def test_persyst_errors():
"""Test reading Persyst files when passed in wrong file path."""
out_dir = mne.utils._TempDir()
new_fname_lay = op.join(out_dir, op.basename(fname_lay))
new_fname_dat = op.join(out_dir, op.basename(fname_dat))
shutil.copy(fname_dat, new_fname_dat)
# reformat the lay file
with open(fname_lay, "r") 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, "r") 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, "r") 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
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_types(eeg=True)
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)
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
out_dir = str(tmp_path)
new_fname_lay = op.join(out_dir, op.basename(fname_lay))
new_fname_dat = op.join(out_dir, op.basename(fname_dat))
shutil.copy(fname_dat, new_fname_dat)
# reformat the lay file to have testdate with
# "/" character
with open(fname_lay, "r") 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, "r") 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
def test_persyst_annotations(tmpdir):
"""Test annotations reading in Persyst."""
out_dir = str(tmpdir)
new_fname_lay = op.join(out_dir, op.basename(fname_lay))
new_fname_dat = op.join(out_dir, op.basename(fname_dat))
shutil.copy(fname_dat, new_fname_dat)
shutil.copy(fname_lay, new_fname_lay)
raw = read_raw_persyst(new_fname_lay)
# 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
def test_persyst_annotations(tmp_path):
"""Test annotations reading in Persyst."""
new_fname_lay = tmp_path / op.basename(fname_lay)
new_fname_dat = tmp_path / op.basename(fname_dat)
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
def test_persyst_moved_file(tmp_path):
"""Test reader - Persyst files need to be in same directory."""
out_dir = str(tmp_path)
new_fname_lay = op.join(out_dir, op.basename(fname_lay))
new_fname_dat = op.join(out_dir, op.basename(fname_dat))
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, "r") 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 = op.join(op.dirname(fname_dat),
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)
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_types(eeg=True)
# 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, :])
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)
out_dir = str(tmp_path)
new_fname_lay = op.join(out_dir, op.basename(fname_lay))
new_fname_dat = op.join(out_dir, op.basename(fname_dat))
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)
