[MRG] Patch writing iEEGCoordinateSystemDescription (#706)

doc/whats_new.rst

@@ -52,11 +52,12 @@ Bug fixes
 - Fix writing MEGIN Triux files, by `Alexandre Gramfort`_ (:gh:`674`)
 - Anonymization of EDF files in :func:`write_raw_bids` will now convert recording date to ``01-01-1985 00:00:00`` if anonymization takes place, while setting the recording date in the ``scans.tsv`` file to the anonymized date, thus making the file EDF/EDFBrowser compliant, by `Adam Li`_ (:gh:`669`)
 - :func:`mne_bids.write_raw_bids` will not overwrite an existing ``coordsystem.json`` anymore, unless explicitly requested, by `Adam Li`_ (:gh:`675`)
-- :func:`mne_bids.read_raw_bids` now properly handles datasets without event descriptions, by `Richard Höchenberger`_ (:gh:`680`) 
+- :func:`mne_bids.read_raw_bids` now properly handles datasets without event descriptions, by `Richard Höchenberger`_ (:gh:`680`)
 - :func:`mne_bids.stats.count_events` now handles files without a ``trial_type`` or ``stim_type`` column gracefully, by `Richard Höchenberger`_ (:gh:`682`)
 - :func:`mne_bids.read_raw_bids` now correctly treats ``coordsystem.json`` as optional for EEG and MEG data, by `Diego Lozano-Soldevilla`_ (:gh:`691`)
 - :func:`mne_bids.read_raw_bids` now ignores ``exclude`` parameters passed via ``extra_params``, by `Richard Höchenberger`_ (:gh:`703`)
 - :func:`mne_bids.write_raw_bids` now retains original event IDs in the ``value`` column of ``*_events.tsv``, by `Richard Höchenberger`_ (:gh:`708`)
+- Fix writing correct ``iEEGCoordinateSystemDescription``, by `Stefan Appelhoff`_ (:gh:`706`)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

mne_bids/dig.py

@@ -239,8 +239,10 @@ def _coordsystem_json(*, raw, unit, hpi_coord_system, sensor_coord_system,
         as in BIDS_COORDINATE_UNITS.
     hpi_coord_system : str
         Name of the coordinate system for the head coils.
-    sensor_coord_system : str
+    sensor_coord_system : str | tuple of str
         Name of the coordinate system for the sensor positions.
+        If a tuple of strings, should be in the form:
+        ``(BIDS coordinate frame, MNE coordinate frame)``.
     fname : str
         Filename to save the coordsystem.json to.
     datatype : str
@@ -269,11 +271,21 @@ def _coordsystem_json(*, raw, unit, hpi_coord_system, sensor_coord_system,
                          .format(coord_frame))
 
     # get the coordinate frame description
+    try:
+        sensor_coord_system, sensor_coord_system_mne = sensor_coord_system
+    except ValueError:
+        sensor_coord_system_mne = "n/a"
     sensor_coord_system_descr = (COORD_FRAME_DESCRIPTIONS
                                  .get(sensor_coord_system.lower(), "n/a"))
-    if sensor_coord_system == 'Other' and verbose:
-        print('Using the `Other` keyword for the CoordinateSystem field. '
-              'Please specify the CoordinateSystemDescription field manually.')
+    if sensor_coord_system == 'Other':
+        if verbose:
+            msg = ('Using the `Other` keyword for the CoordinateSystem field. '
+                   'Please specify the CoordinateSystemDescription field '
+                   'manually.')
+            logger.info(msg)
+        sensor_coord_system_descr = (COORD_FRAME_DESCRIPTIONS
+                                     .get(sensor_coord_system_mne.lower(),
+                                          "n/a"))
 
     # create the coordinate json data structure based on 'datatype'
     if datatype == 'meg':
@@ -393,7 +405,8 @@ def _write_dig_bids(bids_path, raw, overwrite=False, verbose=True):
             _electrodes_tsv(raw, electrodes_path,
                             datatype, overwrite, verbose)
             _coordsystem_json(raw=raw, unit=unit, hpi_coord_system='n/a',
-                              sensor_coord_system=coord_frame,
+                              sensor_coord_system=(coord_frame,
+                                                   mne_coord_frame),
                               fname=coordsystem_path, datatype=datatype,
                               overwrite=overwrite, verbose=verbose)
         else:

mne_bids/tests/test_write.py

@@ -2204,10 +2204,6 @@ def test_coordsystem_json_compliance(
     """Tests that coordsystem.json contents are written correctly.
 
     Tests multiple manufacturer data formats and MEG, EEG, and iEEG.
-
-    TODO: Fix coordinatesystemdescription for iEEG.
-    Currently, iEEG coordinate system descriptions are not written
-    correctly.
     """
     bids_root = _TempDir()
     data_path = op.join(testing.data_path(), dir_name)
@@ -2304,16 +2300,16 @@ def test_coordsystem_json_compliance(
     elif datatype == 'ieeg' and coord_frame == 'mni_tal':
         assert 'space-mni' in coordsystem_fname
         assert coordsystem_json['iEEGCoordinateSystem'] == 'Other'
-        # assert coordsystem_json['iEEGCoordinateSystemDescription'] == \
-        #     COORD_FRAME_DESCRIPTIONS['mni_tal']
+        assert coordsystem_json['iEEGCoordinateSystemDescription'] == \
+            COORD_FRAME_DESCRIPTIONS['mni_tal']
     elif datatype == 'ieeg' and coord_frame == 'fs_tal':
         assert 'space-fs' in coordsystem_fname
         assert coordsystem_json['iEEGCoordinateSystem'] == 'Other'
-        # assert coordsystem_json['iEEGCoordinateSystemDescription'] == \
-        #     COORD_FRAME_DESCRIPTIONS['fs_tal']
+        assert coordsystem_json['iEEGCoordinateSystemDescription'] == \
+            COORD_FRAME_DESCRIPTIONS['fs_tal']
     elif datatype == 'ieeg' and coord_frame == 'unknown':
         assert coordsystem_json['iEEGCoordinateSystem'] == 'Other'
-        # assert coordsystem_json['iEEGCoordinateSystemDescription'] == 'n/a'
+        assert coordsystem_json['iEEGCoordinateSystemDescription'] == 'n/a'
     elif datatype == 'meg' and dir_name == 'CTF':
         assert coordsystem_json['MEGCoordinateSystem'] == 'CTF'
         assert coordsystem_json['MEGCoordinateSystemDescription'] == \