def test_fnirs_channel_naming_and_order_custom_optical_density():
"""Ensure fNIRS channel checking on manually created data."""
data = np.random.normal(size=(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 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850',
'S3_D1 760', 'S3_D1 850']
ch_types = np.repeat("fnirs_od", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.tile([760, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
freqs = np.unique(_channel_frequencies(raw))
picks = _check_channels_ordered(raw, freqs)
assert len(picks) == len(raw.ch_names)
assert len(picks) == 6
# Check block naming for optical density
ch_names = ['S1_D1 760', 'S2_D1 760', 'S3_D1 760',
'S1_D1 850', 'S2_D1 850', 'S3_D1 850']
ch_types = np.repeat("fnirs_od", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.repeat([760, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
with pytest.raises(ValueError, match='channels not ordered correctly'):
_check_channels_ordered(raw, [760, 850])
# and this is how you would fix the ordering, then it should pass
raw.pick(picks=[0, 3, 1, 4, 2, 5])
_check_channels_ordered(raw, [760, 850])
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"])
def test_fnirs_channel_naming_and_order_custom_optical_density():
"""Ensure fNIRS channel checking on manually created data."""
data = np.random.normal(size=(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 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850', 'S3_D1 760',
'S3_D1 850'
]
ch_types = np.repeat("fnirs_od", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.tile([760, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
freqs = np.unique(_channel_frequencies(raw.info))
picks = _check_channels_ordered(raw.info, freqs)
assert len(picks) == len(raw.ch_names)
assert len(picks) == 6
# Check block naming for optical density
ch_names = [
'S1_D1 760', 'S2_D1 760', 'S3_D1 760', 'S1_D1 850', 'S2_D1 850',
'S3_D1 850'
]
ch_types = np.repeat("fnirs_od", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.repeat([760, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
# no problems here
_check_channels_ordered(raw.info, [760, 850])
# or with this (nirx) reordering
raw.pick(picks=[0, 3, 1, 4, 2, 5])
_check_channels_ordered(raw.info, [760, 850])
# Check that if you mix types you get an error
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)
raw2 = RawArray(data, info, verbose=True)
raw.add_channels([raw2])
with pytest.raises(ValueError, match='does not support a combination'):
_check_channels_ordered(raw.info, [760, 850])
def test_fnirs_channel_naming_and_order_custom_raw():
"""Ensure fNIRS channel checking on manually created data."""
data = np.random.normal(size=(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 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850', 'S3_D1 760',
'S3_D1 850'
]
ch_types = np.repeat("fnirs_cw_amplitude", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.tile([760, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
freqs = np.unique(_channel_frequencies(raw.info))
picks = _check_channels_ordered(raw.info, freqs)
assert len(picks) == len(raw.ch_names)
assert len(picks) == 6
# Different systems use different frequencies, so ensure that works
ch_names = [
'S1_D1 920', 'S1_D1 850', 'S2_D1 920', 'S2_D1 850', 'S3_D1 920',
'S3_D1 850'
]
ch_types = np.repeat("fnirs_cw_amplitude", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.tile([920, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
picks = _check_channels_ordered(raw.info, [920, 850])
assert len(picks) == len(raw.ch_names)
assert len(picks) == 6
# Catch expected errors
# The frequencies named in the channel names must match the info loc field
ch_names = [
'S1_D1 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850', 'S3_D1 760',
'S3_D1 850'
]
ch_types = np.repeat("fnirs_cw_amplitude", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.tile([920, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
with pytest.raises(ValueError, match='not ordered'):
_check_channels_ordered(raw.info, [920, 850])
# Catch if someone doesn't set the info field
ch_names = [
'S1_D1 760', 'S1_D1 850', 'S2_D1 760', 'S2_D1 850', 'S3_D1 760',
'S3_D1 850'
]
ch_types = np.repeat("fnirs_cw_amplitude", 6)
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='missing wavelength information'):
_check_channels_ordered(raw.info, [920, 850])
# I have seen data encoded not in alternating frequency, but blocked.
ch_names = [
'S1_D1 760', 'S2_D1 760', 'S3_D1 760', 'S1_D1 850', 'S2_D1 850',
'S3_D1 850'
]
ch_types = np.repeat("fnirs_cw_amplitude", 6)
info = create_info(ch_names=ch_names, ch_types=ch_types, sfreq=1.0)
raw = RawArray(data, info, verbose=True)
freqs = np.repeat([760, 850], 3)
for idx, f in enumerate(freqs):
raw.info["chs"][idx]["loc"][9] = f
with pytest.raises(ValueError, match='channels not ordered correctly'):
_check_channels_ordered(raw.info, [760, 850])
# and this is how you would fix the ordering, then it should pass
raw.pick(picks=[0, 3, 1, 4, 2, 5])
_check_channels_ordered(raw.info, [760, 850])