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'