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# -*- coding: utf-8 -*-
#
# Authors: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>
#
#
# License: BSD (3-clause)
import os.path as op
import numpy as np
from shutil import copyfile
import pytest
from numpy.testing import assert_allclose, assert_array_equal
from mne.annotations import events_from_annotations
from mne.datasets import testing
from mne.event import find_events
from mne.io.constants import FIFF
from mne.io.edf import read_raw_bdf
from mne.io.bti import read_raw_bti
from mne.io.curry import read_raw_curry
from mne.utils import check_version, run_tests_if_main
from mne.annotations import read_annotations
from mne.io.curry.curry import (_get_curry_version, _get_curry_file_structure,
_read_events_curry, FILE_EXTENSIONS)
data_dir = testing.data_path(download=False)
curry_dir = op.join(data_dir, "curry")
bdf_file = op.join(data_dir, 'BDF', 'test_bdf_stim_channel.bdf')
bti_rfDC_file = op.join(data_dir, 'BTi', 'erm_HFH', 'c,rfDC')
curry7_rfDC_file = op.join(curry_dir, "c,rfDC Curry 7.dat")
curry8_rfDC_file = op.join(curry_dir, "c,rfDC Curry 8.cdt")
curry7_bdf_file = op.join(curry_dir, "test_bdf_stim_channel Curry 7.dat")
curry7_bdf_ascii_file = op.join(curry_dir,
"test_bdf_stim_channel Curry 7 ASCII.dat")
curry8_bdf_file = op.join(curry_dir, "test_bdf_stim_channel Curry 8.cdt")
curry8_bdf_ascii_file = op.join(curry_dir,
"test_bdf_stim_channel Curry 8 ASCII.cdt")
missing_event_file = op.join(curry_dir, "test_sfreq_0.dat")
@pytest.fixture(scope='session')
def bdf_curry_ref():
"""Return a view of the reference bdf used to create the curry files."""
raw = read_raw_bdf(bdf_file, preload=True).drop_channels(['Status'])
return raw
@testing.requires_testing_data
@pytest.mark.parametrize('fname,tol', [
pytest.param(curry7_bdf_file, 1e-7, id='curry 7'),
pytest.param(curry8_bdf_file, 1e-7, id='curry 8'),
pytest.param(curry7_bdf_ascii_file, 1e-4, id='curry 7 ascii'),
pytest.param(curry8_bdf_ascii_file, 1e-4, id='curry 8 ascii'),
])
@pytest.mark.parametrize('preload', [True, False])
def test_read_raw_curry(fname, tol, preload, bdf_curry_ref):
"""Test reading CURRY files."""
with pytest.warns(None) as wrn:
raw = read_raw_curry(fname, preload=preload)
if not check_version('numpy', '1.16') and preload and fname.endswith(
'ASCII.dat'):
assert len(wrn) > 0
else:
assert len(wrn) == 0
assert hasattr(raw, '_data') == preload
assert raw.n_times == bdf_curry_ref.n_times
assert raw.info['sfreq'] == bdf_curry_ref.info['sfreq']
for field in ['kind', 'ch_name']:
assert_array_equal([ch[field] for ch in raw.info['chs']],
[ch[field] for ch in bdf_curry_ref.info['chs']])
raw.verbose = 'error' # don't emit warnings about slow reading
assert_allclose(raw.get_data(), bdf_curry_ref.get_data(), atol=tol)
picks, start, stop = ["C3", "C4"], 200, 800
assert_allclose(
raw.get_data(picks=picks, start=start, stop=stop),
bdf_curry_ref.get_data(picks=picks, start=start, stop=stop),
rtol=tol)
@testing.requires_testing_data
@pytest.mark.parametrize('fname,tol', [
pytest.param(curry7_rfDC_file, 1e-6, id='curry 7'),
pytest.param(curry8_rfDC_file, 1e-3, id='curry 8'),
])
def test_read_raw_curry_rfDC(fname, tol):
"""Test reading CURRY files."""
# check data
bti_rfDC = read_raw_bti(pdf_fname=bti_rfDC_file, head_shape_fname=None)
raw = read_raw_curry(fname)
# test on the eeg chans, since these were not renamed by curry
eeg_names = [ch["ch_name"] for ch in raw.info["chs"]
if ch["kind"] == FIFF.FIFFV_EEG_CH]
assert_allclose(raw.get_data(eeg_names),
bti_rfDC.get_data(eeg_names), rtol=tol)
@testing.requires_testing_data
@pytest.mark.parametrize('fname', [
pytest.param(curry7_bdf_file, id='curry 7'),
pytest.param(curry8_bdf_file, id='curry 8'),
])
def test_read_events_curry_are_same_as_bdf(fname):
"""Test events from curry annotations recovers the right events."""
EVENT_ID = {str(ii): ii for ii in range(5)}
REF_EVENTS = find_events(read_raw_bdf(bdf_file, preload=True))
raw = read_raw_curry(fname)
events, _ = events_from_annotations(raw, event_id=EVENT_ID)
assert_allclose(events, REF_EVENTS)
def test_check_missing_files():
"""Test checking for missing curry files (smoke test)."""
invalid_fname = "/invalid/path/name.xy"
with pytest.raises(IOError, match="file type .*? must end with"):
_read_events_curry(invalid_fname)
with pytest.raises(FileNotFoundError, match="files cannot be found"):
_get_curry_file_structure(invalid_fname)
_get_curry_file_structure(missing_event_file,
required=["info", "events"])
def _mock_info_file(src, dst, sfreq, time_step):
with open(src, 'r') as in_file, open(dst, 'w') as out_file:
for line in in_file:
if 'SampleFreqHz' in line:
out_file.write(line.replace('500', str(sfreq)))
elif 'SampleTimeUsec' in line:
out_file.write(line.replace('2000', str(time_step)))
else:
out_file.write(line)
@pytest.fixture(params=[
pytest.param(dict(sfreq=500, time_step=0), id='correct sfreq'),
pytest.param(dict(sfreq=0, time_step=2000), id='correct time_step'),
pytest.param(dict(sfreq=500, time_step=2000), id='both correct'),
pytest.param(dict(sfreq=0, time_step=0), id='both 0',
marks=pytest.mark.xfail(raises=ValueError)),
pytest.param(dict(sfreq=500, time_step=42), id='mismatch',
marks=pytest.mark.xfail(raises=ValueError)),
])
def sfreq_testing_data(tmpdir, request):
"""Generate different sfreq, time_step scenarios to be tested."""
sfreq, time_step = request.param['sfreq'], request.param['time_step']
in_base_name = curry7_bdf_file.strip('dat')
out_base_name = str(tmpdir.join('curry.'))
# create dummy empty files for 'dat' and 'rs3'
for fname in [out_base_name + ext for ext in ['dat', 'rs3']]:
open(fname, 'a').close()
_mock_info_file(src=in_base_name + 'dap', dst=out_base_name + 'dap',
sfreq=sfreq, time_step=time_step)
return out_base_name + 'dat'
@testing.requires_testing_data
def test_sfreq(sfreq_testing_data):
"""Test sfreq and time_step."""
raw = read_raw_curry(sfreq_testing_data, preload=False)
assert raw.info['sfreq'] == 500
@testing.requires_testing_data
@pytest.mark.parametrize('fname', [
pytest.param(curry_dir + '/test_bdf_stim_channel Curry 7.cef', id='7'),
pytest.param(curry_dir + '/test_bdf_stim_channel Curry 8.cdt.cef', id='8'),
pytest.param(curry_dir + '/test_bdf_stim_channel Curry 7 ASCII.cef',
id='7 ascii'),
pytest.param(curry_dir + '/test_bdf_stim_channel Curry 8 ASCII.cdt.cef',
id='8 ascii'),
])
def test_read_curry_annotations(fname):
"""Test reading for Curry events file."""
EXPECTED_ONSET = [0.484, 0.486, 0.62, 0.622, 1.904, 1.906, 3.212, 3.214,
4.498, 4.5, 5.8, 5.802, 7.074, 7.076, 8.324, 8.326, 9.58,
9.582]
EXPECTED_DURATION = np.zeros_like(EXPECTED_ONSET)
EXPECTED_DESCRIPTION = ['4', '50000', '2', '50000', '1', '50000', '1',
'50000', '1', '50000', '1', '50000', '1', '50000',
'1', '50000', '1', '50000']
annot = read_annotations(fname, sfreq='auto')
assert annot.orig_time is None
assert_array_equal(annot.onset, EXPECTED_ONSET)
assert_array_equal(annot.duration, EXPECTED_DURATION)
assert_array_equal(annot.description, EXPECTED_DESCRIPTION)
def _get_read_annotations_mock_info(name_part, mock_dir):
original, modified = dict(), dict()
original['event'] = curry_dir + '/test_bdf_stim_channel ' + name_part
original['base'], ext = original['event'].split(".", maxsplit=1)
version = _get_curry_version(ext)
original['info'] = original['base'] + FILE_EXTENSIONS[version]["info"]
modified['base'] = str(mock_dir.join('curry'))
modified['event'] = modified['base'] + FILE_EXTENSIONS[version]["events"]
modified['info'] = modified['base'] + FILE_EXTENSIONS[version]["info"]
return original, modified
@testing.requires_testing_data
@pytest.mark.parametrize('name_part', [
pytest.param('7.cef', id='7'),
pytest.param('8.cdt.cef', id='8'),
pytest.param('7 ASCII.cef', id='7 (ascii)'),
pytest.param('8 ASCII.cdt.cef', id='8 (ascii)'),
])
def test_read_curry_annotations_using_mocked_info(tmpdir, name_part):
"""Test reading for Curry events file."""
EXPECTED_ONSET = [0.484, 0.486, 0.62, 0.622, 1.904, 1.906, 3.212, 3.214,
4.498, 4.5, 5.8, 5.802, 7.074, 7.076, 8.324, 8.326, 9.58,
9.582]
EXPECTED_DURATION = np.zeros_like(EXPECTED_ONSET)
EXPECTED_DESCRIPTION = ['4', '50000', '2', '50000', '1', '50000', '1',
'50000', '1', '50000', '1', '50000', '1', '50000',
'1', '50000', '1', '50000']
original, fname = _get_read_annotations_mock_info("Curry " + name_part,
tmpdir)
copyfile(src=original['event'], dst=fname['event'])
_msg = 'required files cannot be found'
with pytest.raises(FileNotFoundError, match=_msg):
read_annotations(fname['event'], sfreq='auto')
_mock_info_file(src=original['info'], dst=fname['info'],
sfreq=0, time_step=2000)
annot = read_annotations(fname['event'], sfreq='auto')
assert annot.orig_time is None
assert_array_equal(annot.onset, EXPECTED_ONSET)
assert_array_equal(annot.duration, EXPECTED_DURATION)
assert_array_equal(annot.description, EXPECTED_DESCRIPTION)
run_tests_if_main()
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