bluepyemodel.evaluation.evaluation

Emodels evaluation functions

Functions

check_local_responses_presence(emodels, ...)

Returns True if there is a local response file for each emodel.

compute_responses(access_point, ...[, ...])

Compute the responses of the emodel to the optimisation and validation protocols.

fill_initial_parameters(evaluator, ...)

Freezes the parameters of the evaluator that are present in the informed parameter set.

get_evaluator_from_access_point(access_point)

Create an evaluator for the emodel.

get_responses(to_run)

Compute the voltage responses of a set of parameters.

load_responses_from_local_files(emodels, ...)

Returns responses from locally stored files.

locally_store_responses(emodel)

Locally store the responses.
check_local_responses_presence(emodels, cell_eval)

Returns True if there is a local response file for each emodel.

Parameters:

  • emodels (list of EModel) – the emodel that need a response to be checked.

  • cell_eval (CellEvaluator) – evaluator for the cell model/protocols/e-feature set.

compute_responses(access_point, cell_evaluator, map_function, seeds=None, preselect_for_validation=False, store_responses=False, load_from_local=False, recompute_threshold_protocols=False)

Compute the responses of the emodel to the optimisation and validation protocols.

Parameters:

  • access_point (DataAccessPoint) – API used to access the data.

  • emodel (str) – name of the emodel. Has to match the name of the emodel under which the configuration data are stored.

  • cell_evaluator (CellEvaluator) – evaluator for the cell model/protocols/e-feature set.

  • map_function (map) – used to parallelize the evaluation of the individual in the population.

  • seeds (list) – if not None, filter emodels to keep only the ones with these seeds.

  • preselect_for_validation (bool) – if True, only select models that have not been through validation yet.

  • store_responses (bool) – whether to locally store the responses.

  • load_from_local (bool) – True to load responses from locally saved recordings.

  • recompute_threshold_protocols (bool) – True to re-compute rmp, rin, holding current and threshold current even when threshold output is available.

Returns:

list of emodels.

Return type:

emodels (list)

fill_initial_parameters(evaluator, initial_parameters)

Freezes the parameters of the evaluator that are present in the informed parameter set.

get_evaluator_from_access_point(access_point, stochasticity=None, include_validation_protocols=False, timeout=None, use_fixed_dt_recordings=False, record_ions_and_currents=False)

Create an evaluator for the emodel.

Parameters:

  • access_point (DataAccessPoint) – API used to access the database

  • stochasticity (bool) – should channels behave stochastically if they can.

  • include_validation_protocols (bool) – should the validation protocols and validation efeatures be added to the evaluator.

  • timeout (float) – duration (in second) after which the evaluation of a protocol will be interrupted.

  • use_fixed_dt_recordings (bool) – used for legacy currentscape to record at a fixed dt of 0.1 ms.

  • record_ions_and_currents (bool) – whether to add the ion and non-specific currents and the ionic concentration to the recordings.

Returns:

bluepyopt.ephys.evaluators.CellEvaluator

get_responses(to_run)

Compute the voltage responses of a set of parameters.

Parameters:

to_run (dict) – of the form to_run = {“evaluator”: CellEvaluator, “parameters”: Dict, “threshold_data”: Dict}

load_responses_from_local_files(emodels, cell_eval)

Returns responses from locally stored files.

Parameters:

  • emodels (list of EModel) – the emodel that need a response to be checked.

  • cell_eval (CellEvaluator) – evaluator for the cell model/protocols/e-feature set.

locally_store_responses(emodel)

Locally store the responses.

Parameters:

emodel (EModel) – the emodel which responses are to be stored