Merge branch 'master' of https://github.com/mne-tools/mne-bids into a…

…dd_ieeg_tests

doc/whats_new.rst

@@ -18,6 +18,8 @@ Changelog
 Bug
 ~~~
 
+- Fix logic with inferring unknown channel types for CTF data, by `Mainak Jas`_ (`#129 <https://github.com/mne-tools/mne-bids/pull/16/files>`_)
+
 API
 ~~~
 

examples/convert_eeg_to_bids.py

@@ -25,7 +25,6 @@
 
 import mne
 from mne.datasets import eegbci
-from mne.io.edf.edf import read_annotations_edf
 
 from mne_bids import write_raw_bids, make_bids_basename
 from mne_bids.utils import print_dir_tree
@@ -94,7 +93,7 @@
 ###############################################################################
 # The annotations stored in the file must be read in separately and converted
 # into a 2D numpy array of events that is compatible with MNE.
-annot = read_annotations_edf(edf_path)
+annot = mne.read_annotations(edf_path)
 raw.set_annotations(annot)
 events, event_id = mne.events_from_annotations(raw)
 
@@ -163,7 +162,7 @@
         edf_path = eegbci.load_data(subject=subj_idx, runs=task_idx)[0]
 
         raw = mne.io.read_raw_edf(edf_path, preload=False, stim_channel=None)
-        annot = read_annotations_edf(edf_path)
+        annot = mne.read_annotations(edf_path)
         raw.set_annotations(annot)
         events, event_id = mne.events_from_annotations(raw)
 

mne_bids/mne_bids.py

@@ -127,7 +127,7 @@ def _channels_tsv(raw, fname, overwrite=False, verbose=True):
         status.append('bad' if ch in raw.info['bads'] else 'good')
         _channel_type = channel_type(raw.info, idx)
         if _channel_type in get_specific:
-            _channel_type = coil_type(raw.info, idx)
+            _channel_type = coil_type(raw.info, idx, _channel_type)
         ch_type.append(map_chs[_channel_type])
         description.append(map_desc[_channel_type])
     low_cutoff, high_cutoff = (raw.info['highpass'], raw.info['lowpass'])

mne_bids/pick.py

@@ -44,7 +44,7 @@ def get_coil_types():
                 misc=(FIFF.FIFFV_COIL_NONE,))
 
 
-def coil_type(info, idx):
+def coil_type(info, idx, ch_type='n/a'):
     """Get coil type.
 
     Parameters
@@ -53,6 +53,9 @@ def coil_type(info, idx):
         Measurement info
     idx : int
         Index of channel
+    ch_type : str
+        Channel type to fall back upon if a more specific
+        type is not found
 
     Returns
     -------
@@ -64,5 +67,4 @@ def coil_type(info, idx):
     for key, values in get_coil_types().items():
         if ch['coil_type'] in values:
             return key
-    raise ValueError('Unknown coil of type {0} '
-                     'for channel {1}'.format(ch['coil_type'], ch["ch_name"]))
+    return ch_type

mne_bids/tests/test_pick.py

@@ -1,7 +1,6 @@
 """Test for the coil type picking function"""
 
 import os.path as op
-import pytest
 
 from mne.datasets import testing
 from mne.io import read_raw_fif
@@ -19,5 +18,4 @@ def test_coil_type():
     assert coil_type(raw.info, 306) == 'misc'
     assert coil_type(raw.info, 315) == 'eeg'
     raw.info['chs'][0]['coil_type'] = 1234
-    with pytest.raises(ValueError):
-        coil_type(raw.info, 0)
+    assert coil_type(raw.info, 0) == 'n/a'