MRG: Add fnirs and snirf support to report

doc/changes/latest.inc

@@ -48,6 +48,8 @@ Enhancements
 - Add projections when printing a :class:`mne.Info` in the notebook (:gh:`9403` by `Alex Gramfort`_)
 
 - Add support for interpolating oxy and deoxyhaemoglobin data types (:gh:`9431` by `Robert Luke`_)
+
+- Add support for SNIRF files in :class:`mne.Report` (:gh:`9443` by `Robert Luke`_)
 
 Bugs
 ~~~~

mne/io/_read_raw.py

@@ -12,7 +12,7 @@
                read_raw_fif, read_raw_eeglab, read_raw_cnt, read_raw_egi,
                read_raw_eximia, read_raw_nirx, read_raw_fieldtrip,
                read_raw_artemis123, read_raw_nicolet, read_raw_kit,
-               read_raw_ctf, read_raw_boxy)
+               read_raw_ctf, read_raw_boxy, read_raw_snirf)
 from ..utils import fill_doc
 
 
@@ -39,6 +39,7 @@ def _read_unsupported(fname, **kwargs):
     ".mff": read_raw_egi,
     ".nxe": read_raw_eximia,
     ".hdr": read_raw_nirx,
+    ".snirf": read_raw_snirf,
     ".mat": read_raw_fieldtrip,
     ".bin": read_raw_artemis123,
     ".data": read_raw_nicolet,

mne/report.py

@@ -53,6 +53,7 @@
         RAW_EXTENSIONS.append(f'meg{ext}')
     RAW_EXTENSIONS.append(f'eeg{ext}')
     RAW_EXTENSIONS.append(f'ieeg{ext}')
+    RAW_EXTENSIONS.append(f'nirs{ext}')
 
 # Processed data will always be in (gzipped) FIFF format
 VALID_EXTENSIONS = ('sss.fif', 'sss.fif.gz',
@@ -258,7 +259,7 @@ def _get_toc_property(fname):
         div_klass = 'ssp'
         tooltip = fname
         text = op.basename(fname)
-    elif _endswith(fname, ['raw', 'sss', 'meg']):
+    elif _endswith(fname, ['raw', 'sss', 'meg', 'nirs']):
         div_klass = 'raw'
         tooltip = fname
         text = op.basename(fname)
@@ -314,7 +315,7 @@ def _update_html(html, report_fname, report_sectionlabel):
                     % op.join('...' + report.data_path[-20:],
                               fname))
         try:
-            if _endswith(fname, ['raw', 'sss', 'meg']):
+            if _endswith(fname, ['raw', 'sss', 'meg', 'nirs']):
                 html = report._render_raw(fname, data_path)
                 report_fname = fname
                 report_sectionlabel = 'raw'

mne/tests/test_report.py

@@ -49,6 +49,9 @@
                                'data'))
 evoked_fname = op.join(base_dir, 'test-ave.fif')
 
+nirs_fname = op.join(data_dir, 'SNIRF', 'NIRx', 'NIRSport2', '1.0.3',
+                     '2021-05-05_001.snirf')
+
 
 def _get_example_figures():
     """Create two example figures."""
@@ -70,14 +73,16 @@ def test_render_report(renderer, tmpdir):
     proj_fname_new = op.join(tempdir, 'temp_ecg-proj.fif')
     fwd_fname_new = op.join(tempdir, 'temp_raw-fwd.fif')
     inv_fname_new = op.join(tempdir, 'temp_raw-inv.fif')
+    nirs_fname_new = op.join(tempdir, 'temp_raw-nirs.snirf')
     for a, b in [[raw_fname, raw_fname_new],
                  [raw_fname, raw_fname_new_bids],
                  [ms_fname, ms_fname_new],
                  [event_fname, event_fname_new],
                  [cov_fname, cov_fname_new],
                  [proj_fname, proj_fname_new],
                  [fwd_fname, fwd_fname_new],
-                 [inv_fname, inv_fname_new]]:
+                 [inv_fname, inv_fname_new],
+                 [nirs_fname, nirs_fname_new]]:
         shutil.copyfile(a, b)
 
     # create and add -epo.fif and -ave.fif files
@@ -105,6 +110,7 @@ def test_render_report(renderer, tmpdir):
 
     # Check correct paths and filenames
     fnames = glob.glob(op.join(tempdir, '*.fif'))
+    fnames.extend(glob.glob(op.join(tempdir, '*.snirf')))
     for fname in fnames:
         assert (op.basename(fname) in
                 [op.basename(x) for x in report.fnames])