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Improved ICA based noise removal for reference channels #5959

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jshanna100 wants to merge 13 commits into from
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Improved ICA based noise removal for reference channels #5959

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c472839
bare bones functionality for doing ICA on MEG reference channels and …
Dec 19, 2018
a7f356a
bypassing topography, incomplete work on correlative functions
Jan 10, 2019
28ef93f
woops
Jan 10, 2019
4712690
ICA accepts reference channels, topography functions are skipped,
Jan 16, 2019
7615f17
Solved various backwards compatibility issues.
Jan 19, 2019
ceb6b44
new private function _find_bads_ch now underlies find_bads_ecg/eog/ref
Jan 22, 2019
80dbcfb
should pass ica_test.py now
Jan 22, 2019
5d34d6f
fixed documentation formatting
Jan 29, 2019
c174acc
fix copy paste error in notes
Jan 30, 2019
07b71d5
FIX: Minor fixes
larsoner Feb 1, 2019
e421a4c
FIX: Order
larsoner Feb 1, 2019
b62048e
Merge remote-tracking branch 'upstream/master'
Feb 14, 2019
0c23f3c
fix ICA.label_ bug
Feb 20, 2019
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8 changes: 4 additions & 4 deletions mne/preprocessing/ica.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1066,7 +1066,7 @@ def _find_bads_ch(self, inst, chs, threshold=3.0, start=None,
idx_unique.remove(i)
if len(scores) == 1:
scores = scores[0]
labels[prefix] = list(idx)
labels = list(idx)

return labels, scores

Expand Down Expand Up @@ -1174,7 +1174,7 @@ def find_bads_ecg(self, inst, ch_name=None, threshold=None, start=None,
elif method == 'correlation':
if threshold is None:
threshold = 3.0
self.labels_, scores = self._find_bads_ch(
self.labels_['ecg'], scores = self._find_bads_ch(
inst, [ecg], threshold=threshold, start=start, stop=stop,
l_freq=l_freq, h_freq=h_freq, prefix="ecg",
reject_by_annotation=reject_by_annotation)
Expand Down Expand Up @@ -1244,7 +1244,7 @@ def find_bads_ref(self, inst, ch_name=None, threshold=3.0, start=None,
inds = pick_channels(inst.ch_names, ch_name)
ref_chs = [inst.ch_names[k] for k in inds]

self.labels_, scores = self._find_bads_ch(
self.labels_['ref_meg'], scores = self._find_bads_ch(
inst, ref_chs, threshold=threshold, start=start, stop=stop,
l_freq=l_freq, h_freq=h_freq, prefix="ref_meg",
reject_by_annotation=reject_by_annotation)
Expand Down Expand Up @@ -1306,7 +1306,7 @@ def find_bads_eog(self, inst, ch_name=None, threshold=3.0, start=None,
logger.info('Using EOG channel %s' % inst.ch_names[eog_inds[0]])
eog_chs = [inst.ch_names[k] for k in eog_inds]

self.labels_, scores = self._find_bads_ch(
self.labels_['eog'], scores = self._find_bads_ch(
inst, eog_chs, threshold=threshold, start=start, stop=stop,
l_freq=l_freq, h_freq=h_freq, prefix="eog",
reject_by_annotation=reject_by_annotation)
Expand Down