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MRG: Add fnirs and snirf support to report #9443

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merged 6 commits into from
Jun 6, 2021
Merged

MRG: Add fnirs and snirf support to report #9443

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f6651fc
Add snirf and nirs support to report
rob-luke Jun 3, 2021
dc17a48
Add to tests
rob-luke Jun 3, 2021
e75adff
Add to tests
rob-luke Jun 3, 2021
ac7eea3
Update report.py
rob-luke Jun 5, 2021
a305b14
Update latest.inc
rob-luke Jun 5, 2021
4fe739a
Update latest.inc
rob-luke Jun 5, 2021
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3 changes: 2 additions & 1 deletion mne/io/_read_raw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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


Expand All @@ -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,
Expand Down
5 changes: 3 additions & 2 deletions mne/report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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',
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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'
Expand Down
8 changes: 7 additions & 1 deletion mne/tests/test_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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."""
Expand All @@ -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
Expand Down Expand Up @@ -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])
Expand Down