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nicolet.py
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nicolet.py
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# Author: Jaakko Leppakangas <jaeilepp@student.jyu.fi>
#
# License: BSD (3-clause)
import numpy as np
from os import path
import datetime
import calendar
from ...utils import logger
from ..utils import _read_segments_file, _find_channels, _create_chs
from ..base import BaseRaw, _check_update_montage
from ..meas_info import _empty_info
from ..constants import FIFF
def read_raw_nicolet(input_fname, ch_type, montage=None, eog=(), ecg=(),
emg=(), misc=(), preload=False, verbose=None):
"""Read Nicolet data as raw object.
Note: This reader takes data files with the extension ``.data`` as an
input. The header file with the same file name stem and an extension
``.head`` is expected to be found in the same directory.
Parameters
----------
input_fname : str
Path to the data file.
ch_type : str
Channel type to designate to the data channels. Supported data types
include 'eeg', 'seeg'.
montage : str | None | instance of montage
Path or instance of montage containing electrode positions.
If None, sensor locations are (0,0,0). See the documentation of
:func:`mne.channels.read_montage` for more information.
eog : list | tuple | 'auto'
Names of channels or list of indices that should be designated
EOG channels. If 'auto', the channel names beginning with
``EOG`` are used. Defaults to empty tuple.
ecg : list or tuple | 'auto'
Names of channels or list of indices that should be designated
ECG channels. If 'auto', the channel names beginning with
``ECG`` are used. Defaults to empty tuple.
emg : list or tuple | 'auto'
Names of channels or list of indices that should be designated
EMG channels. If 'auto', the channel names beginning with
``EMG`` are used. Defaults to empty tuple.
misc : list or tuple
Names of channels or list of indices that should be designated
MISC channels. Defaults to empty tuple.
preload : bool or str (default False)
Preload data into memory for data manipulation and faster indexing.
If True, the data will be preloaded into memory (fast, requires
large amount of memory). If preload is a string, preload is the
file name of a memory-mapped file which is used to store the data
on the hard drive (slower, requires less memory).
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
Returns
-------
raw : Instance of Raw
A Raw object containing the data.
See Also
--------
mne.io.Raw : Documentation of attribute and methods.
"""
return RawNicolet(input_fname, ch_type, montage=montage, eog=eog, ecg=ecg,
emg=emg, misc=misc, preload=preload, verbose=verbose)
def _get_nicolet_info(fname, ch_type, eog, ecg, emg, misc):
"""Extract info from Nicolet header files."""
fname = path.splitext(fname)[0]
header = fname + '.head'
logger.info('Reading header...')
header_info = dict()
with open(header, 'r') as fid:
for line in fid:
var, value = line.split('=')
if var == 'elec_names':
value = value[1:-2].split(',') # strip brackets
elif var == 'conversion_factor':
value = float(value)
elif var != 'start_ts':
value = int(value)
header_info[var] = value
ch_names = header_info['elec_names']
if eog == 'auto':
eog = _find_channels(ch_names, 'EOG')
if ecg == 'auto':
ecg = _find_channels(ch_names, 'ECG')
if emg == 'auto':
emg = _find_channels(ch_names, 'EMG')
date, time = header_info['start_ts'].split()
date = date.split('-')
time = time.split(':')
sec, msec = time[2].split('.')
date = datetime.datetime(int(date[0]), int(date[1]), int(date[2]),
int(time[0]), int(time[1]), int(sec), int(msec))
info = _empty_info(header_info['sample_freq'])
info['meas_date'] = (calendar.timegm(date.utctimetuple()), 0)
if ch_type == 'eeg':
ch_coil = FIFF.FIFFV_COIL_EEG
ch_kind = FIFF.FIFFV_EEG_CH
elif ch_type == 'seeg':
ch_coil = FIFF.FIFFV_COIL_EEG
ch_kind = FIFF.FIFFV_SEEG_CH
else:
raise TypeError("Channel type not recognized. Available types are "
"'eeg' and 'seeg'.")
cals = np.repeat(header_info['conversion_factor'] * 1e-6, len(ch_names))
info['chs'] = _create_chs(ch_names, cals, ch_coil, ch_kind, eog, ecg, emg,
misc)
info['highpass'] = 0.
info['lowpass'] = info['sfreq'] / 2.0
info._update_redundant()
return info, header_info
class RawNicolet(BaseRaw):
"""Raw object from Nicolet file.
Parameters
----------
input_fname : str
Path to the Nicolet file.
ch_type : str
Channel type to designate to the data channels. Supported data types
include 'eeg', 'seeg'.
montage : str | None | instance of Montage
Path or instance of montage containing electrode positions.
If None, sensor locations are (0,0,0). See the documentation of
:func:`mne.channels.read_montage` for more information.
eog : list | tuple | 'auto'
Names of channels or list of indices that should be designated
EOG channels. If 'auto', the channel names beginning with
``EOG`` are used. Defaults to empty tuple.
ecg : list or tuple | 'auto'
Names of channels or list of indices that should be designated
ECG channels. If 'auto', the channel names beginning with
``ECG`` are used. Defaults to empty tuple.
emg : list or tuple | 'auto'
Names of channels or list of indices that should be designated
EMG channels. If 'auto', the channel names beginning with
``EMG`` are used. Defaults to empty tuple.
misc : list or tuple
Names of channels or list of indices that should be designated
MISC channels. Defaults to empty tuple.
preload : bool or str (default False)
Preload data into memory for data manipulation and faster indexing.
If True, the data will be preloaded into memory (fast, requires
large amount of memory). If preload is a string, preload is the
file name of a memory-mapped file which is used to store the data
on the hard drive (slower, requires less memory).
verbose : bool, str, int, or None
If not None, override default verbose level (see :func:`mne.verbose`
and :ref:`Logging documentation <tut_logging>` for more).
See Also
--------
mne.io.Raw : Documentation of attribute and methods.
"""
def __init__(self, input_fname, ch_type, montage=None, eog=(), ecg=(),
emg=(), misc=(), preload=False, verbose=None): # noqa: D102
input_fname = path.abspath(input_fname)
info, header_info = _get_nicolet_info(input_fname, ch_type, eog, ecg,
emg, misc)
last_samps = [header_info['num_samples'] - 1]
_check_update_montage(info, montage)
super(RawNicolet, self).__init__(
info, preload, filenames=[input_fname], raw_extras=[header_info],
last_samps=last_samps, orig_format='int',
verbose=verbose)
def _read_segment_file(self, data, idx, fi, start, stop, cals, mult):
"""Read a chunk of raw data."""
_read_segments_file(self, data, idx, fi, start, stop, cals, mult)