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# Authors: Denis A. Engemann <denis.engemann@gmail.com>
# Teon Brooks <teon.brooks@gmail.com>
#
# simplified BSD-3 license
import datetime
import time
import numpy as np
from .egimff import _read_raw_egi_mff
from .events import _combine_triggers
from ..base import BaseRaw, _check_update_montage
from ..utils import _read_segments_file, _create_chs
from ..meas_info import _empty_info
from ..constants import FIFF
from ...utils import verbose, logger, warn
def _read_header(fid):
"""Read EGI binary header."""
version = np.fromfile(fid, np.int32, 1)[0]
if version > 6 & ~np.bitwise_and(version, 6):
version = version.byteswap().astype(np.uint32)
else:
ValueError('Watchout. This does not seem to be a simple '
'binary EGI file.')
def my_fread(*x, **y):
return np.fromfile(*x, **y)[0]
info = dict(
version=version,
year=my_fread(fid, '>i2', 1),
month=my_fread(fid, '>i2', 1),
day=my_fread(fid, '>i2', 1),
hour=my_fread(fid, '>i2', 1),
minute=my_fread(fid, '>i2', 1),
second=my_fread(fid, '>i2', 1),
millisecond=my_fread(fid, '>i4', 1),
samp_rate=my_fread(fid, '>i2', 1),
n_channels=my_fread(fid, '>i2', 1),
gain=my_fread(fid, '>i2', 1),
bits=my_fread(fid, '>i2', 1),
value_range=my_fread(fid, '>i2', 1)
)
unsegmented = 1 if np.bitwise_and(version, 1) == 0 else 0
precision = np.bitwise_and(version, 6)
if precision == 0:
RuntimeError('Floating point precision is undefined.')
if unsegmented:
info.update(dict(n_categories=0,
n_segments=1,
n_samples=np.fromfile(fid, '>i4', 1)[0],
n_events=np.fromfile(fid, '>i2', 1)[0],
event_codes=[],
category_names=[],
category_lengths=[],
pre_baseline=0))
for event in range(info['n_events']):
event_codes = ''.join(np.fromfile(fid, 'S1', 4).astype('U1'))
info['event_codes'].append(event_codes)
info['event_codes'] = np.array(info['event_codes'])
else:
raise NotImplementedError('Only continuous files are supported')
info['unsegmented'] = unsegmented
info['dtype'], info['orig_format'] = {2: ('>i2', 'short'),
4: ('>f4', 'float'),
6: ('>f8', 'double')}[precision]
info['dtype'] = np.dtype(info['dtype'])
return info
def _read_events(fid, info):
"""Read events."""
events = np.zeros([info['n_events'],
info['n_segments'] * info['n_samples']])
fid.seek(36 + info['n_events'] * 4, 0) # skip header
for si in range(info['n_samples']):
# skip data channels
fid.seek(info['n_channels'] * info['dtype'].itemsize, 1)
# read event channels
events[:, si] = np.fromfile(fid, info['dtype'], info['n_events'])
return events
@verbose
def read_raw_egi(input_fname, montage=None, eog=None, misc=None,
include=None, exclude=None, preload=False,
channel_naming='E%d', verbose=None):
"""Read EGI simple binary as raw object.
Parameters
----------
input_fname : str
Path to the raw file. Files with an extension .mff are automatically
considered to be EGI's native MFF format files.
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 or tuple
Names of channels or list of indices that should be designated
EOG channels. Default is None.
misc : list or tuple
Names of channels or list of indices that should be designated
MISC channels. Default is None.
include : None | list
The event channels to be ignored when creating the synthetic
trigger. Defaults to None.
Note. Overrides `exclude` parameter.
exclude : None | list
The event channels to be ignored when creating the synthetic
trigger. Defaults to None. If None, channels that have more than
one event and the ``sync`` and ``TREV`` channels will be
ignored.
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).
..versionadded:: 0.11
channel_naming : str
Channel naming convention for the data channels. Defaults to 'E%d'
(resulting in channel names 'E1', 'E2', 'E3'...). The effective default
prior to 0.14.0 was 'EEG %03d'.
..versionadded:: 0.14.0
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 RawEGI
A Raw object containing EGI data.
Notes
-----
The trigger channel names are based on the arbitrary user dependent event
codes used. However this function will attempt to generate a synthetic
trigger channel named ``STI 014`` in accordance with the general
Neuromag / MNE naming pattern.
The event_id assignment equals ``np.arange(n_events) + 1``. The resulting
``event_id`` mapping is stored as attribute to the resulting raw object but
will be ignored when saving to a fiff. Note. The trigger channel is
artificially constructed based on timestamps received by the Netstation.
As a consequence, triggers have only short durations.
This step will fail if events are not mutually exclusive.
See Also
--------
mne.io.Raw : Documentation of attribute and methods.
"""
if input_fname.endswith('.mff'):
return _read_raw_egi_mff(input_fname, montage, eog, misc, include,
exclude, preload, channel_naming, verbose)
return RawEGI(input_fname, montage, eog, misc, include, exclude, preload,
channel_naming, verbose)
class RawEGI(BaseRaw):
"""Raw object from EGI simple binary file."""
@verbose
def __init__(self, input_fname, montage=None, eog=None, misc=None,
include=None, exclude=None, preload=False,
channel_naming='E%d', verbose=None): # noqa: D102
if eog is None:
eog = []
if misc is None:
misc = []
with open(input_fname, 'rb') as fid: # 'rb' important for py3k
logger.info('Reading EGI header from %s...' % input_fname)
egi_info = _read_header(fid)
logger.info(' Reading events ...')
egi_events = _read_events(fid, egi_info) # update info + jump
if egi_info['value_range'] != 0 and egi_info['bits'] != 0:
cal = egi_info['value_range'] / 2. ** egi_info['bits']
else:
cal = 1e-6
logger.info(' Assembling measurement info ...')
event_codes = []
if egi_info['n_events'] > 0:
event_codes = list(egi_info['event_codes'])
if include is None:
exclude_list = ['sync', 'TREV'] if exclude is None else exclude
exclude_inds = [i for i, k in enumerate(event_codes) if k in
exclude_list]
more_excludes = []
if exclude is None:
for ii, event in enumerate(egi_events):
if event.sum() <= 1 and event_codes[ii]:
more_excludes.append(ii)
if len(exclude_inds) + len(more_excludes) == len(event_codes):
warn('Did not find any event code with more than one '
'event.', RuntimeWarning)
else:
exclude_inds.extend(more_excludes)
exclude_inds.sort()
include_ = [i for i in np.arange(egi_info['n_events']) if
i not in exclude_inds]
include_names = [k for i, k in enumerate(event_codes)
if i in include_]
else:
include_ = [i for i, k in enumerate(event_codes)
if k in include]
include_names = include
for kk, v in [('include', include_names), ('exclude', exclude)]:
if isinstance(v, list):
for k in v:
if k not in event_codes:
raise ValueError('Could find event named "%s"' % k)
elif v is not None:
raise ValueError('`%s` must be None or of type list' % kk)
event_ids = np.arange(len(include_)) + 1
logger.info(' Synthesizing trigger channel "STI 014" ...')
logger.info(' Excluding events {%s} ...' %
", ".join([k for i, k in enumerate(event_codes)
if i not in include_]))
self._new_trigger = _combine_triggers(egi_events[include_],
remapping=event_ids)
self.event_id = dict(zip([e for e in event_codes if e in
include_names], event_ids))
else:
# No events
self.event_id = None
self._new_trigger = None
info = _empty_info(egi_info['samp_rate'])
my_time = datetime.datetime(
egi_info['year'], egi_info['month'], egi_info['day'],
egi_info['hour'], egi_info['minute'], egi_info['second'])
my_timestamp = time.mktime(my_time.timetuple())
info['meas_date'] = (my_timestamp, 0)
ch_names = [channel_naming % (i + 1) for i in
range(egi_info['n_channels'])]
ch_names.extend(list(egi_info['event_codes']))
if self._new_trigger is not None:
ch_names.append('STI 014') # our new_trigger
nchan = len(ch_names)
cals = np.repeat(cal, nchan)
ch_coil = FIFF.FIFFV_COIL_EEG
ch_kind = FIFF.FIFFV_EEG_CH
chs = _create_chs(ch_names, cals, ch_coil, ch_kind, eog, (), (), misc)
sti_ch_idx = [i for i, name in enumerate(ch_names) if
name.startswith('STI') or name in event_codes]
for idx in sti_ch_idx:
chs[idx].update({'unit_mul': 0, 'cal': 1,
'kind': FIFF.FIFFV_STIM_CH,
'coil_type': FIFF.FIFFV_COIL_NONE,
'unit': FIFF.FIFF_UNIT_NONE})
info['chs'] = chs
info._update_redundant()
_check_update_montage(info, montage)
super(RawEGI, self).__init__(
info, preload, orig_format=egi_info['orig_format'],
filenames=[input_fname], last_samps=[egi_info['n_samples'] - 1],
raw_extras=[egi_info], verbose=verbose)
def _read_segment_file(self, data, idx, fi, start, stop, cals, mult):
"""Read a segment of data from a file."""
egi_info = self._raw_extras[fi]
dtype = egi_info['dtype']
n_chan_read = egi_info['n_channels'] + egi_info['n_events']
offset = 36 + egi_info['n_events'] * 4
_read_segments_file(self, data, idx, fi, start, stop, cals, mult,
dtype=dtype, n_channels=n_chan_read, offset=offset,
trigger_ch=self._new_trigger)
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