ENH: Add temperature and galvanic (#11090)

* ENH: Add temperature and galvanic

* FIX: Use correct name

* FIX: Flake

* FIX: Rename

* DOC: Sp

* Update doc/_includes/channel_types.rst

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>

doc/_includes/channel_types.rst

@@ -65,4 +65,8 @@ ias            Internal Active Shielding data
 
 syst           System status channel information
                (Triux systems only)
+
+temperature    Temperature                               Degrees Celsius
+
+gsr            Galvanic skin response                    Siemens
 =============  ========================================= =================

doc/changes/latest.inc

@@ -33,6 +33,7 @@ Enhancements
 - Add ``starting_affine`` keyword argument to :func:`mne.transforms.compute_volume_registration` to initialize an alignment with an affine (:gh:`11020` by `Alex Rockhill`_)
 - The ``trans`` parameter in :func:`mne.make_field_map` now accepts a :class:`~pathlib.Path` object, and uses standardised loading logic (:gh:`10784` by :newcontrib:`Andrew Quinn`)
 - Add HTML representation for `~mne.Evoked` in Jupyter Notebooks (:gh:`11075` by `Valerii Chirkov`_ and `Andrew Quinn`_)
+- Add support for ``temperature`` and ``gsr`` (galvanic skin response, i.e., electrodermal activity) channel types (:gh:`11090` by `Eric Larson`_)
 - Allow :func:`mne.beamformer.make_dics` to take ``pick_ori='vector'`` to compute vector source estimates (:gh:`19080` by `Alex Rockhill`_)
 - Add ``on_missing`` functionality to all of our classes that have a ``drop_channels`` method, to control what happens when channel names are not in the object (:gh:`11077` by `Andrew Quinn`_)
 

mne/channels/channels.py

@@ -328,7 +328,7 @@ def set_channel_types(self, mapping, verbose=None):
 
             ecg, eeg, emg, eog, exci, ias, misc, resp, seeg, dbs, stim, syst,
             ecog, hbo, hbr, fnirs_cw_amplitude, fnirs_fd_ac_amplitude,
-            fnirs_fd_phase, fnirs_od
+            fnirs_fd_phase, fnirs_od, temperature, gsr
 
         .. versionadded:: 0.9.0
         """
@@ -590,11 +590,12 @@ class UpdateChannelsMixin(object):
 
     @verbose
     def pick_types(self, meg=False, eeg=False, stim=False, eog=False,
-                   ecg=False, emg=False, ref_meg='auto', misc=False,
+                   ecg=False, emg=False, ref_meg='auto', *, misc=False,
                    resp=False, chpi=False, exci=False, ias=False, syst=False,
                    seeg=False, dipole=False, gof=False, bio=False,
-                   ecog=False, fnirs=False, csd=False, dbs=False, include=(),
-                   exclude='bads', selection=None, verbose=None):
+                   ecog=False, fnirs=False, csd=False, dbs=False,
+                   temperature=False, gsr=False,
+                   include=(), exclude='bads', selection=None, verbose=None):
         """Pick some channels by type and names.
 
         Parameters
@@ -620,7 +621,8 @@ def pick_types(self, meg=False, eeg=False, stim=False, eog=False,
             ref_meg=ref_meg, misc=misc, resp=resp, chpi=chpi, exci=exci,
             ias=ias, syst=syst, seeg=seeg, dipole=dipole, gof=gof, bio=bio,
             ecog=ecog, fnirs=fnirs, csd=csd, dbs=dbs, include=include,
-            exclude=exclude, selection=selection)
+            exclude=exclude, selection=selection, temperature=temperature,
+            gsr=gsr)
 
         self._pick_drop_channels(idx)
 

mne/defaults.py

@@ -12,25 +12,27 @@
                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', csd='k', whitened='k',
+               gsr='#666633', temperature='#663333'),
     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'),
+                  whitened='Z', gsr='S', temperature='C'),
     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'),
+               whitened='Z', gsr='S', temperature='C'),
     # 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, csd=1e3, whitened=1.,
+                  gsr=1., temperature=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',
@@ -39,7 +41,8 @@
                            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),
+                           dipole=1e-7, gof=1e2,
+                           gsr=1., temperature=1.),
     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.),
@@ -55,7 +58,8 @@
                 fnirs_fd_phase='fNIRS (FD phase)',
                 fnirs_od='fNIRS (OD)', hbr='Deoxyhemoglobin',
                 gof='Goodness of fit', csd='Current source density',
-                stim='Stimulus',
+                stim='Stimulus', gsr='Galvanic skin response',
+                temperature='Temperature',
                 ),
     mask_params=dict(marker='o',
                      markerfacecolor='w',

mne/io/constants.py

@@ -202,6 +202,8 @@
 FIFF.FIFFV_DIPOLE_WAVE  = 1000  # Dipole time curve (xplotter/xfit)
 FIFF.FIFFV_GOODNESS_FIT = 1001  # Goodness of fit (xplotter/xfit)
 FIFF.FIFFV_FNIRS_CH     = 1100  # Functional near-infrared spectroscopy
+FIFF.FIFFV_TEMPERATURE_CH = 1200  # Functional near-infrared spectroscopy
+FIFF.FIFFV_GALVANIC_CH  = 1300  # Galvanic skin response
 _ch_kind_named = {key: key for key in (
     FIFF.FIFFV_BIO_CH,
     FIFF.FIFFV_MEG_CH,
@@ -223,6 +225,8 @@
     FIFF.FIFFV_DIPOLE_WAVE,
     FIFF.FIFFV_GOODNESS_FIT,
     FIFF.FIFFV_FNIRS_CH,
+    FIFF.FIFFV_GALVANIC_CH,
+    FIFF.FIFFV_TEMPERATURE_CH,
 )}
 
 #
@@ -839,7 +843,7 @@
 FIFF.FIFF_UNIT_V   = 107  # volt
 FIFF.FIFF_UNIT_F   = 108  # farad
 FIFF.FIFF_UNIT_OHM = 109  # ohm
-FIFF.FIFF_UNIT_MHO = 110  # one per ohm
+FIFF.FIFF_UNIT_S   = 110  # Siemens (same as Moh, what fiff-constants calls it)
 FIFF.FIFF_UNIT_WB  = 111  # weber
 FIFF.FIFF_UNIT_T   = 112  # tesla
 FIFF.FIFF_UNIT_H   = 113  # Henry
@@ -861,7 +865,7 @@
     FIFF.FIFF_UNIT_CD, FIFF.FIFF_UNIT_MOL_M3, FIFF.FIFF_UNIT_HZ,
     FIFF.FIFF_UNIT_N, FIFF.FIFF_UNIT_PA, FIFF.FIFF_UNIT_J, FIFF.FIFF_UNIT_W,
     FIFF.FIFF_UNIT_C, FIFF.FIFF_UNIT_V, FIFF.FIFF_UNIT_F, FIFF.FIFF_UNIT_OHM,
-    FIFF.FIFF_UNIT_MHO, FIFF.FIFF_UNIT_WB, FIFF.FIFF_UNIT_T, FIFF.FIFF_UNIT_H,
+    FIFF.FIFF_UNIT_S, FIFF.FIFF_UNIT_WB, FIFF.FIFF_UNIT_T, FIFF.FIFF_UNIT_H,
     FIFF.FIFF_UNIT_CEL, FIFF.FIFF_UNIT_LM, FIFF.FIFF_UNIT_LX,
     FIFF.FIFF_UNIT_V_M2, FIFF.FIFF_UNIT_T_M, FIFF.FIFF_UNIT_AM,
     FIFF.FIFF_UNIT_AM_M2, FIFF.FIFF_UNIT_AM_M3,

mne/io/pick.py

@@ -94,7 +94,12 @@ def get_channel_type_constants(include_defaults=False):
                          coil_type=FIFF.FIFFV_COIL_FNIRS_HBR),
                 csd=dict(kind=FIFF.FIFFV_EEG_CH,
                          unit=FIFF.FIFF_UNIT_V_M2,
-                         coil_type=FIFF.FIFFV_COIL_EEG_CSD))
+                         coil_type=FIFF.FIFFV_COIL_EEG_CSD),
+                temperature=dict(kind=FIFF.FIFFV_TEMPERATURE_CH,
+                                 unit=FIFF.FIFF_UNIT_C),
+                gsr=dict(kind=FIFF.FIFFV_GALVANIC_CH,
+                         unit=FIFF.FIFF_UNIT_S),
+                )
     if include_defaults:
         coil_none = dict(coil_type=FIFF.FIFFV_COIL_NONE)
         unit_none = dict(unit=FIFF.FIFF_UNIT_NONE)
@@ -146,6 +151,8 @@ def get_channel_type_constants(include_defaults=False):
     FIFF.FIFFV_GOODNESS_FIT: 'gof',
     FIFF.FIFFV_ECOG_CH: 'ecog',
     FIFF.FIFFV_FNIRS_CH: 'fnirs',
+    FIFF.FIFFV_TEMPERATURE_CH: 'temperature',
+    FIFF.FIFFV_GALVANIC_CH: 'gsr',
 }
 # How to reduce our categories in channel_type (originally)
 _second_rules = {
@@ -186,7 +193,8 @@ def channel_type(info, idx):
 
             {'grad', 'mag', 'eeg', 'csd', 'stim', 'eog', 'emg', 'ecg',
              'ref_meg', 'resp', 'exci', 'ias', 'syst', 'misc', 'seeg', 'dbs',
-              'bio', 'chpi', 'dipole', 'gof', 'ecog', 'hbo', 'hbr'}
+              'bio', 'chpi', 'dipole', 'gof', 'ecog', 'hbo', 'hbr',
+              'temperature', 'gsr'}
     """
     # This is faster than the original _channel_type_old now in test_pick.py
     # because it uses (at most!) two dict lookups plus one conditional
@@ -368,10 +376,11 @@ def _check_info_exclude(info, exclude):
 
 @fill_doc
 def pick_types(info, meg=False, eeg=False, stim=False, eog=False, ecg=False,
-               emg=False, ref_meg='auto', misc=False, resp=False, chpi=False,
-               exci=False, ias=False, syst=False, seeg=False, dipole=False,
-               gof=False, bio=False, ecog=False, fnirs=False, csd=False,
-               dbs=False, include=(), exclude='bads', selection=None):
+               emg=False, ref_meg='auto', *, misc=False, resp=False,
+               chpi=False, exci=False, ias=False, syst=False, seeg=False,
+               dipole=False, gof=False, bio=False, ecog=False, fnirs=False,
+               csd=False, dbs=False, temperature=False, gsr=False,
+               include=(), exclude='bads', selection=None):
     """Pick channels by type and names.
 
     Parameters
@@ -399,7 +408,8 @@ def pick_types(info, meg=False, eeg=False, stim=False, eog=False, ecg=False,
                    len(info['comps']) > 0 and meg is not False)
 
     for param in (eeg, stim, eog, ecg, emg, misc, resp, chpi, exci,
-                  ias, syst, seeg, dipole, gof, bio, ecog, csd, dbs):
+                  ias, syst, seeg, dipole, gof, bio, ecog, csd, dbs,
+                  temperature, gsr):
         if not isinstance(param, bool):
             w = ('Parameters for all channel types (with the exception of '
                  '"meg", "ref_meg" and "fnirs") must be of type bool, not {}.')
@@ -408,7 +418,8 @@ def pick_types(info, meg=False, eeg=False, stim=False, eog=False, ecg=False,
     param_dict = dict(eeg=eeg, stim=stim, eog=eog, ecg=ecg, emg=emg,
                       misc=misc, resp=resp, chpi=chpi, exci=exci,
                       ias=ias, syst=syst, seeg=seeg, dbs=dbs, dipole=dipole,
-                      gof=gof, bio=bio, ecog=ecog, csd=csd)
+                      gof=gof, bio=bio, ecog=ecog, csd=csd,
+                      temperature=temperature, gsr=gsr)
     # avoid triage if possible
     if isinstance(meg, bool):
         for key in ('grad', 'mag'):
@@ -911,7 +922,7 @@ def _check_excludes_includes(chs, info=None, allow_bads=False):
     meg=True, eeg=True, csd=True, stim=False, eog=False, ecg=False, emg=False,
     misc=False, resp=False, chpi=False, exci=False, ias=False, syst=False,
     seeg=True, dipole=False, gof=False, bio=False, ecog=True, fnirs=True,
-    dbs=True)
+    dbs=True, temperature=False, gsr=False)
 _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',

mne/io/tests/test_constants.py

@@ -21,7 +21,7 @@
 
 # https://github.com/mne-tools/fiff-constants/commits/master
 REPO = 'mne-tools'
-COMMIT = 'aa49e20cff5791fbaf01d77ad4ec2e0ecb69840d'
+COMMIT = '6d9ca9ce7fb44c63d429c2986a953500743dfb22'
 
 # These are oddities that we won't address:
 iod_dups = (355, 359)  # these are in both MEGIN and MNE files

mne/utils/docs.py

@@ -2357,6 +2357,10 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
     EEG-CSD channels.
 dbs : bool
     Deep brain stimulation channels.
+temperature : bool
+    Temperature channels.
+gsr : bool
+    Galvanic skin response channels.
 include : list of str
     List of additional channels to include. If empty do not include
     any.

mne/viz/raw.py

@@ -565,7 +565,7 @@ def _setup_channel_selections(raw, kind, order):
                       ecg=True, emg=True, ref_meg=False, misc=True,
                       resp=True, chpi=True, exci=True, ias=True, syst=True,
                       seeg=False, bio=True, ecog=False, fnirs=False, dbs=False,
-                      exclude=())
+                      temperature=True, gsr=True, exclude=())
     if len(misc) and np.in1d(misc, order).any():
         selections_dict['Misc'] = misc
     return selections_dict