amended _write_electrodes_tsv to exclude writing stim channels to e…

…lectrodes.tsv (#1023)

* amended mne_bids.dig._write_electrodes_tsv to skip stim channels so they are not written to electrodes.tsv

* added test for properly writing to electrodes.tsv

* Update mne_bids/tests/test_dig.py

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

* Update mne_bids/tests/test_dig.py

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

* Update mne_bids/tests/test_dig.py

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

* removed second test from test_electrodes_io

* updated change log

* updated test_electrodes_io per reviewer comments

* Update mne_bids/tests/test_dig.py

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

* Update doc/whats_new.rst

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

* Update mne_bids/tests/test_dig.py

Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

* specifying encoding=utf-8 in  per reviewer suggestion

* Rework test a little

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>
Co-authored-by: Mathieu Scheltienne <mathieu.scheltienne@gmail.com>

doc/whats_new.rst

@@ -72,6 +72,8 @@ Detailed list of changes
 
 - :func:`~mne_bids.print_dir_tree` now correctly expands ``~`` to the user's home directory, by `Richard Höchenberger`_ (:gh:`1013`)
 
+- :func:`~mne_bids.write_raw_bids` now correctly excludes stim channels when writing to electrodes.tsv, by `Scott Huberty_` (:gh:`1023`)
+
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 
 .. include:: authors.rst

mne_bids/dig.py

@@ -138,7 +138,11 @@ def _write_electrodes_tsv(raw, fname, datatype, overwrite=False):
     # create list of channel coordinates and names
     x, y, z, names = list(), list(), list(), list()
     for ch in raw.info['chs']:
-        if (
+        if ch['kind'] == FIFF.FIFFV_STIM_CH:
+            logger.debug(f"Not writing stim chan {ch['ch_name']} "
+                         f"to electrodes.tsv")
+            continue
+        elif (
             np.isnan(ch['loc'][:3]).any() or
             np.allclose(ch['loc'][:3], 0)
         ):

mne_bids/tests/test_dig.py

@@ -325,3 +325,28 @@ def test_convert_montage():
     assert pos['coord_frame'] == 'mri'
     assert_almost_equal(pos['ch_pos']['EEG 001'],
                         [-0.0313669, 0.0540269, 0.0949191])
+
+
+def test_electrodes_io(tmp_path):
+    """Ensure only electrodes end up in *_electrodes.json."""
+    raw = _load_raw()
+    raw.pick_types(eeg=True, stim=True)  # we don't need meg channels
+    bids_root = tmp_path / 'bids1'
+    bids_path = _bids_path.copy().update(root=bids_root, datatype='eeg')
+    write_raw_bids(raw=raw, bids_path=bids_path)
+
+    electrodes_path = (
+        bids_path.copy()
+        .update(
+            task=None,
+            run=None,
+            space='CapTrak',
+            suffix='electrodes',
+            extension='.tsv'
+        )
+    )
+    with open(electrodes_path, encoding='utf-8') as sidecar:
+        n_entries = len([line for line in sidecar
+                         if 'name' not in line])  # don't need the header
+        # only eeg chs w/ electrode pos should be written to electrodes.tsv
+        assert n_entries == len(raw.get_channel_types('eeg'))