def test_fnirs_channel_naming_and_order_readers(fname):
"""Ensure fNIRS channel checking on standard readers."""
# fNIRS data requires specific channel naming and ordering.
# All standard readers should pass tests
raw = read_raw_nirx(fname)
freqs = np.unique(_channel_frequencies(raw.info))
assert_array_equal(freqs, [760, 850])
chroma = np.unique(_channel_chromophore(raw.info))
assert len(chroma) == 0
picks = _check_channels_ordered(raw.info, freqs)
assert len(picks) == len(raw.ch_names) # as all fNIRS only data
# Check that dropped channels are detected
# For each source detector pair there must be two channels,
# removing one should throw an error.
raw_dropped = raw.copy().drop_channels(raw.ch_names[4])
with pytest.raises(ValueError, match='not ordered correctly'):
_check_channels_ordered(raw_dropped.info, freqs)
# The ordering must be increasing for the pairs, if provided
raw_names_reversed = raw.copy().ch_names
raw_names_reversed.reverse()
raw_reversed = raw.copy().pick_channels(raw_names_reversed, ordered=True)
with pytest.raises(ValueError, match='The frequencies.*sorted.*'):
_check_channels_ordered(raw_reversed.info, [850, 760])
# So if we flip the second argument it should pass again
picks = _check_channels_ordered(raw_reversed.info, freqs)
got_first = set(raw_reversed.ch_names[pick].split()[1]
for pick in picks[::2])
assert got_first == {'760'}
got_second = set(raw_reversed.ch_names[pick].split()[1]
for pick in picks[1::2])
assert got_second == {'850'}
# Check on OD data
raw = optical_density(raw)
freqs = np.unique(_channel_frequencies(raw.info))
assert_array_equal(freqs, [760, 850])
chroma = np.unique(_channel_chromophore(raw.info))
assert len(chroma) == 0
picks = _check_channels_ordered(raw.info, freqs)
assert len(picks) == len(raw.ch_names) # as all fNIRS only data
# Check on haemoglobin data
raw = beer_lambert_law(raw)
freqs = np.unique(_channel_frequencies(raw.info))
assert len(freqs) == 0
assert len(_channel_chromophore(raw.info)) == len(raw.ch_names)
chroma = np.unique(_channel_chromophore(raw.info))
assert_array_equal(chroma, ["hbo", "hbr"])
picks = _check_channels_ordered(raw.info, chroma)
assert len(picks) == len(raw.ch_names)
with pytest.raises(ValueError, match='chromophore in info'):
_check_channels_ordered(raw.info, ["hbr", "hbo"])
def test_fnirs_channel_naming_and_order_readers(fname):
"""Ensure fNIRS channel checking on standard readers."""
# fNIRS data requires specific channel naming and ordering.
# All standard readers should pass tests
raw = read_raw_nirx(fname)
freqs = np.unique(_channel_frequencies(raw))
assert_array_equal(freqs, [760, 850])
chroma = np.unique(_channel_chromophore(raw))
assert len(chroma) == 0
picks = _check_channels_ordered(raw, freqs)
assert len(picks) == len(raw.ch_names) # as all fNIRS only data
# Check that dropped channels are detected
# For each source detector pair there must be two channels,
# removing one should throw an error.
raw_dropped = raw.copy().drop_channels(raw.ch_names[4])
with pytest.raises(ValueError, match='not ordered correctly'):
_check_channels_ordered(raw_dropped, freqs)
# The ordering must match the passed in argument
raw_names_reversed = raw.copy().ch_names
raw_names_reversed.reverse()
raw_reversed = raw.copy().pick_channels(raw_names_reversed, ordered=True)
with pytest.raises(ValueError, match='not ordered .* frequencies'):
_check_channels_ordered(raw_reversed, freqs)
# So if we flip the second argument it should pass again
_check_channels_ordered(raw_reversed, [850, 760])
# Check on OD data
raw = optical_density(raw)
freqs = np.unique(_channel_frequencies(raw))
assert_array_equal(freqs, [760, 850])
chroma = np.unique(_channel_chromophore(raw))
assert len(chroma) == 0
picks = _check_channels_ordered(raw, freqs)
assert len(picks) == len(raw.ch_names) # as all fNIRS only data
# Check on haemoglobin data
raw = beer_lambert_law(raw)
freqs = np.unique(_channel_frequencies(raw))
assert len(freqs) == 0
assert len(_channel_chromophore(raw)) == len(raw.ch_names)
chroma = np.unique(_channel_chromophore(raw))
assert_array_equal(chroma, ["hbo", "hbr"])
picks = _check_channels_ordered(raw, chroma)
assert len(picks) == len(raw.ch_names)
with pytest.raises(ValueError, match='not ordered .* chromophore'):
_check_channels_ordered(raw, ["hbx", "hbr"])
def test_fnirs_channel_naming_and_order_custom_chroma():
"""Ensure fNIRS channel checking on manually created data."""
data = np.random.RandomState(0).randn(6, 10)
# Start with a correctly named raw intensity dataset
# These are the steps required to build an fNIRS Raw object from scratch
ch_names = [
'S1_D1 hbo', 'S1_D1 hbr', 'S2_D1 hbo', 'S2_D1 hbr', 'S3_D1 hbo',
'S3_D1 hbr'
]
ch_types = np.tile(["hbo", "hbr"], 3)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
chroma = np.unique(_channel_chromophore(raw.info))
picks = _check_channels_ordered(raw.info, chroma)
assert len(picks) == len(raw.ch_names)
assert len(picks) == 6
# Test block creation fails
ch_names = [
'S1_D1 hbo', 'S2_D1 hbo', 'S3_D1 hbo', 'S1_D1 hbr', 'S2_D1 hbr',
'S3_D1 hbr'
]
ch_types = np.repeat(["hbo", "hbr"], 3)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
with pytest.raises(ValueError, match='not ordered .* chromophore'):
_check_channels_ordered(raw.info, ["hbo", "hbr"])
# Reordering should fix
raw.pick(picks=[0, 3, 1, 4, 2, 5])
_check_channels_ordered(raw.info, ["hbo", "hbr"])
# Wrong names should fail
with pytest.raises(ValueError, match='not ordered .* chromophore'):
_check_channels_ordered(raw.info, ["hbb", "hbr"])
# Test weird naming
ch_names = [
'S1_D1 hbb', 'S1_D1 hbr', 'S2_D1 hbb', 'S2_D1 hbr', 'S3_D1 hbb',
'S3_D1 hbr'
]
ch_types = np.tile(["hbo", "hbr"], 3)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
with pytest.raises(ValueError, match='naming conventions'):
_check_channels_ordered(raw.info, ["hbb", "hbr"])
# Check more weird naming
ch_names = [
'S1_DX hbo', 'S1_DX hbr', 'S2_D1 hbo', 'S2_D1 hbr', 'S3_D1 hbo',
'S3_D1 hbr'
]
ch_types = np.tile(["hbo", "hbr"], 3)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
with pytest.raises(ValueError, match='can not be parsed'):
_check_channels_ordered(raw.info, ["hbo", "hbr"])