bluepyefe.recording

Classes

Recording(config_data, reader_data, ...)

Contains the data related to an electrophysiological recording.
class Recording(config_data, reader_data, protocol_name)[source]

Bases: ABC

Contains the data related to an electrophysiological recording.

Constructor

Parameters:

  • config_data (dict) – metadata for the recording considered informed by the user.

  • reader_data (dict) – metadata for the recording considered returned by the recording reader.

  • protocol_name (str) – name of the protocol of the present recording.

call_efel(efeatures, efel_settings=None)[source]

Calls efel to compute the wanted efeatures

compute_efeatures(efeatures, efeature_names=None, efel_settings=None)[source]

Compute a set of efeatures for the present recording.

Parameters:

  • efeatures (list of str) – name of the efeatures to extract from the recordings.

  • efeature_names (list of str) – Optional. Given name for the features. Can and should be used if the same feature is to be extracted several time on different sections of the same recording.

  • efel_settings (dict) – eFEL settings in the form {setting_name: setting_value}.

compute_relative_amp(amp_threshold)[source]

Divide all the amplitude in the stimuli by the spiking amplitude

compute_spikecount(efel_settings=None)[source]

Compute the number of spikes in the trace

abstractmethod generate()[source]

Generate the current array from the parameters of the ecode

get_params()[source]

Returns the eCode parameters

in_target(target, tolerance, absolute_amplitude=False)[source]

Returns a boolean. True if the amplitude of the eCode is close to target and False otherwise.

index_to_ms(name_timing, time_series)[source]

Used by some of the children classes to translate a timing attribute from index to ms.

abstractmethod interpret()[source]

Analyse a current array and extract from it the parameters needed to reconstruct the array

property name

Proxy that can be used to name the recording.

plot(axis_current=None, axis_voltage=None, display_xlabel=True, display_ylabel=True)[source]

Plot the recording

set_amplitudes_ecode(amp_name, config_data, reader_data, value)[source]

Check in the user-provided data or reader-provided data if a given current amplitude is provided. If it isn’t use the value computed from the current series

set_autothreshold(offset_voltage=20.0) → None[source]

Computes the threshold based on the input voltage sets it as an attribute.

set_timing_ecode(name_timings, config_data)[source]

Used by some of the children classes to check that the timing of the ecode is provided by the user and assign it to the correct attribute.

standardize_trace(config_data, reader_data)[source]

Standardize the units of the current and voltage times series. If some metadata are present both in the file itself and the file_metadata dictionary, the latter is used.

property time

Alias of the time attribute