biophysics_fitting ❭ simulator ❭ Simulator_Setup

Simulator_Setup¶

class biophysics_fitting.simulator.Simulator_Setup¶

Class for setting up cells with biophysical details.

This class is an inherent attribute of the Simulator class, and should only be accessed as such. This class concerns with setting up a cell with biophysical details.

Usually, a simulation contains fixed parameters, specific to the cell (e.g. the filename of the morphology) and/or stimulus protocol (e.g. recording sites). Such fixed parameters can be defined by adding set_fixed_params() to param_modify_funs. A typical usecase is to use the fixed parameters to specify to soma distance for a voltage trace of the apical dendrite. Make sure that the Simulator stim_run_fun reads the parameter recSite and sets up the stimulus accordingly (see Simulator).

Example:

>>> def param_modify_function(params):
>>>    # alter params
>>>    return params

>>> def cell_params_generator(params, template):
>>>    cell_params = template.copy()
>>>    # Fill in template with params
>>>    return cell_params

>>> def cell_param_modify_function(cell_params):
>>>     # alter cell_params
>>>     return cell_params

>>> def cell_generator(cell_params):
>>>     return single_cell_parser.create_cell(cell_params)

>>> def cell_modify_functions(cell):
>>>     # alter cell
>>>     return cell

>>> s = Simulator() # instantiate simulator object
>>> fixed_params = {'stim_1.measure_fun.recSite': 835, 'stim_1.stim_setup.dist': 835}
>>> s.setup.params_modify_funs.append([
    'fixed_params',
    partial(set_fixed_params, fixed_params=fixed_params)
    ])
>>> s.setup.cell_param_generator =  cell_params_generator
>>> s.setup.cell_generator = cell_generator
>>> s.setup.params_modify_funs.append(['modify_param_1', param_modify_fun])
>>> s.setup.cell_param_modify_funs.append(['modify_cell_param_1', cell_param_modify_fun])
>>> s.setup.cell_modify_funs.append(['modify_cell_1', cell_modify_fun])

Notable methods:

>>> s.setup.get(params)
cell, params

Each function that receives the biophysical parameter vector (i.e. cell_param_modify_funs and cell_modify_funs) only sees a subset of the parameter vector that is provided by the user. This subset is determined by the name by which the function is registered.

Example:

>>> params = {
>>>     'apical_scaling.scale': 2,
>>>     'ephys.soma.gKv': 0.001,
>>>     'ephys.soma.gNav': 0.01
>>>    }

>>> def scale_apical(params, **kwargs):
>>>     params['scale'] = kwargs['scale']

>>> def ephys(cell, **kwargs):
>>>     cell.soma.gKv = kwargs['soma.gKv']
>>>     cell.soma.gNav = kwargs['soma.Nav']

>>> s.setup.params_modify_funs.append([
    'apical_scaling',  # name must equal the prefix of the parameter, i.e. 'apical_scaling'
    partial(scale_apical, 'scale' = 2)])
>>> s.setup.cell_modify_funs.append([
    'ephys',  # name must equal the prefix of the parameter, i.e. 'ephys'
    partial(ephys, 'soma.gKv'=1, 'soma.gNav'=2)])

Attributes:¶

cell_param_generator¶

A function that generates a ParameterSet cell parameter object.

Type:¶: callable

cell_param_modify_funs¶

list of functions that modify the cell parameters.

Type:¶: list

cell_generator¶

A function that generates a Cell object.

Type:¶: callable

cell_modify_funs¶

List of functions that modify the cell object.

Type:¶: list

stim_setup_funs¶

List of functions that set up the stimulus.

Type:¶: list

stim_run_funs¶

List of functions that each run a simulation.

Type:¶: list

stim_response_measure_funs¶

List of functions that extract voltage traces from the cell.

Type:¶: list

params_modify_funs¶

List of functions that modify the biophysical parameter vector.

Type:¶: list

check_funs¶

List of functions that check the setup. Useful for debugging.

Type:¶: list

Methods:¶

`check`()	Check if the setup is correct.
`_check_not_none`(var, varname, procedure_description)	Convenience method to check if the output of some method is not None.
`_check_first_element_of_name_is_the_same`(list1, list2)	Check if the first element of the names of two lists are the same.
`get_stims`()	Get the names of the stimuli.
`get_stim_setup_fun_by_stim`(stim)	Get the stimulus setup function by stimulus name.
`get_stim_run_fun_by_stim`(stim)	Get the stimulus run function by stimulus name.
`get_stim_response_measure_fun`(stim)	Get the stimulus response measure function by stimulus name.
`get_params`(params)	Get the modified biophysical parameters.
`get_cell_params`(params)	Get the cell parameters as an `ParameterSet` from the parameter vector.
`get_cell_params_with_default_sim_prams`(params, recordingSites, tStart, tStop, dt, Vinit, T)	Get a neuron parameter object.
`get`(params)	Get the cell with set up biophysics and params.