Explicit the value used as a default for the standard deviation

bluepyefe/extract.py

@@ -479,6 +479,7 @@ def create_feature_protocol_files(
     threshold_nvalue_save=1,
     write_files=True,
     save_files_used=False,
+    default_std_value=1e-3
 ):
     """
     Save the efeatures and protocols for each protocol/target combo
@@ -496,6 +497,8 @@ def create_feature_protocol_files(
         save_files_used (bool): if True, the name of the recording files used
             in the computation of the features will be added to the
             efeatures.
+        default_std_value (float): default value used to replace the standard
+            deviation if the standard deviation is 0.
 
     Returns:
         feat (dict)
@@ -523,7 +526,7 @@ def create_feature_protocol_files(
                 )
                 continue
 
-            tmp_feat.append(target.as_legacy_dict(save_files_used))
+            tmp_feat.append(target.as_dict(save_files_used, default_std_value))
 
         if not tmp_feat:
             logger.warning(
@@ -783,7 +786,8 @@ def extract_efeatures_per_cell(
     targets,
     protocol_mode,
     threshold_nvalue_save,
-    write_files
+    write_files,
+    default_std_value=1e-3
 ):
 
     for cell_name in files_metadata:
@@ -808,6 +812,7 @@ def extract_efeatures_per_cell(
                 output_directory=cell_directory,
                 threshold_nvalue_save=threshold_nvalue_save,
                 write_files=write_files,
+                default_std_value=default_std_value
             )
 
 
@@ -830,6 +835,7 @@ def extract_efeatures(
     rheobase_settings=None,
     auto_targets=None,
     pickle_cells=False,
+    default_std_value=1e-3
 ):
     """
     Extract efeatures.
@@ -908,6 +914,8 @@ def extract_efeatures(
             computation function.
         auto_targets (list of AutoTarget): targets with more flexible goals.
         pickle_cells (bool): if True, the cells object will be saved as a pickle file.
+        default_std_value (float): default value used to replace the standard
+            deviation if the standard deviation is 0.
     """
 
     if not files_metadata:
@@ -978,6 +986,7 @@ def extract_efeatures(
         output_directory=output_directory,
         threshold_nvalue_save=threshold_nvalue_save,
         write_files=write_files,
+        default_std_value=default_std_value
     )
 
     if pickle_cells:

bluepyefe/target.py

@@ -37,6 +37,7 @@ def __init__(
             amplitude,
             tolerance,
             efel_settings=None,
+
     ):
         """Constructor.
 
@@ -127,24 +128,7 @@ def add_effective_threshold(self):
         if self._auto_thresholds:
             self.efel_settings["Threshold"] = numpy.median(self._auto_thresholds)
 
-    def as_dict(self):
-        """Returns the target in the form of a dictionary"""
-
-        self.add_effective_threshold()
-
-        return {
-            "efeature_name": self.efeature_name,
-            "feature": self.efel_feature_name,
-            "mean": self.mean,
-            "std": self.std,
-            "values": self._values,
-            "protocol_name": self.protocol_name,
-            "amplitude": self.amplitude,
-            "tolerance": self.tolerance,
-            "efel_settings": self.efel_settings
-        }
-
-    def as_legacy_dict(self, save_files_used=False):
+    def as_dict(self, save_files_used=False, default_std_value=1e-3):
         """Returns the target in the form of a dictionary in a legacy format"""
 
         self.add_effective_threshold()
@@ -153,11 +137,11 @@ def as_legacy_dict(self, save_files_used=False):
         if std == 0.0:
             logger.warning(
                 "Standard deviation for efeatures {} stimulus {} is 0 and"
-                "will be set to 1e-3".format(
-                    self.efel_feature_name, self.protocol_name
+                "will be set to {}".format(
+                    self.efel_feature_name, self.protocol_name, default_std_value
                 )
             )
-            std = 1e-3
+            std = default_std_value
 
         feature_dict = {
             "feature": self.efel_feature_name,

tests/test_target.py

@@ -48,12 +48,9 @@ def test_dict(self):
         self.target.append(1.)
         self.target.append(2.)
         dict_form = self.target.as_dict()
-        self.assertEqual(len(dict_form), 9)
-        self.assertEqual(dict_form['mean'], 1.5)
-        dict_form_legacy = self.target.as_legacy_dict()
-        self.assertEqual(len(dict_form_legacy), 5)
-        self.assertEqual(len(dict_form_legacy['val']), 2)
-        self.assertEqual(len(dict_form_legacy['efel_settings']), 0)
+        self.assertEqual(len(dict_form), 5)
+        self.assertEqual(len(dict_form['val']), 2)
+        self.assertEqual(len(dict_form['efel_settings']), 0)
 
     def test_str(self):
         print(self.target)