suppress channel unit change warnings (#1282)

doc/whats_new.rst

@@ -36,7 +36,7 @@ Detailed list of changes
 🧐 API and behavior changes
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-- nothing yet
+- :func:`mne_bids.read_raw_bids` no longer warns about unit changes in channels upon reading, as that information is taken from ``channels.tsv`` and judged authorative, by `Stefan Appelhoff`_ (:gh:`1282`)
 
 🛠 Requirements
 ^^^^^^^^^^^^^^^

mne_bids/read.py

@@ -683,7 +683,9 @@ def _handle_channels_reading(channels_fname, raw):
             f"Cannot set channel type for the following channels, as they "
             f'are missing in the raw data: {", ".join(sorted(ch_diff))}'
         )
-    raw.set_channel_types(channel_type_bids_mne_map_available_channels)
+    raw.set_channel_types(
+        channel_type_bids_mne_map_available_channels, on_unit_change="ignore"
+    )
 
     # Set bad channels based on _channels.tsv sidecar
     if "status" in channels_dict:

mne_bids/tests/test_read.py

@@ -794,7 +794,6 @@ def test_handle_info_reading(tmp_path):
         assert raw.info["line_freq"] == 55
 
 
-@pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @pytest.mark.filterwarnings(warning_str["maxshield"])
 @testing.requires_testing_data
 def test_handle_chpi_reading(tmp_path):
@@ -827,7 +826,6 @@ def test_handle_chpi_reading(tmp_path):
 
     with (
         pytest.warns(RuntimeWarning, match="Defaulting to .* mne.Raw object"),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
     ):
         raw_read = read_raw_bids(bids_path, extra_params=dict(allow_maxshield="yes"))
 
@@ -842,7 +840,6 @@ def test_handle_chpi_reading(tmp_path):
 
 
 @pytest.mark.filterwarnings(warning_str["nasion_not_found"])
-@pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @testing.requires_testing_data
 def test_handle_eeg_coords_reading(tmp_path):
     """Test reading iEEG coordinates from BIDS files."""
@@ -859,7 +856,7 @@ def test_handle_eeg_coords_reading(tmp_path):
     raw = _read_raw_edf(raw_fname)
 
     # ensure we are writing 'eeg' data
-    raw.set_channel_types({ch: "eeg" for ch in raw.ch_names})
+    raw.set_channel_types({ch: "eeg" for ch in raw.ch_names}, on_unit_change="ignore")
 
     # set a `random` montage
     ch_names = raw.ch_names
@@ -903,19 +900,15 @@ def test_handle_eeg_coords_reading(tmp_path):
         bids_path, suffix="coordsystem", extension=".json"
     )
     _update_sidecar(coordsystem_fname, "EEGCoordinateSystem", "besa")
-    with (
-        pytest.warns(
-            RuntimeWarning, match="is not a BIDS-acceptable coordinate frame for EEG"
-        ),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
+    with pytest.warns(
+        RuntimeWarning, match="is not a BIDS-acceptable coordinate frame for EEG"
     ):
         raw_test = read_raw_bids(bids_path)
         assert raw_test.info["dig"] is None
 
 
 @pytest.mark.parametrize("bids_path", [_bids_path, _bids_path_minimal])
 @pytest.mark.filterwarnings(warning_str["nasion_not_found"])
-@pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @testing.requires_testing_data
 def test_handle_ieeg_coords_reading(bids_path, tmp_path):
     """Test reading iEEG coordinates from BIDS files."""
@@ -926,7 +919,7 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
     raw = _read_raw_edf(raw_fname)
 
     # ensure we are writing 'ecog'/'ieeg' data
-    raw.set_channel_types({ch: "ecog" for ch in raw.ch_names})
+    raw.set_channel_types({ch: "ecog" for ch in raw.ch_names}, on_unit_change="ignore")
 
     # coordinate frames in mne-python should all map correctly
     # set a `random` montage
@@ -978,11 +971,8 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
     for axis in ["x", "y", "z"]:
         electrodes_dict[axis] = np.multiply(orig_electrodes_dict[axis], scaling)
     _to_tsv(electrodes_dict, electrodes_fname)
-    with (
-        pytest.warns(
-            RuntimeWarning, match="Coordinate unit is not an accepted BIDS unit"
-        ),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
+    with pytest.warns(
+        RuntimeWarning, match="Coordinate unit is not an accepted BIDS unit"
     ):
         raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
 
@@ -1012,7 +1002,6 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
         # and make sure all digpoints are MRI coordinate frame
         with (
             pytest.warns(RuntimeWarning, match="not an MNE-Python coordinate frame"),
-            pytest.warns(RuntimeWarning, match="The unit for channel"),
         ):
             raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
             assert raw_test.info["dig"] is not None
@@ -1031,7 +1020,6 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
                 pytest.warns(
                     RuntimeWarning, match="not an MNE-Python coordinate frame"
                 ),
-                pytest.warns(RuntimeWarning, match="The unit for channel"),
             ):
                 raw_test = read_raw_bids(bids_path=bids_fname, verbose=False)
         assert raw_test.info["dig"] is not None
@@ -1061,7 +1049,6 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
     # however, a warning will be raised through mne-python
     with (
         pytest.warns(RuntimeWarning, match="DigMontage is only a subset of info"),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
     ):
         read_raw_bids(bids_path=bids_fname, verbose=False)
 
@@ -1080,7 +1067,6 @@ def test_handle_ieeg_coords_reading(bids_path, tmp_path):
     nan_chs = [electrodes_dict["name"][i] for i in [0, 3]]
     with (
         pytest.warns(RuntimeWarning, match="There are channels without locations"),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
     ):
         raw = read_raw_bids(bids_path=bids_fname, verbose=False)
         for idx, ch in enumerate(raw.info["chs"]):
@@ -1188,7 +1174,6 @@ def test_handle_channel_type_casing(tmp_path):
         read_raw_bids(bids_path)
 
 
-@pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @testing.requires_testing_data
 def test_handle_non_mne_channel_type(tmp_path):
     """Test that channel types not known to MNE will be read as 'misc'."""
@@ -1212,7 +1197,6 @@ def test_handle_non_mne_channel_type(tmp_path):
 
     with (
         pytest.warns(RuntimeWarning, match='will be set to "misc"'),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
     ):
         raw = read_raw_bids(bids_path)
 

mne_bids/tests/test_write.py

@@ -504,7 +504,6 @@ def test_line_freq(line_freq, _bids_validate, tmp_path):
 
 
 @testing.requires_testing_data
-@pytest.mark.filterwarnings(warning_str["channel_unit_changed"])
 @pytest.mark.filterwarnings(warning_str["maxshield"])
 def test_fif(_bids_validate, tmp_path):
     """Test functionality of the write_raw_bids conversion for fif."""
@@ -549,7 +548,8 @@ def test_fif(_bids_validate, tmp_path):
         {
             raw.ch_names[i]: "misc"
             for i in mne.pick_types(raw.info, stim=True, meg=False)
-        }
+        },
+        on_unit_change="ignore",
     )
     bids_root = tmp_path / "bids2"
     bids_path.update(root=bids_root)
@@ -611,7 +611,6 @@ def test_fif(_bids_validate, tmp_path):
     bids_path.update(root=bids_root, datatype="eeg")
     with (
         pytest.warns(RuntimeWarning, match="Not setting position"),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
     ):
         raw2 = read_raw_bids(bids_path=bids_path)
     os.remove(op.join(bids_root, "test-raw.fif"))
@@ -1055,8 +1054,7 @@ def test_kit(_bids_validate, tmp_path):
 
     _bids_validate(bids_root)
     assert op.exists(bids_root / "participants.tsv")
-    with pytest.warns(RuntimeWarning, match=".* changed from V to NA"):
-        read_raw_bids(bids_path=kit_bids_path)
+    read_raw_bids(bids_path=kit_bids_path)
 
     # ensure the marker file is produced in the right place
     marker_fname = BIDSPath(
@@ -1183,7 +1181,6 @@ def test_ctf(_bids_validate, tmp_path):
     _bids_validate(tmp_path)
     with (
         pytest.warns(RuntimeWarning, match="Did not find any events"),
-        pytest.warns(RuntimeWarning, match="The unit for channel"),
     ):
         raw = read_raw_bids(bids_path=bids_path, extra_params=dict(clean_names=False))
 
@@ -1871,11 +1868,7 @@ def test_bdf(_bids_validate, tmp_path):
     # Now read the raw data back from BIDS, with the tampered TSV, to show
     # that the channels.tsv truly influences how read_raw_bids sets ch_types
     # in the raw data object
-    with (
-        pytest.warns(RuntimeWarning, match=r"The unit for channel\(s\) Fp1"),
-        pytest.warns(RuntimeWarning, match=r"The unit for channel\(s\) Status"),
-    ):
-        raw = read_raw_bids(bids_path=bids_path)
+    raw = read_raw_bids(bids_path=bids_path)
     assert coil_type(raw.info, test_ch_idx) == "misc"
     with pytest.raises(TypeError, match="unexpected keyword argument 'foo'"):
         read_raw_bids(bids_path=bids_path, extra_params=dict(foo="bar"))
@@ -4071,8 +4064,7 @@ def test_repeat_write_location(tmpdir):
     bids_path = write_raw_bids(raw, bids_path, verbose=False)
 
     # Read back in
-    with pytest.warns(RuntimeWarning, match=".* has changed from NA to V"):
-        raw = read_raw_bids(bids_path, verbose=False)
+    raw = read_raw_bids(bids_path, verbose=False)
 
     # Re-writing with src == dest should error
     with pytest.raises(FileExistsError, match="Desired output BIDSPath"):