bluepyemodel.efeatures_extraction.efeatures_extraction

Efeatures extraction functions

Functions

attach_efeatures_pdf(emodel, efeatures)	If the efeatures are plotted, attach the path to the plot to the related efeature
define_extraction_reader_function(access_point)	Define the function used to read the ephys data during efeature extraction
extract_save_features_protocols(access_point)	Extract the efeatures and saves the results as a configuration for the fitness calculator.
get_extraction_output_directory(emodel)	Get output directory for extraction figures.
interpolate_RMP(fitness_calculator_configuration)	If we do not have recordings with no holding, we need to estimate the RMP as: RMP = V_hold - R_in*I_Hold
read_extraction_output(filepath)	Returns output of extraction if present.
read_extraction_output_cells(emodel)	Returns cells output of extraction if present.
read_extraction_output_protocols(emodel)	Returns protocols output of extraction if present.
threshold_efeatures_std(...)	Set std as the mean value if std is higher than mean value.
update_minimum_protocols_delay(access_point, ...)	Threshold the minimum delay to the value of minimum_protocol_delay provided in the settings.

attach_efeatures_pdf(emodel, efeatures)

If the efeatures are plotted, attach the path to the plot to the related efeature

define_extraction_reader_function(access_point)

Define the function used to read the ephys data during efeature extraction

extract_save_features_protocols(access_point, mapper=<class 'map'>)

Extract the efeatures and saves the results as a configuration for the fitness calculator.

Parameters:

• access_point (DataAccessPoint) – access point to the model’s data

• mapper (map) – mapper for parallel computations.

get_extraction_output_directory(emodel)

Get output directory for extraction figures.

Parameters:

emodel (str) – emodel name as in emodel_metadata.emodel

interpolate_RMP(fitness_calculator_configuration)

If we do not have recordings with no holding, we need to estimate the RMP as: RMP = V_hold - R_in*I_Hold

read_extraction_output(filepath)

Returns output of extraction if present. Can return cells or protocols file.

Parameters:

filename (str or Path) – path to extraction pickle file

read_extraction_output_cells(emodel)

Returns cells output of extraction if present.

Parameters:

emodel (str) – emodel name as in emodel_metadata.emodel

read_extraction_output_protocols(emodel)

Returns protocols output of extraction if present.

Parameters:

emodel (str) – emodel name as in emodel_metadata.emodel

threshold_efeatures_std(fitness_calculator_configuration, default_std_value)

Set std as the mean value if std is higher than mean value.

update_minimum_protocols_delay(access_point, config)

Threshold the minimum delay to the value of minimum_protocol_delay provided in the settings.