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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import os
import shutil
import numpy as np
import pytest
from numpy.testing import assert_array_equal
from mne.datasets.testing import data_path, requires_testing_data
from mne.io import read_raw_persyst
from mne.io.tests.test_raw import _test_raw_reader
testing_path = data_path(download=False)
fname_lay = (
testing_path / "Persyst" / "sub-pt1_ses-02_task-monitor_acq-ecog_run-01_clip2.lay"
)
fname_dat = (
testing_path / "Persyst" / "sub-pt1_ses-02_task-monitor_acq-ecog_run-01_clip2.dat"
)
@requires_testing_data
def test_persyst_lay_load():
"""Test reading Persyst files using path to header file."""
raw = read_raw_persyst(fname_lay, preload=False)
# Test data import
assert raw.info["sfreq"] == 200
assert raw.preload is False
# load raw data
raw.load_data()
assert raw._data.shape == (83, 847)
assert raw.preload is True
# defaults channels to EEG
raw = raw.pick("eeg")
assert len(raw.ch_names) == 83
# no "-Ref" in channel names
assert all(["-ref" not in ch.lower() for ch in raw.ch_names])
# test with preload True
raw = read_raw_persyst(fname_lay, preload=True)
@requires_testing_data
def test_persyst_raw():
"""Test reading Persyst files using path to header file."""
raw = read_raw_persyst(fname_lay, preload=False)
# defaults channels to EEG
raw = raw.pick("eeg")
# get data
data, times = raw.get_data(start=200, return_times=True)
assert data.shape == (83, 647)
# seconds should match up to what is in the file
assert times.min() == 1.0
assert times.max() == 4.23
# get data
data = raw.get_data(start=200, stop=400)
assert data.shape == (83, 200)
# data should have been set correctly
assert not data.min() == 0 and not data.max() == 0
first_ch_data = raw.get_data(picks=[0], start=200, stop=400)
assert_array_equal(first_ch_data.squeeze(), data[0, :])
@requires_testing_data
def test_persyst_dates(tmp_path):
"""Test different Persyst date formats for meas date."""
# now test what if you change contents of the lay file
new_fname_lay = tmp_path / fname_lay.name
new_fname_dat = tmp_path / fname_dat.name
shutil.copy(fname_dat, new_fname_dat)
# reformat the lay file to have testdate with
# "/" character
with open(fname_lay) as fin:
with open(new_fname_lay, "w") as fout:
# for each line in the input file
for idx, line in enumerate(fin):
if line.startswith("TestDate"):
line = "TestDate=01/23/2000\n"
fout.write(line)
# file should update correctly with datetime
raw = read_raw_persyst(new_fname_lay)
assert raw.info["meas_date"].month == 1
assert raw.info["meas_date"].day == 23
assert raw.info["meas_date"].year == 2000
# reformat the lay file to have testdate with
# "-" character
os.remove(new_fname_lay)
with open(fname_lay) as fin:
with open(new_fname_lay, "w") as fout:
# for each line in the input file
for idx, line in enumerate(fin):
if line.startswith("TestDate"):
line = "TestDate=24-01-2000\n"
fout.write(line)
# file should update correctly with datetime
raw = read_raw_persyst(new_fname_lay)
assert raw.info["meas_date"].month == 1
assert raw.info["meas_date"].day == 24
assert raw.info["meas_date"].year == 2000
@requires_testing_data
def test_persyst_wrong_file(tmp_path):
"""Test reading Persyst files when passed in wrong file path."""
with pytest.raises(FileNotFoundError, match="The path you"):
read_raw_persyst(fname_dat, preload=True)
new_fname_lay = tmp_path / fname_lay.name
new_fname_dat = tmp_path / fname_dat.name
shutil.copy(fname_lay, new_fname_lay)
# without a .dat file, reader should break
desired_err_msg = (
"The data path you specified does "
"not exist for the lay path, "
"sub-pt1_ses-02_task-monitor_acq-ecog_run-01_clip2.lay"
)
with pytest.raises(FileNotFoundError, match=desired_err_msg):
read_raw_persyst(new_fname_lay, preload=True)
# once you copy over the .dat file things should work
shutil.copy(fname_dat, new_fname_dat)
read_raw_persyst(new_fname_lay, preload=True)
@requires_testing_data
def test_persyst_moved_file(tmp_path):
"""Test reader - Persyst files need to be in same directory."""
new_fname_lay = tmp_path / fname_lay.name
new_fname_dat = tmp_path / fname_dat.name
shutil.copy(fname_lay, new_fname_lay)
# original file read should work
read_raw_persyst(fname_lay)
# without a .dat file, reader should break
# when the lay file was moved
desired_err_msg = (
"The data path you specified does "
"not exist for the lay path, "
"sub-pt1_ses-02_task-monitor_acq-ecog_run-01_clip2.lay"
)
with pytest.raises(FileNotFoundError, match=desired_err_msg):
read_raw_persyst(new_fname_lay, preload=True)
# now change the file contents to point
# to the full path, but it should still not work
# as reader requires lay and dat file to be in
# same directory
with open(fname_lay) as fin:
with open(new_fname_lay, "w") as fout:
# for each line in the input file
for idx, line in enumerate(fin):
if line.startswith("File="):
# give it the full path to the old data
test_fpath = fname_dat.parent / line.split("=")[1]
line = f"File={test_fpath}\n"
fout.write(line)
with pytest.raises(FileNotFoundError, match=desired_err_msg):
read_raw_persyst(new_fname_lay, preload=True)
# once we copy the dat file to the same directory, reader
# should work
shutil.copy(fname_dat, new_fname_dat)
read_raw_persyst(new_fname_lay, preload=True)
@requires_testing_data
def test_persyst_standard():
"""Test standard operations."""
_test_raw_reader(read_raw_persyst, fname=fname_lay)
@requires_testing_data
def test_persyst_annotations(tmp_path):
"""Test annotations reading in Persyst."""
new_fname_lay = tmp_path / fname_lay.name
new_fname_dat = tmp_path / fname_dat.name
shutil.copy(fname_dat, new_fname_dat)
shutil.copy(fname_lay, new_fname_lay)
raw = read_raw_persyst(new_fname_lay)
raw.crop(tmin=0, tmax=4)
# get the annotations and make sure that repeated annotations
# are in the dataset
annotations = raw.annotations
assert np.count_nonzero(annotations.description == "seizure") == 2
# make sure annotation with a "," character is in there
assert "seizure1,2" in annotations.description
assert "CLip2" in annotations.description
@requires_testing_data
def test_persyst_errors(tmp_path):
"""Test reading Persyst files when passed in wrong file path."""
new_fname_lay = tmp_path / fname_lay.name
new_fname_dat = tmp_path / fname_dat.name
shutil.copy(fname_dat, new_fname_dat)
# reformat the lay file
with open(fname_lay) as fin:
with open(new_fname_lay, "w") as fout:
# for each line in the input file
for idx, line in enumerate(fin):
if idx == 1:
line = line.replace("=", ",")
fout.write(line)
# file should break
with pytest.raises(RuntimeError, match="The line"):
read_raw_persyst(new_fname_lay)
# reformat the lay file
os.remove(new_fname_lay)
with open(fname_lay) as fin:
with open(new_fname_lay, "w") as fout:
# for each line in the input file
for idx, line in enumerate(fin):
if line.startswith("WaveformCount"):
line = "WaveformCount=1\n"
fout.write(line)
# file should break
with pytest.raises(RuntimeError, match="Channels in lay file do not"):
read_raw_persyst(new_fname_lay)
# reformat the lay file to have testdate
# improperly specified
os.remove(new_fname_lay)
with open(fname_lay) as fin:
with open(new_fname_lay, "w") as fout:
# for each line in the input file
for idx, line in enumerate(fin):
if line.startswith("TestDate"):
line = "TestDate=Jan 23rd 2000\n"
fout.write(line)
# file should not read in meas date
with pytest.warns(RuntimeWarning, match="Cannot read in the measurement date"):
raw = read_raw_persyst(new_fname_lay)
assert raw.info["meas_date"] is None
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