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# -*- coding: UTF-8 -*-
# Authors: Thomas Hartmann <thomas.hartmann@th-ht.de>
# Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>
#
# License: BSD (3-clause)
import mne
import os.path
import pytest
import copy
import itertools
import numpy as np
from mne.datasets import testing
from mne.io.fieldtrip.utils import NOINFO_WARNING, _create_events
from mne.utils import _check_pandas_installed, requires_h5py
from mne.io.fieldtrip.tests.helpers import (check_info_fields, get_data_paths,
get_raw_data, get_epochs,
get_evoked, _has_h5py,
pandas_not_found_warning_msg,
get_raw_info, check_data,
assert_warning_in_record)
# missing: KIT: biggest problem here is that the channels do not have the same
# names.
# EGI: no calibration done in FT. so data is VERY different
all_systems_raw = ['neuromag306', 'CTF', 'CNT', 'BTI', 'eximia']
all_systems_epochs = ['neuromag306', 'CTF', 'CNT']
all_versions = ['v7', 'v73']
use_info = [True, False]
all_test_params_raw = list(itertools.product(all_systems_raw, all_versions,
use_info))
all_test_params_epochs = list(itertools.product(all_systems_epochs,
all_versions,
use_info))
no_info_warning = {'expected_warning': RuntimeWarning,
'message': NOINFO_WARNING}
@testing.requires_testing_data
# Reading the sample CNT data results in a RuntimeWarning because it cannot
# parse the measurement date. We need to ignore that warning.
@pytest.mark.filterwarnings('ignore::RuntimeWarning')
@pytest.mark.parametrize('cur_system, version, use_info',
all_test_params_epochs)
def test_read_evoked(cur_system, version, use_info):
"""Test comparing reading an Evoked object and the FieldTrip version."""
test_data_folder_ft = get_data_paths(cur_system)
mne_avg = get_evoked(cur_system)
if use_info:
info = get_raw_info(cur_system)
pytestwarning = {'expected_warning': None}
else:
info = None
pytestwarning = no_info_warning
cur_fname = os.path.join(test_data_folder_ft,
'averaged_%s.mat' % (version,))
if version == 'v73' and not _has_h5py():
with pytest.raises(ImportError):
mne.io.read_evoked_fieldtrip(cur_fname, info)
return
with pytest.warns(**pytestwarning):
avg_ft = mne.io.read_evoked_fieldtrip(cur_fname, info)
mne_data = mne_avg.data[:, :-1]
ft_data = avg_ft.data
check_data(mne_data, ft_data, cur_system)
check_info_fields(mne_avg, avg_ft, use_info)
@testing.requires_testing_data
# Reading the sample CNT data results in a RuntimeWarning because it cannot
# parse the measurement date. We need to ignore that warning.
@pytest.mark.filterwarnings('ignore::RuntimeWarning')
@pytest.mark.parametrize('cur_system, version, use_info',
all_test_params_epochs)
def test_read_epochs(cur_system, version, use_info):
"""Test comparing reading an Epochs object and the FieldTrip version."""
pandas = _check_pandas_installed(strict=False)
has_pandas = pandas is not False
test_data_folder_ft = get_data_paths(cur_system)
mne_epoched = get_epochs(cur_system)
if use_info:
info = get_raw_info(cur_system)
pytestwarning = {'expected_warning': None}
else:
info = None
pytestwarning = no_info_warning
cur_fname = os.path.join(test_data_folder_ft,
'epoched_%s.mat' % (version,))
if has_pandas:
if version == 'v73' and not _has_h5py():
with pytest.raises(ImportError):
mne.io.read_epochs_fieldtrip(cur_fname, info)
return
with pytest.warns(**pytestwarning):
epoched_ft = mne.io.read_epochs_fieldtrip(cur_fname, info)
assert isinstance(epoched_ft.metadata, pandas.DataFrame)
else:
with pytest.warns(None) as warn_record:
if version == 'v73' and not _has_h5py():
with pytest.raises(ImportError):
mne.io.read_epochs_fieldtrip(cur_fname, info)
return
epoched_ft = mne.io.read_epochs_fieldtrip(cur_fname, info)
assert epoched_ft.metadata is None
assert_warning_in_record(pandas_not_found_warning_msg, warn_record)
if pytestwarning['expected_warning'] is not None:
assert_warning_in_record(pytestwarning['message'], warn_record)
mne_data = mne_epoched.get_data()[:, :, :-1]
ft_data = epoched_ft.get_data()
check_data(mne_data, ft_data, cur_system)
check_info_fields(mne_epoched, epoched_ft, use_info)
@testing.requires_testing_data
# Reading the sample CNT data results in a RuntimeWarning because it cannot
# parse the measurement date. We need to ignore that warning.
@pytest.mark.filterwarnings('ignore::RuntimeWarning')
@pytest.mark.parametrize('cur_system, version, use_info', all_test_params_raw)
def test_raw(cur_system, version, use_info):
"""Test comparing reading a raw fiff file and the FieldTrip version."""
# Load the raw fiff file with mne
test_data_folder_ft = get_data_paths(cur_system)
raw_fiff_mne = get_raw_data(cur_system, drop_extra_chs=True)
if use_info:
info = get_raw_info(cur_system)
pytestwarning = {'expected_warning': None}
else:
info = None
pytestwarning = no_info_warning
cur_fname = os.path.join(test_data_folder_ft,
'raw_%s.mat' % (version,))
if version == 'v73' and not _has_h5py():
with pytest.raises(ImportError):
mne.io.read_raw_fieldtrip(cur_fname, info)
return
with pytest.warns(**pytestwarning):
raw_fiff_ft = mne.io.read_raw_fieldtrip(cur_fname, info)
if cur_system == 'BTI' and not use_info:
raw_fiff_ft.drop_channels(['MzA', 'MxA', 'MyaA',
'MyA', 'MxaA', 'MzaA'])
if cur_system == 'eximia' and not use_info:
raw_fiff_ft.drop_channels(['TRIG2', 'TRIG1', 'GATE'])
# Check that the data was loaded correctly
check_data(raw_fiff_mne.get_data(),
raw_fiff_ft.get_data(),
cur_system)
# Check info field
check_info_fields(raw_fiff_mne, raw_fiff_ft, use_info)
@testing.requires_testing_data
def test_load_epoched_as_raw():
"""Test whether exception is thrown when loading epochs as raw."""
test_data_folder_ft = get_data_paths('neuromag306')
info = get_raw_info('neuromag306')
cur_fname = os.path.join(test_data_folder_ft, 'epoched_v7.mat')
with pytest.raises(RuntimeError):
mne.io.read_raw_fieldtrip(cur_fname, info)
@testing.requires_testing_data
def test_invalid_trialinfocolumn():
"""Test for exceptions when using wrong values for trialinfo parameter."""
test_data_folder_ft = get_data_paths('neuromag306')
info = get_raw_info('neuromag306')
cur_fname = os.path.join(test_data_folder_ft, 'epoched_v7.mat')
with pytest.raises(ValueError):
mne.io.read_epochs_fieldtrip(cur_fname, info, trialinfo_column=-1)
with pytest.raises(ValueError):
mne.io.read_epochs_fieldtrip(cur_fname, info, trialinfo_column=3)
@testing.requires_testing_data
def test_create_events():
"""Test 2dim trialinfo fields."""
from mne.externals.pymatreader import read_mat
test_data_folder_ft = get_data_paths('neuromag306')
cur_fname = os.path.join(test_data_folder_ft, 'epoched_v7.mat')
original_data = read_mat(cur_fname, ['data', ])
new_data = copy.deepcopy(original_data)
new_data['trialinfo'] = np.array([[1, 2, 3, 4],
[1, 2, 3, 4],
[1, 2, 3, 4]])
with pytest.raises(ValueError):
_create_events(new_data, -1)
for cur_col in np.arange(4):
evts = _create_events(new_data, cur_col)
assert np.all(evts[:, 2] == cur_col + 1)
with pytest.raises(ValueError):
_create_events(new_data, 4)
@testing.requires_testing_data
@pytest.mark.parametrize('version', all_versions)
@requires_h5py
def test_one_channel_elec_bug(version):
"""Test if loading data having only one elec in the elec field works."""
fname = os.path.join(mne.datasets.testing.data_path(), 'fieldtrip',
'one_channel_elec_bug_data_%s.mat' % (version, ))
with pytest.warns(**no_info_warning):
mne.io.read_raw_fieldtrip(fname, info=None)
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