efel_feature_means[protocol_name].items():
feature_name = '%s.%s' % (protocol_name, efel_feature_name)
feature = nrpel.efeatures.eFELFeature(
feature_name,
efel_feature_name=efel_feature_name,
recording_names={'': '%s.soma.v' % protocol_name},
stim_start=stim_start,
stim_end=stim_end,
exp_mean=mean,
exp_std=0.05 * mean)
objective = objective = nrpel.objectives.SingletonObjective(
feature_name, feature)
objectives.append(objective)
score_calc = nrpel.scorecalculators.ObjectivesScoreCalculator(objectives)
cell_evaluator = nrpel.cellevaluator.CellEvaluator(
cell_template=simple_cell,
param_names=['gnabar_hh', 'gkbar_hh'],
fitness_protocols=protocols,
fitness_calculator=score_calc)
optimisation = nrp.Optimisation(
evaluator=cell_evaluator,
eval_function=cell_evaluator.evaluate_with_lists,
offspring_size=10,
use_scoop=True)
if __name__ == '__main__':
final_pop, hall_of_fame, logs, hist = optimisation.run(max_ngen=2)
print('BEST:', hall_of_fame[0])
# TODO store definition dicts in json
# TODO rename 'score' into 'objective'
# TODO add functionality to read settings of every object from config format
import l5pc_evaluator
evaluator = l5pc_evaluator.create()
def evaluate(parameter_array):
"""Global evaluate function"""
return evaluator.evaluate(parameter_array)
opt = bluepyopt.Optimisation(
evaluator=evaluator,
eval_function=evaluate,
offspring_size=2,
use_scoop=True)
def main():
"""Main"""
import argparse
parser = argparse.ArgumentParser(description='L5PC example')
parser.add_argument('--start', action="store_true")
parser.add_argument('--continue_cp', action="store_true")
parser.add_argument('--analyse', action="store_true")
# TODO read checkpoint filename from arguments
cp_filename = 'checkpoint.pkl'