bluepyemodel.access_point.access_point¶
DataAccessPoint class.
Classes
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Abstract data access point class. |
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the possible states of an optimisation process. |
- class DataAccessPoint(emodel=None, etype=None, ttype=None, mtype=None, species=None, brain_region=None, iteration_tag=None, synapse_class=None)¶
Bases:
objectAbstract data access point class. This class is not meant to be used directly. Instead, it is used through the classes LocalAccessPoint and NexusAccessPoint.
Init
- download_mechanisms()¶
Download the mod files when not already downloaded
- get_available_efeatures(cleaned=True)¶
Returns a curated list of available eFEL features
- get_available_mechanisms()¶
Get all the available mechanisms
- get_available_traces(filter_species=False, filter_brain_region=False)¶
Get the list of available Traces for the current species from Nexus
- get_distributions()¶
Get the list of available distributions
- get_emodel()¶
Get dict with parameter of single emodel (including seed if any)
- get_emodel_names()¶
Get the list of all the names of emodels
- Returns:
keys are emodel names with seed, values are names without seed.
- Return type:
- get_emodels(emodels)¶
Get the list of emodels dictionaries.
- get_fitness_calculator_configuration(record_ions_and_currents=False)¶
Get the configuration of the fitness calculator (efeatures and protocols)
- get_ion_currents_concentrations()¶
Get all ion currents and ion concentrations.
- Returns:
(list of str): current (ion and non-specific) names for all available mechanisms (list of str): ionic concentration names for all available mechanisms
- Return type:
tuple containing
- get_mechanisms_directory()¶
Return the path to the directory containing the mechanisms for the current emodel
- get_model_configuration(skip_get_available_morph=True)¶
Get the configuration of the model, including parameters, mechanisms and distributions
- get_targets_configuration()¶
Get the configuration of the targets (targets and ephys files used)
- optimisation_state(seed=None, continue_opt=False)¶
Return the state of the optimisation.
- Parameters:
- Raises:
ValueError if optimiser in pipeline settings in neither – “SO-CMA”, “MO-CMA” or “IBEA”
- Returns:
True if completed, False if in progress or empty
- Return type:
- set_emodel(emodel)¶
Setter for the name of the emodel.
- store_distribution(distribution)¶
Store a channel distribution as a resource of type EModelChannelDistribution
- store_efeatures(efeatures, current)¶
Save the efeatures and currents obtained from BluePyEfe
- store_emodel(scores, params, optimiser_name, seed, validated=None, scores_validation=None)¶
Save a model obtained from BluePyOpt
- store_emodels_hoc(only_validated=False, only_best=True, seeds=None, map_function=<class 'map'>, new_emodel_name=None, description=None)¶
Store hoc file produced by export_hoc
- store_emodels_sonata(only_validated=False, only_best=True, seeds=None, map_function=<class 'map'>, new_emodel_name=None, description=None)¶
Store hoc file produced by export_sonata
- store_fitness_calculator_configuration(configuration)¶
Store a fitness calculator configuration
- store_hocs(only_validated=False, only_best=True, seeds=None, map_function=<class 'map'>, new_emodel_name=None, description=None, output_base_dir='export_emodels_hoc')¶
Store the hoc files
- store_model_configuration()¶
Store the configuration of a model, including parameters, mechanisms and distributions
- store_protocols(stimuli)¶
Save the protocols obtained from BluePyEfe
- store_targets_configuration()¶
Store the configuration of the targets (targets and ephys files used)
- update_emodel_images(seed, keep_old_images=False)¶
Update an EModel resource with local emodel plots if access_point is nexus.