Merge pull request autoreject#115 from jasmainak/fix_picks

[MRG] FIX bug in meg picks during interpolation

.travis.yml

@@ -13,7 +13,7 @@ before_install:
 install:
     - conda create -n testenv --yes pip python=${PYTHON_VERSION}
     - source activate testenv
-    - conda install --yes --quiet numpy=1.12 scipy=0.19 scikit-learn=0.18 matplotlib
+    - conda install --yes --quiet numpy scipy scikit-learn matplotlib
     - conda install --yes --quiet nose coverage
     - pip install -q flake8 mne check-manifest
     - pip install coverage coveralls

autoreject/tests/test_utils.py

@@ -63,3 +63,20 @@ def test_utils():
     _interpolate_bads_eeg(evoked_ar, picks=None)
     mne.channels.interpolation._interpolate_bads_eeg(evoked_mne)
     assert_array_equal(evoked_ar.data, evoked_mne.data)
+
+
+def test_interpolate_bads():
+    """Test interpolate bads"""
+    event_id = None
+    events = mne.find_events(raw)
+    tmin, tmax = -0.2, 0.5
+    for ii, ch_name in enumerate(raw.info['ch_names'][:14]):
+        raw.set_channel_types({ch_name: 'bio'})
+        raw.rename_channels({ch_name: 'BIO%02d' % ii})
+
+    picks = mne.pick_types(raw.info, meg='grad', eeg=False, eog=False)
+    epochs = mne.Epochs(raw, events, event_id, tmin, tmax,
+                        baseline=(None, 0), decim=10,
+                        reject=None, preload=True)[:10]
+    epochs.info['bads'] = ['MEG 2212']
+    interpolate_bads(epochs, picks)

autoreject/utils.py

@@ -10,7 +10,7 @@
 
 import mne
 from mne.utils import check_version as version_is_greater_equal
-from mne import pick_types, pick_channels, pick_info
+from mne import pick_types, pick_info
 from mne.channels.interpolation import _do_interp_dots
 from mne.externals import six
 
@@ -356,22 +356,20 @@ def _interpolate_bads_meg_fast(inst, picks, mode='accurate', verbose=None):
     else:
         picked_info = inst.info.copy()
 
-    def get_picks_bad_good(info):
-        picks_meg = pick_types(info, meg=True, eeg=False, exclude=[],
-                               stim=False)
-        ch_names = [info['ch_names'][p] for p in picks_meg]
-        picks_good = pick_types(info, meg=True, eeg=False, exclude='bads',
-                                stim=False)
+    def get_picks_bad_good(info, picks_meg):
+        picks_good = [p for p in picks_meg
+                      if info['ch_names'][p] not in info['bads']]
 
         # select the bad meg channel to be interpolated
         if len(info['bads']) == 0:
             picks_bad = []
         else:
-            picks_bad = pick_channels(ch_names, info['bads'],
-                                      exclude=[])
+            picks_bad = [p for p in picks_meg
+                         if info['ch_names'][p] in info['bads']]
         return picks_meg, picks_good, picks_bad
 
-    picks_meg, picks_good, picks_bad = get_picks_bad_good(picked_info)
+    picks_meg, picks_good, picks_bad = get_picks_bad_good(
+        picked_info, range(picked_info['nchan']))
     # return without doing anything if there are no meg channels
     if len(picks_meg) == 0 or len(picks_bad) == 0:
         return
@@ -386,7 +384,8 @@ def get_picks_bad_good(info):
     # the unpicked info of the data.
     # Since we may have picked the info, we need to double map
     # the indices.
-    _, picks_good_, picks_bad_orig = get_picks_bad_good(inst.info.copy())
+    _, picks_good_, picks_bad_orig = get_picks_bad_good(
+        inst.info.copy(), picks)
     ch_names_a = [picked_info['ch_names'][pp] for pp in picks_bad]
     ch_names_b = [inst.info['ch_names'][pp] for pp in picks_bad_orig]
     assert ch_names_a == ch_names_b

doc/conf.py

@@ -132,6 +132,7 @@
         ("Examples", "auto_examples/index"),
         ("API", "api"),
         ("FAQ", "faq"),
+        ("What's new", "whats_new"),
         ("GitHub", "https://github.com/autoreject/autoreject", True)
     ],
     'bootswatch_theme': "united"

doc/whats_new.rst

@@ -0,0 +1,27 @@
+:orphan:
+
+.. _whats_new:
+
+What's new?
+===========
+
+.. currentmodule:: autoreject
+
+.. _current:
+
+Current
+-------
+
+Changelog
+~~~~~~~~~
+
+Bug
+~~~
+
+- Fixed bug in picking bad channels during interpolation. This bug only affects users who got an assertion
+  error when running :class:`autoreject.Autoreject`. Fixed by `Mainak Jas`_ in `#115 <https://github.com/autoreject/autoreject/pull/115>`_
+
+API
+~~~
+
+.. _Mainak Jas: https://perso.telecom-paristech.fr/mjas/