[MRG, ENH] Get annotation description from snirf stim name (mne-tools#9575)

dsleiter · web-flow · commit 144a58c94665 · 2021-07-16T14:55:46.000-04:00
* Get annotation description from snirf stim name

* Update changelog
diff --git a/doc/changes/latest.inc b/doc/changes/latest.inc
@@ -31,10 +31,14 @@ Current (0.24.dev0)
 
 .. |Pierre-Antoine Bannier| replace:: **Pierre-Antoine Bannier**
 
+.. |Darin Erat Sleiter| replace:: **Darin Erat Sleiter**
+
 Enhancements
 ~~~~~~~~~~~~
 .. - Add something cool (:gh:`9192` **by new contributor** |New Contributor|_)
 
+- Get annotation descriptions from the name field of SNIRF stimulus groups when reading SNIRF files via `mne.io.read_raw_snirf` (:gh:`9575` **by new contributor** |Darin Erat Sleiter|_)
+
 - Add support for NIRSport and NIRSport2 devices to `mne.io.read_raw_nirx` (:gh:`9348` and :gh:`9401` **by new contributor** |David Julien|_, **new contributor** |Romain Derollepot|_, `Robert Luke`_, and `Eric Larson`_)
 
 - New function :func:`mne.label.find_pos_in_annot` to get atlas label for MRI coordinates.  (:gh:`9376` by **by new contributor** |Marian Dovgialo|_)
diff --git a/doc/changes/names.inc b/doc/changes/names.inc
@@ -401,3 +401,5 @@
 .. _Marian Dovgialo: https://github.com/mdovgialo
 
 .. _Pierre-Antoine Bannier: https://github.com/PABannier
+
+.. _Darin Erat Sleiter: https://github.com/dsleiter
diff --git a/mne/io/snirf/_snirf.py b/mne/io/snirf/_snirf.py
@@ -365,7 +365,8 @@ def natural_keys(text):
                     data = np.atleast_2d(np.array(
                         dat.get('/nirs/' + key + '/data')))
                     if data.size > 0:
-                        annot.append(data[:, 0], 1.0, key[4:])
+                        desc = dat.get('/nirs/' + key + '/name')[0]
+                        annot.append(data[:, 0], 1.0, desc.decode('UTF-8'))
             self.set_annotations(annot)
 
             # Reorder channels to match expected ordering in MNE
diff --git a/mne/io/snirf/tests/test_snirf.py b/mne/io/snirf/tests/test_snirf.py
@@ -3,7 +3,7 @@
 #          simplified BSD-3 license
 
 import os.path as op
-from numpy.testing import assert_allclose, assert_almost_equal
+from numpy.testing import assert_allclose, assert_almost_equal, assert_equal
 import shutil
 import pytest
 
@@ -288,3 +288,12 @@ def test_snirf_standard():
     """Test standard operations."""
     _test_raw_reader(read_raw_snirf, fname=sfnirs_homer_103_wShort,
                      boundary_decimal=0)  # low fs
+
+
+@requires_testing_data
+@requires_h5py
+def test_annotation_description_from_stim_groups():
+    """Test annotation descriptions parsed from stim group names."""
+    raw = read_raw_snirf(nirx_nirsport2_103_2, preload=True)
+    expected_descriptions = ['1', '2', '6']
+    assert_equal(expected_descriptions, raw.annotations.description)
