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# -*- coding: utf-8 -*-
# Authors: Alexandre Gramfort <alexandre.gramfort@inria.fr>
# Matti Hämäläinen <msh@nmr.mgh.harvard.edu>
# Teon Brooks <teon.brooks@gmail.com>
# Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#
# License: BSD-3-Clause
from collections import Counter, OrderedDict
from collections.abc import Mapping
import contextlib
from copy import deepcopy
import datetime
from io import BytesIO
import operator
from textwrap import shorten
import string
import numpy as np
from .pick import (channel_type, _get_channel_types,
get_channel_type_constants, pick_types, _contains_ch_type)
from .constants import FIFF, _coord_frame_named
from .open import fiff_open
from .tree import dir_tree_find
from .tag import (read_tag, find_tag, _ch_coord_dict, _update_ch_info_named,
_rename_list)
from .proj import (_read_proj, _write_proj, _uniquify_projs, _normalize_proj,
_proj_equal, Projection)
from .ctf_comp import _read_ctf_comp, write_ctf_comp
from .write import (start_and_end_file, start_block, end_block,
write_string, write_dig_points, write_float, write_int,
write_coord_trans, write_ch_info, write_name_list,
write_julian, write_float_matrix, write_id, DATE_NONE)
from .proc_history import _read_proc_history, _write_proc_history
from ..transforms import (invert_transform, Transform, _coord_frame_name,
_ensure_trans, _frame_to_str)
from ..utils import (logger, verbose, warn, object_diff, _validate_type,
_stamp_to_dt, _dt_to_stamp, _pl, _is_numeric,
_check_option, _on_missing, _check_on_missing, fill_doc,
_check_fname, repr_html)
from ._digitization import (_format_dig_points, _dig_kind_proper, DigPoint,
_dig_kind_rev, _dig_kind_ints, _read_dig_fif)
from ._digitization import write_dig, _get_data_as_dict_from_dig
from .compensator import get_current_comp
from ..defaults import _handle_default
b = bytes # alias
_SCALAR_CH_KEYS = ('scanno', 'logno', 'kind', 'range', 'cal', 'coil_type',
'unit', 'unit_mul', 'coord_frame')
_ALL_CH_KEYS_SET = set(_SCALAR_CH_KEYS + ('loc', 'ch_name'))
# XXX we need to require these except when doing simplify_info
_MIN_CH_KEYS_SET = set(('kind', 'cal', 'unit', 'loc', 'ch_name'))
def _get_valid_units():
"""Get valid units according to the International System of Units (SI).
The International System of Units (SI, :footcite:`WikipediaSI`) is the
default system for describing units in the Brain Imaging Data Structure
(BIDS). For more information, see the BIDS specification
:footcite:`BIDSdocs` and the appendix "Units" therein.
References
----------
.. footbibliography::
"""
valid_prefix_names = ['yocto', 'zepto', 'atto', 'femto', 'pico', 'nano',
'micro', 'milli', 'centi', 'deci', 'deca', 'hecto',
'kilo', 'mega', 'giga', 'tera', 'peta', 'exa',
'zetta', 'yotta']
valid_prefix_symbols = ['y', 'z', 'a', 'f', 'p', 'n', u'µ', 'm', 'c', 'd',
'da', 'h', 'k', 'M', 'G', 'T', 'P', 'E', 'Z', 'Y']
valid_unit_names = ['metre', 'kilogram', 'second', 'ampere', 'kelvin',
'mole', 'candela', 'radian', 'steradian', 'hertz',
'newton', 'pascal', 'joule', 'watt', 'coulomb', 'volt',
'farad', 'ohm', 'siemens', 'weber', 'tesla', 'henry',
'degree Celsius', 'lumen', 'lux', 'becquerel', 'gray',
'sievert', 'katal']
valid_unit_symbols = ['m', 'kg', 's', 'A', 'K', 'mol', 'cd', 'rad', 'sr',
'Hz', 'N', 'Pa', 'J', 'W', 'C', 'V', 'F', u'Ω', 'S',
'Wb', 'T', 'H', u'°C', 'lm', 'lx', 'Bq', 'Gy', 'Sv',
'kat']
# Valid units are all possible combinations of either prefix name or prefix
# symbol together with either unit name or unit symbol. E.g., nV for
# nanovolt
valid_units = []
valid_units += ([''.join([prefix, unit]) for prefix in valid_prefix_names
for unit in valid_unit_names])
valid_units += ([''.join([prefix, unit]) for prefix in valid_prefix_names
for unit in valid_unit_symbols])
valid_units += ([''.join([prefix, unit]) for prefix in valid_prefix_symbols
for unit in valid_unit_names])
valid_units += ([''.join([prefix, unit]) for prefix in valid_prefix_symbols
for unit in valid_unit_symbols])
# units are also valid without a prefix
valid_units += valid_unit_names
valid_units += valid_unit_symbols
# we also accept "n/a" as a unit, which is the default missing value in
# BIDS
valid_units += ["n/a"]
return tuple(valid_units)
@verbose
def _unique_channel_names(ch_names, max_length=None, verbose=None):
"""Ensure unique channel names."""
suffixes = tuple(string.ascii_lowercase)
if max_length is not None:
ch_names[:] = [name[:max_length] for name in ch_names]
unique_ids = np.unique(ch_names, return_index=True)[1]
if len(unique_ids) != len(ch_names):
dups = {ch_names[x]
for x in np.setdiff1d(range(len(ch_names)), unique_ids)}
warn('Channel names are not unique, found duplicates for: '
'%s. Applying running numbers for duplicates.' % dups)
for ch_stem in dups:
overlaps = np.where(np.array(ch_names) == ch_stem)[0]
# We need an extra character since we append '-'.
# np.ceil(...) is the maximum number of appended digits.
if max_length is not None:
n_keep = (
max_length - 1 - int(np.ceil(np.log10(len(overlaps)))))
else:
n_keep = np.inf
n_keep = min(len(ch_stem), n_keep)
ch_stem = ch_stem[:n_keep]
for idx, ch_idx in enumerate(overlaps):
# try idx first, then loop through lower case chars
for suffix in (idx,) + suffixes:
ch_name = ch_stem + '-%s' % suffix
if ch_name not in ch_names:
break
if ch_name not in ch_names:
ch_names[ch_idx] = ch_name
else:
raise ValueError('Adding a single alphanumeric for a '
'duplicate resulted in another '
'duplicate name %s' % ch_name)
return ch_names
class MontageMixin(object):
"""Mixin for Montage getting and setting."""
@fill_doc
def get_montage(self):
"""Get a DigMontage from instance.
Returns
-------
%(montage)s
"""
from ..channels.montage import make_dig_montage
info = self if isinstance(self, Info) else self.info
if info['dig'] is None:
return None
# obtain coord_frame, and landmark coords
# (nasion, lpa, rpa, hsp, hpi) from DigPoints
montage_bunch = _get_data_as_dict_from_dig(info['dig'])
coord_frame = _frame_to_str.get(montage_bunch.coord_frame)
# get the channel names and chs data structure
ch_names, chs = info['ch_names'], info['chs']
picks = pick_types(info, meg=False, eeg=True, seeg=True,
ecog=True, dbs=True, fnirs=True, exclude=[])
# channel positions from dig do not match ch_names one to one,
# so use loc[:3] instead
ch_pos = {ch_names[ii]: chs[ii]['loc'][:3] for ii in picks}
# fNIRS uses multiple channels for the same sensors, we use
# a private function to format these for dig montage.
fnirs_picks = pick_types(info, fnirs=True, exclude=[])
if len(ch_pos) == len(fnirs_picks):
ch_pos = _get_fnirs_ch_pos(info)
elif len(fnirs_picks) > 0:
raise ValueError("MNE does not support getting the montage "
"for a mix of fNIRS and other data types. "
"Please raise a GitHub issue if you "
"require this feature.")
# create montage
montage = make_dig_montage(
ch_pos=ch_pos,
coord_frame=coord_frame,
nasion=montage_bunch.nasion,
lpa=montage_bunch.lpa,
rpa=montage_bunch.rpa,
hsp=montage_bunch.hsp,
hpi=montage_bunch.hpi,
)
return montage
@verbose
def set_montage(self, montage, match_case=True, match_alias=False,
on_missing='raise', verbose=None):
"""Set %(montage_types)s channel positions and digitization points.
Parameters
----------
%(montage)s
%(match_case)s
%(match_alias)s
%(on_missing_montage)s
%(verbose)s
Returns
-------
inst : instance of Raw | Epochs | Evoked
The instance, modified in-place.
See Also
--------
mne.channels.make_standard_montage
mne.channels.make_dig_montage
mne.channels.read_custom_montage
Notes
-----
.. warning::
Only %(montage_types)s channels can have their positions set using
a montage. Other channel types (e.g., MEG channels) should have
their positions defined properly using their data reading
functions.
"""
# How to set up a montage to old named fif file (walk through example)
# https://gist.github.com/massich/f6a9f4799f1fbeb8f5e8f8bc7b07d3df
from ..channels.montage import _set_montage
info = self if isinstance(self, Info) else self.info
_set_montage(info, montage, match_case, match_alias, on_missing)
return self
class ContainsMixin(object):
"""Mixin class for Raw, Evoked, Epochs and Info."""
def __contains__(self, ch_type):
"""Check channel type membership.
Parameters
----------
ch_type : str
Channel type to check for. Can be e.g. 'meg', 'eeg', 'stim', etc.
Returns
-------
in : bool
Whether or not the instance contains the given channel type.
Examples
--------
Channel type membership can be tested as::
>>> 'meg' in inst # doctest: +SKIP
True
>>> 'seeg' in inst # doctest: +SKIP
False
"""
info = self if isinstance(self, Info) else self.info
if ch_type == 'meg':
has_ch_type = (_contains_ch_type(info, 'mag') or
_contains_ch_type(info, 'grad'))
else:
has_ch_type = _contains_ch_type(info, ch_type)
return has_ch_type
@property
def compensation_grade(self):
"""The current gradient compensation grade."""
info = self if isinstance(self, Info) else self.info
return get_current_comp(info)
@fill_doc
def get_channel_types(self, picks=None, unique=False, only_data_chs=False):
"""Get a list of channel type for each channel.
Parameters
----------
%(picks_all)s
unique : bool
Whether to return only unique channel types. Default is ``False``.
only_data_chs : bool
Whether to ignore non-data channels. Default is ``False``.
Returns
-------
channel_types : list
The channel types.
"""
info = self if isinstance(self, Info) else self.info
return _get_channel_types(info, picks=picks, unique=unique,
only_data_chs=only_data_chs)
def _format_trans(obj, key):
try:
t = obj[key]
except KeyError:
pass
else:
if t is not None:
obj[key] = Transform(t['from'], t['to'], t['trans'])
def _check_ch_keys(ch, ci, name='info["chs"]', check_min=True):
ch_keys = set(ch)
bad = sorted(ch_keys.difference(_ALL_CH_KEYS_SET))
if bad:
raise KeyError(
f'key{_pl(bad)} errantly present for {name}[{ci}]: {bad}')
if check_min:
bad = sorted(_MIN_CH_KEYS_SET.difference(ch_keys))
if bad:
raise KeyError(
f'key{_pl(bad)} missing for {name}[{ci}]: {bad}',)
# As options are added here, test_meas_info.py:test_info_bad should be updated
def _check_bads(bads):
_validate_type(bads, list, 'bads')
return bads
def _check_description(description):
_validate_type(description, (None, str), "info['description']")
return description
def _check_dev_head_t(dev_head_t):
_validate_type(dev_head_t, (Transform, None), "info['dev_head_t']")
if dev_head_t is not None:
dev_head_t = _ensure_trans(dev_head_t, 'meg', 'head')
return dev_head_t
def _check_experimenter(experimenter):
_validate_type(experimenter, (None, str), 'experimenter')
return experimenter
def _check_line_freq(line_freq):
_validate_type(line_freq, (None, 'numeric'), 'line_freq')
line_freq = float(line_freq) if line_freq is not None else line_freq
return line_freq
def _check_subject_info(subject_info):
_validate_type(subject_info, (None, dict), 'subject_info')
return subject_info
def _check_device_info(device_info):
_validate_type(device_info, (None, dict, ), 'device_info')
return device_info
def _check_helium_info(helium_info):
_validate_type(helium_info, (None, dict, ), 'helium_info')
return helium_info
class Info(dict, MontageMixin, ContainsMixin):
"""Measurement information.
This data structure behaves like a dictionary. It contains all metadata
that is available for a recording. However, its keys are restricted to
those provided by the
`FIF format specification <https://github.com/mne-tools/fiff-constants>`__,
so new entries should not be manually added.
.. note::
This class should not be instantiated directly via
``mne.Info(...)``. Instead, use :func:`mne.create_info` to create
measurement information from scratch.
.. warning::
The only entries that should be manually changed by the user are:
``info['bads']``, ``info['description']``, ``info['device_info']``
``info['dev_head_t']``, ``info['experimenter']``,
``info['helium_info']``, ``info['line_freq']``, ``info['temp']``,
and ``info['subject_info']``.
All other entries should be considered read-only, though they can be
modified by various MNE-Python functions or methods (which have
safeguards to ensure all fields remain in sync).
Parameters
----------
*args : list
Arguments.
**kwargs : dict
Keyword arguments.
Attributes
----------
acq_pars : str | None
MEG system acquisition parameters.
See :class:`mne.AcqParserFIF` for details.
acq_stim : str | None
MEG system stimulus parameters.
bads : list of str
List of bad (noisy/broken) channels, by name. These channels will by
default be ignored by many processing steps.
ch_names : list of str
The names of the channels.
chs : list of dict
A list of channel information dictionaries, one per channel.
See Notes for more information.
command_line : str
Contains the command and arguments used to create the source space
(used for source estimation).
comps : list of dict
CTF software gradient compensation data.
See Notes for more information.
ctf_head_t : Transform | None
The transformation from 4D/CTF head coordinates to Neuromag head
coordinates. This is only present in 4D/CTF data.
custom_ref_applied : int
Whether a custom (=other than average) reference has been applied to
the EEG data. This flag is checked by some algorithms that require an
average reference to be set.
description : str | None
String description of the recording.
dev_ctf_t : Transform | None
The transformation from device coordinates to 4D/CTF head coordinates.
This is only present in 4D/CTF data.
dev_head_t : Transform | None
The device to head transformation.
device_info : dict | None
Information about the acquisition device. See Notes for details.
.. versionadded:: 0.19
dig : list of dict | None
The Polhemus digitization data in head coordinates.
See Notes for more information.
events : list of dict
Event list, sometimes extracted from the stim channels by Neuromag
systems. In general this should not be used and
:func:`mne.find_events` should be used for event processing.
See Notes for more information.
experimenter : str | None
Name of the person that ran the experiment.
file_id : dict | None
The FIF globally unique ID. See Notes for more information.
gantry_angle : float | None
Tilt angle of the gantry in degrees.
helium_info : dict | None
Information about the device helium. See Notes for details.
.. versionadded:: 0.19
highpass : float
Highpass corner frequency in Hertz. Zero indicates a DC recording.
hpi_meas : list of dict
HPI measurements that were taken at the start of the recording
(e.g. coil frequencies).
See Notes for details.
hpi_results : list of dict
Head position indicator (HPI) digitization points and fit information
(e.g., the resulting transform).
See Notes for details.
hpi_subsystem : dict | None
Information about the HPI subsystem that was used (e.g., event
channel used for cHPI measurements).
See Notes for details.
kit_system_id : int
Identifies the KIT system.
line_freq : float | None
Frequency of the power line in Hertz.
lowpass : float
Lowpass corner frequency in Hertz.
It is automatically set to half the sampling rate if there is
otherwise no low-pass applied to the data.
maxshield : bool
True if active shielding (IAS) was active during recording.
meas_date : datetime
The time (UTC) of the recording.
.. versionchanged:: 0.20
This is stored as a :class:`~python:datetime.datetime` object
instead of a tuple of seconds/microseconds.
meas_file : str | None
Raw measurement file (used for source estimation).
meas_id : dict | None
The ID assigned to this measurement by the acquisition system or
during file conversion. Follows the same format as ``file_id``.
mri_file : str | None
File containing the MRI to head transformation (used for source
estimation).
mri_head_t : dict | None
Transformation from MRI to head coordinates (used for source
estimation).
mri_id : dict | None
MRI unique ID (used for source estimation).
nchan : int
Number of channels.
proc_history : list of dict
The MaxFilter processing history.
See Notes for details.
proj_id : int | None
ID number of the project the experiment belongs to.
proj_name : str | None
Name of the project the experiment belongs to.
projs : list of Projection
List of SSP operators that operate on the data.
See :class:`mne.Projection` for details.
sfreq : float
Sampling frequency in Hertz.
subject_info : dict | None
Information about the subject.
See Notes for details.
temp : object | None
Can be used to store temporary objects in an Info instance. It will not
survive an I/O roundtrip.
.. versionadded:: 0.24
utc_offset : str
"UTC offset of related meas_date (sHH:MM).
.. versionadded:: 0.19
working_dir : str
Working directory used when the source space was created (used for
source estimation).
xplotter_layout : str
Layout of the Xplotter (Neuromag system only).
See Also
--------
mne.create_info
Notes
-----
The following parameters have a nested structure.
* ``chs`` list of dict:
cal : float
The calibration factor to bring the channels to physical
units. Used in product with ``range`` to scale the data read
from disk.
ch_name : str
The channel name.
coil_type : int
Coil type, e.g. ``FIFFV_COIL_MEG``.
coord_frame : int
The coordinate frame used, e.g. ``FIFFV_COORD_HEAD``.
kind : int
The kind of channel, e.g. ``FIFFV_EEG_CH``.
loc : array, shape (12,)
Channel location. For MEG this is the position plus the
normal given by a 3x3 rotation matrix. For EEG this is the
position followed by reference position (with 6 unused).
The values are specified in device coordinates for MEG and in
head coordinates for EEG channels, respectively.
logno : int
Logical channel number, conventions in the usage of this
number vary.
range : float
The hardware-oriented part of the calibration factor.
This should be only applied to the continuous raw data.
Used in product with ``cal`` to scale data read from disk.
scanno : int
Scanning order number, starting from 1.
unit : int
The unit to use, e.g. ``FIFF_UNIT_T_M``.
unit_mul : int
Unit multipliers, most commonly ``FIFF_UNITM_NONE``.
* ``comps`` list of dict:
ctfkind : int
CTF compensation grade.
colcals : ndarray
Column calibrations.
mat : dict
A named matrix dictionary (with entries "data", "col_names", etc.)
containing the compensation matrix.
rowcals : ndarray
Row calibrations.
save_calibrated : bool
Were the compensation data saved in calibrated form.
* ``device_info`` dict:
type : str
Device type.
model : str
Device model.
serial : str
Device serial.
site : str
Device site.
* ``dig`` list of dict:
kind : int
The kind of channel,
e.g. ``FIFFV_POINT_EEG``, ``FIFFV_POINT_CARDINAL``.
r : array, shape (3,)
3D position in m. and coord_frame.
ident : int
Number specifying the identity of the point.
e.g. ``FIFFV_POINT_NASION`` if kind is ``FIFFV_POINT_CARDINAL``, or
42 if kind is ``FIFFV_POINT_EEG``.
coord_frame : int
The coordinate frame used, e.g. ``FIFFV_COORD_HEAD``.
* ``events`` list of dict:
channels : list of int
Channel indices for the events.
list : ndarray, shape (n_events * 3,)
Events in triplets as number of samples, before, after.
* ``file_id`` dict:
version : int
FIF format version, i.e. ``FIFFC_VERSION``.
machid : ndarray, shape (2,)
Unique machine ID, usually derived from the MAC address.
secs : int
Time in seconds.
usecs : int
Time in microseconds.
* ``helium_info`` dict:
he_level_raw : float
Helium level (%) before position correction.
helium_level : float
Helium level (%) after position correction.
orig_file_guid : str
Original file GUID.
meas_date : tuple of int
The helium level meas date.
* ``hpi_meas`` list of dict:
creator : str
Program that did the measurement.
sfreq : float
Sample rate.
nchan : int
Number of channels used.
nave : int
Number of averages used.
ncoil : int
Number of coils used.
first_samp : int
First sample used.
last_samp : int
Last sample used.
hpi_coils : list of dict
Coils, containing:
number: int
Coil number
epoch : ndarray
Buffer containing one epoch and channel.
slopes : ndarray, shape (n_channels,)
HPI data.
corr_coeff : ndarray, shape (n_channels,)
HPI curve fit correlations.
coil_freq : float
HPI coil excitation frequency
* ``hpi_results`` list of dict:
dig_points : list
Digitization points (see ``dig`` definition) for the HPI coils.
order : ndarray, shape (ncoil,)
The determined digitization order.
used : ndarray, shape (nused,)
The indices of the used coils.
moments : ndarray, shape (ncoil, 3)
The coil moments.
goodness : ndarray, shape (ncoil,)
The goodness of fits.
good_limit : float
The goodness of fit limit.
dist_limit : float
The distance limit.
accept : int
Whether or not the fit was accepted.
coord_trans : instance of Transformation
The resulting MEG<->head transformation.
* ``hpi_subsystem`` dict:
ncoil : int
The number of coils.
event_channel : str
The event channel used to encode cHPI status (e.g., STI201).
hpi_coils : list of ndarray
List of length ``ncoil``, each 4-element ndarray contains the
event bits used on the event channel to indicate cHPI status
(using the first element of these arrays is typically
sufficient).
* ``mri_id`` dict:
version : int
FIF format version, i.e. ``FIFFC_VERSION``.
machid : ndarray, shape (2,)
Unique machine ID, usually derived from the MAC address.
secs : int
Time in seconds.
usecs : int
Time in microseconds.
* ``proc_history`` list of dict:
block_id : dict
See ``id`` above.
date : ndarray, shape (2,)
2-element tuple of seconds and microseconds.
experimenter : str
Name of the person who ran the program.
creator : str
Program that did the processing.
max_info : dict
Maxwel filtering info, can contain:
sss_info : dict
SSS processing information.
max_st
tSSS processing information.
sss_ctc : dict
Cross-talk processing information.
sss_cal : dict
Fine-calibration information.
smartshield : dict
MaxShield information. This dictionary is (always?) empty,
but its presence implies that MaxShield was used during
acquisition.
* ``subject_info`` dict:
id : int
Integer subject identifier.
his_id : str
String subject identifier.
last_name : str
Last name.
first_name : str
First name.
middle_name : str
Middle name.
birthday : tuple of int
Birthday in (year, month, day) format.
sex : int
Subject sex (0=unknown, 1=male, 2=female).
hand : int
Handedness (1=right, 2=left, 3=ambidextrous).
weight : float
Weight in kilograms.
height : float
Height in meters.
"""
_attributes = {
'acq_pars': 'acq_pars cannot be set directly. '
'See mne.AcqParserFIF() for details.',
'acq_stim': 'acq_stim cannot be set directly.',
'bads': _check_bads,
'ch_names': 'ch_names cannot be set directly. '
'Please use methods inst.add_channels(), '
'inst.drop_channels(), inst.pick_channels(), '
'inst.rename_channels(), inst.reorder_channels() '
'and inst.set_channel_types() instead.',
'chs': 'chs cannot be set directly. '
'Please use methods inst.add_channels(), '
'inst.drop_channels(), inst.pick_channels(), '
'inst.rename_channels(), inst.reorder_channels() '
'and inst.set_channel_types() instead.',
'command_line': 'command_line cannot be set directly.',
'comps': 'comps cannot be set directly. '
'Please use method Raw.apply_gradient_compensation() '
'instead.',
'ctf_head_t': 'ctf_head_t cannot be set directly.',
'custom_ref_applied': 'custom_ref_applied cannot be set directly. '
'Please use method inst.set_eeg_reference() '
'instead.',
'description': _check_description,
'dev_ctf_t': 'dev_ctf_t cannot be set directly.',
'dev_head_t': _check_dev_head_t,
'device_info': _check_device_info,
'dig': 'dig cannot be set directly. '
'Please use method inst.set_montage() instead.',
'events': 'events cannot be set directly.',
'experimenter': _check_experimenter,
'file_id': 'file_id cannot be set directly.',
'gantry_angle': 'gantry_angle cannot be set directly.',
'helium_info': _check_helium_info,
'highpass': 'highpass cannot be set directly. '
'Please use method inst.filter() instead.',
'hpi_meas': 'hpi_meas can not be set directly.',
'hpi_results': 'hpi_results cannot be set directly.',
'hpi_subsystem': 'hpi_subsystem cannot be set directly.',
'kit_system_id': 'kit_system_id cannot be set directly.',
'line_freq': _check_line_freq,
'lowpass': 'lowpass cannot be set directly. '
'Please use method inst.filter() instead.',
'maxshield': 'maxshield cannot be set directly.',
'meas_date': 'meas_date cannot be set directly. '
'Please use method inst.set_meas_date() instead.',
'meas_file': 'meas_file cannot be set directly.',
'meas_id': 'meas_id cannot be set directly.',
'mri_file': 'mri_file cannot be set directly.',
'mri_head_t': 'mri_head_t cannot be set directly.',
'mri_id': 'mri_id cannot be set directly.',
'nchan': 'nchan cannot be set directly. '
'Please use methods inst.add_channels(), '
'inst.drop_channels(), and inst.pick_channels() instead.',
'proc_history': 'proc_history cannot be set directly.',
'proj_id': 'proj_id cannot be set directly.',
'proj_name': 'proj_name cannot be set directly.',
'projs': 'projs cannot be set directly. '
'Please use methods inst.add_proj() and inst.del_proj() '
'instead.',
'sfreq': 'sfreq cannot be set directly. '
'Please use method inst.resample() instead.',
'subject_info': _check_subject_info,
'temp': lambda x: x,
'utc_offset': 'utc_offset cannot be set directly.',
'working_dir': 'working_dir cannot be set directly.',
'xplotter_layout': 'xplotter_layout cannot be set directly.'
}
def __init__(self, *args, **kwargs):
self._unlocked = True
super().__init__(*args, **kwargs)
# Deal with h5io writing things as dict
for key in ('dev_head_t', 'ctf_head_t', 'dev_ctf_t'):
_format_trans(self, key)
for res in self.get('hpi_results', []):
_format_trans(res, 'coord_trans')
if self.get('dig', None) is not None and len(self['dig']):
if isinstance(self['dig'], dict): # needs to be unpacked
self['dig'] = _dict_unpack(self['dig'], _DIG_CAST)
if not isinstance(self['dig'][0], DigPoint):
self['dig'] = _format_dig_points(self['dig'])
if isinstance(self.get('chs', None), dict):
self['chs']['ch_name'] = [str(x) for x in np.char.decode(
self['chs']['ch_name'], encoding='utf8')]
self['chs'] = _dict_unpack(self['chs'], _CH_CAST)
for pi, proj in enumerate(self.get('projs', [])):
if not isinstance(proj, Projection):
self['projs'][pi] = Projection(**proj)
# Old files could have meas_date as tuple instead of datetime
try:
meas_date = self['meas_date']
except KeyError:
pass
else:
self['meas_date'] = _ensure_meas_date_none_or_dt(meas_date)
self._unlocked = False
def __getstate__(self):
"""Get state (for pickling)."""
return {'_unlocked': self._unlocked}
def __setstate__(self, state):
"""Set state (for pickling)."""
self._unlocked = state['_unlocked']
def __setitem__(self, key, val):
"""Attribute setter."""
# During unpickling, the _unlocked attribute has not been set, so
# let __setstate__ do it later and act unlocked now
unlocked = getattr(self, '_unlocked', True)
if key in self._attributes:
if isinstance(self._attributes[key], str):
if not unlocked:
raise RuntimeError(self._attributes[key])
else:
val = self._attributes[key](val) # attribute checker function
else:
raise RuntimeError(
f"Info does not support directly setting the key {repr(key)}. "
"You can set info['temp'] to store temporary objects in an "
"Info instance, but these will not survive an I/O round-trip.")
super().__setitem__(key, val)
def update(self, other=None, **kwargs):
"""Update method using __setitem__()."""
iterable = other.items() if isinstance(other, Mapping) else other
if other is not None:
for key, val in iterable:
self[key] = val
for key, val in kwargs.items():
self[key] = val
@contextlib.contextmanager
def _unlock(self, *, update_redundant=False, check_after=False):
"""Context manager unlocking access to attributes."""
# needed for nested _unlock()
state = self._unlocked if hasattr(self, '_unlocked') else False
self._unlocked = True
try:
yield
except Exception:
raise
else:
if update_redundant:
self._update_redundant()
if check_after:
self._check_consistency()
finally:
self._unlocked = state
def copy(self):
"""Copy the instance.
Returns
-------
info : instance of Info
The copied info.
"""
return deepcopy(self)
def normalize_proj(self):
"""(Re-)Normalize projection vectors after subselection.
Applying projection after sub-selecting a set of channels that
were originally used to compute the original projection vectors
can be dangerous (e.g., if few channels remain, most power was
in channels that are no longer picked, etc.). By default, mne
will emit a warning when this is done.
This function will re-normalize projectors to use only the
remaining channels, thus avoiding that warning. Only use this
function if you're confident that the projection vectors still
adequately capture the original signal of interest.
"""
_normalize_proj(self)
def __repr__(self):
"""Summarize info instead of printing all."""
MAX_WIDTH = 68
strs = ['<Info | %s non-empty values']
non_empty = 0
titles = _handle_default('titles')
for k, v in self.items():
if k == 'ch_names':
if v:
entr = shorten(', '.join(v), MAX_WIDTH, placeholder=' ...')
else:
entr = '[]' # always show
non_empty -= 1 # don't count as non-empty
elif k == 'bads':
if v:
entr = '{} items ('.format(len(v))
entr += ', '.join(v)
entr = shorten(entr, MAX_WIDTH, placeholder=' ...') + ')'
else:
entr = '[]' # always show
non_empty -= 1 # don't count as non-empty
elif k == 'projs':
if v:
entr = ', '.join(p['desc'] + ': o%s' %
{0: 'ff', 1: 'n'}[p['active']] for p in v)
entr = shorten(entr, MAX_WIDTH, placeholder=' ...')
else:
entr = '[]' # always show projs
non_empty -= 1 # don't count as non-empty
elif k == 'meas_date':
if v is None:
entr = 'unspecified'
else:
entr = v.strftime('%Y-%m-%d %H:%M:%S %Z')
elif k == 'kit_system_id' and v is not None:
from .kit.constants import KIT_SYSNAMES
entr = '%i (%s)' % (v, KIT_SYSNAMES.get(v, 'unknown'))
elif k == 'dig' and v is not None:
counts = Counter(d['kind'] for d in v)
counts = ['%d %s' % (counts[ii],
_dig_kind_proper[_dig_kind_rev[ii]])
for ii in _dig_kind_ints if ii in counts]
counts = (' (%s)' % (', '.join(counts))) if len(counts) else ''
entr = '%d item%s%s' % (len(v), _pl(len(v)), counts)
elif isinstance(v, Transform):
# show entry only for non-identity transform
if not np.allclose(v["trans"], np.eye(v["trans"].shape[0])):
frame1 = _coord_frame_name(v['from'])
frame2 = _coord_frame_name(v['to'])
entr = '%s -> %s transform' % (frame1, frame2)
else:
entr = ''
elif k in ['sfreq', 'lowpass', 'highpass']:
entr = '{:.1f} Hz'.format(v)
elif isinstance(v, str):
entr = shorten(v, MAX_WIDTH, placeholder=' ...')
elif k == 'chs':
# TODO someday we should refactor with _repr_html_ with
# bad vs good
ch_types = [channel_type(self, idx) for idx in range(len(v))]
ch_counts = Counter(ch_types)
entr = ', '.join(
f'{count} {titles.get(ch_type, ch_type.upper())}'
for ch_type, count in ch_counts.items())
elif k == 'custom_ref_applied':
entr = str(bool(v))
if not v:
non_empty -= 1 # don't count if 0
else:
try:
this_len = len(v)
except TypeError:
entr = '{}'.format(v) if v is not None else ''
else:
if this_len > 0:
entr = ('%d item%s (%s)' % (this_len, _pl(this_len),
type(v).__name__))
else:
entr = ''
if entr != '':
non_empty += 1
strs.append('%s: %s' % (k, entr))
st = '\n '.join(sorted(strs))
st += '\n>'
st %= non_empty
return st
def __deepcopy__(self, memodict):
"""Make a deepcopy."""
result = Info.__new__(Info)
result._unlocked = True
for k, v in self.items():
# chs is roughly half the time but most are immutable
if k == 'chs':
# dict shallow copy is fast, so use it then overwrite
result[k] = list()
for ch in v:
ch = ch.copy() # shallow
ch['loc'] = ch['loc'].copy()
result[k].append(ch)
elif k == 'ch_names':
# we know it's list of str, shallow okay and saves ~100 µs
result[k] = v.copy()
elif k == 'hpi_meas':
hms = list()
for hm in v:
hm = hm.copy()
# the only mutable thing here is some entries in coils
hm['hpi_coils'] = [coil.copy() for coil in hm['hpi_coils']]
# There is a *tiny* risk here that someone could write
# raw.info['hpi_meas'][0]['hpi_coils'][1]['epoch'] = ...
# and assume that info.copy() will make an actual copy,
# but copying these entries has a 2x slowdown penalty so
# probably not worth it for such a deep corner case:
# for coil in hpi_coils:
# for key in ('epoch', 'slopes', 'corr_coeff'):
# coil[key] = coil[key].copy()
hms.append(hm)
result[k] = hms
else:
result[k] = deepcopy(v, memodict)
result._unlocked = False
return result
def _check_consistency(self, prepend_error=''):
"""Do some self-consistency checks and datatype tweaks."""
missing = [bad for bad in self['bads'] if bad not in self['ch_names']]
if len(missing) > 0:
msg = '%sbad channel(s) %s marked do not exist in info'
raise RuntimeError(msg % (prepend_error, missing,))
meas_date = self.get('meas_date')
if meas_date is not None:
if (not isinstance(self['meas_date'], datetime.datetime) or
self['meas_date'].tzinfo is None or
self['meas_date'].tzinfo is not datetime.timezone.utc):
raise RuntimeError('%sinfo["meas_date"] must be a datetime '
'object in UTC or None, got %r'
% (prepend_error, repr(self['meas_date']),))
chs = [ch['ch_name'] for ch in self['chs']]
if len(self['ch_names']) != len(chs) or any(
ch_1 != ch_2 for ch_1, ch_2 in zip(self['ch_names'], chs)) or \
self['nchan'] != len(chs):
raise RuntimeError('%sinfo channel name inconsistency detected, '
'please notify mne-python developers'
% (prepend_error,))
# make sure we have the proper datatypes
with self._unlock():
for key in ('sfreq', 'highpass', 'lowpass'):
if self.get(key) is not None:
self[key] = float(self[key])
for pi, proj in enumerate(self.get('projs', [])):
_validate_type(proj, Projection, f'info["projs"][{pi}]')
for key in ('kind', 'active', 'desc', 'data', 'explained_var'):
if key not in proj:
raise RuntimeError(f'Projection incomplete, missing {key}')
# Ensure info['chs'] has immutable entries (copies much faster)
for ci, ch in enumerate(self['chs']):
_check_ch_keys(ch, ci)
ch_name = ch['ch_name']
if not isinstance(ch_name, str):
raise TypeError(
'Bad info: info["chs"][%d]["ch_name"] is not a string, '
'got type %s' % (ci, type(ch_name)))
for key in _SCALAR_CH_KEYS:
val = ch.get(key, 1)
if not _is_numeric(val):
raise TypeError(
'Bad info: info["chs"][%d][%r] = %s is type %s, must '
'be float or int' % (ci, key, val, type(val)))
loc = ch['loc']
if not (isinstance(loc, np.ndarray) and loc.shape == (12,)):
raise TypeError(
'Bad info: info["chs"][%d]["loc"] must be ndarray with '
'12 elements, got %r' % (ci, loc))
# make sure channel names are unique
with self._unlock():
self['ch_names'] = _unique_channel_names(self['ch_names'])
for idx, ch_name in enumerate(self['ch_names']):
self['chs'][idx]['ch_name'] = ch_name
def _update_redundant(self):
"""Update the redundant entries."""
with self._unlock():
self['ch_names'] = [ch['ch_name'] for ch in self['chs']]
self['nchan'] = len(self['chs'])
@property
def ch_names(self):
return self['ch_names']
def _get_chs_for_repr(self):
titles = _handle_default('titles')
# good channels
channels = {}
ch_types = [channel_type(self, idx) for idx in range(len(self['chs']))]
ch_counts = Counter(ch_types)
for ch_type, count in ch_counts.items():
if ch_type == 'meg':
channels['mag'] = len(pick_types(self, meg='mag'))
channels['grad'] = len(pick_types(self, meg='grad'))
elif ch_type == 'eog':
pick_eog = pick_types(self, eog=True)
eog = ', '.join(
np.array(self['ch_names'])[pick_eog])
elif ch_type == 'ecg':
pick_ecg = pick_types(self, ecg=True)
ecg = ', '.join(
np.array(self['ch_names'])[pick_ecg])
channels[ch_type] = count
good_channels = ', '.join(
[f'{v} {titles.get(k, k.upper())}' for k, v in channels.items()])
if 'ecg' not in channels.keys():
ecg = 'Not available'
if 'eog' not in channels.keys():
eog = 'Not available'
# bad channels
if len(self['bads']) > 0:
bad_channels = ', '.join(self['bads'])
else:
bad_channels = 'None'
return good_channels, bad_channels, ecg, eog
@repr_html
def _repr_html_(self, caption=None):
"""Summarize info for HTML representation."""
from ..html_templates import repr_templates_env
if isinstance(caption, str):
html = f'<h4>{caption}</h4>'
else:
html = ''
good_channels, bad_channels, ecg, eog = self._get_chs_for_repr()
# TODO
# Most of the following checks are to ensure that we get a proper repr
# for Forward['info'] (and probably others like
# InverseOperator['info']??), which doesn't seem to follow our standard
# Info structure used elsewhere.
# Proposed solution for a future refactoring:
# Forward['info'] should get its own Info subclass (with respective
# repr).
# meas date
meas_date = self.get('meas_date')
if meas_date is not None:
meas_date = meas_date.strftime("%B %d, %Y %H:%M:%S") + ' GMT'
projs = self.get('projs')
if projs:
projs = [
f'{p["desc"]} : {"on" if p["active"] else "off"}'
for p in self['projs']
]
else:
projs = None
info_template = repr_templates_env.get_template('info.html.jinja')
return html + info_template.render(
caption=caption,
meas_date=meas_date,
projs=projs,
ecg=ecg,
eog=eog,
good_channels=good_channels,
bad_channels=bad_channels,
dig=self.get('dig'),
subject_info=self.get('subject_info'),
lowpass=self.get('lowpass'),
highpass=self.get('highpass'),
sfreq=self.get('sfreq'),
experimenter=self.get('experimenter'),
)
def _simplify_info(info):
"""Return a simplified info structure to speed up picking."""
chs = [{key: ch[key]
for key in ('ch_name', 'kind', 'unit', 'coil_type', 'loc', 'cal')}
for ch in info['chs']]
sub_info = Info(chs=chs, bads=info['bads'], comps=info['comps'],
projs=info['projs'],
custom_ref_applied=info['custom_ref_applied'])
sub_info._update_redundant()
return sub_info
@verbose
def read_fiducials(fname, verbose=None):
"""Read fiducials from a fiff file.
Parameters
----------
fname : path-like
The filename to read.
%(verbose)s
Returns
-------
pts : list of dict
List of digitizer points (each point in a dict).
coord_frame : int
The coordinate frame of the points (one of
``mne.io.constants.FIFF.FIFFV_COORD_...``).
"""
fname = _check_fname(
fname=fname,
overwrite='read',
must_exist=True
)
fid, tree, _ = fiff_open(fname)
with fid:
isotrak = dir_tree_find(tree, FIFF.FIFFB_ISOTRAK)
isotrak = isotrak[0]
pts = []
coord_frame = FIFF.FIFFV_COORD_HEAD
for k in range(isotrak['nent']):
kind = isotrak['directory'][k].kind
pos = isotrak['directory'][k].pos
if kind == FIFF.FIFF_DIG_POINT:
tag = read_tag(fid, pos)
pts.append(DigPoint(tag.data))
elif kind == FIFF.FIFF_MNE_COORD_FRAME:
tag = read_tag(fid, pos)
coord_frame = tag.data[0]
coord_frame = _coord_frame_named.get(coord_frame, coord_frame)
# coord_frame is not stored in the tag
for pt in pts:
pt['coord_frame'] = coord_frame
return pts, coord_frame
@verbose
def write_fiducials(fname, pts, coord_frame='unknown', *, overwrite=False,
verbose=None):
"""Write fiducials to a fiff file.
Parameters
----------
fname : path-like
Destination file name.
pts : iterator of dict
Iterator through digitizer points. Each point is a dictionary with
the keys 'kind', 'ident' and 'r'.
coord_frame : str | int
The coordinate frame of the points. If a string, must be one of
``'meg'``, ``'mri'``, ``'mri_voxel'``, ``'head'``,
``'mri_tal'``, ``'ras'``, ``'fs_tal'``, ``'ctf_head'``,
``'ctf_meg'``, and ``'unknown'``
If an integer, must be one of the constants defined as
``mne.io.constants.FIFF.FIFFV_COORD_...``.
%(overwrite)s
.. versionadded:: 1.0
%(verbose)s
"""
write_dig(fname, pts, coord_frame, overwrite=overwrite)
@verbose
def read_info(fname, verbose=None):
"""Read measurement info from a file.
Parameters
----------
fname : str
File name.
%(verbose)s
Returns
-------
%(info_not_none)s
"""
f, tree, _ = fiff_open(fname)
with f as fid:
info = read_meas_info(fid, tree)[0]
return info
def read_bad_channels(fid, node):
"""Read bad channels.
Parameters
----------
fid : file
The file descriptor.
node : dict
The node of the FIF tree that contains info on the bad channels.
Returns
-------
bads : list
A list of bad channel's names.
"""
return _read_bad_channels(fid, node)
def _read_bad_channels(fid, node, ch_names_mapping):
ch_names_mapping = {} if ch_names_mapping is None else ch_names_mapping
nodes = dir_tree_find(node, FIFF.FIFFB_MNE_BAD_CHANNELS)
bads = []
if len(nodes) > 0:
for node in nodes:
tag = find_tag(fid, node, FIFF.FIFF_MNE_CH_NAME_LIST)
if tag is not None and tag.data is not None:
bads = tag.data.split(':')
bads[:] = _rename_list(bads, ch_names_mapping)
return bads
@verbose
def read_meas_info(fid, tree, clean_bads=False, verbose=None):
"""Read the measurement info.
Parameters
----------
fid : file
Open file descriptor.
tree : tree
FIF tree structure.
clean_bads : bool
If True, clean info['bads'] before running consistency check.
Should only be needed for old files where we did not check bads
before saving.
%(verbose)s
Returns
-------
%(info_not_none)s
meas : dict
Node in tree that contains the info.
"""
# Find the desired blocks
meas = dir_tree_find(tree, FIFF.FIFFB_MEAS)
if len(meas) == 0:
raise ValueError('Could not find measurement data')
if len(meas) > 1:
raise ValueError('Cannot read more that 1 measurement data')
meas = meas[0]
meas_info = dir_tree_find(meas, FIFF.FIFFB_MEAS_INFO)
if len(meas_info) == 0:
raise ValueError('Could not find measurement info')
if len(meas_info) > 1:
raise ValueError('Cannot read more that 1 measurement info')
meas_info = meas_info[0]
# Read measurement info
dev_head_t = None
ctf_head_t = None
dev_ctf_t = None
meas_date = None
utc_offset = None
highpass = None
lowpass = None
nchan = None
sfreq = None
chs = []
experimenter = None
description = None
proj_id = None
proj_name = None
line_freq = None
gantry_angle = None
custom_ref_applied = FIFF.FIFFV_MNE_CUSTOM_REF_OFF
xplotter_layout = None
kit_system_id = None
for k in range(meas_info['nent']):
kind = meas_info['directory'][k].kind
pos = meas_info['directory'][k].pos
if kind == FIFF.FIFF_NCHAN:
tag = read_tag(fid, pos)
nchan = int(tag.data)
elif kind == FIFF.FIFF_SFREQ:
tag = read_tag(fid, pos)
sfreq = float(tag.data)
elif kind == FIFF.FIFF_CH_INFO:
tag = read_tag(fid, pos)
chs.append(tag.data)
elif kind == FIFF.FIFF_LOWPASS:
tag = read_tag(fid, pos)
if not np.isnan(tag.data):
lowpass = float(tag.data)
elif kind == FIFF.FIFF_HIGHPASS:
tag = read_tag(fid, pos)
if not np.isnan(tag.data):
highpass = float(tag.data)
elif kind == FIFF.FIFF_MEAS_DATE:
tag = read_tag(fid, pos)
meas_date = tuple(tag.data)
if len(meas_date) == 1: # can happen from old C conversions
meas_date = (meas_date[0], 0)
elif kind == FIFF.FIFF_UTC_OFFSET:
tag = read_tag(fid, pos)
utc_offset = str(tag.data)
elif kind == FIFF.FIFF_COORD_TRANS:
tag = read_tag(fid, pos)
cand = tag.data
if cand['from'] == FIFF.FIFFV_COORD_DEVICE and \
cand['to'] == FIFF.FIFFV_COORD_HEAD:
dev_head_t = cand
elif cand['from'] == FIFF.FIFFV_COORD_HEAD and \
cand['to'] == FIFF.FIFFV_COORD_DEVICE:
# this reversal can happen with BabyMEG data
dev_head_t = invert_transform(cand)
elif cand['from'] == FIFF.FIFFV_MNE_COORD_CTF_HEAD and \
cand['to'] == FIFF.FIFFV_COORD_HEAD:
ctf_head_t = cand
elif cand['from'] == FIFF.FIFFV_MNE_COORD_CTF_DEVICE and \
cand['to'] == FIFF.FIFFV_MNE_COORD_CTF_HEAD:
dev_ctf_t = cand
elif kind == FIFF.FIFF_EXPERIMENTER:
tag = read_tag(fid, pos)
experimenter = tag.data
elif kind == FIFF.FIFF_DESCRIPTION:
tag = read_tag(fid, pos)
description = tag.data
elif kind == FIFF.FIFF_PROJ_ID:
tag = read_tag(fid, pos)
proj_id = tag.data
elif kind == FIFF.FIFF_PROJ_NAME:
tag = read_tag(fid, pos)
proj_name = tag.data
elif kind == FIFF.FIFF_LINE_FREQ:
tag = read_tag(fid, pos)
line_freq = float(tag.data)
elif kind == FIFF.FIFF_GANTRY_ANGLE:
tag = read_tag(fid, pos)
gantry_angle = float(tag.data)
elif kind in [FIFF.FIFF_MNE_CUSTOM_REF, 236]: # 236 used before v0.11
tag = read_tag(fid, pos)
custom_ref_applied = int(tag.data)
elif kind == FIFF.FIFF_XPLOTTER_LAYOUT:
tag = read_tag(fid, pos)
xplotter_layout = str(tag.data)
elif kind == FIFF.FIFF_MNE_KIT_SYSTEM_ID:
tag = read_tag(fid, pos)
kit_system_id = int(tag.data)
ch_names_mapping = _read_extended_ch_info(chs, meas_info, fid)
# Check that we have everything we need
if nchan is None:
raise ValueError('Number of channels is not defined')
if sfreq is None:
raise ValueError('Sampling frequency is not defined')
if len(chs) == 0:
raise ValueError('Channel information not defined')
if len(chs) != nchan:
raise ValueError('Incorrect number of channel definitions found')
if dev_head_t is None or ctf_head_t is None:
hpi_result = dir_tree_find(meas_info, FIFF.FIFFB_HPI_RESULT)
if len(hpi_result) == 1:
hpi_result = hpi_result[0]
for k in range(hpi_result['nent']):
kind = hpi_result['directory'][k].kind
pos = hpi_result['directory'][k].pos
if kind == FIFF.FIFF_COORD_TRANS:
tag = read_tag(fid, pos)
cand = tag.data
if (cand['from'] == FIFF.FIFFV_COORD_DEVICE and
cand['to'] == FIFF.FIFFV_COORD_HEAD and
dev_head_t is None):
dev_head_t = cand
elif (cand['from'] == FIFF.FIFFV_MNE_COORD_CTF_HEAD and
cand['to'] == FIFF.FIFFV_COORD_HEAD and
ctf_head_t is None):
ctf_head_t = cand
# Locate the Polhemus data
dig = _read_dig_fif(fid, meas_info)
# Locate the acquisition information
acqpars = dir_tree_find(meas_info, FIFF.FIFFB_DACQ_PARS)
acq_pars = None
acq_stim = None
if len(acqpars) == 1:
acqpars = acqpars[0]
for k in range(acqpars['nent']):
kind = acqpars['directory'][k].kind
pos = acqpars['directory'][k].pos
if kind == FIFF.FIFF_DACQ_PARS:
tag = read_tag(fid, pos)
acq_pars = tag.data
elif kind == FIFF.FIFF_DACQ_STIM:
tag = read_tag(fid, pos)
acq_stim = tag.data
# Load the SSP data
projs = _read_proj(
fid, meas_info, ch_names_mapping=ch_names_mapping)
# Load the CTF compensation data
comps = _read_ctf_comp(
fid, meas_info, chs, ch_names_mapping=ch_names_mapping)
# Load the bad channel list
bads = _read_bad_channels(
fid, meas_info, ch_names_mapping=ch_names_mapping)
#
# Put the data together
#
info = Info(file_id=tree['id'])
info._unlocked = True
# Locate events list
events = dir_tree_find(meas_info, FIFF.FIFFB_EVENTS)
evs = list()
for event in events:
ev = dict()
for k in range(event['nent']):
kind = event['directory'][k].kind
pos = event['directory'][k].pos
if kind == FIFF.FIFF_EVENT_CHANNELS:
ev['channels'] = read_tag(fid, pos).data
elif kind == FIFF.FIFF_EVENT_LIST:
ev['list'] = read_tag(fid, pos).data
evs.append(ev)
info['events'] = evs
# Locate HPI result
hpi_results = dir_tree_find(meas_info, FIFF.FIFFB_HPI_RESULT)
hrs = list()
for hpi_result in hpi_results:
hr = dict()
hr['dig_points'] = []
for k in range(hpi_result['nent']):
kind = hpi_result['directory'][k].kind
pos = hpi_result['directory'][k].pos
if kind == FIFF.FIFF_DIG_POINT:
hr['dig_points'].append(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_HPI_DIGITIZATION_ORDER:
hr['order'] = read_tag(fid, pos).data
elif kind == FIFF.FIFF_HPI_COILS_USED:
hr['used'] = read_tag(fid, pos).data
elif kind == FIFF.FIFF_HPI_COIL_MOMENTS:
hr['moments'] = read_tag(fid, pos).data
elif kind == FIFF.FIFF_HPI_FIT_GOODNESS:
hr['goodness'] = read_tag(fid, pos).data
elif kind == FIFF.FIFF_HPI_FIT_GOOD_LIMIT:
hr['good_limit'] = float(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_HPI_FIT_DIST_LIMIT:
hr['dist_limit'] = float(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_HPI_FIT_ACCEPT:
hr['accept'] = int(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_COORD_TRANS:
hr['coord_trans'] = read_tag(fid, pos).data
hrs.append(hr)
info['hpi_results'] = hrs
# Locate HPI Measurement
hpi_meass = dir_tree_find(meas_info, FIFF.FIFFB_HPI_MEAS)
hms = list()
for hpi_meas in hpi_meass:
hm = dict()
for k in range(hpi_meas['nent']):
kind = hpi_meas['directory'][k].kind
pos = hpi_meas['directory'][k].pos
if kind == FIFF.FIFF_CREATOR:
hm['creator'] = str(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_SFREQ:
hm['sfreq'] = float(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_NCHAN:
hm['nchan'] = int(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_NAVE:
hm['nave'] = int(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_HPI_NCOIL:
hm['ncoil'] = int(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_FIRST_SAMPLE:
hm['first_samp'] = int(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_LAST_SAMPLE:
hm['last_samp'] = int(read_tag(fid, pos).data)
hpi_coils = dir_tree_find(hpi_meas, FIFF.FIFFB_HPI_COIL)
hcs = []
for hpi_coil in hpi_coils:
hc = dict()
for k in range(hpi_coil['nent']):
kind = hpi_coil['directory'][k].kind
pos = hpi_coil['directory'][k].pos
if kind == FIFF.FIFF_HPI_COIL_NO:
hc['number'] = int(read_tag(fid, pos).data)
elif kind == FIFF.FIFF_EPOCH:
hc['epoch'] = read_tag(fid, pos).data
hc['epoch'].flags.writeable = False
elif kind == FIFF.FIFF_HPI_SLOPES:
hc['slopes'] = read_tag(fid, pos).data
hc['slopes'].flags.writeable = False
elif kind == FIFF.FIFF_HPI_CORR_COEFF:
hc['corr_coeff'] = read_tag(fid, pos).data
hc['corr_coeff'].flags.writeable = False
elif kind == FIFF.FIFF_HPI_COIL_FREQ:
hc['coil_freq'] = float(read_tag(fid, pos).data)
hcs.append(hc)
hm['hpi_coils'] = hcs
hms.append(hm)
info['hpi_meas'] = hms
del hms
subject_info = dir_tree_find(meas_info, FIFF.FIFFB_SUBJECT)
si = None
if len(subject_info) == 1:
subject_info = subject_info[0]
si = dict()
for k in range(subject_info['nent']):
kind = subject_info['directory'][k].kind
pos = subject_info['directory'][k].pos
if kind == FIFF.FIFF_SUBJ_ID:
tag = read_tag(fid, pos)
si['id'] = int(tag.data)
elif kind == FIFF.FIFF_SUBJ_HIS_ID:
tag = read_tag(fid, pos)
si['his_id'] = str(tag.data)
elif kind == FIFF.FIFF_SUBJ_LAST_NAME:
tag = read_tag(fid, pos)
si['last_name'] = str(tag.data)
elif kind == FIFF.FIFF_SUBJ_FIRST_NAME:
tag = read_tag(fid, pos)
si['first_name'] = str(tag.data)
elif kind == FIFF.FIFF_SUBJ_MIDDLE_NAME:
tag = read_tag(fid, pos)
si['middle_name'] = str(tag.data)
elif kind == FIFF.FIFF_SUBJ_BIRTH_DAY:
try:
tag = read_tag(fid, pos)
except OverflowError:
warn('Encountered an error while trying to read the '
'birthday from the input data. No birthday will be '
'set. Please check the integrity of the birthday '
'information in the input data.')
continue
si['birthday'] = tag.data
elif kind == FIFF.FIFF_SUBJ_SEX:
tag = read_tag(fid, pos)
si['sex'] = int(tag.data)
elif kind == FIFF.FIFF_SUBJ_HAND:
tag = read_tag(fid, pos)
si['hand'] = int(tag.data)
elif kind == FIFF.FIFF_SUBJ_WEIGHT:
tag = read_tag(fid, pos)
si['weight'] = tag.data
elif kind == FIFF.FIFF_SUBJ_HEIGHT:
tag = read_tag(fid, pos)
si['height'] = tag.data
info['subject_info'] = si
del si
device_info = dir_tree_find(meas_info, FIFF.FIFFB_DEVICE)
di = None
if len(device_info) == 1:
device_info = device_info[0]
di = dict()
for k in range(device_info['nent']):
kind = device_info['directory'][k].kind
pos = device_info['directory'][k].pos
if kind == FIFF.FIFF_DEVICE_TYPE:
tag = read_tag(fid, pos)
di['type'] = str(tag.data)
elif kind == FIFF.FIFF_DEVICE_MODEL:
tag = read_tag(fid, pos)
di['model'] = str(tag.data)
elif kind == FIFF.FIFF_DEVICE_SERIAL:
tag = read_tag(fid, pos)
di['serial'] = str(tag.data)
elif kind == FIFF.FIFF_DEVICE_SITE:
tag = read_tag(fid, pos)
di['site'] = str(tag.data)
info['device_info'] = di
del di
helium_info = dir_tree_find(meas_info, FIFF.FIFFB_HELIUM)
hi = None
if len(helium_info) == 1:
helium_info = helium_info[0]
hi = dict()
for k in range(helium_info['nent']):
kind = helium_info['directory'][k].kind
pos = helium_info['directory'][k].pos
if kind == FIFF.FIFF_HE_LEVEL_RAW:
tag = read_tag(fid, pos)
hi['he_level_raw'] = float(tag.data)
elif kind == FIFF.FIFF_HELIUM_LEVEL:
tag = read_tag(fid, pos)
hi['helium_level'] = float(tag.data)
elif kind == FIFF.FIFF_ORIG_FILE_GUID:
tag = read_tag(fid, pos)
hi['orig_file_guid'] = str(tag.data)
elif kind == FIFF.FIFF_MEAS_DATE:
tag = read_tag(fid, pos)
hi['meas_date'] = tuple(int(t) for t in tag.data)
info['helium_info'] = hi
del hi
hpi_subsystem = dir_tree_find(meas_info, FIFF.FIFFB_HPI_SUBSYSTEM)
hs = None
if len(hpi_subsystem) == 1:
hpi_subsystem = hpi_subsystem[0]
hs = dict()
for k in range(hpi_subsystem['nent']):
kind = hpi_subsystem['directory'][k].kind
pos = hpi_subsystem['directory'][k].pos
if kind == FIFF.FIFF_HPI_NCOIL:
tag = read_tag(fid, pos)
hs['ncoil'] = int(tag.data)
elif kind == FIFF.FIFF_EVENT_CHANNEL:
tag = read_tag(fid, pos)
hs['event_channel'] = str(tag.data)
hpi_coils = dir_tree_find(hpi_subsystem, FIFF.FIFFB_HPI_COIL)
hc = []
for coil in hpi_coils:
this_coil = dict()
for j in range(coil['nent']):
kind = coil['directory'][j].kind
pos = coil['directory'][j].pos
if kind == FIFF.FIFF_EVENT_BITS:
tag = read_tag(fid, pos)
this_coil['event_bits'] = np.array(tag.data)
hc.append(this_coil)
hs['hpi_coils'] = hc
info['hpi_subsystem'] = hs
# Read processing history
info['proc_history'] = _read_proc_history(fid, tree)
# Make the most appropriate selection for the measurement id
if meas_info['parent_id'] is None:
if meas_info['id'] is None:
if meas['id'] is None:
if meas['parent_id'] is None:
info['meas_id'] = info['file_id']
else:
info['meas_id'] = meas['parent_id']
else:
info['meas_id'] = meas['id']
else:
info['meas_id'] = meas_info['id']
else:
info['meas_id'] = meas_info['parent_id']
info['experimenter'] = experimenter
info['description'] = description
info['proj_id'] = proj_id
info['proj_name'] = proj_name
if meas_date is None:
meas_date = (info['meas_id']['secs'], info['meas_id']['usecs'])
info['meas_date'] = _ensure_meas_date_none_or_dt(meas_date)
info['utc_offset'] = utc_offset
info['sfreq'] = sfreq
info['highpass'] = highpass if highpass is not None else 0.
info['lowpass'] = lowpass if lowpass is not None else info['sfreq'] / 2.0
info['line_freq'] = line_freq
info['gantry_angle'] = gantry_angle
# Add the channel information and make a list of channel names
# for convenience
info['chs'] = chs
#
# Add the coordinate transformations
#
info['dev_head_t'] = dev_head_t
info['ctf_head_t'] = ctf_head_t
info['dev_ctf_t'] = dev_ctf_t
if dev_head_t is not None and ctf_head_t is not None and dev_ctf_t is None:
from ..transforms import Transform
head_ctf_trans = np.linalg.inv(ctf_head_t['trans'])
dev_ctf_trans = np.dot(head_ctf_trans, info['dev_head_t']['trans'])
info['dev_ctf_t'] = Transform('meg', 'ctf_head', dev_ctf_trans)
# All kinds of auxliary stuff
info['dig'] = _format_dig_points(dig)
info['bads'] = bads
info._update_redundant()
if clean_bads:
info['bads'] = [b for b in bads if b in info['ch_names']]
info['projs'] = projs
info['comps'] = comps
info['acq_pars'] = acq_pars
info['acq_stim'] = acq_stim
info['custom_ref_applied'] = custom_ref_applied
info['xplotter_layout'] = xplotter_layout
info['kit_system_id'] = kit_system_id
info._check_consistency()
info._unlocked = False
return info, meas
def _read_extended_ch_info(chs, parent, fid):
ch_infos = dir_tree_find(parent, FIFF.FIFFB_CH_INFO)
if len(ch_infos) == 0:
return
_check_option('length of channel infos', len(ch_infos), [len(chs)])
logger.info(' Reading extended channel information')
# Here we assume that ``remap`` is in the same order as the channels
# themselves, which is hopefully safe enough.
ch_names_mapping = dict()
for new, ch in zip(ch_infos, chs):
for k in range(new['nent']):
kind = new['directory'][k].kind
try:
key, cast = _CH_READ_MAP[kind]
except KeyError:
# This shouldn't happen if we're up to date with the FIFF
# spec
warn(f'Discarding extra channel information kind {kind}')
continue
assert key in ch
data = read_tag(fid, new['directory'][k].pos).data
if data is not None:
data = cast(data)
if key == 'ch_name':
ch_names_mapping[ch[key]] = data
ch[key] = data
_update_ch_info_named(ch)
# we need to return ch_names_mapping so that we can also rename the
# bad channels
return ch_names_mapping
def _rename_comps(comps, ch_names_mapping):
if not (comps and ch_names_mapping):
return
for comp in comps:
data = comp['data']
for key in ('row_names', 'col_names'):
data[key][:] = _rename_list(data[key], ch_names_mapping)
def _ensure_meas_date_none_or_dt(meas_date):
if meas_date is None or np.array_equal(meas_date, DATE_NONE):
meas_date = None
elif not isinstance(meas_date, datetime.datetime):
meas_date = _stamp_to_dt(meas_date)
return meas_date
def _check_dates(info, prepend_error=''):
"""Check dates before writing as fif files.
It's needed because of the limited integer precision
of the fix standard.
"""
for key in ('file_id', 'meas_id'):
value = info.get(key)
if value is not None:
assert 'msecs' not in value
for key_2 in ('secs', 'usecs'):
if (value[key_2] < np.iinfo('>i4').min or
value[key_2] > np.iinfo('>i4').max):
raise RuntimeError('%sinfo[%s][%s] must be between '
'"%r" and "%r", got "%r"'
% (prepend_error, key, key_2,
np.iinfo('>i4').min,
np.iinfo('>i4').max,
value[key_2]),)
meas_date = info.get('meas_date')
if meas_date is None:
return
meas_date_stamp = _dt_to_stamp(meas_date)
if (meas_date_stamp[0] < np.iinfo('>i4').min or
meas_date_stamp[0] > np.iinfo('>i4').max):
raise RuntimeError(
'%sinfo["meas_date"] seconds must be between "%r" '
'and "%r", got "%r"'
% (prepend_error, (np.iinfo('>i4').min, 0),
(np.iinfo('>i4').max, 0), meas_date_stamp[0],))
@fill_doc
def write_meas_info(fid, info, data_type=None, reset_range=True):
"""Write measurement info into a file id (from a fif file).
Parameters
----------
fid : file
Open file descriptor.
%(info_not_none)s
data_type : int
The data_type in case it is necessary. Should be 4 (FIFFT_FLOAT),
5 (FIFFT_DOUBLE), or 16 (FIFFT_DAU_PACK16) for
raw data.
reset_range : bool
If True, info['chs'][k]['range'] will be set to unity.
Notes
-----
Tags are written in a particular order for compatibility with maxfilter.
"""
info._check_consistency()
_check_dates(info)
# Measurement info
start_block(fid, FIFF.FIFFB_MEAS_INFO)
# Add measurement id
if info['meas_id'] is not None:
write_id(fid, FIFF.FIFF_PARENT_BLOCK_ID, info['meas_id'])
for event in info['events']:
start_block(fid, FIFF.FIFFB_EVENTS)
if event.get('channels') is not None:
write_int(fid, FIFF.FIFF_EVENT_CHANNELS, event['channels'])
if event.get('list') is not None:
write_int(fid, FIFF.FIFF_EVENT_LIST, event['list'])
end_block(fid, FIFF.FIFFB_EVENTS)
# HPI Result
for hpi_result in info['hpi_results']:
start_block(fid, FIFF.FIFFB_HPI_RESULT)
write_dig_points(fid, hpi_result['dig_points'])
if 'order' in hpi_result:
write_int(fid, FIFF.FIFF_HPI_DIGITIZATION_ORDER,
hpi_result['order'])
if 'used' in hpi_result:
write_int(fid, FIFF.FIFF_HPI_COILS_USED, hpi_result['used'])
if 'moments' in hpi_result:
write_float_matrix(fid, FIFF.FIFF_HPI_COIL_MOMENTS,
hpi_result['moments'])
if 'goodness' in hpi_result:
write_float(fid, FIFF.FIFF_HPI_FIT_GOODNESS,
hpi_result['goodness'])
if 'good_limit' in hpi_result:
write_float(fid, FIFF.FIFF_HPI_FIT_GOOD_LIMIT,
hpi_result['good_limit'])
if 'dist_limit' in hpi_result:
write_float(fid, FIFF.FIFF_HPI_FIT_DIST_LIMIT,
hpi_result['dist_limit'])
if 'accept' in hpi_result:
write_int(fid, FIFF.FIFF_HPI_FIT_ACCEPT, hpi_result['accept'])
if 'coord_trans' in hpi_result:
write_coord_trans(fid, hpi_result['coord_trans'])
end_block(fid, FIFF.FIFFB_HPI_RESULT)
# HPI Measurement
for hpi_meas in info['hpi_meas']:
start_block(fid, FIFF.FIFFB_HPI_MEAS)
if hpi_meas.get('creator') is not None:
write_string(fid, FIFF.FIFF_CREATOR, hpi_meas['creator'])
if hpi_meas.get('sfreq') is not None:
write_float(fid, FIFF.FIFF_SFREQ, hpi_meas['sfreq'])
if hpi_meas.get('nchan') is not None:
write_int(fid, FIFF.FIFF_NCHAN, hpi_meas['nchan'])
if hpi_meas.get('nave') is not None:
write_int(fid, FIFF.FIFF_NAVE, hpi_meas['nave'])
if hpi_meas.get('ncoil') is not None:
write_int(fid, FIFF.FIFF_HPI_NCOIL, hpi_meas['ncoil'])
if hpi_meas.get('first_samp') is not None:
write_int(fid, FIFF.FIFF_FIRST_SAMPLE, hpi_meas['first_samp'])
if hpi_meas.get('last_samp') is not None:
write_int(fid, FIFF.FIFF_LAST_SAMPLE, hpi_meas['last_samp'])
for hpi_coil in hpi_meas['hpi_coils']:
start_block(fid, FIFF.FIFFB_HPI_COIL)
if hpi_coil.get('number') is not None:
write_int(fid, FIFF.FIFF_HPI_COIL_NO, hpi_coil['number'])
if hpi_coil.get('epoch') is not None:
write_float_matrix(fid, FIFF.FIFF_EPOCH, hpi_coil['epoch'])
if hpi_coil.get('slopes') is not None:
write_float(fid, FIFF.FIFF_HPI_SLOPES, hpi_coil['slopes'])
if hpi_coil.get('corr_coeff') is not None:
write_float(fid, FIFF.FIFF_HPI_CORR_COEFF,
hpi_coil['corr_coeff'])
if hpi_coil.get('coil_freq') is not None:
write_float(fid, FIFF.FIFF_HPI_COIL_FREQ,
hpi_coil['coil_freq'])
end_block(fid, FIFF.FIFFB_HPI_COIL)
end_block(fid, FIFF.FIFFB_HPI_MEAS)
# Polhemus data
write_dig_points(fid, info['dig'], block=True)
# megacq parameters
if info['acq_pars'] is not None or info['acq_stim'] is not None:
start_block(fid, FIFF.FIFFB_DACQ_PARS)
if info['acq_pars'] is not None:
write_string(fid, FIFF.FIFF_DACQ_PARS, info['acq_pars'])
if info['acq_stim'] is not None:
write_string(fid, FIFF.FIFF_DACQ_STIM, info['acq_stim'])
end_block(fid, FIFF.FIFFB_DACQ_PARS)
# Coordinate transformations if the HPI result block was not there
if info['dev_head_t'] is not None:
write_coord_trans(fid, info['dev_head_t'])
if info['ctf_head_t'] is not None:
write_coord_trans(fid, info['ctf_head_t'])
if info['dev_ctf_t'] is not None:
write_coord_trans(fid, info['dev_ctf_t'])
# Projectors
ch_names_mapping = _make_ch_names_mapping(info['chs'])
_write_proj(fid, info['projs'], ch_names_mapping=ch_names_mapping)
# Bad channels
if len(info['bads']) > 0:
bads = _rename_list(info['bads'], ch_names_mapping)
start_block(fid, FIFF.FIFFB_MNE_BAD_CHANNELS)
write_name_list(fid, FIFF.FIFF_MNE_CH_NAME_LIST, bads)
end_block(fid, FIFF.FIFFB_MNE_BAD_CHANNELS)
# General
if info.get('experimenter') is not None:
write_string(fid, FIFF.FIFF_EXPERIMENTER, info['experimenter'])
if info.get('description') is not None:
write_string(fid, FIFF.FIFF_DESCRIPTION, info['description'])
if info.get('proj_id') is not None:
write_int(fid, FIFF.FIFF_PROJ_ID, info['proj_id'])
if info.get('proj_name') is not None:
write_string(fid, FIFF.FIFF_PROJ_NAME, info['proj_name'])
if info.get('meas_date') is not None:
write_int(fid, FIFF.FIFF_MEAS_DATE, _dt_to_stamp(info['meas_date']))
if info.get('utc_offset') is not None:
write_string(fid, FIFF.FIFF_UTC_OFFSET, info['utc_offset'])
write_int(fid, FIFF.FIFF_NCHAN, info['nchan'])
write_float(fid, FIFF.FIFF_SFREQ, info['sfreq'])
if info['lowpass'] is not None:
write_float(fid, FIFF.FIFF_LOWPASS, info['lowpass'])
if info['highpass'] is not None:
write_float(fid, FIFF.FIFF_HIGHPASS, info['highpass'])
if info.get('line_freq') is not None:
write_float(fid, FIFF.FIFF_LINE_FREQ, info['line_freq'])
if info.get('gantry_angle') is not None:
write_float(fid, FIFF.FIFF_GANTRY_ANGLE, info['gantry_angle'])
if data_type is not None:
write_int(fid, FIFF.FIFF_DATA_PACK, data_type)
if info.get('custom_ref_applied'):
write_int(fid, FIFF.FIFF_MNE_CUSTOM_REF, info['custom_ref_applied'])
if info.get('xplotter_layout'):
write_string(fid, FIFF.FIFF_XPLOTTER_LAYOUT, info['xplotter_layout'])
# Channel information
_write_ch_infos(fid, info['chs'], reset_range, ch_names_mapping)
# Subject information
if info.get('subject_info') is not None:
start_block(fid, FIFF.FIFFB_SUBJECT)
si = info['subject_info']
if si.get('id') is not None:
write_int(fid, FIFF.FIFF_SUBJ_ID, si['id'])
if si.get('his_id') is not None:
write_string(fid, FIFF.FIFF_SUBJ_HIS_ID, si['his_id'])
if si.get('last_name') is not None:
write_string(fid, FIFF.FIFF_SUBJ_LAST_NAME, si['last_name'])
if si.get('first_name') is not None:
write_string(fid, FIFF.FIFF_SUBJ_FIRST_NAME, si['first_name'])
if si.get('middle_name') is not None:
write_string(fid, FIFF.FIFF_SUBJ_MIDDLE_NAME, si['middle_name'])
if si.get('birthday') is not None:
write_julian(fid, FIFF.FIFF_SUBJ_BIRTH_DAY, si['birthday'])
if si.get('sex') is not None:
write_int(fid, FIFF.FIFF_SUBJ_SEX, si['sex'])
if si.get('hand') is not None:
write_int(fid, FIFF.FIFF_SUBJ_HAND, si['hand'])
if si.get('weight') is not None:
write_float(fid, FIFF.FIFF_SUBJ_WEIGHT, si['weight'])
if si.get('height') is not None:
write_float(fid, FIFF.FIFF_SUBJ_HEIGHT, si['height'])
end_block(fid, FIFF.FIFFB_SUBJECT)
del si
if info.get('device_info') is not None:
start_block(fid, FIFF.FIFFB_DEVICE)
di = info['device_info']
write_string(fid, FIFF.FIFF_DEVICE_TYPE, di['type'])
for key in ('model', 'serial', 'site'):
if di.get(key) is not None:
write_string(fid, getattr(FIFF, 'FIFF_DEVICE_' + key.upper()),
di[key])
end_block(fid, FIFF.FIFFB_DEVICE)
del di
if info.get('helium_info') is not None:
start_block(fid, FIFF.FIFFB_HELIUM)
hi = info['helium_info']
if hi.get('he_level_raw') is not None:
write_float(fid, FIFF.FIFF_HE_LEVEL_RAW, hi['he_level_raw'])
if hi.get('helium_level') is not None:
write_float(fid, FIFF.FIFF_HELIUM_LEVEL, hi['helium_level'])
if hi.get('orig_file_guid') is not None:
write_string(fid, FIFF.FIFF_ORIG_FILE_GUID, hi['orig_file_guid'])
write_int(fid, FIFF.FIFF_MEAS_DATE, hi['meas_date'])
end_block(fid, FIFF.FIFFB_HELIUM)
del hi
if info.get('hpi_subsystem') is not None:
hs = info['hpi_subsystem']
start_block(fid, FIFF.FIFFB_HPI_SUBSYSTEM)
if hs.get('ncoil') is not None:
write_int(fid, FIFF.FIFF_HPI_NCOIL, hs['ncoil'])
if hs.get('event_channel') is not None:
write_string(fid, FIFF.FIFF_EVENT_CHANNEL, hs['event_channel'])
if hs.get('hpi_coils') is not None:
for coil in hs['hpi_coils']:
start_block(fid, FIFF.FIFFB_HPI_COIL)
if coil.get('event_bits') is not None:
write_int(fid, FIFF.FIFF_EVENT_BITS,
coil['event_bits'])
end_block(fid, FIFF.FIFFB_HPI_COIL)
end_block(fid, FIFF.FIFFB_HPI_SUBSYSTEM)
del hs
# CTF compensation info
comps = info['comps']
if ch_names_mapping:
comps = deepcopy(comps)
_rename_comps(comps, ch_names_mapping)
write_ctf_comp(fid, comps)
# KIT system ID
if info.get('kit_system_id') is not None:
write_int(fid, FIFF.FIFF_MNE_KIT_SYSTEM_ID, info['kit_system_id'])
end_block(fid, FIFF.FIFFB_MEAS_INFO)
# Processing history
_write_proc_history(fid, info)
@fill_doc
def write_info(fname, info, data_type=None, reset_range=True):
"""Write measurement info in fif file.
Parameters
----------
fname : str
The name of the file. Should end by -info.fif.
%(info_not_none)s
data_type : int
The data_type in case it is necessary. Should be 4 (FIFFT_FLOAT),
5 (FIFFT_DOUBLE), or 16 (FIFFT_DAU_PACK16) for
raw data.
reset_range : bool
If True, info['chs'][k]['range'] will be set to unity.
"""
with start_and_end_file(fname) as fid:
start_block(fid, FIFF.FIFFB_MEAS)
write_meas_info(fid, info, data_type, reset_range)
end_block(fid, FIFF.FIFFB_MEAS)
@verbose
def _merge_info_values(infos, key, verbose=None):
"""Merge things together.
Fork for {'dict', 'list', 'array', 'other'}
and consider cases where one or all are of the same type.
Does special things for "projs", "bads", and "meas_date".
"""
values = [d[key] for d in infos]
msg = ("Don't know how to merge '%s'. Make sure values are "
"compatible, got types:\n %s"
% (key, [type(v) for v in values]))
def _flatten(lists):
return [item for sublist in lists for item in sublist]
def _check_isinstance(values, kind, func):
return func([isinstance(v, kind) for v in values])
def _where_isinstance(values, kind):
"""Get indices of instances."""
return np.where([isinstance(v, type) for v in values])[0]
# list
if _check_isinstance(values, list, all):
lists = (d[key] for d in infos)
if key == 'projs':
return _uniquify_projs(_flatten(lists))
elif key == 'bads':
return sorted(set(_flatten(lists)))
else:
return _flatten(lists)
elif _check_isinstance(values, list, any):
idx = _where_isinstance(values, list)
if len(idx) == 1:
return values[int(idx)]
elif len(idx) > 1:
lists = (d[key] for d in infos if isinstance(d[key], list))
return _flatten(lists)
# dict
elif _check_isinstance(values, dict, all):
is_qual = all(object_diff(values[0], v) == '' for v in values[1:])
if is_qual:
return values[0]
else:
RuntimeError(msg)
elif _check_isinstance(values, dict, any):
idx = _where_isinstance(values, dict)
if len(idx) == 1:
return values[int(idx)]
elif len(idx) > 1:
raise RuntimeError(msg)
# ndarray
elif _check_isinstance(values, np.ndarray, all) or \
_check_isinstance(values, tuple, all):
is_qual = all(np.array_equal(values[0], x) for x in values[1:])
if is_qual:
return values[0]
elif key == 'meas_date':
logger.info('Found multiple entries for %s. '
'Setting value to `None`' % key)
return None
else:
raise RuntimeError(msg)
elif _check_isinstance(values, (np.ndarray, tuple), any):
idx = _where_isinstance(values, np.ndarray)
if len(idx) == 1:
return values[int(idx)]
elif len(idx) > 1:
raise RuntimeError(msg)
# other
else:
unique_values = set(values)
if len(unique_values) == 1:
return list(values)[0]
elif isinstance(list(unique_values)[0], BytesIO):
logger.info('Found multiple StringIO instances. '
'Setting value to `None`')
return None
elif isinstance(list(unique_values)[0], str):
logger.info('Found multiple filenames. '
'Setting value to `None`')
return None
else:
raise RuntimeError(msg)
@verbose
def _merge_info(infos, force_update_to_first=False, verbose=None):
"""Merge multiple measurement info dictionaries.
- Fields that are present in only one info object will be used in the
merged info.
- Fields that are present in multiple info objects and are the same
will be used in the merged info.
- Fields that are present in multiple info objects and are different
will result in a None value in the merged info.
- Channels will be concatenated. If multiple info objects contain
channels with the same name, an exception is raised.
Parameters
----------
infos | list of instance of Info
Info objects to merge into one info object.
force_update_to_first : bool
If True, force the fields for objects in `info` will be updated
to match those in the first item. Use at your own risk, as this
may overwrite important metadata.
%(verbose)s
Returns
-------
info : instance of Info
The merged info object.
"""
for info in infos:
info._check_consistency()
if force_update_to_first is True:
infos = deepcopy(infos)
_force_update_info(infos[0], infos[1:])
info = Info()
info._unlocked = True
info['chs'] = []
for this_info in infos:
info['chs'].extend(this_info['chs'])
info._update_redundant()
duplicates = {ch for ch in info['ch_names']
if info['ch_names'].count(ch) > 1}
if len(duplicates) > 0:
msg = ("The following channels are present in more than one input "
"measurement info objects: %s" % list(duplicates))
raise ValueError(msg)
transforms = ['ctf_head_t', 'dev_head_t', 'dev_ctf_t']
for trans_name in transforms:
trans = [i[trans_name] for i in infos if i[trans_name]]
if len(trans) == 0:
info[trans_name] = None
elif len(trans) == 1:
info[trans_name] = trans[0]
elif all(np.all(trans[0]['trans'] == x['trans']) and
trans[0]['from'] == x['from'] and
trans[0]['to'] == x['to']
for x in trans[1:]):
info[trans_name] = trans[0]
else:
msg = ("Measurement infos provide mutually inconsistent %s" %
trans_name)
raise ValueError(msg)
# KIT system-IDs
kit_sys_ids = [i['kit_system_id'] for i in infos if i['kit_system_id']]
if len(kit_sys_ids) == 0:
info['kit_system_id'] = None
elif len(set(kit_sys_ids)) == 1:
info['kit_system_id'] = kit_sys_ids[0]
else:
raise ValueError("Trying to merge channels from different KIT systems")
# hpi infos and digitization data:
fields = ['hpi_results', 'hpi_meas', 'dig']
for k in fields:
values = [i[k] for i in infos if i[k]]
if len(values) == 0:
info[k] = []
elif len(values) == 1:
info[k] = values[0]
elif all(object_diff(values[0], v) == '' for v in values[1:]):
info[k] = values[0]
else:
msg = ("Measurement infos are inconsistent for %s" % k)
raise ValueError(msg)
# other fields
other_fields = ['acq_pars', 'acq_stim', 'bads',
'comps', 'custom_ref_applied', 'description',
'experimenter', 'file_id', 'highpass', 'utc_offset',
'hpi_subsystem', 'events', 'device_info', 'helium_info',
'line_freq', 'lowpass', 'meas_id',
'proj_id', 'proj_name', 'projs', 'sfreq', 'gantry_angle',
'subject_info', 'sfreq', 'xplotter_layout', 'proc_history']
for k in other_fields:
info[k] = _merge_info_values(infos, k)
info['meas_date'] = infos[0]['meas_date']
info._unlocked = False
return info
@verbose
def create_info(ch_names, sfreq, ch_types='misc', verbose=None):
"""Create a basic Info instance suitable for use with create_raw.
Parameters
----------
ch_names : list of str | int
Channel names. If an int, a list of channel names will be created
from ``range(ch_names)``.
sfreq : float
Sample rate of the data.
ch_types : list of str | str
Channel types, default is ``'misc'`` which is not a
:term:`data channel <data channels>`.
Currently supported fields are 'ecg', 'bio', 'stim', 'eog', 'misc',
'seeg', 'dbs', 'ecog', 'mag', 'eeg', 'ref_meg', 'grad', 'emg', 'hbr'
or 'hbo'. If str, then all channels are assumed to be of the same type.
%(verbose)s
Returns
-------
%(info_not_none)s
Notes
-----
The info dictionary will be sparsely populated to enable functionality
within the rest of the package. Advanced functionality such as source
localization can only be obtained through substantial, proper
modifications of the info structure (not recommended).
Note that the MEG device-to-head transform ``info['dev_head_t']`` will
be initialized to the identity transform.
Proper units of measure:
* V: eeg, eog, seeg, dbs, emg, ecg, bio, ecog
* T: mag
* T/m: grad
* M: hbo, hbr
* Am: dipole
* AU: misc
"""
try:
ch_names = operator.index(ch_names) # int-like
except TypeError:
pass
else:
ch_names = list(np.arange(ch_names).astype(str))
_validate_type(ch_names, (list, tuple), "ch_names",
("list, tuple, or int"))
sfreq = float(sfreq)
if sfreq <= 0:
raise ValueError('sfreq must be positive')
nchan = len(ch_names)
if isinstance(ch_types, str):
ch_types = [ch_types] * nchan
ch_types = np.atleast_1d(np.array(ch_types, np.str_))
if ch_types.ndim != 1 or len(ch_types) != nchan:
raise ValueError('ch_types and ch_names must be the same length '
'(%s != %s) for ch_types=%s'
% (len(ch_types), nchan, ch_types))
info = _empty_info(sfreq)
ch_types_dict = get_channel_type_constants(include_defaults=True)
for ci, (ch_name, ch_type) in enumerate(zip(ch_names, ch_types)):
_validate_type(ch_name, 'str', "each entry in ch_names")
_validate_type(ch_type, 'str', "each entry in ch_types")
if ch_type not in ch_types_dict:
raise KeyError(f'kind must be one of {list(ch_types_dict)}, '
f'not {ch_type}')
this_ch_dict = ch_types_dict[ch_type]
kind = this_ch_dict['kind']
# handle chpi, where kind is a *list* of FIFF constants:
kind = kind[0] if isinstance(kind, (list, tuple)) else kind
# mirror what tag.py does here
coord_frame = _ch_coord_dict.get(kind, FIFF.FIFFV_COORD_UNKNOWN)
coil_type = this_ch_dict.get('coil_type', FIFF.FIFFV_COIL_NONE)
unit = this_ch_dict.get('unit', FIFF.FIFF_UNIT_NONE)
chan_info = dict(loc=np.full(12, np.nan),
unit_mul=FIFF.FIFF_UNITM_NONE, range=1., cal=1.,
kind=kind, coil_type=coil_type, unit=unit,
coord_frame=coord_frame, ch_name=str(ch_name),
scanno=ci + 1, logno=ci + 1)
info['chs'].append(chan_info)
info._update_redundant()
info._check_consistency()
info._unlocked = False
return info
RAW_INFO_FIELDS = (
'acq_pars', 'acq_stim', 'bads', 'ch_names', 'chs',
'comps', 'ctf_head_t', 'custom_ref_applied', 'description', 'dev_ctf_t',
'dev_head_t', 'dig', 'experimenter', 'events', 'utc_offset', 'device_info',
'file_id', 'highpass', 'hpi_meas', 'hpi_results', 'helium_info',
'hpi_subsystem', 'kit_system_id', 'line_freq', 'lowpass', 'meas_date',
'meas_id', 'nchan', 'proj_id', 'proj_name', 'projs', 'sfreq',
'subject_info', 'xplotter_layout', 'proc_history', 'gantry_angle',
)
def _empty_info(sfreq):
"""Create an empty info dictionary."""
_none_keys = (
'acq_pars', 'acq_stim', 'ctf_head_t', 'description',
'dev_ctf_t', 'dig', 'experimenter', 'utc_offset', 'device_info',
'file_id', 'highpass', 'hpi_subsystem', 'kit_system_id', 'helium_info',
'line_freq', 'lowpass', 'meas_date', 'meas_id', 'proj_id', 'proj_name',
'subject_info', 'xplotter_layout', 'gantry_angle',
)
_list_keys = ('bads', 'chs', 'comps', 'events', 'hpi_meas', 'hpi_results',
'projs', 'proc_history')
info = Info()
info._unlocked = True
for k in _none_keys:
info[k] = None
for k in _list_keys:
info[k] = list()
info['custom_ref_applied'] = FIFF.FIFFV_MNE_CUSTOM_REF_OFF
info['highpass'] = 0.
info['sfreq'] = float(sfreq)
info['lowpass'] = info['sfreq'] / 2.
info['dev_head_t'] = Transform('meg', 'head')
info._update_redundant()
info._check_consistency()
return info
def _force_update_info(info_base, info_target):
"""Update target info objects with values from info base.
Note that values in info_target will be overwritten by those in info_base.
This will overwrite all fields except for: 'chs', 'ch_names', 'nchan'.
Parameters
----------
info_base : mne.Info
The Info object you want to use for overwriting values
in target Info objects.
info_target : mne.Info | list of mne.Info
The Info object(s) you wish to overwrite using info_base. These objects
will be modified in-place.
"""
exclude_keys = ['chs', 'ch_names', 'nchan']
info_target = np.atleast_1d(info_target).ravel()
all_infos = np.hstack([info_base, info_target])
for ii in all_infos:
if not isinstance(ii, Info):
raise ValueError('Inputs must be of type Info. '
'Found type %s' % type(ii))
for key, val in info_base.items():
if key in exclude_keys:
continue
for i_targ in info_target:
with i_targ._unlock():
i_targ[key] = val
def _add_timedelta_to_stamp(meas_date_stamp, delta_t):
"""Add a timedelta to a meas_date tuple."""
if meas_date_stamp is not None:
meas_date_stamp = _dt_to_stamp(_stamp_to_dt(meas_date_stamp) + delta_t)
return meas_date_stamp
@verbose
def anonymize_info(info, daysback=None, keep_his=False, verbose=None):
"""Anonymize measurement information in place.
.. warning:: If ``info`` is part of an object like
:class:`raw.info <mne.io.Raw>`, you should directly use
the method :meth:`raw.anonymize() <mne.io.Raw.anonymize>`
to ensure that all parts of the data are anonymized and
stay synchronized (e.g.,
:class:`raw.annotations <mne.Annotations>`).
Parameters
----------
%(info_not_none)s
%(daysback_anonymize_info)s
%(keep_his_anonymize_info)s
%(verbose)s
Returns
-------
info : instance of Info
The anonymized measurement information.
Notes
-----
%(anonymize_info_notes)s
"""
_validate_type(info, 'info', "self")
default_anon_dos = datetime.datetime(2000, 1, 1, 0, 0, 0,
tzinfo=datetime.timezone.utc)
default_str = "mne_anonymize"
default_subject_id = 0
default_sex = 0
default_desc = ("Anonymized using a time shift"
" to preserve age at acquisition")
none_meas_date = info['meas_date'] is None
if none_meas_date:
if daysback is not None:
warn('Input info has "meas_date" set to None. '
'Removing all information from time/date structures, '
'*NOT* performing any time shifts!')
else:
# compute timeshift delta
if daysback is None:
delta_t = info['meas_date'] - default_anon_dos
else:
delta_t = datetime.timedelta(days=daysback)
with info._unlock():
info['meas_date'] = info['meas_date'] - delta_t
# file_id and meas_id
for key in ('file_id', 'meas_id'):
value = info.get(key)
if value is not None:
assert 'msecs' not in value
if (none_meas_date or
((value['secs'], value['usecs']) == DATE_NONE)):
# Don't try to shift backwards in time when no measurement
# date is available or when file_id is already a place holder
tmp = DATE_NONE
else:
tmp = _add_timedelta_to_stamp(
(value['secs'], value['usecs']), -delta_t)
value['secs'] = tmp[0]
value['usecs'] = tmp[1]
# The following copy is needed for a test CTF dataset
# otherwise value['machid'][:] = 0 would suffice
_tmp = value['machid'].copy()
_tmp[:] = 0
value['machid'] = _tmp
# subject info
subject_info = info.get('subject_info')
if subject_info is not None:
if subject_info.get('id') is not None:
subject_info['id'] = default_subject_id
if keep_his:
logger.info('Not fully anonymizing info - keeping '
'his_id, sex, and hand info')
else:
if subject_info.get('his_id') is not None:
subject_info['his_id'] = str(default_subject_id)
if subject_info.get('sex') is not None:
subject_info['sex'] = default_sex
if subject_info.get('hand') is not None:
del subject_info['hand'] # there's no "unknown" setting
for key in ('last_name', 'first_name', 'middle_name'):
if subject_info.get(key) is not None:
subject_info[key] = default_str
# anonymize the subject birthday
if none_meas_date:
subject_info.pop('birthday', None)
elif subject_info.get('birthday') is not None:
dob = datetime.datetime(subject_info['birthday'][0],
subject_info['birthday'][1],
subject_info['birthday'][2])
dob -= delta_t
subject_info['birthday'] = dob.year, dob.month, dob.day
for key in ('weight', 'height'):
if subject_info.get(key) is not None:
subject_info[key] = 0
info['experimenter'] = default_str
info['description'] = default_desc
with info._unlock():
if info['proj_id'] is not None:
info['proj_id'] = np.zeros_like(info['proj_id'])
if info['proj_name'] is not None:
info['proj_name'] = default_str
if info['utc_offset'] is not None:
info['utc_offset'] = None
proc_hist = info.get('proc_history')
if proc_hist is not None:
for record in proc_hist:
record['block_id']['machid'][:] = 0
record['experimenter'] = default_str
if none_meas_date:
record['block_id']['secs'] = DATE_NONE[0]
record['block_id']['usecs'] = DATE_NONE[1]
record['date'] = DATE_NONE
else:
this_t0 = (record['block_id']['secs'],
record['block_id']['usecs'])
this_t1 = _add_timedelta_to_stamp(
this_t0, -delta_t)
record['block_id']['secs'] = this_t1[0]
record['block_id']['usecs'] = this_t1[1]
record['date'] = _add_timedelta_to_stamp(
record['date'], -delta_t)
hi = info.get('helium_info')
if hi is not None:
if hi.get('orig_file_guid') is not None:
hi['orig_file_guid'] = default_str
if none_meas_date and hi.get('meas_date') is not None:
hi['meas_date'] = DATE_NONE
elif hi.get('meas_date') is not None:
hi['meas_date'] = _add_timedelta_to_stamp(
hi['meas_date'], -delta_t)
di = info.get('device_info')
if di is not None:
for k in ('serial', 'site'):
if di.get(k) is not None:
di[k] = default_str
err_mesg = ('anonymize_info generated an inconsistent info object. '
'Underlying Error:\n')
info._check_consistency(prepend_error=err_mesg)
err_mesg = ('anonymize_info generated an inconsistent info object. '
'daysback parameter was too large. '
'Underlying Error:\n')
_check_dates(info, prepend_error=err_mesg)
return info
@fill_doc
def _bad_chans_comp(info, ch_names):
"""Check if channel names are consistent with current compensation status.
Parameters
----------
%(info_not_none)s
ch_names : list of str
The channel names to check.
Returns
-------
status : bool
True if compensation is *currently* in use but some compensation
channels are not included in picks
False if compensation is *currently* not being used
or if compensation is being used and all compensation channels
in info and included in picks.
missing_ch_names: array-like of str, shape (n_missing,)
The names of compensation channels not included in picks.
Returns [] if no channels are missing.
"""
if 'comps' not in info:
# should this be thought of as a bug?
return False, []
# only include compensation channels that would affect selected channels
ch_names_s = set(ch_names)
comp_names = []
for comp in info['comps']:
if len(ch_names_s.intersection(comp['data']['row_names'])) > 0:
comp_names.extend(comp['data']['col_names'])
comp_names = sorted(set(comp_names))
missing_ch_names = sorted(set(comp_names).difference(ch_names))
if get_current_comp(info) != 0 and len(missing_ch_names) > 0:
return True, missing_ch_names
return False, missing_ch_names
_DIG_CAST = dict(
kind=int, ident=int, r=lambda x: x, coord_frame=int)
# key -> const, cast, write
_CH_INFO_MAP = OrderedDict(
scanno=(FIFF.FIFF_CH_SCAN_NO, int, write_int),
logno=(FIFF.FIFF_CH_LOGICAL_NO, int, write_int),
kind=(FIFF.FIFF_CH_KIND, int, write_int),
range=(FIFF.FIFF_CH_RANGE, float, write_float),
cal=(FIFF.FIFF_CH_CAL, float, write_float),
coil_type=(FIFF.FIFF_CH_COIL_TYPE, int, write_int),
loc=(FIFF.FIFF_CH_LOC, lambda x: x, write_float),
unit=(FIFF.FIFF_CH_UNIT, int, write_int),
unit_mul=(FIFF.FIFF_CH_UNIT_MUL, int, write_int),
ch_name=(FIFF.FIFF_CH_DACQ_NAME, str, write_string),
coord_frame=(FIFF.FIFF_CH_COORD_FRAME, int, write_int),
)
# key -> cast
_CH_CAST = OrderedDict((key, val[1]) for key, val in _CH_INFO_MAP.items())
# const -> key, cast
_CH_READ_MAP = OrderedDict((val[0], (key, val[1]))
for key, val in _CH_INFO_MAP.items())
@contextlib.contextmanager
def _writing_info_hdf5(info):
# Make info writing faster by packing chs and dig into numpy arrays
orig_dig = info.get('dig', None)
orig_chs = info['chs']
with info._unlock():
try:
if orig_dig is not None and len(orig_dig) > 0:
info['dig'] = _dict_pack(info['dig'], _DIG_CAST)
info['chs'] = _dict_pack(info['chs'], _CH_CAST)
info['chs']['ch_name'] = np.char.encode(
info['chs']['ch_name'], encoding='utf8')
yield
finally:
if orig_dig is not None:
info['dig'] = orig_dig
info['chs'] = orig_chs
def _dict_pack(obj, casts):
# pack a list of dict into dict of array
return {key: np.array([o[key] for o in obj]) for key in casts}
def _dict_unpack(obj, casts):
# unpack a dict of array into a list of dict
n = len(obj[list(casts)[0]])
return [{key: cast(obj[key][ii]) for key, cast in casts.items()}
for ii in range(n)]
def _make_ch_names_mapping(chs):
orig_ch_names = [c['ch_name'] for c in chs]
ch_names = orig_ch_names.copy()
_unique_channel_names(ch_names, max_length=15, verbose='error')
ch_names_mapping = dict()
if orig_ch_names != ch_names:
ch_names_mapping.update(zip(orig_ch_names, ch_names))
return ch_names_mapping
def _write_ch_infos(fid, chs, reset_range, ch_names_mapping):
ch_names_mapping = dict() if ch_names_mapping is None else ch_names_mapping
for k, c in enumerate(chs):
# Scan numbers may have been messed up
c = c.copy()
c['ch_name'] = ch_names_mapping.get(c['ch_name'], c['ch_name'])
assert len(c['ch_name']) <= 15
c['scanno'] = k + 1
# for float/double, the "range" param is unnecessary
if reset_range:
c['range'] = 1.0
write_ch_info(fid, c)
# only write new-style channel information if necessary
if len(ch_names_mapping):
logger.info(
' Writing channel names to FIF truncated to 15 characters '
'with remapping')
for ch in chs:
start_block(fid, FIFF.FIFFB_CH_INFO)
assert set(ch) == set(_CH_INFO_MAP)
for (key, (const, _, write)) in _CH_INFO_MAP.items():
write(fid, const, ch[key])
end_block(fid, FIFF.FIFFB_CH_INFO)
def _ensure_infos_match(info1, info2, name, *, on_mismatch='raise'):
"""Check if infos match.
Parameters
----------
info1, info2 : instance of Info
The infos to compare.
name : str
The name of the object appearing in the error message of the comparison
fails.
on_mismatch : 'raise' | 'warn' | 'ignore'
What to do in case of a mismatch of ``dev_head_t`` between ``info1``
and ``info2``.
"""
_check_on_missing(on_missing=on_mismatch, name='on_mismatch')
info1._check_consistency()
info2._check_consistency()
if info1['nchan'] != info2['nchan']:
raise ValueError(f'{name}.info[\'nchan\'] must match')
if set(info1['bads']) != set(info2['bads']):
raise ValueError(f'{name}.info[\'bads\'] must match')
if info1['sfreq'] != info2['sfreq']:
raise ValueError(f'{name}.info[\'sfreq\'] must match')
if set(info1['ch_names']) != set(info2['ch_names']):
raise ValueError(f'{name}.info[\'ch_names\'] must match')
if len(info2['projs']) != len(info1['projs']):
raise ValueError(f'SSP projectors in {name} must be the same')
if any(not _proj_equal(p1, p2) for p1, p2 in
zip(info2['projs'], info1['projs'])):
raise ValueError(f'SSP projectors in {name} must be the same')
if (info1['dev_head_t'] is None) != (info2['dev_head_t'] is None) or \
(info1['dev_head_t'] is not None and not
np.allclose(info1['dev_head_t']['trans'],
info2['dev_head_t']['trans'], rtol=1e-6)):
msg = (f"{name}.info['dev_head_t'] differs. The "
f"instances probably come from different runs, and "
f"are therefore associated with different head "
f"positions. Manually change info['dev_head_t'] to "
f"avoid this message but beware that this means the "
f"MEG sensors will not be properly spatially aligned. "
f"See mne.preprocessing.maxwell_filter to realign the "
f"runs to a common head position.")
_on_missing(on_missing=on_mismatch, msg=msg,
name='on_mismatch')
def _get_fnirs_ch_pos(info):
"""Return positions of each fNIRS optode.
fNIRS uses two types of optodes, sources and detectors.
There can be multiple connections between each source
and detector at different wavelengths. This function
returns the location of each source and detector.
"""
from ..preprocessing.nirs import _fnirs_optode_names, _optode_position
srcs, dets = _fnirs_optode_names(info)
ch_pos = {}
for optode in [*srcs, *dets]:
ch_pos[optode] = _optode_position(info, optode)
return ch_pos
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