/
egi.py
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/
egi.py
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# Authors: Denis A. Engemann <denis.engemann@gmail.com>
# Teon Brooks <teon.brooks@gmail.com>
#
# simplified BSD-3 license
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import datetime
import time
import numpy as np
from ..._fiff.constants import FIFF
from ..._fiff.meas_info import _empty_info
from ..._fiff.utils import _create_chs, _read_segments_file
from ...utils import _check_fname, _validate_type, logger, verbose, warn
from ..base import BaseRaw
from .egimff import _read_raw_egi_mff
from .events import _combine_triggers
def _read_header(fid):
"""Read EGI binary header."""
version = np.fromfile(fid, "<i4", 1)[0]
if version > 6 & ~np.bitwise_and(version, 6):
version = version.byteswap().astype(np.uint32)
else:
raise ValueError("Watchout. This does not seem to be a simple binary EGI file.")
def my_fread(*x, **y):
return int(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:
raise RuntimeError("Floating point precision is undefined.")
if unsegmented:
info.update(
dict(
n_categories=0,
n_segments=1,
n_samples=int(np.fromfile(fid, ">i4", 1)[0]),
n_events=int(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)
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,
eog=None,
misc=None,
include=None,
exclude=None,
preload=False,
channel_naming="E%d",
verbose=None,
) -> "RawEGI":
"""Read EGI simple binary as raw object.
.. note:: This function attempts to create a synthetic trigger channel.
See the Notes section below.
Parameters
----------
input_fname : path-like
Path to the raw file. Files with an extension ``.mff`` are
automatically considered to be EGI's native MFF format files.
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)s
.. 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)s
Returns
-------
raw : instance of RawEGI
A Raw object containing EGI data.
See :class:`mne.io.Raw` for documentation of attributes and methods.
See Also
--------
mne.io.Raw : Documentation of attributes and methods of RawEGI.
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.
"""
_validate_type(input_fname, "path-like", "input_fname")
input_fname = str(input_fname)
if input_fname.rstrip("/\\").endswith(".mff"): # allows .mff or .mff/
return _read_raw_egi_mff(
input_fname, eog, misc, include, exclude, preload, channel_naming, verbose
)
return RawEGI(
input_fname, eog, misc, include, exclude, preload, channel_naming, verbose
)
class RawEGI(BaseRaw):
"""Raw object from EGI simple binary file."""
_extra_attributes = ("event_id",)
@verbose
def __init__(
self,
input_fname,
eog=None,
misc=None,
include=None,
exclude=None,
preload=False,
channel_naming="E%d",
verbose=None,
):
input_fname = str(_check_fname(input_fname, "read", True, "input_fname"))
if eog is None:
eog = []
if misc is None:
misc = []
with open(input_fname, "rb") as fid: # 'rb' important for py3k
logger.info(f"Reading EGI header from {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"] / 2.0 ** 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(f'Could find event named "{k}"')
elif v is not None:
raise ValueError(f"`{kk}` must be None or of type list")
event_ids = np.arange(len(include_)) + 1
logger.info(' Synthesizing trigger channel "STI 014" ...')
excl_events = ", ".join(
k for i, k in enumerate(event_codes) if i not in include_
)
logger.info(f" Excluding events {{{excl_events}}} ...")
egi_info["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
egi_info["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 egi_info["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": FIFF.FIFF_UNITM_NONE,
"cal": 1.0,
"kind": FIFF.FIFFV_STIM_CH,
"coil_type": FIFF.FIFFV_COIL_NONE,
"unit": FIFF.FIFF_UNIT_NONE,
"loc": np.zeros(12),
}
)
info["chs"] = chs
info._unlocked = False
info._update_redundant()
orig_format = (
egi_info["orig_format"] if egi_info["orig_format"] != "float" else "single"
)
super().__init__(
info,
preload,
orig_format=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
trigger_ch = egi_info["new_trigger"]
_read_segments_file(
self,
data,
idx,
fi,
start,
stop,
cals,
mult,
dtype=dtype,
n_channels=n_chan_read,
offset=offset,
trigger_ch=trigger_ch,
)