MRG: Fix writing preloaded data of a non-BIDS format with automated f…

…ormat conversion (#1102)

* Fix writing preloaded data of a non-BIDS format with automated format conversion

Fixes #1101

* Simpler

* Better error message

* Add test

* Better error message

* Add changelog entry

* Fix error message

* Add requires_testing_data decorator

doc/whats_new.rst

@@ -60,6 +60,7 @@ Detailed list of changes
 
 - When writing data containing :class:`mne.Annotations` **and** passing events to :func:`~mne_bids.write_raw_bids`, previously, annotations whose description did not appear in ``event_id`` were silently dropped. We now raise an exception and request users to specify mappings between descriptions and event codes in this case. It is still possible to omit ``event_id`` if no ``events`` are passed, by `Richard Höchenberger`_ (:gh:`1084`)
 - When working with NIRS data, raise the correct error message when a faulty ``format`` argument is passed to :func:`~mne_bids.write_raw_bids`, by `Stefan Appelhoff`_ (:gh:`1092`)
+- Fixed writing data preloaded from a format that's not supported by BIDS, by `Richard Höchenberger`_ (:gh:`1101`)
 
 :doc:`Find out what was new in previous releases <whats_new_previous_releases>`
 

mne_bids/tests/test_write.py

@@ -681,12 +681,6 @@ def test_fif(_bids_validate, tmp_path):
     for FILE in files:
         assert 'split' in FILE
 
-    # test unknown extension
-    raw = _read_raw_fif(raw_fname)
-    raw._filenames = (raw.filenames[0].replace('.fif', '.foo'),)
-    with pytest.raises(ValueError, match='Unrecognized file format'):
-        write_raw_bids(raw, bids_path)
-
     # test whether extra points in raw.info['dig'] are correctly used
     # to set DigitizedHeadShape in the JSON sidecar
     # unchanged sample data includes extra points
@@ -3948,3 +3942,26 @@ def test_events_data_deprecation(tmp_path):
             raw=raw, bids_path=bids_path, events=events, events_data=events,
             event_id=event_id
         )
+
+
+@testing.requires_testing_data
+def test_unknown_extension(_bids_validate, tmp_path):
+    """Write data with unknown extension to BIDS."""
+    bids_root = tmp_path / 'bids'
+    bids_path = _bids_path.copy().update(root=bids_root, datatype='meg')
+    raw_fname = data_path / 'MEG' / 'sample' / 'sample_audvis_trunc_raw.fif'
+
+    raw = _read_raw_fif(raw_fname)
+    raw._filenames = (raw.filenames[0].replace('.fif', '.foo'),)
+
+    # When data is not preloaded, we should raise an exception.
+    with pytest.raises(ValueError, match='file format not supported by BIDS'):
+        write_raw_bids(raw, bids_path)
+
+    # With preloaded data, writing should work.
+    raw._filenames = (raw.filenames[0].replace('.foo', '.fif'),)
+    raw.load_data()
+    raw._filenames = (raw.filenames[0].replace('.fif', '.foo'),)
+
+    write_raw_bids(raw, bids_path, allow_preload=True, format='FIF')
+    _bids_validate(bids_root)

mne_bids/write.py

@@ -112,8 +112,7 @@ def _channels_tsv(raw, fname, overwrite=False):
 
     # get the manufacturer from the file in the Raw object
     _, ext = _parse_ext(raw.filenames[0])
-    manufacturer = MANUFACTURERS[ext]
-
+    manufacturer = MANUFACTURERS.get(ext, '')
     ignored_channels = IGNORED_CHANNELS.get(manufacturer, list())
 
     status, ch_type, description = list(), list(), list()
@@ -1542,8 +1541,10 @@ def write_raw_bids(
                          'got %s' % type(raw))
 
     if raw.preload is not False and not allow_preload:
-        raise ValueError('The data is already loaded from disk and may be '
-                         'altered. See warning for "allow_preload".')
+        raise ValueError(
+            'The data has already been loaded from disk. To write it to BIDS, '
+            'pass "allow_preload=True" and the "format" parameter.'
+        )
 
     if not isinstance(bids_path, BIDSPath):
         raise RuntimeError('"bids_path" must be a BIDSPath object. Please '
@@ -1609,7 +1610,12 @@ def write_raw_bids(
             ext = '.bdf'
 
         if ext not in ALLOWED_INPUT_EXTENSIONS:
-            raise ValueError(f'Unrecognized file format {ext}')
+            raise ValueError(
+                f'The input data is in a file format not supported by '
+                f'BIDS: "{ext}". You can try to preload the data and call '
+                f'write_raw_bids() with the "allow_preload=True" and the '
+                f'"format" parameters.'
+            )
 
         if symlink and ext != '.fif':
             raise NotImplementedError('Symlinks are currently only supported '