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Merged
agramfort merged 3 commits into from
May 29, 2021
Merged

MRG: Enable interpolation for all fNIRS types #9431

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fea17f7
Enable interpolation for all fNIRS types
rob-luke May 29, 2021
a7d5e0f
Update interpolation.py
rob-luke May 29, 2021
45875b6
Update latest.inc
rob-luke May 29, 2021
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2 changes: 2 additions & 0 deletions doc/changes/latest.inc
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Expand Up @@ -47,6 +47,8 @@ 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`_)

Bugs
~~~~
- Fix bug with :meth:`mne.Epochs.crop` and :meth:`mne.Evoked.crop` when ``include_tmax=False``, where the last sample was always cut off, even when ``tmax > epo.times[-1]`` (:gh:`9378` **by new contributor** |Jan Sosulski|_)
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6 changes: 2 additions & 4 deletions mne/channels/interpolation.py
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Expand Up @@ -205,12 +205,10 @@ def _interpolate_bads_meeg(inst, mode='accurate', origin=(0., 0., 0.04),
@verbose
def _interpolate_bads_nirs(inst, method='nearest', exclude=(), verbose=None):
from scipy.spatial.distance import pdist, squareform
from mne.preprocessing.nirs import _channel_frequencies,\
_check_channels_ordered
from mne.preprocessing.nirs import _validate_nirs_info

# Returns pick of all nirs and ensures channels are correctly ordered
freqs = np.unique(_channel_frequencies(inst.info))
picks_nirs = _check_channels_ordered(inst.info, freqs)
picks_nirs = _validate_nirs_info(inst.info)
if len(picks_nirs) == 0:
return

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8 changes: 7 additions & 1 deletion mne/channels/tests/test_interpolation.py
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Expand Up @@ -8,7 +8,8 @@
from mne import io, pick_types, pick_channels, read_events, Epochs
from mne.channels.interpolation import _make_interpolation_matrix
from mne.datasets import testing
from mne.preprocessing.nirs import optical_density, scalp_coupling_index
from mne.preprocessing.nirs import (optical_density, scalp_coupling_index,
beer_lambert_law)
from mne.datasets.testing import data_path
from mne.io import read_raw_nirx
from mne.io.proj import _has_eeg_average_ref_proj
Expand Down Expand Up @@ -303,3 +304,8 @@ def test_interpolation_nirs():
raw_od.interpolate_bads()
assert raw_od.info['bads'] == []
assert bad_0_std_pre_interp > np.std(raw_od._data[bad_0])
raw_haemo = beer_lambert_law(raw_od)
raw_haemo.info['bads'] = raw_haemo.ch_names[2:4]
assert raw_haemo.info['bads'] == ['S1_D2 hbo', 'S1_D2 hbr']
raw_haemo.interpolate_bads()
assert raw_haemo.info['bads'] == []