def main(args):
trial = args[0]
config = args[1]
input_params = config["input_parameters"]
connection_params = config["connection_parameters"]
neuron_params = config["neuron_parameters"]
simulation_time_per_pattern = (input_params["pattern_delay"] +
input_params["pattern_duration"])
config["simulation_time"] = (
simulation_time_per_pattern * input_params["num_assemblies"] * (
input_params["num_patterns_per_assembly"] +
input_params["num_assemblies"] *
input_params["num_test_patterns_per_assembly"]))
# Directory for simulation results and log files.
output_directory = os.path.join("results", "rewiring_ex6", str(input_params["num_assembly_neurons"]),
time.strftime("%y%m%d_%H%M%S"), str(trial), "data")
# Initialize the simulation environment.
core.init(directory=output_directory)
# Write config file to the output directory.
utils.write_configuration(os.path.join(output_directory, "..", "config_rewiring_ex6.yaml"), config)
# Set the random seed.
core.kernel.set_master_seed(config["master_seed"])
# Create input neurons.
inp = PoissonPatternGroup(input_params["num_inputs"], input_params["rate"], input_params["rate_bg"],
params=input_params)
# Here we randomly chose the assembly neurons.
unique_size = input_params["assembly_size"] - input_params["shared_size"]
assembly_neurons_idc = [list(range(i * unique_size, (i + 1) * unique_size))
for i in range(input_params["num_assemblies"])]
shared_neurons = range(unique_size * input_params["num_assemblies"], input_params["num_inputs"])
for i in range(input_params["num_assemblies"]):
assembly_neurons_idc[i] += list(np.random.choice(shared_neurons, input_params["shared_size"],
replace=False))
assembly_neurons_idc = np.array(assembly_neurons_idc)
np.savetxt(os.path.join(output_directory, "assembly_neurons_idc"),
np.sort(assembly_neurons_idc), fmt="%d")
# Set the indices of the assembly neurons.
inp.set_assembly_neurons_idc(assembly_neurons_idc)
# Create the neuron.
neuron = McLifGroup(1, neuron_params["num_branches"], neuron_params)
# Connect input to neuron.
conn = RewiringConnection(inp, neuron, neuron.branch.syn_current, connection_params)
# Create some monitors which will record the simulation data.
sm_inp = SpikeMonitor(inp, core.kernel.fn("input", "ras"))
sm_nrn = SpikeMonitor(neuron, core.kernel.fn("output", "ras"))
vm_nrn = VoltageMonitor(neuron.soma, 0, core.kernel.fn("soma", "mem"))
vm_br = []
for i in range(neuron_params["num_branches"]):
vm_br.append(VoltageMonitor(neuron.branch, (i, 0), core.kernel.fn("branch", "mem", i)))
WeightMatrixMonitor(conn, core.kernel.fn("weights", "dat"),
interval=config["sampling_interval_weights"])
# Now simulate the model.
simulation_time = config["simulation_time"]
for assembly in range(input_params["num_assemblies"]):
conn.learn = True
sm_inp.active = False
vm_nrn.active = False
for vm in vm_br:
vm.active = False
inp.set_assemblies(assembly)
core.kernel.run_chunk(input_params["num_patterns_per_assembly"] * simulation_time_per_pattern,
0, simulation_time)
for assembly in range(input_params["num_assemblies"]):
conn.learn = False
sm_inp.active = True
sm_nrn.active = True
vm_nrn.active = True
for vm in vm_br:
vm.active = True
inp.set_assemblies(assembly)
core.kernel.run_chunk(
input_params["num_test_patterns_per_assembly"] * simulation_time_per_pattern,
0, simulation_time)
def main(args):
trial = args[0]
config = args[1]
input_params = config["input_parameters"]
connection_params = config["connection_parameters"]
neuron_params = config["neuron_parameters"]
# Directory for simulation results and log files.
output_directory = os.path.join("results", "rewiring_ex1",
time.strftime("%y%m%d_%H%M%S"), str(trial),
"data")
# Initialize the simulation environment.
core.init(directory=output_directory)
# Write config file to the output directory.
utils.write_configuration(
os.path.join(output_directory, "..", "config_rewiring_ex1.yaml"),
config)
# Set the random seed.
core.kernel.set_master_seed(config["master_seed"])
# Create input neurons.
inp = PoissonPatternGroup(input_params["num_inputs"],
input_params["rate"],
input_params["rate_bg"],
params=input_params)
# Create the neuron.
neuron = McLifGroup(1, neuron_params["num_branches"], neuron_params)
# Connect input to neuron.
conn = RewiringConnection(inp, neuron, neuron.branch.syn_current,
connection_params)
# Create some monitors which will record the simulation data.
WeightMatrixMonitor(conn,
core.kernel.fn("weights", "dat"),
interval=config["sampling_interval_weights"])
SpikeMonitor(neuron, core.kernel.fn("output", "ras"))
sm_inp = SpikeMonitor(inp, core.kernel.fn("input", "ras"))
vm_nrn = VoltageMonitor(neuron.soma, 0, core.kernel.fn("soma", "mem"))
vm_br = []
for i in range(neuron_params["num_branches"]):
vm_br.append(
VoltageMonitor(neuron.branch, (i, 0),
core.kernel.fn("branch", "mem", i)))
# Now simulate the model.
simulation_time = config["simulation_time"]
core.kernel.run_chunk(20.0, 0, simulation_time)
sm_inp.active = False
vm_nrn.active = False
for vm in vm_br:
vm.active = False
core.kernel.run_chunk(simulation_time - 40, 0, simulation_time)
sm_inp.active = True
vm_nrn.active = True
for vm in vm_br:
vm.active = True
core.kernel.run_chunk(20.0, 0, simulation_time)
def main(args):
trial = args[0]
config = args[1]
input_params = config["input_parameters"]
connection_params = config["connection_parameters"]
neuron_params = config["neuron_parameters"]
# Directory for simulation results and log files.
output_directory = os.path.join("results", "rewiring_ex10",
"T" + str(connection_params["T"]),
time.strftime("%y%m%d_%H%M%S"), str(trial),
"data")
# Initialize the simulation environment.
core.init(directory=output_directory)
# Write config file to the output directory.
utils.write_configuration(
os.path.join(output_directory, "..", "config_rewiring_ex10.yaml"),
config)
# Set the random seed.
core.kernel.set_master_seed(config["master_seed"])
# Create input neurons.
inp = PoissonPatternGroup(input_params["num_inputs"],
input_params["rate"],
input_params["rate_bg"],
params=input_params)
# Create the neuron.
neuron = McLifGroup(1, neuron_params["num_branches"], neuron_params)
# Connect input to neuron.
conn = RewiringConnection(inp, neuron, neuron.branch.syn_current,
connection_params)
# Set the weights.
size = (neuron_params["num_branches"], input_params["num_inputs"])
theta_ini = connection_params["theta_ini"]
theta = np.full(size, theta_ini, np.float32)
assembly_neurons_idc = [
i * input_params["assembly_size"] +
np.arange(input_params["assembly_size"])
for i in range(input_params["num_assemblies"] + 1)
]
for idc, row in zip(assembly_neurons_idc, theta):
row[core.kernel.rng.choice(idc, connection_params["n_syn_start"], replace=False)] = \
core.kernel.rng.uniform(low=connection_params["w_ini_min"],
high=connection_params["w_ini_max"],
size=connection_params["n_syn_start"])
conn.set_weights(theta)
# Create some monitors which will record the simulation data.
WeightMatrixMonitor(conn,
core.kernel.fn("weights", "dat"),
interval=config["sampling_interval_weights"])
SpikeMonitor(neuron, core.kernel.fn("output", "ras"))
sm_inp = SpikeMonitor(inp, core.kernel.fn("input", "ras"))
vm_nrn = VoltageMonitor(neuron.soma, 0, core.kernel.fn("soma", "mem"))
vm_br = []
for i in range(neuron_params["num_branches"]):
vm_br.append(
VoltageMonitor(neuron.branch, (i, 0),
core.kernel.fn("branch", "mem", i)))
# Now simulate the model.
simulation_time = config["simulation_time"]
core.kernel.run_chunk(20.0, 0, simulation_time)
sm_inp.active = False
vm_nrn.active = False
for vm in vm_br:
vm.active = False
core.kernel.run_chunk(simulation_time - 40, 0, simulation_time)
sm_inp.active = True
vm_nrn.active = True
for vm in vm_br:
vm.active = True
core.kernel.run_chunk(20.0, 0, simulation_time)
