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# Author: Adonay Nunes <adonay.s.nunes@gmail.com>
#
# License: BSD-3-Clause
import os.path as op
import numpy as np
import pytest
from numpy.testing import assert_allclose, assert_array_equal
from mne.chpi import read_head_pos
from mne.datasets import testing
from mne.io import read_raw_fif
from mne.preprocessing import (annotate_movement, compute_average_dev_head_t,
annotate_muscle_zscore, annotate_break)
from mne import Annotations, events_from_annotations
from mne.tests.test_annotations import _assert_annotations_equal
data_path = testing.data_path(download=False)
sss_path = op.join(data_path, 'SSS')
pos_fname = op.join(sss_path, 'test_move_anon_raw.pos')
raw_fname = op.join(sss_path, 'test_move_anon_raw.fif')
@testing.requires_testing_data
@pytest.mark.parametrize('meas_date', (None, 'orig'))
def test_movement_annotation_head_correction(meas_date):
"""Test correct detection movement artifact and dev_head_t."""
raw = read_raw_fif(raw_fname, allow_maxshield='yes').load_data()
pos = read_head_pos(pos_fname)
if meas_date is None:
raw.set_meas_date(None)
else:
assert meas_date == 'orig'
# Check 5 rotation segments are detected
annot_rot, [] = annotate_movement(raw, pos, rotation_velocity_limit=5)
assert annot_rot.orig_time == raw.info["meas_date"]
assert annot_rot.duration.size == 5
# Check 2 translation vel. segments are detected
annot_tra, [] = annotate_movement(raw, pos, translation_velocity_limit=.05)
assert annot_tra.duration.size == 2
# Check 1 movement distance segment is detected
annot_dis, _ = annotate_movement(raw, pos, mean_distance_limit=.02)
assert annot_dis.duration.size == 1
# Check correct trans mat
annot_all_2 = annotate_movement(
raw, pos, rotation_velocity_limit=5,
translation_velocity_limit=.05,
mean_distance_limit=.02)[0]
assert (annot_rot.orig_time ==
annot_tra.orig_time ==
annot_dis.orig_time ==
raw.info['meas_date'])
annot_all = annot_rot + annot_tra + annot_dis
_assert_annotations_equal(annot_all_2, annot_all)
assert annot_all.orig_time == raw.info['meas_date']
raw.set_annotations(annot_all)
dev_head_t = compute_average_dev_head_t(raw, pos)
dev_head_t_ori = np.array([
[0.9957292, -0.08688804, 0.03120615, 0.00698271],
[0.09020767, 0.9875856, -0.12859731, -0.0159098],
[-0.01964518, 0.1308631, 0.99120578, 0.07258289],
[0., 0., 0., 1.]])
assert_allclose(dev_head_t_ori, dev_head_t['trans'], rtol=1e-5, atol=0)
# Smoke test skipping time due to previous annotations.
raw.set_annotations(Annotations([raw.times[0]], 0.1, 'bad'))
annot_dis, _ = annotate_movement(raw, pos, mean_distance_limit=.02)
assert annot_dis.duration.size == 1
@testing.requires_testing_data
@pytest.mark.parametrize('meas_date', (None, 'orig'))
def test_muscle_annotation(meas_date, events):
"""Test correct detection muscle artifacts."""
raw = read_raw_fif(raw_fname, allow_maxshield='yes').load_data()
if meas_date is None:
raw.set_meas_date(None)
raw.notch_filter([50, 110, 150])
# Check 2 muscle segments are detected
annot_muscle, scores = annotate_muscle_zscore(raw, ch_type='mag',
threshold=10)
assert annot_muscle.orig_time == raw.info["meas_date"]
onset = annot_muscle.onset * raw.info['sfreq']
if meas_date is not None:
onset -= raw.first_samp
onset = onset.astype(int)
assert_array_equal(scores[onset].astype(int), np.array([23, 10]))
assert annot_muscle.duration.size == 2
raw.set_annotations(annot_muscle)
@testing.requires_testing_data
@pytest.mark.parametrize('meas_date', (None, 'orig'))
def test_muscle_annotation_without_meeg_data(meas_date):
"""Call annotate_muscle_zscore with data without meg or eeg."""
raw = read_raw_fif(raw_fname, allow_maxshield='yes')
if meas_date is None:
raw.set_meas_date(None)
raw.crop(0, .1).load_data()
raw.pick_types(meg=False, stim=True)
with pytest.raises(ValueError, match="No M/EEG channel types found"):
annotate_muscle_zscore(raw, threshold=10)
@pytest.mark.parametrize('meas_date', (None, "orig"))
@testing.requires_testing_data
def test_annotate_breaks(meas_date):
"""Test annotate_breaks."""
raw = read_raw_fif(raw_fname, allow_maxshield='yes')
if meas_date is None:
raw.set_meas_date(None)
annots = Annotations(onset=[12, 15, 16, 20, 21],
duration=[1, 1, 1, 2, 0.5],
description=['test'],
orig_time=raw.info['meas_date'])
if raw.info['meas_date'] is None:
annots.onset -= raw.first_time
raw.set_annotations(annots)
min_break_duration = 0.5
t_start_after_previous = 0.1
t_stop_before_next = 0.1
expected_onsets = np.array(
[
raw.first_time,
13 + t_start_after_previous,
17 + t_start_after_previous,
22 + t_start_after_previous
]
)
if raw.info['meas_date'] is None:
expected_onsets -= raw.first_time
expected_durations = np.array(
[
12 - raw.first_time - t_stop_before_next,
15 - 13 - t_start_after_previous - t_stop_before_next,
20 - 17 - t_start_after_previous - t_stop_before_next,
raw._last_time - 22 - t_start_after_previous
]
)
break_annots = annotate_break(
raw=raw,
min_break_duration=min_break_duration,
t_start_after_previous=t_start_after_previous,
t_stop_before_next=t_stop_before_next
)
assert break_annots.orig_time == raw.info["meas_date"]
assert_allclose(break_annots.onset, expected_onsets)
assert_allclose(break_annots.duration, expected_durations)
assert all(description == 'BAD_break'
for description in break_annots.description)
# try setting the annotations, this should not omit anything
raw.set_annotations(break_annots)
current_annotations = raw.annotations
if raw.info['meas_date'] is None:
current_annotations.onset -= raw.first_time
raw.set_annotations(current_annotations + break_annots)
# reset before next test
raw.set_annotations(annots)
# `ignore` parameter should be respected
raw.annotations.description[0] = 'BAD_'
break_annots = annotate_break(
raw=raw,
min_break_duration=min_break_duration,
t_start_after_previous=t_start_after_previous,
t_stop_before_next=t_stop_before_next
)
assert_allclose(break_annots.onset,
expected_onsets[[True, False, True, True]])
assert_allclose(
break_annots.duration,
[15 - raw.first_time - t_stop_before_next] +
list(expected_durations[2:])
)
# try setting the annotations, this should not omit anything
raw.set_annotations(break_annots)
current_annotations = raw.annotations
if raw.info['meas_date'] is None:
current_annotations.onset -= raw.first_time
raw.set_annotations(current_annotations + break_annots)
# Restore annotations for next test
raw.set_annotations(annots)
raw.annotations.description[0] = 'test'
# Test with events
events, _ = events_from_annotations(raw=raw)
raw.set_annotations(None)
expected_onsets = np.array(
[
raw.first_time,
12 + t_start_after_previous,
15 + t_start_after_previous,
16 + t_start_after_previous,
20 + t_start_after_previous,
21 + t_start_after_previous
]
)
expected_durations = np.array(
[
12 - raw.first_time - t_stop_before_next,
15 - 12 - t_start_after_previous - t_stop_before_next,
16 - 15 - t_start_after_previous - t_stop_before_next,
20 - 16 - t_start_after_previous - t_stop_before_next,
21 - 20 - t_start_after_previous - t_stop_before_next,
raw._last_time - 21 - t_start_after_previous
]
)
break_annots = annotate_break(
raw=raw,
events=events,
min_break_duration=min_break_duration,
t_start_after_previous=t_start_after_previous,
t_stop_before_next=t_stop_before_next
)
if raw.info['meas_date'] is None:
expected_onsets -= raw.first_time
assert_allclose(break_annots.onset, expected_onsets)
assert_allclose(break_annots.duration, expected_durations)
# try setting the annotations, this should not omit anything
raw.set_annotations(break_annots)
current_annotations = raw.annotations
if raw.info['meas_date'] is None:
current_annotations.onset -= raw.first_time
raw.set_annotations(current_annotations + break_annots)
# reset before next test
raw.set_annotations(annots)
# Not finding any break periods
break_annots = annotate_break(
raw=raw,
events=events,
min_break_duration=1000,
)
assert len(break_annots) == 0
# Implausible parameters (would produce break annot of duration < 0)
with pytest.raises(ValueError, match='must be greater than 0'):
annotate_break(
raw=raw,
min_break_duration=5,
t_start_after_previous=5,
t_stop_before_next=5
)
# Empty events array
with pytest.raises(ValueError, match='events array must not be empty'):
annotate_break(raw=raw, events=np.array([]))
# Invalid `ignore` value
with pytest.raises(TypeError, match='must be an instance of str'):
annotate_break(raw=raw, ignore=('foo', 1))
# No annotations to work with
raw.set_annotations(None)
with pytest.raises(ValueError, match='Could not find.*annotations'):
annotate_break(raw=raw)
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