Merge pull request #84 from BlueBrain/fix-default-std-value

Fix: FCC Ignoring 'default_std_value' parameter issue
BlueBrain · Nov 27, 2023 · ca5c960 · ca5c960
2 parents f8b2742 + 4d22992
commit ca5c960
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diff --git 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
@@ -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":