ENH: Support TD data

mne/cov.py

@@ -1237,9 +1237,11 @@ def _auto_low_rank_model(data, mode, n_jobs, method_params, cv,
 class _RegCovariance(BaseEstimator):
     """Aux class."""
 
-    def __init__(self, info, grad=0.1, mag=0.1, eeg=0.1, seeg=0.1,
+    def __init__(self, info, grad=0.1, mag=0.1, eeg=0.1, *, seeg=0.1,
                  ecog=0.1, hbo=0.1, hbr=0.1, fnirs_cw_amplitude=0.1,
                  fnirs_fd_ac_amplitude=0.1, fnirs_fd_phase=0.1, fnirs_od=0.1,
+                 fnirs_td_gated_amplitude=0.1,
+                 fnirs_td_moments_amplitude=0.1,
                  csd=0.1, dbs=0.1, store_precision=False,
                  assume_centered=False):
         self.info = info
@@ -1540,9 +1542,12 @@ def _smart_eigh(C, info, rank, scalings=None, projs=None,
 
 @verbose
 def regularize(cov, info, mag=0.1, grad=0.1, eeg=0.1, exclude='bads',
-               proj=True, seeg=0.1, ecog=0.1, hbo=0.1, hbr=0.1,
+               proj=True, *, seeg=0.1, ecog=0.1, hbo=0.1, hbr=0.1,
                fnirs_cw_amplitude=0.1, fnirs_fd_ac_amplitude=0.1,
-               fnirs_fd_phase=0.1, fnirs_od=0.1, csd=0.1, dbs=0.1,
+               fnirs_fd_phase=0.1, fnirs_od=0.1,
+               fnirs_td_gated_amplitude=0.1,
+               fnirs_td_moments_amplitude=0.1,
+               csd=0.1, dbs=0.1,
                rank=None, scalings=None, verbose=None):
     """Regularize noise covariance matrix.
 
@@ -1590,6 +1595,10 @@ def regularize(cov, info, mag=0.1, grad=0.1, eeg=0.1, exclude='bads',
         Regularization factor for fNIRS raw phase signals.
     fnirs_od : float (default 0.1)
         Regularization factor for fNIRS optical density signals.
+    fnirs_td_gated_amplitude : float (default 0.1)
+        Regularization factor for fNIRS time domain gated amplitude signals.
+    fnirs_td_moments_amplitude : float (default 0.1)
+        Regularization factor for fNIRS time domain moments amplitude signals.
     csd : float (default 0.1)
         Regularization factor for EEG-CSD signals.
     dbs : float (default 0.1)
@@ -1623,7 +1632,10 @@ def regularize(cov, info, mag=0.1, grad=0.1, eeg=0.1, exclude='bads',
     regs = dict(eeg=eeg, seeg=seeg, dbs=dbs, ecog=ecog, hbo=hbo, hbr=hbr,
                 fnirs_cw_amplitude=fnirs_cw_amplitude,
                 fnirs_fd_ac_amplitude=fnirs_fd_ac_amplitude,
-                fnirs_fd_phase=fnirs_fd_phase, fnirs_od=fnirs_od, csd=csd)
+                fnirs_fd_phase=fnirs_fd_phase, fnirs_od=fnirs_od,
+                fnirs_td_gated_amplitude=fnirs_td_gated_amplitude,
+                fnirs_td_moments_amplitude=fnirs_td_moments_amplitude,
+                csd=csd)
 
     if exclude is None:
         raise ValueError('exclude must be a list of strings or "bads"')

mne/defaults.py

@@ -12,34 +12,47 @@
                exci='k', ias='k', syst='k', seeg='saddlebrown', dbs='seagreen',
                dipole='k', gof='k', bio='k', ecog='k', hbo='#AA3377', hbr='b',
                fnirs_cw_amplitude='k', fnirs_fd_ac_amplitude='k',
-               fnirs_fd_phase='k', fnirs_od='k', csd='k', whitened='k'),
+               fnirs_fd_phase='k', fnirs_od='k',
+               fnirs_td_gated_amplitude='k',
+               fnirs_td_moments_amplitude='k',
+               csd='k', whitened='k'),
     si_units=dict(mag='T', grad='T/m', eeg='V', eog='V', ecg='V', emg='V',
                   misc='AU', seeg='V', dbs='V', dipole='Am', gof='GOF',
                   bio='V', ecog='V', hbo='M', hbr='M', ref_meg='T',
                   fnirs_cw_amplitude='V', fnirs_fd_ac_amplitude='V',
-                  fnirs_fd_phase='rad', fnirs_od='V', csd='V/m²',
-                  whitened='Z'),
+                  fnirs_fd_phase='rad', fnirs_od='V',
+                  # TODO: These units and scalings are wrong
+                  fnirs_td_gated_amplitude='Au',
+                  fnirs_td_moments_amplitude='Au',
+                  csd='V/m²', whitened='Z'),
     units=dict(mag='fT', grad='fT/cm', eeg='µV', eog='µV', ecg='µV', emg='µV',
                misc='AU', seeg='mV', dbs='µV', dipole='nAm', gof='GOF',
                bio='µV', ecog='µV', hbo='µM', hbr='µM', ref_meg='fT',
                fnirs_cw_amplitude='V', fnirs_fd_ac_amplitude='V',
-               fnirs_fd_phase='rad', fnirs_od='V', csd='mV/m²',
-               whitened='Z'),
+               fnirs_fd_phase='rad', fnirs_od='V',
+               fnirs_td_gated_amplitude='Au',
+               fnirs_td_moments_amplitude='Au',
+               csd='mV/m²', whitened='Z'),
     # scalings for the units
     scalings=dict(mag=1e15, grad=1e13, eeg=1e6, eog=1e6, emg=1e6, ecg=1e6,
                   misc=1.0, seeg=1e3, dbs=1e6, ecog=1e6, dipole=1e9, gof=1.0,
                   bio=1e6, hbo=1e6, hbr=1e6, ref_meg=1e15,
                   fnirs_cw_amplitude=1.0, fnirs_fd_ac_amplitude=1.0,
-                  fnirs_fd_phase=1., fnirs_od=1.0, csd=1e3, whitened=1.),
+                  fnirs_fd_phase=1., fnirs_od=1.0,
+                  fnirs_td_gated_amplitude=1.,
+                  fnirs_td_moments_amplitude=1.,
+                  csd=1e3, whitened=1.),
     # rough guess for a good plot
     scalings_plot_raw=dict(mag=1e-12, grad=4e-11, eeg=20e-6, eog=150e-6,
                            ecg=5e-4, emg=1e-3, ref_meg=1e-12, misc='auto',
                            stim=1, resp=1, chpi=1e-4, exci=1, ias=1, syst=1,
                            seeg=1e-4, dbs=1e-4, bio=1e-6, ecog=1e-4, hbo=10e-6,
                            hbr=10e-6, whitened=10., fnirs_cw_amplitude=2e-2,
                            fnirs_fd_ac_amplitude=2e-2, fnirs_fd_phase=2e-1,
-                           fnirs_od=2e-2, csd=200e-4,
-                           dipole=1e-7, gof=1e2),
+                           fnirs_od=2e-2,
+                           fnirs_td_gated_amplitude=1.,
+                           fnirs_td_moments_amplitude=1.,
+                           csd=200e-4, dipole=1e-7, gof=1e2),
     scalings_cov_rank=dict(mag=1e12, grad=1e11, eeg=1e5,  # ~100x scalings
                            seeg=1e1, dbs=1e4, ecog=1e4, hbo=1e4, hbr=1e4),
     ylim=dict(mag=(-600., 600.), grad=(-200., 200.), eeg=(-200., 200.),
@@ -54,6 +67,8 @@
                 fnirs_fd_ac_amplitude='fNIRS (FD AC amplitude)',
                 fnirs_fd_phase='fNIRS (FD phase)',
                 fnirs_od='fNIRS (OD)', hbr='Deoxyhemoglobin',
+                fnirs_td_gated_amplitude='fNIRS (TD amplitude)',
+                fnirs_td_moments_amplitude='fNIRS (TD moment)',
                 gof='Goodness of fit', csd='Current source density',
                 stim='Stimulus',
                 ),

mne/io/constants.py

@@ -916,6 +916,8 @@
 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_MCG_42             = 1000  # For testing the MCG software
 
@@ -1002,7 +1004,9 @@
     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_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,

mne/io/pick.py

@@ -76,6 +76,14 @@ 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_fd_ac_amplitude=dict(
                     kind=FIFF.FIFFV_FNIRS_CH,
                     unit=FIFF.FIFF_UNIT_V,
@@ -160,6 +168,10 @@ 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',
                             }),
     'eeg': ('coil_type', {FIFF.FIFFV_COIL_EEG: 'eeg',
                           FIFF.FIFFV_COIL_EEG_BIPOLAR: 'eeg',
@@ -717,9 +729,8 @@ def channel_indices_by_type(info, picks=None):
     """
     idx_by_type = {key: list() for key in _PICK_TYPES_KEYS if
                    key not in ('meg', 'fnirs')}
-    idx_by_type.update(mag=list(), grad=list(), hbo=list(), hbr=list(),
-                       fnirs_cw_amplitude=list(), fnirs_fd_ac_amplitude=list(),
-                       fnirs_fd_phase=list(), fnirs_od=list())
+    idx_by_type.update(mag=list(), grad=list())
+    idx_by_type.update((key, list()) for key in _FNIRS_CH_TYPES_SPLIT)
     picks = _picks_to_idx(info, picks,
                           none='all', exclude=(), allow_empty=True)
     for k in picks:
@@ -914,8 +925,11 @@ 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',
+)
 _DATA_CH_TYPES_ORDER_DEFAULT = (
     'mag', 'grad', 'eeg', 'csd', 'eog', 'ecg', 'resp', 'emg', 'ref_meg',
     'misc', 'stim', 'chpi', 'exci', 'ias', 'syst', 'seeg', 'bio', 'ecog',