bluepyefe.protocol

Protocol class

Classes

Protocol(name, amplitude, tolerance[, ...])

Protocol informs about the current stimulus that was used to obtain efeatures at a given amplitude for a given protocol name.
class Protocol(name, amplitude, tolerance, feature_targets=None, global_rheobase=None, mode='mean')[source]

Bases: object

Protocol informs about the current stimulus that was used to obtain efeatures at a given amplitude for a given protocol name. This class is mainly used to produce a description of the experimental protocol that can be used in BluePyOpt

Constructor

Parameters:

  • name (str) – name of the protocol (ex: ‘APWaveform’)

  • amplitude (float) – amplitude of the current stimuli for the present protocol (expressed as a percentage of the threshold amplitude or in absolute current depending on the setting absolute_amplitude)

  • tolerance (float) – tolerance around the target amplitude in which an experimental recording will be seen as a hit during efeatures extraction (expressed as a percentage of the threshold amplitude or in absolute current depending on the setting absolute_amplitude)

  • feature_targets (list) – list of EFeatureTarget associated to the protocol

  • global_rheobase (float) – average rheobase across all cells

  • mode (str) – if the protocol matches several recordings, the mode set the logic of how the output will be generating. Must be ‘mean’, ‘median’ or ‘lnmc’

append(recording)[source]

Append a Recording to the present protocol

as_dict()[source]

Returns a dictionary that defines the present protocol. This definition is computed differently depending on the mode of the protocol

property ecode

Create a temporary eCode that matches all the recordings for the present protocol. The eCode’s parameters are computed differently depending on the mode of the protocol

property n_match

Number of recordings whose amplitude matched the present protocol

reduce_ecode(ecode, operator)[source]

Creates an eCode defined from the parameters of all the recordings matching the present protocol

property stimulus_name

Name of the stimulus associated to the protocol