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import os.path as op
import numpy as np
from numpy.testing import (assert_allclose, assert_array_equal)
import pytest
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.utils import run_tests_if_main
base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
raw_fname = op.join(base_dir, 'test_raw.fif')
event_name = op.join(base_dir, 'test-eve.fif')
raw_fname_ctf = op.join(base_dir, 'test_ctf_raw.fif')
event_id, tmin, tmax = 1, -0.2, 0.5
event_id_2 = 2
def _load_data(kind):
"""Load data."""
# It is more memory efficient to load data in a separate
# function so it's loaded on-demand
raw = io.read_raw_fif(raw_fname)
events = read_events(event_name)
# subselect channels for speed
if kind == 'eeg':
picks = pick_types(raw.info, meg=False, eeg=True, exclude=[])[:15]
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True, reject=dict(eeg=80e-6))
else:
picks = pick_types(raw.info, meg=True, eeg=False, exclude=[])[1:200:2]
assert kind == 'meg'
with pytest.warns(RuntimeWarning, match='projection'):
epochs = Epochs(raw, events, event_id, tmin, tmax, picks=picks,
preload=True,
reject=dict(grad=1000e-12, mag=4e-12))
return raw, epochs
def test_interpolation_eeg():
"""Test interpolation of EEG channels."""
raw, epochs_eeg = _load_data('eeg')
# check that interpolation does nothing if no bads are marked
epochs_eeg.info['bads'] = []
evoked_eeg = epochs_eeg.average()
with pytest.warns(RuntimeWarning, match='Doing nothing'):
evoked_eeg.interpolate_bads()
# create good and bad channels for EEG
epochs_eeg.info['bads'] = []
goods_idx = np.ones(len(epochs_eeg.ch_names), dtype=bool)
goods_idx[epochs_eeg.ch_names.index('EEG 012')] = False
bads_idx = ~goods_idx
evoked_eeg = epochs_eeg.average()
ave_before = evoked_eeg.data[bads_idx]
# interpolate bad channels for EEG
pos = epochs_eeg._get_channel_positions()
pos_good = pos[goods_idx]
pos_bad = pos[bads_idx]
interpolation = _make_interpolation_matrix(pos_good, pos_bad)
assert interpolation.shape == (1, len(epochs_eeg.ch_names) - 1)
ave_after = np.dot(interpolation, evoked_eeg.data[goods_idx])
epochs_eeg.info['bads'] = ['EEG 012']
evoked_eeg = epochs_eeg.average()
assert_array_equal(ave_after, evoked_eeg.interpolate_bads().data[bads_idx])
assert_allclose(ave_before, ave_after, atol=2e-6)
# check that interpolation fails when preload is False
epochs_eeg.preload = False
pytest.raises(RuntimeError, epochs_eeg.interpolate_bads)
epochs_eeg.preload = True
# check that interpolation changes the data in raw
raw_eeg = io.RawArray(data=epochs_eeg._data[0], info=epochs_eeg.info)
raw_before = raw_eeg._data[bads_idx]
raw_after = raw_eeg.interpolate_bads()._data[bads_idx]
assert not np.all(raw_before == raw_after)
# check that interpolation fails when preload is False
for inst in [raw, epochs_eeg]:
assert hasattr(inst, 'preload')
inst.preload = False
inst.info['bads'] = [inst.ch_names[1]]
pytest.raises(RuntimeError, inst.interpolate_bads)
# check that interpolation works with few channels
raw_few = raw.copy().crop(0, 0.1).load_data()
raw_few.pick_channels(raw_few.ch_names[:1] + raw_few.ch_names[3:4])
assert len(raw_few.ch_names) == 2
raw_few.del_proj()
raw_few.info['bads'] = [raw_few.ch_names[-1]]
orig_data = raw_few[1][0]
with pytest.warns(None) as w:
raw_few.interpolate_bads(reset_bads=False)
assert len(w) == 0
new_data = raw_few[1][0]
assert (new_data == 0).mean() < 0.5
assert np.corrcoef(new_data, orig_data)[0, 1] > 0.1
def test_interpolation_meg():
"""Test interpolation of MEG channels."""
# speed accuracy tradeoff: channel subselection is faster but the
# correlation drops
thresh = 0.7
raw, epochs_meg = _load_data('meg')
# check that interpolation works when non M/EEG channels are present
# before MEG channels
raw.crop(0, 0.1).load_data().pick_channels(epochs_meg.ch_names)
raw.info.normalize_proj()
with pytest.warns(RuntimeWarning, match='unit .* changed from .* to .*'):
raw.set_channel_types({raw.ch_names[0]: 'stim'})
raw.info['bads'] = [raw.ch_names[1]]
raw.load_data()
raw.interpolate_bads(mode='fast')
del raw
# check that interpolation works for MEG
epochs_meg.info['bads'] = ['MEG 0141']
evoked = epochs_meg.average()
pick = pick_channels(epochs_meg.info['ch_names'], epochs_meg.info['bads'])
# MEG -- raw
raw_meg = io.RawArray(data=epochs_meg._data[0], info=epochs_meg.info)
raw_meg.info['bads'] = ['MEG 0141']
data1 = raw_meg[pick, :][0][0]
raw_meg.info.normalize_proj()
data2 = raw_meg.interpolate_bads(reset_bads=False,
mode='fast')[pick, :][0][0]
assert np.corrcoef(data1, data2)[0, 1] > thresh
# the same number of bads as before
assert len(raw_meg.info['bads']) == len(raw_meg.info['bads'])
# MEG -- epochs
data1 = epochs_meg.get_data()[:, pick, :].ravel()
epochs_meg.info.normalize_proj()
epochs_meg.interpolate_bads(mode='fast')
data2 = epochs_meg.get_data()[:, pick, :].ravel()
assert np.corrcoef(data1, data2)[0, 1] > thresh
assert len(epochs_meg.info['bads']) == 0
# MEG -- evoked (plus auto origin)
data1 = evoked.data[pick]
evoked.info.normalize_proj()
data2 = evoked.interpolate_bads(origin='auto').data[pick]
assert np.corrcoef(data1, data2)[0, 1] > thresh
def _this_interpol(inst, ref_meg=False):
from mne.channels.interpolation import _interpolate_bads_meg
_interpolate_bads_meg(inst, ref_meg=ref_meg, mode='fast')
return inst
def test_interpolate_meg_ctf():
"""Test interpolation of MEG channels from CTF system."""
thresh = .7
tol = .05 # assert the new interpol correlates at least .05 "better"
bad = 'MLC22-2622' # select a good channel to test the interpolation
raw = io.read_raw_fif(raw_fname_ctf, preload=True) # 3 secs
raw.apply_gradient_compensation(3)
# Show that we have to exclude ref_meg for interpolating CTF MEG-channels
# (fixed in #5965):
raw.info['bads'] = [bad]
pick_bad = pick_channels(raw.info['ch_names'], raw.info['bads'])
data_orig = raw[pick_bad, :][0]
# mimic old behavior (the ref_meg-arg in _interpolate_bads_meg only serves
# this purpose):
data_interp_refmeg = _this_interpol(raw, ref_meg=True)[pick_bad, :][0]
# new:
data_interp_no_refmeg = _this_interpol(raw, ref_meg=False)[pick_bad, :][0]
R = dict()
R['no_refmeg'] = np.corrcoef(data_orig, data_interp_no_refmeg)[0, 1]
R['with_refmeg'] = np.corrcoef(data_orig, data_interp_refmeg)[0, 1]
print('Corrcoef of interpolated with original channel: ', R)
assert R['no_refmeg'] > R['with_refmeg'] + tol
assert R['no_refmeg'] > thresh
@testing.requires_testing_data
def test_interpolation_ctf_comp():
"""Test interpolation with compensated CTF data."""
ctf_dir = op.join(testing.data_path(download=False), 'CTF')
raw_fname = op.join(ctf_dir, 'somMDYO-18av.ds')
raw = io.read_raw_ctf(raw_fname, preload=True)
raw.info['bads'] = [raw.ch_names[5], raw.ch_names[-5]]
raw.interpolate_bads(mode='fast')
assert raw.info['bads'] == []
run_tests_if_main()
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