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Feature/td nirs snirf #9661

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3f875d3
adding the new snirf data types to the constants
Zahra-M-Aghajan Aug 11, 2021
cc92adc
more places to add the data types and constants
Zahra-M-Aghajan Aug 11, 2021
0d2fe87
adding constants for the allowed dataTypeLabels for the processed dat…
Zahra-M-Aghajan Aug 11, 2021
21ecb90
updating the snirf reader to accept other data types: gated histogram…
Zahra-M-Aghajan Aug 11, 2021
4491064
setting the formatter line length
Zahra-M-Aghajan Aug 11, 2021
dbdcebc
the reordering of the channels does not make much sense, need to inquire
Zahra-M-Aghajan Aug 12, 2021
80de954
Merge remote-tracking branch 'upstream/main' into feature/TD-nirs_snirf
Zahra-M-Aghajan Aug 19, 2021
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26 changes: 25 additions & 1 deletion mne/io/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -916,6 +916,9 @@
FIFF.FIFFV_COIL_FNIRS_FD_AC_AMPLITUDE = 304 # fNIRS frequency domain AC amplitude
FIFF.FIFFV_COIL_FNIRS_FD_PHASE = 305 # fNIRS frequency domain phase
FIFF.FIFFV_COIL_FNIRS_RAW = FIFF.FIFFV_COIL_FNIRS_CW_AMPLITUDE # old alias
FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE = 306 # fNIRS time-domain gated amplitude
FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE = 307 # fNIRS time-domain moments amplitude
FIFF.FIFFV_COIL_FNIRS_PROCESSED = 308 # fNIRS processed data

FIFF.FIFFV_COIL_MCG_42 = 1000 # For testing the MCG software

Expand Down Expand Up @@ -1002,7 +1005,9 @@
FIFF.FIFFV_COIL_DIPOLE, FIFF.FIFFV_COIL_FNIRS_HBO,
FIFF.FIFFV_COIL_FNIRS_HBR, FIFF.FIFFV_COIL_FNIRS_RAW,
FIFF.FIFFV_COIL_FNIRS_OD, FIFF.FIFFV_COIL_FNIRS_FD_AC_AMPLITUDE,
FIFF.FIFFV_COIL_FNIRS_FD_PHASE, FIFF.FIFFV_COIL_MCG_42,
FIFF.FIFFV_COIL_FNIRS_FD_PHASE, FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE,
FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE, FIFF.FIFFV_COIL_FNIRS_PROCESSED,
FIFF.FIFFV_COIL_MCG_42,
FIFF.FIFFV_COIL_POINT_MAGNETOMETER, FIFF.FIFFV_COIL_AXIAL_GRAD_5CM,
FIFF.FIFFV_COIL_VV_PLANAR_W, FIFF.FIFFV_COIL_VV_PLANAR_T1,
FIFF.FIFFV_COIL_VV_PLANAR_T2, FIFF.FIFFV_COIL_VV_PLANAR_T3,
Expand Down Expand Up @@ -1059,3 +1064,22 @@
# add a comment here (with doi of a published source) above any new
# aliases, as they are added
}

# SNIRF: Supported measurementList(k).dataTypeLabel values in dataTimeSeries
FNIRS_SNIRF_DATATYPELABELS = {
# These types are specified `here <https://github.com/fNIRS/snirf/blob/master/snirf_specification.md#supported-measurementlistkdatatypelabel-values-in-datatimeseries>`_
"HbO": 1, # Oxygenated hemoglobin (oxyhemoglobin) concentration
"HbR": 2, # Deoxygenated hemoglobin (deoxyhemoglobin) concentration
"HbT": 3, # Total hemoglobin concentration
"dOD": 4, # Change in optical density
"mua": 5, # Absorption coefficient
"musp": 6, # Scattering coefficient
"H2O": 7, # Water content
"Lipid": 8, # Lipid concentration
"BFi": 9, # Blood flow index
"HRF dOD": 10, # Hemodynamic response function for change in optical density
"HRF HbO": 11, # Hemodynamic response function for oxyhemoglobin concentration
"HRF HbR": 12, # Hemodynamic response function for deoxyhemoglobin concentration
"HRF HbT": 13, # Hemodynamic response function for total hemoglobin concentration
"HRF BFi": 14, # Hemodynamic response function for blood flow index
}
24 changes: 22 additions & 2 deletions mne/io/pick.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,18 @@ def get_channel_type_constants(include_defaults=False):
kind=FIFF.FIFFV_FNIRS_CH,
unit=FIFF.FIFF_UNIT_V,
coil_type=FIFF.FIFFV_COIL_FNIRS_CW_AMPLITUDE),
fnirs_td_gated_amplitude=dict(
kind=FIFF.FIFFV_FNIRS_CH,
unit=FIFF.FIFF_UNIT_V,
coil_type=FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE),
fnirs_td_moments_amplitude=dict(
kind=FIFF.FIFFV_FNIRS_CH,
unit=FIFF.FIFF_UNIT_V,
coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE),
fnirs_processed=dict(
kind=FIFF.FIFFV_FNIRS_CH,
unit=FIFF.FIFF_UNIT_V,
coil_type=FIFF.FIFFV_COIL_FNIRS_PROCESSED),
fnirs_fd_ac_amplitude=dict(
kind=FIFF.FIFFV_FNIRS_CH,
unit=FIFF.FIFF_UNIT_V,
Expand Down Expand Up @@ -160,6 +172,12 @@ def get_channel_type_constants(include_defaults=False):
FIFF.FIFFV_COIL_FNIRS_FD_PHASE:
'fnirs_fd_phase',
FIFF.FIFFV_COIL_FNIRS_OD: 'fnirs_od',
FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE:
'fnirs_td_gated_amplitude',
FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE:
'fnirs_td_moments_amplitude',
FIFF.FIFFV_COIL_FNIRS_PROCESSED:
'fnirs_processed',
}),
'eeg': ('coil_type', {FIFF.FIFFV_COIL_EEG: 'eeg',
FIFF.FIFFV_COIL_EEG_BIPOLAR: 'eeg',
Expand Down Expand Up @@ -966,8 +984,10 @@ def _check_excludes_includes(chs, info=None, allow_bads=False):
dbs=True)
_PICK_TYPES_KEYS = tuple(list(_PICK_TYPES_DATA_DICT) + ['ref_meg'])
_MEG_CH_TYPES_SPLIT = ('mag', 'grad', 'planar1', 'planar2')
_FNIRS_CH_TYPES_SPLIT = ('hbo', 'hbr', 'fnirs_cw_amplitude',
'fnirs_fd_ac_amplitude', 'fnirs_fd_phase', 'fnirs_od')
_FNIRS_CH_TYPES_SPLIT = (
'hbo', 'hbr', 'fnirs_cw_amplitude', 'fnirs_fd_ac_amplitude',
'fnirs_fd_phase', 'fnirs_od', 'fnirs_td_gated_amplitude',
'fnirs_td_moments_amplitude', 'fnirs_processed')
_DATA_CH_TYPES_ORDER_DEFAULT = (
'mag', 'grad', 'eeg', 'csd', 'eog', 'ecg', 'resp', 'emg', 'ref_meg',
'misc', 'stim', 'chpi', 'exci', 'ias', 'syst', 'seeg', 'bio', 'ecog',
Expand Down
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