diff --git a/bluepyemodel/efeatures_extraction/efeatures_extraction.py b/bluepyemodel/efeatures_extraction/efeatures_extraction.py index 9c2b9c04..3e43ec0b 100644 --- a/bluepyemodel/efeatures_extraction/efeatures_extraction.py +++ b/bluepyemodel/efeatures_extraction/efeatures_extraction.py @@ -153,6 +153,7 @@ def extract_save_features_protocols(access_point, mapper=map): name_rin_protocol=access_point.pipeline_settings.name_Rin_protocol, validation_protocols=access_point.pipeline_settings.validation_protocols, stochasticity=access_point.pipeline_settings.stochasticity, + default_std_value=access_point.pipeline_settings.default_std_value, ) fitness_calculator_config.init_from_bluepyefe( diff --git a/bluepyemodel/evaluation/fitness_calculator_configuration.py b/bluepyemodel/evaluation/fitness_calculator_configuration.py index 56799fd7..57ca55d2 100644 --- a/bluepyemodel/evaluation/fitness_calculator_configuration.py +++ b/bluepyemodel/evaluation/fitness_calculator_configuration.py @@ -221,6 +221,7 @@ def __init__( self.name_rin_protocol = name_rin_protocol self.workflow_id = None + self.default_std_value = default_std_value def protocol_exist(self, protocol_name): return bool(p for p in self.protocols if p.name == protocol_name) @@ -281,6 +282,7 @@ def _add_bluepyefe_efeature(self, feature, protocol_name, recording, threshold_e efel_settings=feature.get("efel_settings", {}), threshold_efeature_std=threshold_efeature_std, sample_size=feature.get("n", None), + default_std_value=self.default_std_value, ) if ( @@ -350,6 +352,7 @@ def init_from_bluepyefe(self, efeatures, protocols, currents, threshold_efeature mean=currents["holding_current"][0], std=currents["holding_current"][1], threshold_efeature_std=threshold_efeature_std, + default_std_value=self.default_std_value, ) ) @@ -361,6 +364,7 @@ def init_from_bluepyefe(self, efeatures, protocols, currents, threshold_efeature mean=currents["threshold_current"][0], std=currents["threshold_current"][1], threshold_efeature_std=threshold_efeature_std, + default_std_value=self.default_std_value, ) ) @@ -425,6 +429,7 @@ def _add_legacy_efeature(self, feature, protocol_name, recording, threshold_efea efeature_name=feature.get("efeature_name", None), efel_settings=feature.get("efel_settings", {}), threshold_efeature_std=threshold_efeature_std, + default_std_value=self.default_std_value, ) if protocol_name == "Rin":