MAINT: Split bad-finding step

docs/source/changes.md

@@ -205,6 +205,9 @@ authors:
 - Make report generation happen within relevant steps instead of at the end
   of all steps
   ({{ gh(652) }} by {{ authors.larsoner }})
+- Initial raw data plots are now added to reports and bad channel detection
+  is executed in a dedicated step
+  ({{ gh(666) }} by {{ authors.larsoner }})
 
 ### Behavior changes
 

mne_bids_pipeline/_config_import.py

@@ -34,6 +34,7 @@ def _import_config(
         overrides=overrides,
         log=log,
     )
+
     # Check it
     if check:
         _check_config(config)
@@ -59,9 +60,9 @@ def _import_config(
         # Caching
         'memory_location', 'memory_verbose', 'memory_file_method',
         # Misc
-        'deriv_root',
+        'deriv_root', 'config_path',
     )
-    in_both = {'deriv_root', 'interactive'}
+    in_both = {'deriv_root'}
     exec_params = SimpleNamespace(**{k: getattr(config, k) for k in keys})
     for k in keys:
         if k not in in_both:

mne_bids_pipeline/_config_utils.py

@@ -260,8 +260,9 @@ def get_channels_to_analyze(
     # Return names of the channels of the channel types we wish to analyze.
     # We also include channels marked as "bad" here.
     # `exclude=[]`: keep "bad" channels, too.
+    kwargs = dict(eog=True, ecg=True, exclude=())
     if get_datatype(config) == 'meg' and _meg_in_ch_types(config.ch_types):
-        pick_idx = mne.pick_types(info, eog=True, ecg=True, exclude=[])
+        pick_idx = mne.pick_types(info, **kwargs)
 
         if 'mag' in config.ch_types:
             pick_idx = np.concatenate(
@@ -270,8 +271,8 @@ def get_channels_to_analyze(
             pick_idx = np.concatenate(
                 [pick_idx, mne.pick_types(info, meg='grad', exclude=[])])
         if 'meg' in config.ch_types:
-            pick_idx = mne.pick_types(info, meg=True, eog=True, ecg=True,
-                                      exclude=[])
+            pick_idx = mne.pick_types(info, meg=True, exclude=[])
+        pick_idx.sort()
     elif config.ch_types == ['eeg']:
         pick_idx = mne.pick_types(info, meg=False, eeg=True, eog=True,
                                   ecg=True, exclude=[])