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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import shutil
from datetime import date, datetime, timedelta, timezone
import numpy as np
import scipy.io as sio
from numpy.testing import assert_array_almost_equal, assert_array_equal, assert_equal
from mne import events_from_annotations, find_events, pick_types
from mne.datasets import testing
from mne.io import read_raw_gdf
from mne.io.tests.test_raw import _test_raw_reader
data_path = testing.data_path(download=False)
gdf1_path = data_path / "GDF" / "test_gdf_1.25"
gdf2_path = data_path / "GDF" / "test_gdf_2.20"
gdf_1ch_path = data_path / "GDF" / "test_1ch.gdf"
@testing.requires_testing_data
def test_gdf_data():
"""Test reading raw GDF 1.x files."""
raw = read_raw_gdf(
gdf1_path.with_name(gdf1_path.name + ".gdf"),
eog=None,
misc=None,
preload=True,
)
picks = pick_types(raw.info, meg=False, eeg=True, exclude="bads")
data, _ = raw[picks]
# Test Status is added as event
EXPECTED_EVS_ONSETS = raw._raw_extras[0]["events"][1]
EXPECTED_EVS_ID = {
f"{evs}": i
for i, evs in enumerate(
[
32769,
32770,
33024,
33025,
33026,
33027,
33028,
33029,
33040,
33041,
33042,
33043,
33044,
33045,
33285,
33286,
],
1,
)
}
evs, evs_id = events_from_annotations(raw)
assert_array_equal(evs[:, 0], EXPECTED_EVS_ONSETS)
assert evs_id == EXPECTED_EVS_ID
# this .npy was generated using the official biosig python package
raw_biosig = np.load(gdf1_path.with_name(gdf1_path.name + "_biosig.npy"))
raw_biosig = raw_biosig * 1e-6 # data are stored in microvolts
data_biosig = raw_biosig[picks]
# Assert data are almost equal
assert_array_almost_equal(data, data_biosig, 8)
# Test for events
assert len(raw.annotations.duration == 963)
# gh-5604
assert raw.info["meas_date"] is None
@testing.requires_testing_data
def test_gdf2_birthday(tmp_path):
"""Test reading raw GDF 2.x files."""
new_fname = tmp_path / "temp.gdf"
shutil.copyfile(gdf2_path.with_name(gdf2_path.name + ".gdf"), new_fname)
# go back 44.5 years so the subject should show up as 44
offset_edf = datetime.now(tz=timezone.utc) - datetime( # to their ref
1, 1, 1, tzinfo=timezone.utc
)
offset_44_yr = offset_edf - timedelta(days=int(365 * 44.5)) # 44.5 yr ago
offset_44_yr_days = offset_44_yr.total_seconds() / (24 * 60 * 60) # days
d = (int(offset_44_yr_days) + 367) * 2**32 # with their conversion
with open(new_fname, "r+b") as fid:
fid.seek(176, 0)
assert np.fromfile(fid, np.uint64, 1)[0] == 0
fid.seek(176, 0)
fid.write(np.array([d], np.uint64).tobytes())
fid.seek(176, 0)
assert np.fromfile(fid, np.uint64, 1)[0] == d
raw = read_raw_gdf(new_fname, eog=None, misc=None, preload=True)
assert "subject_info" not in raw._raw_extras[0]
assert raw.info["subject_info"] is not None
birthdate = datetime(1, 1, 1, tzinfo=timezone.utc) + offset_44_yr
assert raw.info["subject_info"]["birthday"] == date(
birthdate.year,
birthdate.month,
birthdate.day,
)
@testing.requires_testing_data
def test_gdf2_data():
"""Test reading raw GDF 2.x files."""
raw = read_raw_gdf(
gdf2_path.with_name(gdf2_path.name + ".gdf"),
eog=None,
misc=None,
preload=True,
)
assert raw.info["subject_info"]["birthday"] == date(1, 1, 1)
picks = pick_types(raw.info, meg=False, eeg=True, exclude="bads")
data, _ = raw[picks]
# This .mat was generated using the official biosig matlab package
mat = sio.loadmat(gdf2_path.with_name(gdf2_path.name + "_biosig.mat"))
data_biosig = mat["dat"] * 1e-6 # data are stored in microvolts
data_biosig = data_biosig[picks]
# Assert data are almost equal
assert_array_almost_equal(data, data_biosig, 8)
# Find events
events = find_events(raw, verbose=1)
events[:, 2] >>= 8 # last 8 bits are system events in biosemi files
assert_equal(events.shape[0], 2) # 2 events in file
assert_array_equal(events[:, 2], [20, 28])
# gh-5604
assert raw.info["meas_date"] is None
_test_raw_reader(
read_raw_gdf,
input_fname=gdf2_path.with_name(gdf2_path.name + ".gdf"),
eog=None,
misc=None,
test_scaling=False, # XXX this should be True
)
@testing.requires_testing_data
def test_one_channel_gdf():
"""Test a one-channel GDF file."""
ecg = read_raw_gdf(gdf_1ch_path, preload=True)
assert ecg["ECG"][0].shape == (1, 4500)
assert 150.0 == ecg.info["sfreq"]
@testing.requires_testing_data
def test_gdf_exclude_channels():
"""Test reading GDF data with excluded channels."""
raw = read_raw_gdf(
gdf1_path.with_name(gdf1_path.name + ".gdf"), exclude=("FP1", "O1")
)
assert "FP1" not in raw.ch_names
assert "O1" not in raw.ch_names
raw = read_raw_gdf(
gdf2_path.with_name(gdf2_path.name + ".gdf"), exclude=("Fp1", "O1")
)
assert "Fp1" not in raw.ch_names
assert "O1" not in raw.ch_names
raw = read_raw_gdf(gdf2_path.with_name(gdf2_path.name + ".gdf"), exclude=".+z$")
assert "AFz" not in raw.ch_names
assert "Cz" not in raw.ch_names
assert "Pz" not in raw.ch_names
assert "Oz" not in raw.ch_names
@testing.requires_testing_data
def test_gdf_include():
"""Test reading GDF data with include."""
raw = read_raw_gdf(
gdf1_path.with_name(gdf1_path.name + ".gdf"), include=("FP1", "O1")
)
assert sorted(raw.ch_names) == ["FP1", "O1"]
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