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379
mne/defaults.py
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379
mne/defaults.py
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# Authors: The MNE-Python contributors.
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# License: BSD-3-Clause
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# Copyright the MNE-Python contributors.
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from copy import deepcopy
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DEFAULTS = dict(
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color=dict(
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mag="darkblue",
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grad="b",
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eeg="k",
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eog="k",
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ecg="m",
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emg="k",
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ref_meg="steelblue",
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misc="k",
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stim="k",
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resp="k",
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chpi="k",
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exci="k",
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ias="k",
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syst="k",
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seeg="saddlebrown",
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dbs="seagreen",
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dipole="k",
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gof="k",
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bio="k",
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ecog="k",
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hbo="#AA3377",
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hbr="b",
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fnirs_cw_amplitude="k",
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fnirs_fd_ac_amplitude="k",
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fnirs_fd_phase="k",
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fnirs_od="k",
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csd="k",
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whitened="k",
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gsr="#666633",
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temperature="#663333",
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eyegaze="k",
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pupil="k",
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),
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si_units=dict(
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mag="T",
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grad="T/m",
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eeg="V",
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eog="V",
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ecg="V",
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emg="V",
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misc="AU",
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seeg="V",
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dbs="V",
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dipole="Am",
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gof="GOF",
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bio="V",
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ecog="V",
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hbo="M",
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hbr="M",
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ref_meg="T",
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fnirs_cw_amplitude="V",
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fnirs_fd_ac_amplitude="V",
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fnirs_fd_phase="rad",
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fnirs_od="V",
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csd="V/m²",
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whitened="Z",
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gsr="S",
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temperature="C",
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eyegaze="rad",
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pupil="m",
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),
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units=dict(
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mag="fT",
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grad="fT/cm",
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eeg="µV",
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eog="µV",
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ecg="µV",
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emg="µV",
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misc="AU",
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seeg="mV",
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dbs="µV",
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dipole="nAm",
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gof="GOF",
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bio="µV",
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ecog="µV",
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hbo="µM",
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hbr="µM",
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ref_meg="fT",
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fnirs_cw_amplitude="V",
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fnirs_fd_ac_amplitude="V",
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fnirs_fd_phase="rad",
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fnirs_od="V",
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csd="mV/m²",
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whitened="Z",
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gsr="S",
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temperature="C",
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eyegaze="rad",
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pupil="µm",
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),
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# scalings for the units
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scalings=dict(
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mag=1e15,
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grad=1e13,
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eeg=1e6,
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eog=1e6,
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emg=1e6,
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ecg=1e6,
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misc=1.0,
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seeg=1e3,
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dbs=1e6,
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ecog=1e6,
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dipole=1e9,
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gof=1.0,
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bio=1e6,
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hbo=1e6,
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hbr=1e6,
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ref_meg=1e15,
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fnirs_cw_amplitude=1.0,
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fnirs_fd_ac_amplitude=1.0,
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fnirs_fd_phase=1.0,
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fnirs_od=1.0,
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csd=1e3,
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whitened=1.0,
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gsr=1.0,
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temperature=1.0,
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eyegaze=1.0,
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pupil=1e6,
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),
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# rough guess for a good plot
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scalings_plot_raw=dict(
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mag=1e-12,
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grad=4e-11,
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eeg=20e-6,
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eog=150e-6,
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ecg=5e-4,
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emg=1e-3,
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ref_meg=1e-12,
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misc="auto",
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stim=1,
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resp=1,
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chpi=1e-4,
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exci=1,
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ias=1,
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syst=1,
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seeg=1e-4,
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dbs=1e-4,
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bio=1e-6,
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ecog=1e-4,
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hbo=10e-6,
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hbr=10e-6,
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whitened=10.0,
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fnirs_cw_amplitude=2e-2,
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fnirs_fd_ac_amplitude=2e-2,
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fnirs_fd_phase=2e-1,
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fnirs_od=2e-2,
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csd=200e-4,
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dipole=1e-7,
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gof=1e2,
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gsr=1.0,
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temperature=0.1,
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eyegaze=2e-1,
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pupil=1e-2,
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),
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scalings_cov_rank=dict(
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mag=1e12,
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grad=1e11,
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eeg=1e5, # ~100x scalings
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seeg=1e1,
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dbs=1e4,
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ecog=1e4,
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hbo=1e4,
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hbr=1e4,
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),
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ylim=dict(
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mag=(-600.0, 600.0),
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grad=(-200.0, 200.0),
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eeg=(-200.0, 200.0),
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misc=(-5.0, 5.0),
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seeg=(-20.0, 20.0),
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dbs=(-200.0, 200.0),
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dipole=(-100.0, 100.0),
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gof=(0.0, 1.0),
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bio=(-500.0, 500.0),
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ecog=(-200.0, 200.0),
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hbo=(0, 20),
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hbr=(0, 20),
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csd=(-50.0, 50.0),
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eyegaze=(-1, 1),
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pupil=(-1.0, 1.0),
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),
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titles=dict(
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mag="Magnetometers",
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grad="Gradiometers",
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eeg="EEG",
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eog="EOG",
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ecg="ECG",
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emg="EMG",
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misc="misc",
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seeg="sEEG",
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dbs="DBS",
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bio="BIO",
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dipole="Dipole",
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ecog="ECoG",
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hbo="Oxyhemoglobin",
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ref_meg="Reference Magnetometers",
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fnirs_cw_amplitude="fNIRS (CW amplitude)",
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fnirs_fd_ac_amplitude="fNIRS (FD AC amplitude)",
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fnirs_fd_phase="fNIRS (FD phase)",
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fnirs_od="fNIRS (OD)",
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hbr="Deoxyhemoglobin",
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gof="Goodness of fit",
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csd="Current source density",
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stim="Stimulus",
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gsr="Galvanic skin response",
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temperature="Temperature",
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eyegaze="Eye-tracking (Gaze position)",
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pupil="Eye-tracking (Pupil size)",
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resp="Respiration monitoring channel",
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chpi="Continuous head position indicator (HPI) coil channels",
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exci="Flux excitation channel",
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ias="Internal Active Shielding data (Triux systems)",
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syst="System status channel information (Triux systems)",
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whitened="Whitened data",
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),
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mask_params=dict(
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marker="o",
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markerfacecolor="w",
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markeredgecolor="k",
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linewidth=0,
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markeredgewidth=1,
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markersize=4,
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),
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coreg=dict(
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mri_fid_opacity=1.0,
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dig_fid_opacity=1.0,
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# go from unit scaling (e.g., unit-radius sphere) to meters
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mri_fid_scale=5e-3,
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dig_fid_scale=8e-3,
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extra_scale=4e-3,
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eeg_scale=4e-3,
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eegp_scale=20e-3,
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eegp_height=0.1,
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ecog_scale=2e-3,
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seeg_scale=2e-3,
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meg_scale=1.0, # sensors are already in SI units
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ref_meg_scale=1.0,
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dbs_scale=5e-3,
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fnirs_scale=5e-3,
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source_scale=5e-3,
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detector_scale=5e-3,
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hpi_scale=4e-3,
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head_color=(0.988, 0.89, 0.74),
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hpi_color=(1.0, 0.0, 1.0),
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extra_color=(1.0, 1.0, 1.0),
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meg_color=(0.0, 0.25, 0.5),
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ref_meg_color=(0.5, 0.5, 0.5),
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helmet_color=(0.0, 0.0, 0.6),
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eeg_color=(1.0, 0.596, 0.588),
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eegp_color=(0.839, 0.15, 0.16),
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ecog_color=(1.0, 1.0, 1.0),
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dbs_color=(0.82, 0.455, 0.659),
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seeg_color=(1.0, 1.0, 0.3),
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fnirs_color=(1.0, 0.647, 0.0),
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source_color=(1.0, 0.05, 0.0),
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detector_color=(0.3, 0.15, 0.15),
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lpa_color=(1.0, 0.0, 0.0),
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nasion_color=(0.0, 1.0, 0.0),
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rpa_color=(0.0, 0.0, 1.0),
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),
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noise_std=dict(grad=5e-13, mag=20e-15, eeg=0.2e-6),
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eloreta_options=dict(eps=1e-6, max_iter=20, force_equal=False),
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depth_mne=dict(
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exp=0.8,
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limit=10.0,
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limit_depth_chs=True,
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combine_xyz="spectral",
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allow_fixed_depth=False,
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),
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depth_sparse=dict(
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exp=0.8,
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limit=None,
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limit_depth_chs="whiten",
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combine_xyz="fro",
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allow_fixed_depth=True,
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),
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interpolation_method=dict(
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eeg="spline", meg="MNE", fnirs="nearest", ecog="spline", seeg="spline"
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),
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volume_options=dict(
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alpha=None,
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resolution=1.0,
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surface_alpha=None,
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blending="mip",
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silhouette_alpha=None,
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silhouette_linewidth=2.0,
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),
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prefixes={
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"k": 1e-3,
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"h": 1e-2,
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"": 1e0,
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"d": 1e1,
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"c": 1e2,
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"m": 1e3,
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"µ": 1e6,
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"u": 1e6,
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"n": 1e9,
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"p": 1e12,
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"f": 1e15,
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},
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transform_zooms=dict(translation=None, rigid=None, affine=None, sdr=None),
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transform_niter=dict(
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translation=(10000, 1000, 100),
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rigid=(10000, 1000, 100),
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affine=(10000, 1000, 100),
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sdr=(10, 10, 5),
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),
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volume_label_indices=(
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# Left and middle
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4, # Left-Lateral-Ventricle
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5, # Left-Inf-Lat-Vent
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8, # Left-Cerebellum-Cortex
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10, # Left-Thalamus-Proper
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11, # Left-Caudate
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12, # Left-Putamen
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13, # Left-Pallidum
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14, # 3rd-Ventricle
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15, # 4th-Ventricle
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16, # Brain-Stem
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17, # Left-Hippocampus
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18, # Left-Amygdala
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26, # Left-Accumbens-area
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28, # Left-VentralDC
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# Right
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43, # Right-Lateral-Ventricle
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44, # Right-Inf-Lat-Vent
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47, # Right-Cerebellum-Cortex
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49, # Right-Thalamus-Proper
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50, # Right-Caudate
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51, # Right-Putamen
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52, # Right-Pallidum
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53, # Right-Hippocampus
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54, # Right-Amygdala
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58, # Right-Accumbens-area
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60, # Right-VentralDC
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),
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report_stc_plot_kwargs=dict(
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views=("lateral", "medial"),
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hemi="split",
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backend="pyvistaqt",
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time_viewer=False,
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show_traces=False,
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size=(450, 450),
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background="white",
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time_label=None,
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add_data_kwargs={"colorbar_kwargs": {"label_font_size": 12, "n_labels": 5}},
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),
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)
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def _handle_default(k, v=None):
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"""Avoid dicts as default keyword arguments.
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Use this function instead to resolve default dict values. Example usage::
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scalings = _handle_default('scalings', scalings)
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"""
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this_mapping = deepcopy(DEFAULTS[k])
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if v is not None:
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if isinstance(v, dict):
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this_mapping.update(v)
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else:
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for key in this_mapping:
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this_mapping[key] = v
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return this_mapping
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HEAD_SIZE_DEFAULT = 0.095 # in [m]
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_BORDER_DEFAULT = "mean"
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_INTERPOLATION_DEFAULT = "cubic"
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_EXTRAPOLATE_DEFAULT = "auto"
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