emodelrunner.factsheets.output

Functionality to save factsheets output.

Functions

get_stim_params_from_config_for_physiology_factsheet(...)	Get step amplitude, delay and duration for phisiology factsheet.
write_emodel_json(emodel, morphology_prefix, ...)	Write the e-model factsheet json file.
write_etype_factsheet(data_path, ...)	Write the e-type factsheet json file.
write_metype_json(data_path, ...)	Write the me-type factsheet json file of SSCX packages.
write_metype_json_from_config(config, ...)	Write the me-type factsheet json file from config input.

emodelrunner.factsheets.output.get_stim_params_from_config_for_physiology_factsheet(prot_path, protocol_key)[source]

Get step amplitude, delay and duration for phisiology factsheet.

Parameters:

• prot_path (str or Path) – path to the json file containing the protocols

• protocol_key (str) – name of the protocol used for physiology features extraction

Returns:

a tuple containing

• current_amplitude (int or float): the amplitude current of the step protocol (mA)

• stim_start (int or float): the start of the stimulus (ms)

• stim_duration (int or float): the duration of the stimulus (ms)

Raises:

TypeError – If a step protocol with multiple steps has been provided

emodelrunner.factsheets.output.write_emodel_json(emodel, morphology_prefix, features_dict, unoptimized_params_dict, optimized_params_dict, output_path)[source]

Write the e-model factsheet json file.

The output metype factsheet contains experimental features and channel mechanisms data.

Parameters:

• emodel (str) – name of the emodel

• morphology_prefix (str) – prefix used in the fitness key to the experimental feature

• features_dict (dict) – contains the experimental features

• unoptimized_params_dict (dict) – contains the unoptimized parameters, and also contains the decay and exponential equations

• optimized_params_dict (dict) – contains the optimized parameters, as well as the original morphology path

• output_path (str) – path to the e-model factsheet output

emodelrunner.factsheets.output.write_etype_factsheet(data_path, current_amplitude, stim_start, stim_duration, output_path)[source]

Write the e-type factsheet json file.

Parameters:

• data_path (str) – path to the trace data (usually output of emodelrunner run)

• current_amplitude (float) – current amplitude of the stimulus (nA)

• stim_start (float) – time at which the stimulus begins (ms)

• stim_duration (float) – stimulus duration (ms)

• output_path (str) – path to the etype factsheet output

emodelrunner.factsheets.output.write_metype_json(data_path, current_amplitude, stim_start, stim_duration, morphology_path, output_path)[source]

Write the me-type factsheet json file of SSCX packages.

The output metype factsheet contains anatomy, physiology and morphology data.

Parameters:

• data_path (str) – path to the trace data (usually output of emodelrunner run)

• current_amplitude (float) – current amplitude of the stimulus (nA)

• stim_start (float) – time at which the stimulus begins (ms)

• stim_duration (float) – stimulus duration (ms)

• morphology_path (str or Path) – Path to the morphology file.

• output_path (str) – path to the metype factsheet output

emodelrunner.factsheets.output.write_metype_json_from_config(config, voltage_path, morphology_path, output_path, protocol_key)[source]

Write the me-type factsheet json file from config input.

Parameters:

• config (configparser.ConfigParser) – configuration

• voltage_path (str) – path to the trace data (usually output of emodelrunner run)

• morphology_path (str) – Path to the morphology file.

• output_path (str) – path to the metype factsheet output

• protocol_key (str) – name of the protocol used for physiology features extraction