def test_user_tags(self):
pre = '0;0'
post = 'mon;mon**2-1'
raw = Raw(pre_expr=pre, post_expr=post)
tags = raw._transform_user_tags()
self.assertIn('user_tag_1', tags)
self.assertIn('user_tag_2', tags)
self.assertEqual(tags['user_tag_1'], pre)
self.assertEqual(tags['user_tag_2'], post)
def build_simulator(self, n=4):
self.conn = numpy.zeros((n, n)) # , numpy.int32)
for i in range(self.conn.shape[0] - 1):
self.conn[i, i + 1] = 1
self.dist = numpy.r_[:n * n].reshape((n, n))
self.dist = numpy.array(self.dist, dtype=float)
self.sim = Simulator(
conduction_speed=1.0,
coupling=IdCoupling(),
surface=None,
stimulus=None,
integrator=Identity(dt=1.0),
initial_conditions=numpy.ones((n * n, 1, n, 1)),
simulation_length=10.0,
connectivity=Connectivity(region_labels=numpy.array(['']),
weights=self.conn,
tract_lengths=self.dist,
speed=numpy.array([1.0]),
centres=numpy.array([0.0])),
model=Sum(),
monitors=(Raw(), ),
)
self.sim.configure()
def _create_sim(self, integrator=None, inhom_mmpr=False, delays=False,
run_sim=True):
mpr = MontbrioPazoRoxin()
conn = Connectivity.from_file()
if inhom_mmpr:
dispersion = 1 + np.random.randn(conn.weights.shape[0])*0.1
mpr = MontbrioPazoRoxin(eta=mpr.eta*dispersion)
conn.speed = np.r_[3.0 if delays else np.inf]
if integrator is None:
dt = 0.01
integrator = EulerDeterministic(dt=dt)
else:
dt = integrator.dt
sim = Simulator(connectivity=conn, model=mpr, integrator=integrator,
monitors=[Raw()],
simulation_length=0.1) # 10 steps
sim.configure()
if not delays:
self.assertTrue((conn.idelays == 0).all())
buf = sim.history.buffer[...,0]
# kernel has history in reverse order except 1st element 🤕
rbuf = np.concatenate((buf[0:1], buf[1:][::-1]), axis=0)
state = np.transpose(rbuf, (1, 0, 2)).astype('f')
self.assertEqual(state.shape[0], 2)
self.assertEqual(state.shape[2], conn.weights.shape[0])
if isinstance(sim.integrator, IntegratorStochastic):
sim.integrator.noise.reset_random_stream()
if run_sim:
(t,y), = sim.run()
return sim, state, t, y
else:
return sim
def test_expr_pre(self):
sim, ys = self._run_sim(5, models.Generic2dOscillator(),
Raw(pre_expr='V;W;V**2;W-V', post_expr=''))
self.assertTrue(hasattr(sim.monitors[0], '_transforms'))
v, w, v2, wmv = ys.transpose((1, 0, 2, 3))
self.assertTrue(numpy.allclose(v**2, v2))
self.assertTrue(numpy.allclose(w - v, wmv))
def test_expr_post(self):
sim, ys = self._run_sim(
5, models.Generic2dOscillator(),
Raw(pre_expr='V;W;V;W', post_expr=';;mon**2; exp(mon)'))
self.assertTrue(hasattr(sim.monitors[0], '_transforms'))
v, w, v2, ew = ys.transpose((1, 0, 2, 3))
self.assertTrue(numpy.allclose(v**2, v2))
self.assertTrue(numpy.allclose(numpy.exp(w), ew))
def test(dt=0.1, noise_strength=0.001, config=CONFIGURED):
# Select the regions for the fine scale modeling with NEST spiking networks
nest_nodes_ids = [] # the indices of fine scale regions modeled with NEST
# In this example, we model parahippocampal cortices (left and right) with NEST
connectivity = Connectivity.from_file(CONFIGURED.DEFAULT_CONNECTIVITY_ZIP)
for id in range(connectivity.region_labels.shape[0]):
if connectivity.region_labels[id].find("hippo") > 0:
nest_nodes_ids.append(id)
connectivity.configure()
# Create a TVB simulator and set all desired inputs
# (connectivity, model, surface, stimuli etc)
# We choose all defaults in this example
simulator = Simulator()
simulator.integrator.dt = dt
simulator.integrator.noise.nsig = np.array([noise_strength])
simulator.model = ReducedWongWangExcIOInhI()
simulator.connectivity = connectivity
mon_raw = Raw(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, )
# Build a NEST network model with the corresponding builder
# Using all default parameters for this example
nest_model_builder = RedWWExcIOInhIMultisynapseBuilder(simulator,
nest_nodes_ids,
config=config)
nest_model_builder.configure()
for prop in [
"min_delay", "tvb_dt", "tvb_model", "tvb_connectivity",
"tvb_weights", "tvb_delays", "number_of_nodes",
"number_of_spiking_nodes", "spiking_nodes_labels",
"number_of_populations", "populations_models", "populations_nodes",
"populations_scales", "populations_sizes", "populations_params",
"populations_connections_labels", "populations_connections_models",
"populations_connections_nodes", "populations_connections_weights",
"populations_connections_delays",
"populations_connections_receptor_types",
"populations_connections_conn_spec", "nodes_connections_labels",
"nodes_connections_models", "nodes_connections_source_nodes",
"nodes_connections_target_nodes", "nodes_connections_weights",
"nodes_connections_delays", "nodes_connections_receptor_types",
"nodes_connections_conn_spec"
]:
print("%s:\n%s\n\n" % (prop, str(getattr(nest_model_builder, prop))))
def _prep_sim(self, coupling) -> Simulator:
"Prepare simulator for testing a coupling function."
con = Connectivity.from_file()
con.weights[:] = 1.0
# con = Connectivity(
# region_labels=np.array(['']),
# weights=con.weights[:5][:,:5],
# tract_lengths=con.tract_lengths[:5][:,:5],
# speed=np.array([10.0]),
# centres=np.array([0.0]))
sim = Simulator(connectivity=con,
model=LinearModel(gamma=np.r_[0.0]),
coupling=coupling,
integrator=Identity(dt=1.0),
monitors=[Raw()],
simulation_length=0.5)
sim.configure()
return sim
def test(dt=0.1, noise_strength=0.001, config=CONFIGURED):
# Select the regions for the fine scale modeling with ANNarchy spiking networks
anarchy_nodes_ids = list(
range(10)) # the indices of fine scale regions modeled with ANNarchy
# In this example, we model parahippocampal cortices (left and right) with ANNarchy
connectivity = Connectivity.from_file(CONFIGURED.DEFAULT_CONNECTIVITY_ZIP)
connectivity.configure()
# Create a TVB simulator and set all desired inputs
# (connectivity, model, surface, stimuli etc)
# We choose all defaults in this example
simulator = Simulator()
simulator.integrator.dt = dt
# simulator.integrator.noise.nsig = np.array([noise_strength])
simulator.model = ReducedWongWangExcIOInhI()
simulator.connectivity = connectivity
mon_raw = Raw(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, )
# Build a ANNarchy network model with the corresponding builder
# Using all default parameters for this example
anarchy_model_builder = BasalGangliaIzhikevichBuilder(simulator,
anarchy_nodes_ids,
config=config)
anarchy_model_builder.configure()
for prop in [
"min_delay", "tvb_dt", "tvb_model", "tvb_connectivity",
"tvb_weights", "tvb_delays", "number_of_nodes",
"number_of_spiking_nodes", "spiking_nodes_labels",
"number_of_populations", "populations_models", "populations_nodes",
"populations_scales", "populations_sizes", "populations_params",
"populations_connections_labels", "populations_connections_models",
"populations_connections_nodes", "populations_connections_weights",
"populations_connections_delays",
"populations_connections_receptor_types",
"populations_connections_conn_spec", "nodes_connections_labels",
"nodes_connections_models", "nodes_connections_source_nodes",
"nodes_connections_target_nodes", "nodes_connections_weights",
"nodes_connections_delays", "nodes_connections_receptor_types",
"nodes_connections_conn_spec"
]:
print("%s:\n%s\n\n" %
(prop, str(getattr(anarchy_model_builder, prop))))
def main_example(tvb_sim_model,
connectivity_zip=CONFIGURED.DEFAULT_CONNECTIVITY_ZIP,
dt=0.1,
noise_strength=0.001,
simulation_length=100.0,
config=CONFIGURED):
plotter = Plotter(config)
# --------------------------------------1. Load TVB connectivity----------------------------------------------------
connectivity = Connectivity.from_file(connectivity_zip)
connectivity.configure()
plotter.plot_tvb_connectivity(connectivity)
# ----------------------2. Define a TVB simulator (model, integrator, monitors...)----------------------------------
# Create a TVB simulator and set all desired inputs
# (connectivity, model, surface, stimuli etc)
# We choose all defaults in this example
simulator = Simulator()
simulator.integrator = HeunStochastic(dt=dt)
simulator.integrator.noise.nsig = np.array(ensure_list(noise_strength))
simulator.model = tvb_sim_model
simulator.connectivity = connectivity
mon_raw = Raw(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, )
# -----------------------------------3. Simulate and gather results-------------------------------------------------
# Configure the simulator with the TVB-NEST interface...
# simulator.configure(tvb_nest_interface=tvb_nest_model)
simulator.configure()
# ...and simulate!
t_start = time.time()
results = simulator.run(simulation_length=simulation_length)
print("\nSimulated in %f secs!" % (time.time() - t_start))
# -------------------------------------------6. Plot results--------------------------------------------------------
plot_results(results, simulator, None, "State Variables",
simulator.model.variables_of_interest, plotter)
return connectivity, results
def create_time_series_region_object():
config = CONFIGURED
connectivity = Connectivity.from_file(config.DEFAULT_CONNECTIVITY_ZIP)
connectivity.configure()
simulator = Simulator()
simulator.model = ReducedWongWangExcIOInhI()
def boundary_fun(state):
state[state < 0] = 0.0
state[state > 1] = 1.0
return state
simulator.boundary_fun = boundary_fun
simulator.connectivity = connectivity
simulator.integrator.dt = \
float(int(numpy.round(simulator.integrator.dt /
config.nest.NEST_MIN_DT))) * config.nest.NEST_MIN_DT
mon_raw = Raw(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, )
number_of_regions = simulator.connectivity.region_labels.shape[0]
nest_nodes_ids = []
for id in range(number_of_regions):
if simulator.connectivity.region_labels[id].find("hippo") > 0:
nest_nodes_ids.append(id)
nest_model_builder = \
RedWWExcIOInhIBuilder(simulator, nest_nodes_ids, config=config)
nest_network = nest_model_builder.build_nest_network()
tvb_nest_builder = \
RedWWexcIOinhIBuilder(simulator, nest_network, nest_nodes_ids, config=config)
tvb_nest_builder.tvb_to_nest_interfaces = \
[{"model": "current", "parameter": "I_e", "sign": 1,
"connections": {"S_e": ["E", "I"]}}]
connections = OrderedDict()
connections["R_e"] = "E"
connections["R_i"] = "I"
tvb_nest_builder.nest_to_tvb_interfaces = \
[{"model": "spike_detector", "params": {}, "connections": connections}]
tvb_nest_model = tvb_nest_builder.build_interface()
simulator.configure(tvb_nest_interface=tvb_nest_model)
results = simulator.run(simulation_length=100.0)
time = results[0][0]
source = results[0][1]
source_ts = TimeSeriesRegion(
data=source,
time=time,
connectivity=simulator.connectivity,
labels_ordering=[
"Time", "Synaptic Gating Variable", "Region", "Neurons"
],
labels_dimensions={
"Synaptic Gating Variable": ["S_e", "S_i"],
"Region": simulator.connectivity.region_labels.tolist()
},
sample_period=simulator.integrator.dt)
return source_ts
def _sample_with_tvb_monitor(self, step, state):
return Raw.sample(self, step, state)
def prepare_launch_default_simulation():
config = Config(output_base="outputs/")
config.figures.SAVE_FLAG = False
config.figures.SHOW_FLAG = False
config.figures.MATPLOTLIB_BACKEND = "Agg"
plotter = Plotter(config)
connectivity = Connectivity.from_file(
os.path.join(Config.DEFAULT_SUBJECT_PATH,
Config.DEFAULT_CONNECTIVITY_ZIP))
connectivity.configure()
# Create a TVB simulator and set all desired inputs
# (connectivity, model, surface, stimuli etc)
# We choose all defaults in this example
simulator = Simulator()
simulator.model = ReducedWongWangExcIOInhI()
simulator.connectivity = connectivity
simulator.integrator.dt = float(
int(np.round(simulator.integrator.dt /
config.nest.NEST_MIN_DT))) * config.nest.NEST_MIN_DT
# Some extra monitors for neuroimaging measures:
mon_raw = Raw(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, ) # mon_bold, mon_eeg
# Select the regions for the fine scale modeling with NEST spiking networks
number_of_regions = simulator.connectivity.region_labels.shape[0]
nest_nodes_ids = [] # the indices of fine scale regions modeled with NEST
# In this example, we model parahippocampal cortices (left and right) with NEST
for rid in range(number_of_regions):
if simulator.connectivity.region_labels[rid].find("hippo") > 0:
nest_nodes_ids.append(rid)
# Build a NEST network model with the corresponding builder
# Using all default parameters for this example
nest_model_builder = RedWWExcIOInhIBuilder(simulator, nest_nodes_ids)
nest_model_builder.populations_names = ["E", "I"]
nest_model_builder.populations_scales = [1.0, 0.7]
nest_model_builder.default_synapse["params"]["rule"] = "fixed_indegree"
# Connection weights
# Choosing the values resulting from J_N = 150 pA and J_i = 1000 pA
w_ee = 150.0
w_ei = -1000.0
w_ie = 150.0
w_ii = -1000.0
# Within node connections' weights
# TODO: take care of J_N units conversion from TVB to NEST!
nest_model_builder.population_connectivity_synapses_weights = np.array([
[w_ee, w_ei], # exc_i -> exc_i, inh_i -> exc_i
[w_ie, w_ii]
]) # exc_i -> inh_i, inh_i -> inh_i
nest_model_builder.population_connectivity_synapses_delays = np.array(
nest_model_builder.tvb_dt / 4)
# Between node connections
# Given that w_ee == w_ie = J_N, we need only one connection type
nest_model_builder.node_connections = [{
"src_population":
"E",
"trg_population": ["E", "I"],
"model":
nest_model_builder.default_synapse["model"],
"params":
nest_model_builder.default_synapse["params"],
"weight":
w_ee, # weight scaling the TVB connectivity weight
"delay":
0.0
}] # additional delay to the one of TVB connectivity
connections = OrderedDict()
connections["E"] = "E"
connections["I"] = "I"
nest_model_builder.output_devices = [{
"model":
"spike_detector",
"props":
config.nest.NEST_OUTPUT_DEVICES_PARAMS_DEF["spike_detector"],
"nodes":
None,
"connections":
connections
}]
nest_network = nest_model_builder.build_nest_network()
# Build a TVB-NEST interface with all the appropriate connections between the
# TVB and NEST modelled regions
# Using all default parameters for this example
tvb_nest_builder = RedWWexcIOinhIBuilder(simulator, nest_network,
nest_nodes_ids)
# NEST -> TVB:
# For current transmission from TVB to NEST,
# either choose a NEST dc_generator device:
# tvb_nest_builder.tvb_to_nest_interfaces = [{"model": "dc_generator", "sign": 1,
# "connections": {"S_e": ["E", "I"]}}]
# or modify directly the external current stimulus parameter:
tvb_nest_builder.tvb_to_nest_interfaces = [{
"model": "current",
"parameter": "I_e",
"sign": 1,
"connections": {
"S_e": ["E", "I"]
}
}]
# NEST -> TVB:
# Use S_e and S_i instead of r_e and r_i
# for transmitting to the TVB state variables directly
connections = OrderedDict()
connections["r_e"] = "E"
connections["r_i"] = "I"
tvb_nest_builder.nest_to_tvb_interfaces = [{
"model": "spike_detector",
"params": {},
"connections": connections
}]
tvb_nest_model = tvb_nest_builder.build_interface()
# Configure the simulator with the TVB-NEST interface...
simulator.configure(tvb_nest_interface=tvb_nest_model)
# ...and simulate!
t = time.time()
results = simulator.run(simulation_length=100.0)
return connectivity.weights, connectivity.tract_lengths, results[0][1]
simulator = Simulator()
simulator.model = ReducedWongWangExcIOInhI()
def boundary_fun(state):
state[state < 0] = 0.0
state[state > 1] = 1.0
return state
# Synaptic gating state variables S_e, S_i need to be in the interval [0, 1]
simulator.boundary_fun = boundary_fun
simulator.connectivity = connectivity
# TODO: Try to make this part of the __init__ of the Simulator!
simulator.integrator.dt = \
float(int(np.round(simulator.integrator.dt / config.nest.NEST_MIN_DT))) * config.nest.NEST_MIN_DT
# Some extra monitors for neuroimaging measures:
mon_raw = Raw(period=simulator.integrator.dt)
# mon_bold = Bold(period=2000.)
# mon_eeg = EEG(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, ) # mon_bold, mon_eeg
# ------3. Build the NEST network model (fine-scale regions' nodes, stimulation devices, spike_detectors etc)--------
# Select the regions for the fine scale modeling with NEST spiking networks
number_of_regions = simulator.connectivity.region_labels.shape[0]
nest_nodes_ids = [] # the indices of fine scale regions modeled with NEST
# In this example, we model parahippocampal cortices (left and right) with NEST
for id in range(number_of_regions):
if simulator.connectivity.region_labels[id].find("hippo") > 0:
nest_nodes_ids.append(id)
# Build a NEST network model with the corresponding builder
def test_expr_tim(self):
sim, ys = self._run_sim(5, models.Epileptor(),
Raw(pre_expr='-y0+y3;y2', post_expr='mon;mon'))
self.assertTrue(hasattr(sim.monitors[0], '_transforms'))
lfp, slow = ys.transpose((1, 0, 2, 3))
def main_example(tvb_sim_model,
nest_model_builder,
tvb_nest_builder,
nest_nodes_ids,
nest_populations_order=100,
connectivity=None,
connectivity_zip=CONFIGURED.DEFAULT_CONNECTIVITY_ZIP,
simulation_length=100.0,
tvb_state_variable_type_label="Synaptic Gating Variable",
delays=True,
dt=0.1,
noise_strength=0.001,
exclusive_nodes=False,
config=CONFIGURED):
plotter = Plotter(config)
# --------------------------------------1. Load TVB connectivity----------------------------------------------------
if connectivity is None:
connectivity = Connectivity.from_file(connectivity_zip)
connectivity.configure()
plotter.plot_tvb_connectivity(connectivity)
if not delays:
connectivity.tract_lengths /= 100000.0
connectivity.configure()
plotter.base.plot_regions2regions(connectivity.delays,
connectivity.region_labels, 111,
"Delays")
plotter.base._save_figure(figure_name="Delays")
# ----------------------2. Define a TVB simulator (model, integrator, monitors...)----------------------------------
# Create a TVB simulator and set all desired inputs
# (connectivity, model, surface, stimuli etc)
# We choose all defaults in this example
simulator = Simulator()
simulator.integrator.dt = dt
simulator.integrator.noise.nsig = np.array([noise_strength])
simulator.model = tvb_sim_model
simulator.connectivity = connectivity
mon_raw = Raw(period=simulator.integrator.dt)
simulator.monitors = (mon_raw, )
# ------3. Build the NEST network model (fine-scale regions' nodes, stimulation devices, spike_detectors etc)-------
print("Building NEST network...")
tic = time.time()
# Build a NEST network model with the corresponding builder
# Using all default parameters for this example
nest_model_builder = nest_model_builder(simulator,
nest_nodes_ids,
config=config)
# Common order of neurons' number per population:
nest_model_builder.populations_order = nest_populations_order
nest_network = nest_model_builder.build_nest_network()
print("Done! in %f min" % ((time.time() - tic) / 60))
# -----------------------------------4. Build the TVB-NEST interface model -----------------------------------------
print("Building TVB-NEST interface...")
tic = time.time()
# Build a TVB-NEST interface with all the appropriate connections between the
# TVB and NEST modelled regions
# Using all default parameters for this example
tvb_nest_builder = tvb_nest_builder(simulator, nest_network,
nest_nodes_ids, exclusive_nodes)
tvb_nest_model = tvb_nest_builder.build_interface()
print("Done! in %f min" % ((time.time() - tic) / 60))
# -----------------------------------5. Simulate and gather results-------------------------------------------------
# Configure the simulator with the TVB-NEST interface...
simulator.configure(tvb_nest_interface=tvb_nest_model)
# ...and simulate!
t_start = time.time()
results = simulator.run(simulation_length=simulation_length)
# Integrate NEST one more NEST time step so that multimeters get the last time point
# unless you plan to continue simulation later
simulator.run_spiking_simulator(
simulator.tvb_nest_interface.nest_instance.GetKernelStatus(
"resolution"))
# Clean-up NEST simulation
if simulator.run_spiking_simulator == simulator.tvb_nest_interface.nest_instance.Run:
simulator.tvb_nest_interface.nest_instance.Cleanup()
print("\nSimulated in %f secs!" % (time.time() - t_start))
# -------------------------------------------6. Plot results--------------------------------------------------------
plot_results(results, simulator, tvb_nest_model,
tvb_state_variable_type_label,
simulator.model.variables_of_interest, plotter)
return connectivity, results