def fix_channel_infos(mne_data_filepath, verbose=True):
log.info('Loading raw fif data from: {}'.format(mne_data_filepath))
raw = mne.io.Raw(mne_data_filepath, preload=True, verbose=verbose)
raw.info['bads'] = [
] # reset bad channels as they have been removed already
montage = Biosemi64Layout().as_montage()
log.info('Applying channel montage: {}'.format(montage))
## change EEG channel names
mapping = dict()
bdf_channel_names = raw.ch_names
for i, channel_name in enumerate(montage.ch_names):
log.debug('renaming channel {}: {} -> {}'.format(
i, bdf_channel_names[i], channel_name))
mapping[bdf_channel_names[i]] = channel_name
rename_channels(raw.info, mapping)
# mne.channels.apply_montage(raw.info, montage) # in mne 0.9
raw.set_montage(montage) # in mne 0.9
log.info('Saving raw fif data to: {}'.format(mne_data_filepath))
raw.save(mne_data_filepath, overwrite=True, verbose=False)
return raw
def test_rename_channels():
"""Test rename channels
"""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to EEG channel
mapping = {'EOG 061': ('EEG 061', 'eeg')}
with warnings.catch_warnings(record=True):
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to illegal channel type
mapping = {'EOG 061': ('MEG 061', 'meg')}
with warnings.catch_warnings(record=True):
assert_raises(ValueError, rename_channels, info, mapping)
# Test channel type which you are changing from e.g. MEG
mapping = {'MEG 2641': ('MEG2641', 'eeg')}
with warnings.catch_warnings(record=True):
assert_raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
assert_raises(ValueError, rename_channels, info, mapping)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
assert_true(info2['ch_names'][374] == 'EEG060')
assert_true('EEG060' in info2['bads'])
assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
assert_true(info2['ch_names'][375] == 'EOG061')
assert_true('EOG061' in info2['bads'])
def fix_channel_infos(mne_data_filepath, verbose=True):
log.info('Loading raw fif data from: {}'.format(mne_data_filepath))
raw = mne.io.Raw(mne_data_filepath, preload=True, verbose=verbose)
raw.info['bads'] = [] # reset bad channels as they have been removed already
montage = Biosemi64Layout().as_montage()
log.info('Applying channel montage: {}'.format(montage))
## change EEG channel names
mapping = dict()
bdf_channel_names = raw.ch_names
for i, channel_name in enumerate(montage.ch_names):
log.debug('renaming channel {}: {} -> {}'.format(
i, bdf_channel_names[i], channel_name))
mapping[bdf_channel_names[i]] = channel_name
rename_channels(raw.info, mapping)
# mne.channels.apply_montage(raw.info, montage) # in mne 0.9
raw.set_montage(montage) # in mne 0.9
log.info('Saving raw fif data to: {}'.format(mne_data_filepath))
raw.save(mne_data_filepath, overwrite=True, verbose=False)
return raw
def test_rename_channels():
"""Test rename channels
"""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to EEG channel
mapping = {'EOG 061': ('EEG 061', 'eeg')}
with warnings.catch_warnings(record=True):
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to illegal channel type
mapping = {'EOG 061': ('MEG 061', 'meg')}
with warnings.catch_warnings(record=True):
assert_raises(ValueError, rename_channels, info, mapping)
# Test channel type which you are changing from e.g. MEG
mapping = {'MEG 2641': ('MEG2641', 'eeg')}
with warnings.catch_warnings(record=True):
assert_raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
assert_raises(ValueError, rename_channels, info, mapping)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
assert_true(info2['ch_names'][374] == 'EEG060')
assert_true('EEG060' in info2['bads'])
assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
assert_true(info2['ch_names'][375] == 'EOG061')
assert_true('EOG061' in info2['bads'])
def test_rename_channels():
"""Test rename channels
"""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to EEG channel
mapping = {'EOG 061': ('EEG 061', 'eeg')}
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to illegal channel type
mapping = {'EOG 061': ('MEG 061', 'meg')}
assert_raises(ValueError, rename_channels, info, mapping)
# Test channel type which you are changing from e.g. MEG
mapping = {'MEG 2641': ('MEG2641', 'eeg')}
assert_raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
assert_raises(ValueError, rename_channels, info, mapping)
# Test duplicate named channels
mapping = {'EEG 060': 'EOG 061'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
assert_true(info2['ch_names'][374] == 'EEG060')
assert_true('EEG060' in info2['bads'])
assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
assert_true(info2['ch_names'][375] == 'EOG061')
assert_true('EOG061' in info2['bads'])
# Test type change
info2 = deepcopy(info)
info2['bads'] = ['EEG 059', 'EEG 060', 'EOG 061']
mapping = {
'EEG 060': ('EOG 060', 'eog'),
'EEG 059': ('EOG 059', 'eog'),
'EOG 061': ("OT'7", 'seeg')
}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EOG 060')
assert_true(info2['ch_names'][374] == 'EOG 060')
assert_true('EOG 060' in info2['bads'])
assert_true(info2['chs'][374]['kind'] is FIFF.FIFFV_EOG_CH)
assert_true(info2['chs'][373]['ch_name'] == 'EOG 059')
assert_true(info2['ch_names'][373] == 'EOG 059')
assert_true('EOG 059' in info2['bads'])
assert_true(info2['chs'][373]['kind'] is FIFF.FIFFV_EOG_CH)
assert_true(info2['chs'][375]['ch_name'] == "OT'7")
assert_true(info2['ch_names'][375] == "OT'7")
assert_true("OT'7" in info2['bads'])
assert_true(info2['chs'][375]['kind'] is FIFF.FIFFV_SEEG_CH)
def test_rename_channels():
"""Test rename channels
"""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to EEG channel
mapping = {'EOG 061': ('EEG 061', 'eeg')}
assert_raises(ValueError, rename_channels, info, mapping)
# Test change to illegal channel type
mapping = {'EOG 061': ('MEG 061', 'meg')}
assert_raises(ValueError, rename_channels, info, mapping)
# Test channel type which you are changing from e.g. MEG
mapping = {'MEG 2641': ('MEG2641', 'eeg')}
assert_raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
assert_raises(ValueError, rename_channels, info, mapping)
# Test duplicate named channels
mapping = {'EEG 060': 'EOG 061'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
assert_true(info2['ch_names'][374] == 'EEG060')
assert_true('EEG060' in info2['bads'])
assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
assert_true(info2['ch_names'][375] == 'EOG061')
assert_true('EOG061' in info2['bads'])
# Test type change
info2 = deepcopy(info)
info2['bads'] = ['EEG 059', 'EEG 060', 'EOG 061']
mapping = {'EEG 060': ('EOG 060', 'eog'), 'EEG 059': ('EOG 059', 'eog'),
'EOG 061': ("OT'7", 'seeg')}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EOG 060')
assert_true(info2['ch_names'][374] == 'EOG 060')
assert_true('EOG 060' in info2['bads'])
assert_true(info2['chs'][374]['kind'] is FIFF.FIFFV_EOG_CH)
assert_true(info2['chs'][373]['ch_name'] == 'EOG 059')
assert_true(info2['ch_names'][373] == 'EOG 059')
assert_true('EOG 059' in info2['bads'])
assert_true(info2['chs'][373]['kind'] is FIFF.FIFFV_EOG_CH)
assert_true(info2['chs'][375]['ch_name'] == "OT'7")
assert_true(info2['ch_names'][375] == "OT'7")
assert_true("OT'7" in info2['bads'])
assert_true(info2['chs'][375]['kind'] is FIFF.FIFFV_SEEG_CH)
def test_rename_channels():
"""Test rename channels"""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
assert_raises(ValueError, rename_channels, info, mapping)
# Test non-unique mapping configuration
mapping = {'MEG 2641': 'MEG 2642'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test bad input
assert_raises(ValueError, rename_channels, info, 1.)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
assert_true(info2['ch_names'][374] == 'EEG060')
assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
assert_true(info2['ch_names'][375] == 'EOG061')
assert_array_equal(['EEG060', 'EOG061'], info2['bads'])
info2 = deepcopy(info)
rename_channels(info2, lambda x: x.replace(' ', ''))
assert_true(info2['chs'][373]['ch_name'] == 'EEG059')
info2 = deepcopy(info)
info2['bads'] = ['EEG 060', 'EEG 060']
rename_channels(info2, mapping)
assert_array_equal(['EEG060', 'EEG060'], info2['bads'])
def test_rename_channels():
"""Test rename channels"""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
assert_raises(ValueError, rename_channels, info, mapping)
# Test non-unique mapping configuration
mapping = {'MEG 2641': 'MEG 2642'}
assert_raises(ValueError, rename_channels, info, mapping)
# Test bad input
assert_raises(ValueError, rename_channels, info, 1.)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert_true(info2['chs'][374]['ch_name'] == 'EEG060')
assert_true(info2['ch_names'][374] == 'EEG060')
assert_true(info2['chs'][375]['ch_name'] == 'EOG061')
assert_true(info2['ch_names'][375] == 'EOG061')
assert_array_equal(['EEG060', 'EOG061'], info2['bads'])
info2 = deepcopy(info)
rename_channels(info2, lambda x: x.replace(' ', ''))
assert_true(info2['chs'][373]['ch_name'] == 'EEG059')
info2 = deepcopy(info)
info2['bads'] = ['EEG 060', 'EEG 060']
rename_channels(info2, mapping)
assert_array_equal(['EEG060', 'EEG060'], info2['bads'])
def test_rename_channels():
"""Test rename channels."""
info = read_info(raw_fname)
# Error Tests
# Test channel name exists in ch_names
mapping = {'EEG 160': 'EEG060'}
pytest.raises(ValueError, rename_channels, info, mapping)
# Test improper mapping configuration
mapping = {'MEG 2641': 1.0}
pytest.raises(TypeError, rename_channels, info, mapping)
# Test non-unique mapping configuration
mapping = {'MEG 2641': 'MEG 2642'}
pytest.raises(ValueError, rename_channels, info, mapping)
# Test bad input
pytest.raises(ValueError, rename_channels, info, 1.)
pytest.raises(ValueError, rename_channels, info, 1.)
# Test name too long (channel names must be less than 15 characters)
A16 = 'A' * 16
mapping = {'MEG 2641': A16}
pytest.raises(ValueError, rename_channels, info, mapping)
# Test successful changes
# Test ch_name and ch_names are changed
info2 = deepcopy(info) # for consistency at the start of each test
info2['bads'] = ['EEG 060', 'EOG 061']
mapping = {'EEG 060': 'EEG060', 'EOG 061': 'EOG061'}
rename_channels(info2, mapping)
assert info2['chs'][374]['ch_name'] == 'EEG060'
assert info2['ch_names'][374] == 'EEG060'
assert info2['chs'][375]['ch_name'] == 'EOG061'
assert info2['ch_names'][375] == 'EOG061'
assert_array_equal(['EEG060', 'EOG061'], info2['bads'])
info2 = deepcopy(info)
rename_channels(info2, lambda x: x.replace(' ', ''))
assert info2['chs'][373]['ch_name'] == 'EEG059'
info2 = deepcopy(info)
info2['bads'] = ['EEG 060', 'EEG 060']
rename_channels(info2, mapping)
assert_array_equal(['EEG060', 'EEG060'], info2['bads'])
# test that keys in Raw._orig_units will be renamed, too
raw = read_raw_fif(raw_fname).crop(0, 0.1)
old, new = 'EEG 060', 'New'
raw._orig_units = {old: 'V'}
raw.rename_channels({old: new})
assert old not in raw._orig_units
assert new in raw._orig_units
