brian2modelfitting.simulator module

class brian2modelfitting.simulator.CPPStandaloneSimulator

Bases: brian2modelfitting.simulator.Simulator

Simulation class created for use with CPPStandaloneDevice

initialize(network, var_init, name='fit')

Prepares the simulation for running

Parameters:

• network (Network) – Network consisting of a NeuronGroup named neurons and either a monitor named spikemonitor or a monitor named ``statemonitor``(or both).
• var_init (dict) – dictionary to initialize the variable states
• name (str, optional) – name of the network

neurons

run(duration, params, params_names, iteration, name='fit')

Simulation has to be run in two stages in order to initialize the code generation

spikemonitor

statemonitor

class brian2modelfitting.simulator.RuntimeSimulator

Bases: brian2modelfitting.simulator.Simulator

Simulation class created for use with RuntimeDevice

initialize(network, var_init, name='fit')

Prepares the simulation for running

Parameters:

• network (Network) – Network consisting of a NeuronGroup named neurons and either a monitor named spikemonitor or a monitor named ``statemonitor``(or both).
• var_init (dict) – dictionary to initialize the variable states
• name (str, optional) – name of the network

neurons

run(duration, params, params_names, iteration, name='fit')

Restores the network, sets neurons to required parameters and runs the simulation

Parameters:

• duration (Quantity) – Simulation duration
• params (dict) – parameters to be set
• params_names (list[str]) – names of parameters to set the dictionary

spikemonitor

statemonitor

class brian2modelfitting.simulator.Simulator

Bases: object

Simulation class created to perform a simulation for fitting traces or spikes.

initialize(network, var_init, name='fit')

Prepares the simulation for running

Parameters:

• network (Network) – Network consisting of a NeuronGroup named neurons and either a monitor named spikemonitor or a monitor named ``statemonitor``(or both).
• var_init (dict) – dictionary to initialize the variable states
• name (str, optional) – name of the network

neurons

run(duration, params, params_names, iteration, name)

Restores the network, sets neurons to required parameters and runs the simulation

Parameters:

• duration (Quantity) – Simulation duration
• params (dict) – parameters to be set
• params_names (list[str]) – names of parameters to set the dictionary

spikemonitor

statemonitor

brian2modelfitting.simulator.initialize_neurons(params_names, neurons, params)

initialize each parameter for NeuronGroup returns dictionary of Dummy devices

brian2modelfitting.simulator.initialize_parameter(variableview, value)

initialize parameter variable in static file, returns Dummy device

brian2modelfitting.simulator.run_again()

re-run the NeuronGroup on cpp file

brian2modelfitting.simulator.set_parameter_value(identifier, value)

change parameter value in cpp file

brian2modelfitting.simulator.set_states(init_dict, values)

set parameters values in the file for the NeuronGroup