[MRG] auto-add event_id key for BAD_ACQ_SKIP (#1258)

doc/whats_new.rst

@@ -28,6 +28,7 @@ The following authors had contributed before. Thank you for sticking around! 
 * `Laetitia Fesselier`_
 * `Richard Höchenberger`_
 * `Stefan Appelhoff`_
+* `Daniel McCloy`_
 
 Detailed list of changes
 ~~~~~~~~~~~~~~~~~~~~~~~~
@@ -46,6 +47,8 @@ Detailed list of changes
   For example, If ``run=1`` is passed to MNE-BIDS, it will no longer be silently auto-converted to ``run-01``, by `Alex Rockhill`_ (:gh:`1215`)
 - MNE-BIDS will no longer warn about missing leading punctuation marks for extensions passed :class:`~mne_bids.BIDSPath`.
   For example, MNE-BIDS will now silently auto-convert ``edf`` to ```.edf``, by `Alex Rockhill`_ (:gh:`1215`)
+- MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if there are ``BAD_ACQ_SKIP`` annotations in the raw file and no corresponding key in ``event_id``.
+  Instead, it will automatically add the necessary key and assign an unused integer event code to it. By `Daniel McCloy`_ (:gh:`1258`)
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^

mne_bids/read.py

@@ -151,9 +151,18 @@ def _read_events(events, event_id, raw, bids_path=None):
                 'To specify custom event codes, please pass "event_id".'
             )
         else:
+            special_annots = {"BAD_ACQ_SKIP"}
             desc_without_id = sorted(
                 set(raw.annotations.description) - set(event_id.keys())
             )
+            # auto-add entries to `event_id` for "special" annotation values
+            # (but only if they're needed)
+            if set(desc_without_id) & special_annots:
+                for annot in special_annots:
+                    # use a value guaranteed to not be in use
+                    event_id = {annot: max(event_id.values()) + 90000} | event_id
+                # remove the "special" annots from the list of problematic annots
+                desc_without_id = sorted(set(desc_without_id) - special_annots)
             if desc_without_id:
                 raise ValueError(
                     f"The provided raw data contains annotations, but "

mne_bids/tests/test_read.py

@@ -46,6 +46,15 @@
 acq = "01"
 task = "testing"
 
+sample_data_event_id = {
+    "Auditory/Left": 1,
+    "Auditory/Right": 2,
+    "Visual/Left": 3,
+    "Visual/Right": 4,
+    "Smiley": 5,
+    "Button": 32,
+}
+
 _bids_path = BIDSPath(
     subject=subject_id, session=session_id, run=run, acquisition=acq, task=task
 )
@@ -214,14 +223,6 @@ def test_get_head_mri_trans(tmp_path):
     """Test getting a trans object from BIDS data."""
     nib = pytest.importorskip("nibabel")
 
-    event_id = {
-        "Auditory/Left": 1,
-        "Auditory/Right": 2,
-        "Visual/Left": 3,
-        "Visual/Right": 4,
-        "Smiley": 5,
-        "Button": 32,
-    }
     events_fname = op.join(
         data_path, "MEG", "sample", "sample_audvis_trunc_raw-eve.fif"
     )
@@ -234,7 +235,9 @@ def test_get_head_mri_trans(tmp_path):
     # Write it to BIDS
     raw = _read_raw_fif(raw_fname)
     bids_path = _bids_path.copy().update(root=tmp_path, datatype="meg", suffix="meg")
-    write_raw_bids(raw, bids_path, events=events, event_id=event_id, overwrite=False)
+    write_raw_bids(
+        raw, bids_path, events=events, event_id=sample_data_event_id, overwrite=False
+    )
 
     # We cannot recover trans if no MRI has yet been written
     with pytest.raises(FileNotFoundError, match="Did not find"):
@@ -300,7 +303,7 @@ def test_get_head_mri_trans(tmp_path):
     # sidecar, and also accept "nasion" instead of just "NAS"
     raw = _read_raw_fif(raw_fname)
     write_raw_bids(
-        raw, bids_path, events=events, event_id=event_id, overwrite=True
+        raw, bids_path, events=events, event_id=sample_data_event_id, overwrite=True
     )  # overwrite with new acq
     t1w_bids_path = write_anat(
         t1w_mgh, bids_path=t1w_bids_path, landmarks=landmarks, overwrite=True
@@ -578,6 +581,27 @@ def test_keep_essential_annotations(tmp_path):
     assert raw_read.annotations[0]["description"] == raw.annotations[0]["description"]
 
 
+@testing.requires_testing_data
+def test_adding_essential_annotations_to_dict(tmp_path):
+    """Test that essential Annotations are auto-added to the `event_id` dictionary."""
+    raw = _read_raw_fif(raw_fname)
+    annotations = mne.Annotations(
+        onset=[raw.times[0]], duration=[1], description=["BAD_ACQ_SKIP"]
+    )
+    raw.set_annotations(annotations)
+    events = mne.find_events(raw)
+    event_id = sample_data_event_id.copy()
+    obj_id = id(event_id)
+
+    # see that no error is raised for missing event_id key for BAD_ACQ_SKIP
+    bids_path = BIDSPath(subject="01", task="task", datatype="meg", root=tmp_path)
+    with pytest.warns(RuntimeWarning, match="Acquisition skips detected"):
+        write_raw_bids(raw, bids_path, overwrite=True, events=events, event_id=event_id)
+    # make sure we didn't modify the user-passed dict
+    assert event_id == sample_data_event_id
+    assert obj_id == id(event_id)
+
+
 @pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @testing.requires_testing_data
 def test_handle_scans_reading(tmp_path):