WIP: More constants

Author: larsoner

environment.yml

@@ -23,6 +23,7 @@ dependencies:
   - joblib
   - jupyter
   - lazy_loader >=0.3
+  - libxml2 !=2.14.0
   - mamba
   - matplotlib >=3.7
   - mffpy >=0.5.7

mne/_fiff/constants.py

@@ -1044,7 +1044,9 @@
 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_TD_MOMENTS_INTENSITY = 307  # fNIRS time-domain moments intensity
+FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN = 308  # fNIRS time-domain moments mean
+FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE = 309  # fNIRS time-domain moments variance
 
 FIFF.FIFFV_COIL_EYETRACK_POS = 400  # Eye-tracking gaze position
 FIFF.FIFFV_COIL_EYETRACK_PUPIL = 401  # Eye-tracking pupil size
@@ -1145,7 +1147,9 @@
         FIFF.FIFFV_COIL_FNIRS_FD_AC_AMPLITUDE,
         FIFF.FIFFV_COIL_FNIRS_FD_PHASE,
         FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE,
-        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE,
+        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_INTENSITY,
+        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN,
+        FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE,
         FIFF.FIFFV_COIL_MCG_42,
         FIFF.FIFFV_COIL_EYETRACK_POS,
         FIFF.FIFFV_COIL_EYETRACK_PUPIL,

mne/_fiff/pick.py

@@ -109,10 +109,20 @@ def get_channel_type_constants(include_defaults=False):
             unit=FIFF.FIFF_UNIT_V,
             coil_type=FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE,
         ),
-        fnirs_td_moments_amplitude=dict(
+        fnirs_td_moments_intensity=dict(
             kind=FIFF.FIFFV_FNIRS_CH,
-            unit=FIFF.FIFF_UNIT_V,
-            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE,
+            unit=FIFF.FIFF_UNIT_UNITLESS,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_INTENSITY,
+        ),
+        fnirs_td_moments_mean=dict(
+            kind=FIFF.FIFFV_FNIRS_CH,
+            unit=FIFF.FIFF_UNIT_S,
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN,
+        ),
+        fnirs_td_moments_variance=dict(
+            kind=FIFF.FIFFV_FNIRS_CH,
+            unit=FIFF.FIFF_UNIT_NONE,  # TODO: Maybe someday add s^2
+            coil_type=FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE,
         ),
         fnirs_od=dict(kind=FIFF.FIFFV_FNIRS_CH, coil_type=FIFF.FIFFV_COIL_FNIRS_OD),
         hbo=dict(
@@ -208,7 +218,9 @@ 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_TD_MOMENTS_INTENSITY: "fnirs_td_moments_intensity",
+            FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN: "fnirs_td_moments_mean",
+            FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE: "fnirs_td_moments_variance",
         },
     ),
     "eeg": (
@@ -398,13 +410,23 @@ def _triage_fnirs_pick(ch, fnirs, warned):
     elif ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_OD and "fnirs_od" in fnirs:
         return True
     elif (
-        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_AMPLITUDE
-        and "fnirs_td_moments_amplitude" in fnirs
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE
+        and "fnirs_td_gated_amplitude" in fnirs
     ):
         return True
     elif (
-        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_GATED_AMPLITUDE
-        and "fnirs_td_gated_amplitude" in fnirs
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_INTENSITY
+        and "fnirs_td_moments_intensity" in fnirs
+    ):
+        return True
+    elif (
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_MEAN
+        and "fnirs_td_moments_mean" in fnirs
+    ):
+        return True
+    elif (
+        ch["coil_type"] == FIFF.FIFFV_COIL_FNIRS_TD_MOMENTS_VARIANCE
+        and "fnirs_td_moments_variance" in fnirs
     ):
         return True
     return False
@@ -885,7 +907,9 @@ def channel_indices_by_type(info, picks=None):
         fnirs_fd_phase=list(),
         fnirs_od=list(),
         fnirs_td_gated_amplitude=list(),
-        fnirs_td_moments_amplitude=list(),
+        fnirs_td_moments_intensity=list(),
+        fnirs_td_moments_mean=list(),
+        fnirs_td_moments_variance=list(),
         eyegaze=list(),
         pupil=list(),
     )
@@ -1123,8 +1147,10 @@ def _check_excludes_includes(chs, info=None, allow_bads=False):
     "fnirs_fd_ac_amplitude",
     "fnirs_fd_phase",
     "fnirs_od",
-    "fnirs_td_moments_amplitude",
     "fnirs_td_gated_amplitude",
+    "fnirs_td_moments_intensity",
+    "fnirs_td_moments_mean",
+    "fnirs_td_moments_variance",
 )
 _EYETRACK_CH_TYPES_SPLIT = ("eyegaze", "pupil")
 _DATA_CH_TYPES_ORDER_DEFAULT = (

mne/_fiff/tests/test_constants.py

@@ -27,8 +27,8 @@
 from mne.utils import requires_good_network
 
 # https://github.com/mne-tools/fiff-constants/commits/master
-REPO = "mne-tools"
-COMMIT = "e27f68cbf74dbfc5193ad429cc77900a59475181"
+REPO = "larsoner"  # TODO: Replace with upstream once merged
+COMMIT = "ba2288355b61b00d65d4f1d8a47ef82b83414201"
 
 # These are oddities that we won't address:
 iod_dups = (355, 359)  # these are in both MEGIN and MNE files
@@ -91,7 +91,9 @@
     304,  # fNIRS frequency domain AC amplitude
     305,  # fNIRS frequency domain phase
     306,  # fNIRS time domain gated amplitude
-    307,  # fNIRS time domain moments amplitude
+    307,  # fNIRS time domain moments intensity
+    308,  # fNIRS time domain moments mean
+    309,  # fNIRS time domain moments variance
     400,  # Eye-tracking gaze position
     401,  # Eye-tracking pupil size
     1000,  # For testing the MCG software

mne/cov.py

@@ -1527,7 +1527,9 @@ def __init__(
         fnirs_fd_phase=0.1,
         fnirs_od=0.1,
         fnirs_td_gated_amplitude=0.1,
-        fnirs_td_moments_amplitude=0.1,
+        fnirs_td_moments_intensity=0.1,
+        fnirs_td_moments_mean=0.1,
+        fnirs_td_moments_variance=0.1,
         csd=0.1,
         dbs=0.1,
         store_precision=False,
@@ -1548,6 +1550,10 @@ def __init__(
         self.fnirs_fd_ac_amplitude = fnirs_fd_ac_amplitude
         self.fnirs_fd_phase = fnirs_fd_phase
         self.fnirs_od = fnirs_od
+        self.fnirs_td_gated_amplitude = fnirs_td_gated_amplitude
+        self.fnirs_td_moments_intensity = fnirs_td_moments_intensity
+        self.fnirs_td_moments_mean = fnirs_td_moments_mean
+        self.fnirs_td_moments_variance = fnirs_td_moments_variance
         self.csd = csd
         self.store_precision = store_precision
         self.assume_centered = assume_centered
@@ -1580,6 +1586,15 @@ def fit(self, X):
             dbs=self.dbs,
             hbo=self.hbo,
             hbr=self.hbr,
+            fnirs_cw_amplitude=self.fnirs_cw_amplitude,
+            fnirs_fd_ac_amplitude=self.fnirs_fd_ac_amplitude,
+            fnirs_fd_phase=self.fnirs_fd_phase,
+            fnirs_od=self.fnirs_od,
+            fnirs_td_gated_amplitude=self.fnirs_td_gated_amplitude,
+            fnirs_td_moments_intensity=self.fnirs_td_moments_intensity,
+            fnirs_td_moments_mean=self.fnirs_td_moments_mean,
+            fnirs_td_moments_variance=self.fnirs_td_moments_variance,
+            csd=self.csd,
             rank="full",
         )
         self.estimator_.covariance_ = self.covariance_ = cov_.data
@@ -1917,7 +1932,9 @@ def regularize(
     fnirs_fd_phase=0.1,
     fnirs_od=0.1,
     fnirs_td_gated_amplitude=0.1,
-    fnirs_td_moments_amplitude=0.1,
+    fnirs_td_moments_intensity=0.1,
+    fnirs_td_moments_mean=0.1,
+    fnirs_td_moments_variance=0.1,
     csd=0.1,
     dbs=0.1,
     rank=None,
@@ -1971,8 +1988,12 @@ def regularize(
         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)
+    fnirs_td_moments_intensity : float (default 0.1)
         Regularization factor for fNIRS time domain moments amplitude signals.
+    fnirs_td_moments_mean : float (default 0.1)
+        Regularization factor for fNIRS time domain moments mean signals.
+    fnirs_td_moments_variance : float (default 0.1)
+        Regularization factor for fNIRS time domain moments variance signals.
     csd : float (default 0.1)
         Regularization factor for EEG-CSD signals.
     dbs : float (default 0.1)
@@ -2014,7 +2035,9 @@ def regularize(
         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,
+        fnirs_td_moments_intensity=fnirs_td_moments_intensity,
+        fnirs_td_moments_mean=fnirs_td_moments_mean,
+        fnirs_td_moments_variance=fnirs_td_moments_variance,
         csd=csd,
     )
 

mne/defaults.py

@@ -33,7 +33,9 @@
         fnirs_fd_phase="k",
         fnirs_od="k",
         fnirs_td_gated_amplitude="k",
-        fnirs_td_moments_amplitude="k",
+        fnirs_td_moments_intensity="k",
+        fnirs_td_moments_mean="k",
+        fnirs_td_moments_variance="k",
         csd="k",
         whitened="k",
         gsr="#666633",
@@ -62,8 +64,10 @@
         fnirs_fd_ac_amplitude="V",
         fnirs_fd_phase="rad",
         fnirs_od="V",
-        fnirs_td_gated_amplitude="M",
-        fnirs_td_moments_amplitude="M",
+        fnirs_td_gated_amplitude="AU",  # counts
+        fnirs_td_moments_intensity="AU",  # counts
+        fnirs_td_moments_mean="s",
+        fnirs_td_moments_variance="s²",
         csd="V/m²",
         whitened="Z",
         gsr="S",
@@ -92,8 +96,10 @@
         fnirs_fd_ac_amplitude="V",
         fnirs_fd_phase="rad",
         fnirs_od="V",
-        fnirs_td_gated_amplitude="µM",
-        fnirs_td_moments_amplitude="µM",
+        fnirs_td_gated_amplitude="AU",
+        fnirs_td_moments_intensity="AU",
+        fnirs_td_moments_mean="s",
+        fnirs_td_moments_variance="s²",
         csd="mV/m²",
         whitened="Z",
         gsr="S",
@@ -123,8 +129,10 @@
         fnirs_fd_ac_amplitude=1.0,
         fnirs_fd_phase=1.0,
         fnirs_od=1.0,
-        fnirs_td_gated_amplitude=1e6,
-        fnirs_td_moments_amplitude=1e6,
+        fnirs_td_gated_amplitude=1.0,
+        fnirs_td_moments_intensity=1.0,
+        fnirs_td_moments_mean=1.0,
+        fnirs_td_moments_variance=1.0,
         csd=1e3,
         whitened=1.0,
         gsr=1.0,
@@ -160,7 +168,9 @@
         fnirs_fd_phase=2e-1,
         fnirs_od=2e-2,
         fnirs_td_gated_amplitude=1.0,
-        fnirs_td_moments_amplitude=1.0,
+        fnirs_td_moments_intensity=1.0,
+        fnirs_td_moments_mean=1.0,
+        fnirs_td_moments_variance=1.0,
         csd=200e-4,
         dipole=1e-7,
         gof=1e2,
@@ -217,7 +227,9 @@
         fnirs_od="fNIRS (OD)",
         hbr="Deoxyhemoglobin",
         fnirs_td_gated_amplitude="fNIRS (TD amplitude)",
-        fnirs_td_moments_amplitude="fNIRS (TD moment)",
+        fnirs_td_moments_intensity="fNIRS (TD moment intensity)",
+        fnirs_td_moments_mean="fNIRS (TD moment mean)",
+        fnirs_td_moments_variance="fNIRS (TD moment variance)",
         gof="Goodness of fit",
         csd="Current source density",
         stim="Stimulus",

mne/io/snirf/_snirf.py

@@ -316,7 +316,8 @@ def natural_keys(text):
                         ch_name = (
                             f"{ch_name} moment{fnirs_moment_orders[moment_idx - 1]}"
                         )
-                        ch_type = "fnirs_td_moments_amplitude"
+                        ch_type = "fnirs_td_moments_intensity"  # TODO: FIX AND TRIAGE!
+                        # raise RuntimeError("FIX THE TYPE")
                         need_data_scale = True
 
                 elif snirf_data_type == SNIRF_PROCESSED:

mne/io/snirf/tests/test_snirf.py

@@ -101,7 +101,10 @@ def test_basic_reading_and_min_process(fname):
         raw = optical_density(raw)
     if "fnirs_od" in raw:
         raw = beer_lambert_law(raw, ppf=6)
-    if "fnirs_td_moments_amplitude" in raw:
+    if "fnirs_td_moments_intensity" in raw:
+        # TODO: Re-enable once types are triaged
+        # assert "fnirs_td_moments_mean" in raw
+        # assert "fnirs_td_moments_variance" in raw
         pass
     else:
         assert "hbo" in raw
@@ -436,7 +439,8 @@ def test_snirf_kernel(kind):
         n_nan = 20
     else:
         assert raw._data.shape == (1080, 14)
-        data = raw.get_data("fnirs_td_moments_amplitude")
+        data = raw.get_data("fnirs_td_moments_intensity")
+        # TODO: This will need to update once we triage properly
         assert data.shape == raw._data.shape
         norm = np.nanmedian(np.linalg.norm(data, axis=-1))
         assert 1e5 < norm < 1e6  # TODO: 429256, is this reasonable Molars!??

mne/preprocessing/nirs/nirs.py

@@ -105,9 +105,12 @@ def _check_channels_ordered(info, pair_vals, *, throw_errors=True, check_bads=Tr
     picks_chroma = _picks_to_idx(info, ["hbo", "hbr"], exclude=[], allow_empty=True)
 
     # All TD moments
-    picks_moments = _picks_to_idx(
-        info, ["fnirs_td_moments_amplitude"], exclude=[], allow_empty=True
-    )
+    td_moments = [
+        "fnirs_td_moments_intensity",
+        "fnirs_td_moments_mean",
+        "fnirs_td_moments_variance",
+    ]
+    picks_moments = _picks_to_idx(info, td_moments, exclude=[], allow_empty=True)
 
     # All TD gated
     picks_gated = _picks_to_idx(

tools/hooks/update_environment_file.py

@@ -22,7 +22,12 @@
         deps |= set(section_deps)
 recursive_deps = set(d for d in deps if d.startswith("mne["))
 deps -= recursive_deps
-deps |= {"pip", "mamba", "nomkl"}
+deps |= {  # ones we add to environment.yml in addition to those from pyproject.toml
+    "pip",
+    "mamba",
+    "nomkl",
+    "libxml2 !=2.14.0",  # https://github.com/conda-forge/libxml2-feedstock/issues/146
+}
 
 
 def remove_spaces(version_spec):