Add support for reading SNIRF files with optical density data (#10408)

* Add support for reading SNIRF files with optical density data

* Remove debug code

* Add tests

* Flake

* Increase testing release

* Increase testing release

* Apply suggestions from code review

* Update latest.inc

* FIX: Dec

Co-authored-by: Eric Larson <larson.eric.d@gmail.com>

Author: rob-luke

Diff for: doc/changes/latest.inc

@@ -124,6 +124,8 @@ Enhancements
 
 - Add support for passing time-frequency data to :func:`mne.stats.spatio_temporal_cluster_test` and :func:`mne.stats.spatio_temporal_cluster_1samp_test` and added an example to :ref:`tut-cluster-spatiotemporal-sensor` (:gh:`10384` by `Alex Rockhill`_)
 
+- Add support for reading optical density fNIRS data to :func:`mne.io.read_raw_snirf` (:gh:`10408` by `Robert Luke`_)   
+
 Bugs
 ~~~~
 

Diff for: mne/datasets/config.py

@@ -87,7 +87,7 @@
 # respective repos, and make a new release of the dataset on GitHub. Then
 # update the checksum in the MNE_DATASETS dict below, and change version
 # here:                  ↓↓↓↓↓         ↓↓↓
-RELEASES = dict(testing='0.130', misc='0.23')
+RELEASES = dict(testing='0.132', misc='0.23')
 TESTING_VERSIONED = f'mne-testing-data-{RELEASES["testing"]}'
 MISC_VERSIONED = f'mne-misc-data-{RELEASES["misc"]}'
 
@@ -111,7 +111,7 @@
 # Testing and misc are at the top as they're updated most often
 MNE_DATASETS['testing'] = dict(
     archive_name=f'{TESTING_VERSIONED}.tar.gz',  # 'mne-testing-data',
-    hash='md5:b2bf6517c3d457b70cb5519ce8ab70a7',
+    hash='md5:2ff8bcd18053af3ee0587dce9d6ab516',
     url=('https://codeload.github.com/mne-tools/mne-testing-data/'
          f'tar.gz/{RELEASES["testing"]}'),
     folder_name='MNE-testing-data',

Diff for: mne/io/snirf/_snirf.py

@@ -230,14 +230,27 @@ def natural_keys(text):
                     ch_types.append('fnirs_cw_amplitude')
 
                 elif snirf_data_type == 99999:
-                    hb_id = _correct_shape(
+                    dt_id = _correct_shape(
                         np.array(dat.get('nirs/data1/' + chan +
                                          '/dataTypeLabel')))[0].decode('UTF-8')
+
+                    # Convert between SNIRF processed names and MNE type names
+                    dt_id = dt_id.lower().replace("dod", "fnirs_od")
+
                     ch_name = sources[src_idx - 1] + '_' + \
-                        detectors[det_idx - 1] + ' ' + \
-                        hb_id.lower()
+                        detectors[det_idx - 1]
+
+                    if dt_id == "fnirs_od":
+                        wve_idx = int(_correct_shape(np.array(
+                            dat.get('nirs/data1/' + chan +
+                                    '/wavelengthIndex')))[0])
+                        suffix = ' ' + str(fnirs_wavelengths[wve_idx - 1])
+                    else:
+                        suffix = ' ' + dt_id.lower()
+                    ch_name = ch_name + suffix
+
                     chnames.append(ch_name)
-                    ch_types.append(hb_id.lower())
+                    ch_types.append(dt_id)
 
             # Create mne structure
             info = create_info(chnames,
@@ -309,7 +322,9 @@ def natural_keys(text):
                 info['chs'][idx]['loc'][0:3] = midpoint
                 info['chs'][idx]['coord_frame'] = coord_frame
 
-                if snirf_data_type in [1]:
+                if (snirf_data_type in [1]) or \
+                    ((snirf_data_type == 99999) and
+                        (ch_types[idx] == "fnirs_od")):
                     wve_idx = int(_correct_shape(np.array(dat.get(
                         'nirs/data1/' + chan + '/wavelengthIndex')))[0])
                     info['chs'][idx]['loc'][9] = fnirs_wavelengths[wve_idx - 1]

Diff for: mne/io/snirf/tests/test_snirf.py

@@ -46,6 +46,10 @@
 
 h5py = pytest.importorskip('h5py')  # module-level
 
+# Fieldtrip
+ft_od = op.join(testing_path, 'SNIRF', 'FieldTrip',
+                '220307_opticaldensity.snirf')
+
 
 @requires_testing_data
 @pytest.mark.filterwarnings('ignore:.*contains 2D location.*:')
@@ -286,6 +290,23 @@ def test_snirf_nirsport2_w_positions():
     assert len(mon.dig) == 43
 
 
+@requires_testing_data
+def test_snirf_fieldtrip_od():
+    """Test reading FieldTrip SNIRF files with optical density data."""
+    raw = read_raw_snirf(ft_od, preload=True)
+
+    # Test data import
+    assert raw._data.shape == (72, 500)
+    assert raw.copy().pick('fnirs')._data.shape == (72, 500)
+    assert raw.copy().pick('fnirs_od')._data.shape == (72, 500)
+    with pytest.raises(ValueError, match='not be interpreted as channel'):
+        raw.copy().pick('hbo')
+    with pytest.raises(ValueError, match='not be interpreted as channel'):
+        raw.copy().pick('hbr')
+
+    assert_allclose(raw.info['sfreq'], 50)
+
+
 @requires_testing_data
 def test_snirf_kernel_hb():
     """Test reading Kernel SNIRF files with haemoglobin data."""

Diff for: mne/tests/test_surface.py

@@ -261,6 +261,7 @@ def test_marching_cubes(dtype, value, smooth):
 
 
 @requires_nibabel()
+@testing.requires_testing_data
 def test_get_montage_volume_labels():
     """Test finding ROI labels near montage channel locations."""
     ch_coords = np.array([[-8.7040273, 17.99938754, 10.29604017],