RFC, WIP: proposal to add optional steps to config

Author: scott-huberty

pylossless/assets/ll_default_config_adults.yaml

@@ -26,7 +26,8 @@ project:
 
 ######################## Task break detection ########################
 # See arguments definition from mne.preprocessing.annotate_breaks
-find_breaks:
+# Uncomment dict to enable task break detection with default values
+find_breaks:  # {}
 
 ############################## epoching ##############################
 epoching:
@@ -53,6 +54,12 @@ nearest_neighbors:
   n_nbr_epoch: 3
 
 ####################### Pipeline steps config ########################
+
+# The following two steps are optional and are not enabled by default.
+# Uncomment the {} to enable them with default values.
+flag_channels_fixed_threshold: # {}
+flag_epochs_fixed_threshold: # {}
+
 bridged_channels:
   bridge_trim: 40
   bridge_z: 6

pylossless/assets/ll_default_config_infants.yaml

@@ -26,7 +26,8 @@ project:
 
 ######################## Task break detection ########################
 # See arguments definition from mne.preprocessing.annotate_breaks
-find_breaks:
+# Uncomment dict to enable task break detection with default values
+find_breaks:  # {}
 
 ############################## epoching ##############################
 epoching:
@@ -53,6 +54,12 @@ nearest_neighbors:
   n_nbr_epoch: 3
 
 ####################### Pipeline steps config ########################
+
+# The following two steps are optional and are not enabled by default.
+# Uncomment the {} to enable them with default values.
+flag_channels_fixed_threshold: # {}
+flag_epochs_fixed_threshold: # {}
+
 bridged_channels:
   bridge_trim: 40
   bridge_z: 6

pylossless/pipeline.py

@@ -721,7 +721,7 @@ def find_breaks(self):
         for example would unpack two keyword arguments from
         mne.preprocessing.annotate_break
         """
-        if "find_breaks" not in self.config or not self.config["find_breaks"]:
+        if "find_breaks" not in self.config or self.config["find_breaks"] is None:
             return
         if not self.raw.annotations:
             logger.debug("No annotations found in raw object. Skipping find_breaks.")
@@ -861,7 +861,10 @@ def flag_channels_fixed_threshold(self, threshold=5e-5, picks="eeg"):
         with. You may need to assess a more appropriate value for your own
         data.
         """
-        if "flag_channels_fixed_threshold" not in self.config:
+        try:
+            if self.config["flag_channels_fixed_threshold"] is None:
+                return
+        except KeyError:
             return
         if "threshold" in self.config["flag_channels_fixed_threshold"]:
             threshold = self.config["flag_channels_fixed_threshold"]["threshold"]