.sum(np.abs(rate_2 - rate_1)) < 1e-12)
def test_non_linear_dendrite(self):
MAX_SSE = 1E-12
I_dend_alias_name = 'I_dend' # synaptic current
I_dend_internal_name = 'I_kernel2__X__I_2' # alias for the synaptic current
input_path = os.path.join(
os.path.realpath(
os.path.join(os.path.dirname(__file__), "resources")),
"iaf_psc_exp_nonlineardendrite.nestml")
nest_path = nest.ll_api.sli_func("statusdict/prefix ::")
target_path = 'target'
logging_level = 'INFO'
module_name = 'nestmlmodule'
store_log = False
suffix = '_nestml'
dev = True
to_nest(input_path, target_path, logging_level, module_name, store_log,
suffix, dev)
install_nest(target_path, nest_path)
nest.set_verbosity("M_ALL")
nest.ResetKernel()
nest.Install("nestmlmodule")
nrn = nest.Create("iaf_psc_exp_nonlineardendrite_nestml")
sg = nest.Create("spike_generator",
params={"spike_times": [10., 20., 30.]})
nest.Connect(sg,
nrn,
syn_spec={
"receptor_type": 2,
"weight": 30.,
"delay": 1.
})
mm = nest.Create('multimeter')
mm.set({
"record_from": [
I_dend_alias_name, I_dend_internal_name, 'V_m',
'dend_curr_enabled', 'I_dend_ap'
]
})
nest.Connect(mm, nrn)
nest.Simulate(100.0)
timevec = mm.get("events")["times"]
I_dend_alias_ts = mm.get("events")[I_dend_alias_name]
I_dend_internal_ts = mm.get("events")[I_dend_internal_name]
if TEST_PLOTS:
fig, ax = plt.subplots(3, 1)
ax[0].plot(timevec, I_dend_alias_ts, label="aliased I_dend_syn")
ax[0].plot(timevec,
I_dend_internal_ts,
label="internal I_dend_syn")
ax[0].legend()
ax_ = ax[0].twinx()
ax_.plot(timevec, mm.get("events")["dend_curr_enabled"])
ax_.set_ylabel("dend_curr_enabled")
ax[1].plot(timevec, mm.get("events")["I_dend_ap"])
ax[1].set_ylabel("I_dend_AP")
ax[2].plot(timevec, mm.get("events")["V_m"], label="V_m")
for _ax in ax:
_ax.legend()
_ax.grid()
plt.ylabel("Dendritic current $I_{dend}$")
plt.suptitle("Reset of synaptic integration after dendritic spike")
plt.savefig("/tmp/nestml_triplet_stdp_test.png")
assert np.all(
I_dend_alias_ts == I_dend_internal_ts
), "Variable " + str(
I_dend_alias_name
) + " and (internal) variable " + str(
I_dend_internal_name
) + " should measure the same thing, but discrepancy in values occurred."
tidx = np.argmin((timevec - 40)**2)
assert mm.get("events")["I_dend_ap"][
tidx] > 0., "Expected a dendritic action potential around t = 40 ms, but dendritic action potential current is zero"
assert mm.get("events")["dend_curr_enabled"][
tidx] == 0., "Dendritic synaptic current should be disabled during dendritic action potential"
tidx_ap_end = tidx + np.where(
mm.get("events")["dend_curr_enabled"][tidx:] == 1.)[0][0]
assert np.all(
I_dend_alias_ts[tidx_ap_end:] == 0.
), "After dendritic spike, dendritic current should be reset to 0 and stay at 0."
def NESTSimulation(self,retina_spikes):
# NEST Kernel and Network settings
nest.ResetKernel()
nest.ResetNetwork()
nest.SetKernelStatus(
{"local_num_threads": self.Params['NEST_threads'],
'resolution': self.Params['resolution'], "rng_seeds": list(self.seeds)})
# import network description
import thalamocortical_system
# get network info
models, layers, conns = thalamocortical_system.get_Network(self.Params)
# Create models
for m in models:
nest.CopyModel(m[0], m[1], m[2])
print ("\n---Creating layers---\n")
# Create layers, store layer info in Python variable
layer_IDs = []
for l in layers:
exec ("%s = tp.CreateLayer(%s)" % (l[0],l[1]),globals())
exec ("copy_var = %s" % l[0],globals())
layer_IDs.append([l[0],copy_var,l[1]['elements']])
# print (l[0])
print ("\n---Connecting layers---\n")
# Create connections, need to insert variable names
for c in conns:
eval('tp.ConnectLayers(%s,%s,c[2])' % (c[0], c[1]))
# print ('tp.ConnectLayers(%s,%s)' % (c[0], c[1]))
# Initialize spike generators
Midget_ganglion_cells_L_ON_spikes = retina_spikes[0]
Midget_ganglion_cells_L_OFF_spikes = retina_spikes[1]
Midget_ganglion_cells_M_ON_spikes = retina_spikes[2]
Midget_ganglion_cells_M_OFF_spikes = retina_spikes[3]
cell = 0
for x in np.arange(self.Params['N_LGN']):
for y in np.arange(self.Params['N_LGN']):
nest.SetStatus([tp.GetElement(Midget_ganglion_cells_L_ON,(x,y))[0]],
[{'spike_times':Midget_ganglion_cells_L_ON_spikes[cell],
'spike_weights':[]}])
nest.SetStatus([tp.GetElement(Midget_ganglion_cells_L_OFF,(x,y))[0]],
[{'spike_times':Midget_ganglion_cells_L_OFF_spikes[cell],
'spike_weights':[]}])
nest.SetStatus([tp.GetElement(Midget_ganglion_cells_M_ON,(x,y))[0]],
[{'spike_times':Midget_ganglion_cells_M_ON_spikes[cell],
'spike_weights':[]}])
nest.SetStatus([tp.GetElement(Midget_ganglion_cells_M_OFF,(x,y))[0]],
[{'spike_times':Midget_ganglion_cells_M_OFF_spikes[cell],
'spike_weights':[]}])
cell+=1
## Check-point: Visualization functions
# fig = tp.PlotLayer(Color_Luminance_inh_L_ON_L_OFF_vertical,nodesize =80)
# ctr = tp.FindCenterElement(Parvo_LGN_relay_cell_L_ON)
# tp.PlotTargets(ctr,Color_Luminance_inh_L_ON_L_OFF_vertical,fig = fig,mask=conns[26][2]['mask'],
# kernel=conns[26][2]['kernel'],src_size=250,tgt_color='red',tgt_size=20,
# kernel_color='green')
# plt.show()
# ctr = tp.FindCenterElement(Color_Luminance_inh_L_ON_L_OFF_vertical)
# print ("ctr = ",ctr," L-ON = ",tp.FindCenterElement(Parvo_LGN_relay_cell_L_ON)," L-OFF = ",tp.FindCenterElement(Parvo_LGN_relay_cell_L_OFF))
# for xx in np.arange(5):
# for yy in np.arange(5):
# ctr = [tp.GetElement(Color_Luminance_inh_L_ON_L_OFF_vertical,(xx,yy))[0]]
# conns = nest.GetConnections(target = [ctr[0]])
# print ("Cell ",ctr)
# for nn in np.arange(len(conns)):
# print ("conns = ",conns[nn])
# ctr = tp.FindCenterElement(Parvo_LGN_relay_cell_L_ON)
# targets = tp.GetTargetNodes(ctr,Color_Luminance_L_ON_L_OFF_vertical)
# print ("targets = ",targets)
return layer_IDs
def _test_model_subthreshold(self,
referenceModel,
testant,
gsl_error_tol,
tolerance=0.000001,
nest_ref_model_opts=None,
custom_model_opts=None):
t_stop = 1000. # [ms]
I_stim_vec = np.linspace(10E-12, 1E-9, 100) # [A]
rate_testant = float("nan") * np.ones_like(I_stim_vec)
rate_reference = float("nan") * np.ones_like(I_stim_vec)
for i, I_stim in enumerate(I_stim_vec):
nest.ResetKernel()
neuron1 = nest.Create(referenceModel, params=nest_ref_model_opts)
neuron2 = nest.Create(testant, params=custom_model_opts)
if gsl_error_tol is not None:
nest.SetStatus(neuron2, {"gsl_error_tol": gsl_error_tol})
dc = nest.Create("dc_generator",
params={"amplitude":
I_stim * 1E12}) # 1E12: convert A to pA
nest.Connect(dc, neuron1)
nest.Connect(dc, neuron2)
multimeter1 = nest.Create('multimeter')
multimeter2 = nest.Create('multimeter')
V_m_specifier = 'V_m' # 'delta_V_m'
nest.SetStatus(multimeter1, {"record_from": [V_m_specifier]})
nest.SetStatus(multimeter2, {"record_from": [V_m_specifier]})
nest.Connect(multimeter1, neuron1)
nest.Connect(multimeter2, neuron2)
sd_reference = nest.Create('spike_recorder')
nest.Connect(neuron1, sd_reference)
sd_testant = nest.Create('spike_recorder')
nest.Connect(neuron2, sd_testant)
nest.Simulate(t_stop)
dmm1 = nest.GetStatus(multimeter1)[0]
Vms1 = dmm1["events"][V_m_specifier]
ts1 = dmm1["events"]["times"]
dmm2 = nest.GetStatus(multimeter2)[0]
Vms2 = dmm2["events"][V_m_specifier]
ts2 = dmm2["events"]["times"]
rate_testant[i] = sd_testant.n_events / t_stop * 1000
rate_reference[i] = sd_reference.n_events / t_stop * 1000
if TEST_PLOTS and False:
fig, ax = plt.subplots(2, 1)
ax[0].plot(ts1, Vms1, label="Reference " + referenceModel)
ax[1].plot(ts2, Vms2, label="Testant " + testant)
for _ax in ax:
_ax.legend(loc='upper right')
_ax.grid()
fig.suptitle("Rate: " + str(rate_testant[i]) + " Hz")
plt.savefig(
"/tmp/nestml_nest_integration_test_subthreshold_[" +
referenceModel + "]_[" + testant + "]_[I_stim=" +
str(I_stim) + "].png")
plt.close(fig)
if TEST_PLOTS:
if len(I_stim_vec) < 20:
marker = "o"
else:
marker = None
fig, ax = plt.subplots(2, 1)
ax[0].plot(I_stim_vec * 1E12,
rate_reference,
marker=marker,
label="Reference " + referenceModel)
ax[1].plot(I_stim_vec * 1E12,
rate_testant,
marker=marker,
label="Testant " + testant)
for _ax in ax:
_ax.legend(loc='upper right')
_ax.grid()
_ax.set_ylabel("Firing rate [Hz]")
ax[1].set_xlabel("$I_{inj}$ [pA]")
plt.savefig("/tmp/nestml_nest_integration_test_subthreshold_[" +
referenceModel + "]_[" + testant + "].png")
plt.close(fig)
if TEST_PLOTS:
if len(I_stim_vec) < 20:
marker = "o"
else:
marker = None
for figsize, fname_snip in zip([(8, 5), (4, 3)], ["", "_small"]):
fig, ax = plt.subplots(1, 1, figsize=figsize)
ax = [ax]
ax[0].plot(I_stim_vec * 1E12,
rate_testant,
marker=marker,
label=referenceModel)
for _ax in ax:
_ax.grid()
_ax.set_ylabel("Firing rate [Hz]")
ax[0].set_xlabel("$I_{inj}$ [pA]")
plt.tight_layout()
plt.savefig("/tmp/nestml_models_library_[" + referenceModel +
"]_f-I_curve" + fname_snip + ".png")
plt.close(fig)
print(testant + " PASSED")
def eSTDP (alpha, step, mu_plus, mu_minus, initweight, maxweight, tau_m, tau_p):
import matplotlib.pyplot as plt
import numpy as np
import sys
sys.path.append("/home/vasco/Documenti/NEST/lib/x86_64-linux-gnu/python2.7/site-packages")
import nest
import nest.raster_plot
#nest.Install("albertomodule")
nest.ResetKernel()
nest.set_verbosity('M_WARNING')
maxweight = 20.0
delay = 1.0
num_parr = 400
parrot = nest.Create("parrot_neuron", num_parr)
nest.SetStatus(parrot, {'tau_minus': tau_m})
senders_e= parrot[:num_parr/4]
receivers_e = parrot[num_parr/4:num_parr/2]
senders_i = parrot[num_parr/2: 3*num_parr/4]
receivers_i = parrot[3*num_parr/4:]
nest.CopyModel('istdp_synapse', 'stdp',{'alpha': alpha, 'lambda': step, 'mu_plus': mu_plus,'mu_minus': mu_minus, 'Wmax': maxweight, 'tau_plus': tau_p})
spikes_in = nest.Create('spike_detector', 1)
spikes_out = nest.Create('spike_detector', 1)
stimuli = nest.Create("spike_generator", 3)
stimulus_e = stimuli[0]
nest.SetStatus([stimulus_e], {'spike_times': [5.0, 10003.0]})
''' LTP '''
for i,senders_ei in enumerate(senders_e):
nest.Connect([stimulus_e], [senders_ei], {'rule': 'all_to_all'}, {'delay' : delay})
for i,receivers_ei in enumerate(receivers_e):
nest.Connect([senders_e[i]], [receivers_ei], {'rule': 'all_to_all'}, {'model':'stdp', 'weight': initweight, 'delay' : delay})
delay = delay + 1
nest.Connect(senders_e, spikes_in)
nest.Connect(receivers_e, spikes_out)
''' LTD '''
delay = 1.0
stimulus_i = stimuli[1]
stimulus_i_out = stimuli[2]
nest.SetStatus([stimulus_i], {'spike_times': [7.0, 10005.0]})
nest.SetStatus([stimulus_i_out], {'spike_times': [5.0]})
nest.Connect([stimulus_i_out], receivers_i, {'rule': 'all_to_all'}, {'model': 'static_synapse'})
for i,senders_ii in enumerate(senders_i):
nest.Connect([stimulus_i], [senders_ii], {'rule': 'all_to_all'}, {'model': 'static_synapse', 'delay': delay})
delay = delay + 1
for i, receivers_ii in enumerate(receivers_i):
nest.Connect([senders_i[i]], [receivers_ii], {'rule': 'all_to_all'}, {'model': 'stdp', 'weight': initweight, 'delay': 1.0})
nest.Simulate(10006)
deltaTime = range(-100, 100)
Exc = nest.GetConnections(senders_e, receivers_e)
weights = nest.GetStatus(Exc, "weight")
#print(weights)
weights_e = np.zeros(100)
weights_e_perc = np.zeros(100)
for i in range(0, 100):
a = weights[i] - initweight
weights_e[i] = a
weights_e_perc[i] = (a/initweight) * 100
Inh = nest.GetConnections(senders_i, receivers_i)
weights = nest.GetStatus(Inh, "weight")
weights_i = np.zeros(100)
weights_i_perc = np.zeros(100)
for i in range(0, 100):
a = weights[i] - initweight
weights_i[99 - i] = a
weights_i_perc[99 -i] = (a/initweight) * 100
W = np.concatenate(( weights_i,weights_e))
W_perc = np.concatenate((weights_i_perc, weights_e_perc))
pesi = np.concatenate((W, W_perc))
return(pesi)
def test_nest_integration(self):
# N.B. all models are assumed to have been already built (see .travis.yml)
nest.ResetKernel()
nest.set_verbosity("M_ALL")
nest.Install("nestml_allmodels_module")
models = []
"""models.append(("iaf_psc_delta", "iaf_psc_delta_nestml", None, 1E-3))
models.append(("iaf_psc_exp", "iaf_psc_exp_nestml", None, .01))
models.append(("iaf_psc_alpha", "iaf_psc_alpha_nestml", None, 1E-3))
models.append(("iaf_cond_exp", "iaf_cond_exp_nestml", 1E-3, 1E-3))
models.append(("iaf_cond_alpha", "iaf_cond_alpha_nestml", 1E-3, 1E-3))
models.append(("iaf_cond_beta", "iaf_cond_beta_nestml", 1E-3, 1E-3, {"tau_rise_ex": 2., "tau_decay_ex": 10., "tau_rise_in": 2., "tau_decay_in": 10.}, {"tau_syn_rise_E": 2., "tau_syn_decay_E": 10., "tau_syn_rise_I": 2., "tau_syn_decay_I": 10.})) # XXX: TODO: does not work yet when tau_rise = tau_fall (numerical singularity occurs in the propagators)"""
models.append(
("izhikevich", "izhikevich_nestml", 1E-3, 1)
) # large tolerance because NEST Simulator model does not use GSL solver, but simple forward Euler
models.append(("hh_psc_alpha", "hh_psc_alpha_nestml", 1E-3, 1E-3))
models.append(("iaf_chxk_2008", "iaf_chxk_2008_nestml", 1E-3, 1E-3))
models.append(("aeif_cond_exp", "aeif_cond_exp_nestml", 1.e-3, 1E-3))
models.append(
("aeif_cond_alpha", "aeif_cond_alpha_nestml", 1.e-3, 1E-3))
# --------------
# XXX: TODO!
# models.append(("hh_cond_exp_traub", "hh_cond_exp_traub_nestml", 1.e-3, 1E-3))
# models.append(("ht_neuron", "hill_tononi_nestml", None, 1E-3))
# models.append(("iaf_cond_exp_sfa_rr", "iaf_cond_exp_sfa_rr_nestml", 1.e-3, 1E-3))
# models.append(("iaf_tum_2000", "iaf_tum_2000_nestml", None, 0.01))
# models.append(("mat2_psc_exp", "mat2_psc_exp_nestml", None, 0.1))
for model in models:
reference = model[0]
testant = model[1]
gsl_error_tol = model[2]
tolerance = model[3]
if len(model) > 4:
nest_ref_model_opts = model[4]
else:
nest_ref_model_opts = None
if len(model) > 5:
custom_model_opts = model[5]
else:
custom_model_opts = None
print("Now testing model: " + str(testant) +
" (reference model: " + str(reference) + ")")
self._test_model(reference, testant, gsl_error_tol, tolerance,
nest_ref_model_opts, custom_model_opts)
self._test_model_subthreshold(reference, testant, gsl_error_tol,
tolerance, nest_ref_model_opts,
custom_model_opts)
all_models = [
s[:-7] for s in list(os.walk("models/neurons"))[0][2]
if s[-7:] == ".nestml"
]
self.generate_models_documentation(models, all_models)
def __initialize_test_data(params_file_):
plot = False
display = True
save = True
# ##################################################################################################################
# Extract parameters from file and build global ParameterSet
# ==================================================================================================================
parameter_set = ParameterSpace(params_file_)[0]
parameter_set = parameter_set.clean(termination='pars')
if not isinstance(parameter_set, ParameterSet):
if isinstance(parameter_set, basestring) or isinstance(
parameter_set, dict):
parameter_set = ParameterSet(parameter_set)
else:
raise TypeError(
"parameter_set must be ParameterSet, string with full path to parameter file or dictionary"
)
# ##################################################################################################################
# Setup extra variables and parameters
# ==================================================================================================================
if plot:
set_global_rcParams(parameter_set.kernel_pars['mpl_path'])
paths = set_storage_locations(parameter_set, save)
np.random.seed(parameter_set.kernel_pars['np_seed'])
# ##################################################################################################################
# Set kernel and simulation parameters
# ==================================================================================================================
print '\nRuning ParameterSet {0}'.format(parameter_set.label)
nest.ResetKernel()
nest.set_verbosity('M_WARNING')
nest.SetKernelStatus(
extract_nestvalid_dict(parameter_set.kernel_pars.as_dict(),
param_type='kernel'))
# ##################################################################################################################
# Build network
# ==================================================================================================================
net = Network(parameter_set.net_pars)
# ##################################################################################################################
# Randomize initial variable values
# ==================================================================================================================
for idx, n in enumerate(list(iterate_obj_list(net.populations))):
if hasattr(parameter_set.net_pars, "randomize_neuron_pars"):
randomize = parameter_set.net_pars.randomize_neuron_pars[idx]
for k, v in randomize.items():
n.randomize_initial_states(k,
randomization_function=v[0],
**v[1])
####################################################################################################################
# Build Input Signal Sets
# ==================================================================================================================
assert hasattr(parameter_set, "input_pars")
total_stimulation_time = parameter_set.kernel_pars.sim_time + parameter_set.kernel_pars.transient_t
# Current input (need to build 2 separate noise signals for the 2 input channels)
# Generate input for channel 1
input_noise_ch1 = InputNoise(parameter_set.input_pars.noise,
rng=np.random,
stop_time=total_stimulation_time)
input_noise_ch1.generate()
input_noise_ch1.re_seed(parameter_set.kernel_pars.np_seed)
# Generate input for channel 2
input_noise_ch2 = InputNoise(parameter_set.input_pars.noise,
rng=np.random,
stop_time=total_stimulation_time)
input_noise_ch2.generate()
input_noise_ch2.re_seed(parameter_set.kernel_pars.np_seed)
if plot:
inp_plot = InputPlots(stim_obj=None,
input_obj=None,
noise_obj=input_noise_ch1)
inp_plot.plot_noise_component(display=display,
save=paths['figures'] +
"/InputNoise_CH1")
inp_plot = InputPlots(stim_obj=None,
input_obj=None,
noise_obj=input_noise_ch2)
inp_plot.plot_noise_component(display=display,
save=paths['figures'] +
"/InputNoise_CH2")
# ##################################################################################################################
# Build and connect input
# ==================================================================================================================
enc_layer_ch1 = EncodingLayer(parameter_set.encoding_ch1_pars,
signal=input_noise_ch1)
enc_layer_ch1.connect(parameter_set.encoding_ch1_pars, net)
enc_layer_ch2 = EncodingLayer(parameter_set.encoding_ch2_pars,
signal=input_noise_ch2)
enc_layer_ch2.connect(parameter_set.encoding_ch2_pars, net)
# ##################################################################################################################
# Connect Devices
# ==================================================================================================================
net.connect_devices()
# ##################################################################################################################
# Simulate
# ==================================================================================================================
if parameter_set.kernel_pars.transient_t:
net.simulate(parameter_set.kernel_pars.transient_t)
net.flush_records()
net.simulate(parameter_set.kernel_pars.sim_time +
nest.GetKernelStatus()['resolution'])
# ##################################################################################################################
# Extract and store data
# ==================================================================================================================
net.extract_population_activity(
t_start=parameter_set.kernel_pars.transient_t,
t_stop=parameter_set.kernel_pars.sim_time +
parameter_set.kernel_pars.transient_t)
net.extract_network_activity()
# ##################################################################################################################
# Analyse / plot data
# ==================================================================================================================
analysis_interval = [
parameter_set.kernel_pars.transient_t,
parameter_set.kernel_pars.transient_t +
parameter_set.kernel_pars.sim_time
]
results = dict()
for idd, nam in enumerate(net.population_names):
results.update({nam: {}})
results[nam] = single_neuron_responses(net.populations[idd],
parameter_set,
pop_idx=idd,
start=analysis_interval[0],
stop=analysis_interval[1],
plot=plot,
display=display,
save=paths['figures'] +
paths['label'])
if results[nam]['rate']:
print('Output Rate [{0}] = {1} spikes/s'.format(
str(nam), str(results[nam]['rate'])))
# ######################################################################################################################
# Save data
# ======================================================================================================================
data = dict()
data['connections_from'] = {
pop.name: nest.GetConnections(source=pop.gids)
for (idx, pop) in enumerate(net.populations)
}
data['connections_to'] = {
pop.name: nest.GetConnections(target=pop.gids)
for (idx, pop) in enumerate(net.populations)
}
data['results'] = results
data['input'] = {
'channel1': input_noise_ch1.noise_signal.analog_signals[.0].signal,
'channel2': input_noise_ch2.noise_signal.analog_signals[.0].signal
}
data['network'] = {
'populations': {
net.populations[0].name: net.populations[0]
}
}
return data
See Also ~~~~~~~~ :doc:`brunel_alpha_nest` """ ############################################################################### # Import all necessary modules for simulation, analysis and plotting. import time import nest import nest.raster_plot import matplotlib.pyplot as plt nest.ResetKernel() ############################################################################### # Assigning the current time to a variable in order to determine the build # time of the network. startbuild = time.time() ############################################################################### # Assigning the simulation parameters to variables. dt = 0.1 # the resolution in ms simtime = 1000.0 # Simulation time in ms delay = 1.5 # synaptic delay in ms ###############################################################################
def run_post_trace_test_nest_(self,
show_all_nest_trace_samples=False):
nest.set_verbosity("M_WARNING")
nest.ResetKernel()
nest.resolution = self.resolution_
wr = nest.Create('weight_recorder')
nest.CopyModel("stdp_synapse", "stdp_synapse_rec",
{"weight_recorder": wr, "weight": 1.})
# create spike_generators with these times
pre_sg_ps = nest.Create("spike_generator",
params={"spike_times": self.pre_spike_times_,
'precise_times': True})
post_sg_ps = nest.Create("spike_generator",
params={"spike_times": self.post_spike_times_,
'precise_times': True})
# create parrot neurons and connect spike_generators
pre_parrot_ps = nest.Create("parrot_neuron_ps")
post_parrot_ps = nest.Create("parrot_neuron_ps",
params={"tau_minus": self.tau_minus_})
nest.Connect(pre_sg_ps, pre_parrot_ps,
syn_spec={"delay": self.delay_})
nest.Connect(post_sg_ps, post_parrot_ps,
syn_spec={"delay": self.delay_})
# create spike recorder --- debugging only
spikes = nest.Create("spike_recorder")
nest.Connect(pre_parrot_ps + post_parrot_ps, spikes)
# connect both parrot neurons with a stdp synapse onto port 1
# thereby spikes transmitted through the stdp connection are
# not repeated postsynaptically.
nest.Connect(
pre_parrot_ps, post_parrot_ps,
syn_spec={'synapse_model': 'stdp_synapse_rec',
'receptor_type': 1,
'delay': self.delay_})
# get STDP synapse
syn_ps = nest.GetConnections(source=pre_parrot_ps,
synapse_model="stdp_synapse_rec")
print("[py] Total simulation time: " + str(self.sim_time_) + " ms")
n_steps = int(np.ceil(self.sim_time_ / self.delay_))
trace_nest = []
trace_nest_t = []
t = nest.biological_time
trace_nest_t.append(t)
post_tr = nest.GetStatus(post_parrot_ps)[0]['post_trace']
trace_nest.append(post_tr)
for step in range(n_steps):
print("\n[py] simulating for " + str(self.delay_) + " ms")
nest.Simulate(self.delay_)
t = nest.biological_time
nearby_pre_spike = np.any(
np.abs(t - np.array(self.pre_spike_times_) - self.delay_) < self.resolution_ / 2.)
if show_all_nest_trace_samples or nearby_pre_spike:
trace_nest_t.append(t)
post_tr = nest.GetStatus(post_parrot_ps)[0]['post_trace']
trace_nest.append(post_tr)
print("[py] Received NEST trace: " +
str(post_tr) + " at time t = " + str(t))
return trace_nest_t, trace_nest
