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
from tvb_nest.interfaces.builders.red_ww_exc_io_inh_i import RedWWexcIOinhIBuilder
from tvb_nest.simulator_nest.models_builders.red_ww_exc_io_inh_i import RedWWExcIOInhIBuilder
from tvb_nest.simulator_tvb.model_reduced_wong_wang_exc_io_inh_i import ReducedWongWangExcIOInhI
from tvb_nest.plot.plotter import Plotter
from tvb_scripts.time_series.model import TimeSeriesRegion
from tvb.datatypes.connectivity import Connectivity
from tvb.simulator.monitors import Raw # , Bold # , EEG
if __name__ == "__main__":
config = CONFIGURED
plotter = Plotter(config)
connectivity = Connectivity.from_file(config.DEFAULT_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.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]
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