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"""Conversion tool from Neuroscan CNT to FIF."""
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from os import path
import numpy as np
from ..._fiff._digitization import _make_dig_points
from ..._fiff.constants import FIFF
from ..._fiff.meas_info import _empty_info
from ..._fiff.utils import _create_chs, _find_channels, _mult_cal_one, read_str
from ...annotations import Annotations
from ...channels.layout import _topo_to_sphere
from ...utils import _check_option, _explain_exception, _validate_type, fill_doc, warn
from ..base import BaseRaw
from ._utils import (
CNTEventType3,
_compute_robust_event_table_position,
_get_event_parser,
_read_teeg,
_session_date_2_meas_date,
)
def _read_annotations_cnt(fname, data_format="int16"):
"""CNT Annotation File Reader.
This method opens the .cnt files, searches all the metadata to construct
the annotations and parses the event table. Notice that CNT files, can
point to a different file containing the events. This case when the
event table is separated from the main .cnt is not supported.
Parameters
----------
fname: path-like
Path to CNT file containing the annotations.
data_format : 'int16' | 'int32'
Defines the data format the data is read in.
Returns
-------
annot : instance of Annotations
The annotations.
"""
# Offsets from SETUP structure in http://paulbourke.net/dataformats/eeg/
SETUP_NCHANNELS_OFFSET = 370
SETUP_RATE_OFFSET = 376
def _accept_reject_function(keypad_accept):
accept_list = []
for code in keypad_accept:
if "xd0" in str(code):
accept_list.append("good")
elif "xc0" in str(code):
accept_list.append("bad")
else:
accept_list.append("NA")
return np.array(accept_list)
def _translating_function(offset, n_channels, event_type, data_format=data_format):
n_bytes = 2 if data_format == "int16" else 4
if event_type == CNTEventType3:
offset *= n_bytes * n_channels
event_time = offset - 900 - (75 * n_channels)
event_time //= n_channels * n_bytes
event_time = event_time - 1
# Prevent negative event times
np.clip(event_time, 0, None, out=event_time)
return event_time
def _update_bad_span_onset(accept_reject, onset, duration, description):
accept_reject = accept_reject.tolist()
onset = onset.tolist()
duration = duration.tolist()
description = description.tolist()
# If there are no bad spans, return original parameters
if "bad" not in accept_reject:
return np.array(onset), np.array(duration), np.array(description)
# Create lists of bad and good span markers and onset
bad_good_span_markers = [i for i in accept_reject if i in ["bad", "good"]]
bad_good_onset = [
onset[i]
for i, value in enumerate(accept_reject)
if value in ["bad", "good"]
]
# Calculate duration of bad span
first_bad_index = bad_good_span_markers.index("bad")
duration_list = [
bad_good_onset[i + 1] - bad_good_onset[i]
for i in range(first_bad_index, len(bad_good_span_markers), 2)
]
# Add bad event marker duration and description
duration_list_index = 0
for i in range(len(onset)):
if accept_reject[i] == "bad":
duration[i] = duration_list[duration_list_index]
description[i] = "BAD_" + description[i]
duration_list_index += 1
# Remove good span markers
final_onset, final_duration, final_description = [], [], []
for i in range(len(accept_reject)):
if accept_reject[i] != "good":
final_onset.append(onset[i])
final_duration.append(duration[i])
final_description.append(description[i])
return (
np.array(final_onset),
np.array(final_duration),
np.array(final_description),
)
with open(fname, "rb") as fid:
fid.seek(SETUP_NCHANNELS_OFFSET)
(n_channels,) = np.frombuffer(fid.read(2), dtype="<u2")
fid.seek(SETUP_RATE_OFFSET)
(sfreq,) = np.frombuffer(fid.read(2), dtype="<u2")
event_table_pos = _compute_robust_event_table_position(
fid=fid, data_format=data_format
)
with open(fname, "rb") as fid:
teeg = _read_teeg(fid, teeg_offset=event_table_pos)
event_parser = _get_event_parser(event_type=teeg.event_type)
with open(fname, "rb") as fid:
fid.seek(event_table_pos + 9) # the real table stats at +9
buffer = fid.read(teeg.total_length)
my_events = list(event_parser(buffer))
if not my_events:
return Annotations(list(), list(), list(), None)
else:
onset = _translating_function(
np.array([e.Offset for e in my_events], dtype=float),
n_channels=n_channels,
event_type=type(my_events[0]),
data_format=data_format,
)
# There is a Latency field but it's not useful for durations, see
# https://github.com/mne-tools/mne-python/pull/11828
duration = np.zeros(len(my_events), dtype=float)
accept_reject = _accept_reject_function(
np.array([e.KeyPad_Accept for e in my_events])
)
# Check to see if there are any button presses
description = []
for event in my_events:
# Extract the 4-bit fields
# Upper nibble (4 bits) currently not used
# accept = (event.KeyPad_Accept[0] & 0xF0) >> 4
# Lower nibble (4 bits) keypad button press
keypad = event.KeyPad_Accept[0] & 0x0F
if str(keypad) != "0":
description.append(f"KeyPad Response {keypad}")
elif event.KeyBoard != 0:
description.append(f"Keyboard Response {event.KeyBoard}")
else:
description.append(str(event.StimType))
description = np.array(description)
onset, duration, description = _update_bad_span_onset(
accept_reject, onset / sfreq, duration, description
)
return Annotations(
onset=onset, duration=duration, description=description, orig_time=None
)
@fill_doc
def read_raw_cnt(
input_fname,
eog=(),
misc=(),
ecg=(),
emg=(),
data_format="auto",
date_format="mm/dd/yy",
*,
header="auto",
preload=False,
verbose=None,
) -> "RawCNT":
"""Read CNT data as raw object.
.. Note::
2d spatial coordinates (x, y) for EEG channels are read from the file
header and fit to a sphere to compute corresponding z-coordinates.
If channels assigned as EEG channels have locations
far away from the head (i.e. x and y coordinates don't fit to a
sphere), all the channel locations will be distorted
(all channels that are not assigned with keywords ``eog``, ``ecg``,
``emg`` and ``misc`` are assigned as EEG channels). If you are not
sure that the channel locations in the header are correct, it is
probably safer to replace them with :meth:`mne.io.Raw.set_montage`.
Montages can be created/imported with:
- Standard montages with :func:`mne.channels.make_standard_montage`
- Montages for `Compumedics systems
<https://compumedicsneuroscan.com>`__ with
:func:`mne.channels.read_dig_dat`
- Other reader functions are listed under *See Also* at
:class:`mne.channels.DigMontage`
Parameters
----------
input_fname : path-like
Path to the data file.
eog : list | tuple | ``'auto'`` | ``'header'``
Names of channels or list of indices that should be designated
EOG channels. If 'header', VEOG and HEOG channels assigned in the file
header are used. If ``'auto'``, channel names containing ``'EOG'`` are
used. Defaults to empty tuple.
misc : list | tuple
Names of channels or list of indices that should be designated
MISC channels. Defaults to empty tuple.
ecg : list | tuple | ``'auto'``
Names of channels or list of indices that should be designated
ECG channels. If ``'auto'``, the channel names containing ``'ECG'`` are
used. Defaults to empty tuple.
emg : list | tuple
Names of channels or list of indices that should be designated
EMG channels. If 'auto', the channel names containing 'EMG' are used.
Defaults to empty tuple.
data_format : ``'auto'`` | ``'int16'`` | ``'int32'``
Defines the data format the data is read in. If ``'auto'``, it is
determined from the file header using ``numsamples`` field.
Defaults to ``'auto'``.
date_format : ``'mm/dd/yy'`` | ``'dd/mm/yy'``
Format of date in the header. Defaults to ``'mm/dd/yy'``.
header : ``'auto'`` | ``'new'`` | ``'old'``
Defines the header format. Used to describe how bad channels
are formatted. If auto, reads using old and new header and
if either contain a bad channel make channel bad.
Defaults to ``'auto'``.
.. versionadded:: 1.6
%(preload)s
%(verbose)s
Returns
-------
raw : instance of RawCNT.
The raw data.
See :class:`mne.io.Raw` for documentation of attributes and methods.
See Also
--------
mne.io.Raw : Documentation of attributes and methods of RawCNT.
Notes
-----
.. versionadded:: 0.12
"""
return RawCNT(
input_fname,
eog=eog,
misc=misc,
ecg=ecg,
emg=emg,
data_format=data_format,
date_format=date_format,
header=header,
preload=preload,
verbose=verbose,
)
def _get_cnt_info(input_fname, eog, ecg, emg, misc, data_format, date_format, header):
"""Read the cnt header."""
data_offset = 900 # Size of the 'SETUP' header.
cnt_info = dict()
# Reading only the fields of interest. Structure of the whole header at
# http://paulbourke.net/dataformats/eeg/
with open(input_fname, "rb", buffering=0) as fid:
fid.seek(21)
patient_id = read_str(fid, 20)
patient_id = int(patient_id) if patient_id.isdigit() else 0
fid.seek(121)
patient_name = read_str(fid, 20).split()
last_name = patient_name[0] if len(patient_name) > 0 else ""
first_name = patient_name[-1] if len(patient_name) > 0 else ""
fid.seek(2, 1)
sex = read_str(fid, 1)
if sex == "M":
sex = FIFF.FIFFV_SUBJ_SEX_MALE
elif sex == "F":
sex = FIFF.FIFFV_SUBJ_SEX_FEMALE
else: # can be 'U'
sex = FIFF.FIFFV_SUBJ_SEX_UNKNOWN
hand = read_str(fid, 1)
if hand == "R":
hand = FIFF.FIFFV_SUBJ_HAND_RIGHT
elif hand == "L":
hand = FIFF.FIFFV_SUBJ_HAND_LEFT
else: # can be 'M' for mixed or 'U'
hand = None
fid.seek(205)
session_label = read_str(fid, 20)
session_date = f"{read_str(fid, 10)} {read_str(fid, 12)}"
meas_date = _session_date_2_meas_date(session_date, date_format)
fid.seek(370)
n_channels = np.fromfile(fid, dtype="<u2", count=1).item()
fid.seek(376)
sfreq = np.fromfile(fid, dtype="<u2", count=1).item()
if eog == "header":
fid.seek(402)
eog = [idx for idx in np.fromfile(fid, dtype="i2", count=2) if idx >= 0]
fid.seek(438)
lowpass_toggle = np.fromfile(fid, "i1", count=1).item()
highpass_toggle = np.fromfile(fid, "i1", count=1).item()
# Header has a field for number of samples, but it does not seem to be
# too reliable. That's why we have option for setting n_bytes manually.
fid.seek(864)
n_samples = np.fromfile(fid, dtype="<u4", count=1).item()
n_samples_header = n_samples
fid.seek(869)
lowcutoff = np.fromfile(fid, dtype="f4", count=1).item()
fid.seek(2, 1)
highcutoff = np.fromfile(fid, dtype="f4", count=1).item()
event_offset = _compute_robust_event_table_position(
fid=fid, data_format=data_format
)
fid.seek(890)
cnt_info["continuous_seconds"] = np.fromfile(fid, dtype="<f4", count=1).item()
if event_offset < data_offset: # no events
data_size = n_samples * n_channels
else:
data_size = event_offset - (data_offset + 75 * n_channels)
_check_option("data_format", data_format, ["auto", "int16", "int32"])
if data_format == "auto":
if n_samples == 0 or data_size // (n_samples * n_channels) not in [2, 4]:
warn(
"Could not define the number of bytes automatically. "
"Defaulting to 2."
)
n_bytes = 2
n_samples = data_size // (n_bytes * n_channels)
# See: PR #12393
annotations = _read_annotations_cnt(input_fname, data_format="int16")
# See: PR #12986
if len(annotations) and annotations.onset[-1] * sfreq > n_samples:
n_bytes = 4
n_samples = n_samples_header
warn(
"Annotations are outside data range. "
"Changing data format to 'int32'."
)
else:
n_bytes = data_size // (n_samples * n_channels)
else:
n_bytes = 2 if data_format == "int16" else 4
n_samples = data_size // (n_bytes * n_channels)
# See PR #12393
if n_samples_header != 0:
n_samples = n_samples_header
# Channel offset refers to the size of blocks per channel in the file.
cnt_info["channel_offset"] = np.fromfile(fid, dtype="<i4", count=1).item()
if cnt_info["channel_offset"] > 1:
cnt_info["channel_offset"] //= n_bytes
else:
cnt_info["channel_offset"] = 1
ch_names, cals, baselines, chs, pos = (list(), list(), list(), list(), list())
bads = list()
_validate_type(header, str, "header")
_check_option("header", header, ("auto", "new", "old"))
for ch_idx in range(n_channels): # ELECTLOC fields
fid.seek(data_offset + 75 * ch_idx)
ch_name = read_str(fid, 10)
ch_names.append(ch_name)
# Some files have bad channels marked differently in the header.
if header in ("new", "auto"):
fid.seek(data_offset + 75 * ch_idx + 14)
if np.fromfile(fid, dtype="u1", count=1).item():
bads.append(ch_name)
if header in ("old", "auto"):
fid.seek(data_offset + 75 * ch_idx + 4)
if np.fromfile(fid, dtype="u1", count=1).item():
bads.append(ch_name)
fid.seek(data_offset + 75 * ch_idx + 19)
xy = np.fromfile(fid, dtype="f4", count=2)
xy[1] *= -1 # invert y-axis
pos.append(xy)
fid.seek(data_offset + 75 * ch_idx + 47)
# Baselines are subtracted before scaling the data.
baselines.append(np.fromfile(fid, dtype="i2", count=1).item())
fid.seek(data_offset + 75 * ch_idx + 59)
sensitivity = np.fromfile(fid, dtype="f4", count=1).item()
fid.seek(data_offset + 75 * ch_idx + 71)
cal = np.fromfile(fid, dtype="f4", count=1).item()
cals.append(cal * sensitivity * 1e-6 / 204.8)
info = _empty_info(sfreq)
if lowpass_toggle == 1:
info["lowpass"] = highcutoff
if highpass_toggle == 1:
info["highpass"] = lowcutoff
subject_info = {
"hand": hand,
"id": patient_id,
"sex": sex,
"first_name": first_name,
"last_name": last_name,
}
subject_info = {key: val for key, val in subject_info.items() if val is not None}
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")
chs = _create_chs(
ch_names, cals, FIFF.FIFFV_COIL_EEG, FIFF.FIFFV_EEG_CH, eog, ecg, emg, misc
)
eegs = [idx for idx, ch in enumerate(chs) if ch["coil_type"] == FIFF.FIFFV_COIL_EEG]
coords = _topo_to_sphere(pos, eegs)
locs = np.full((len(chs), 12), np.nan)
locs[:, :3] = coords
dig = _make_dig_points(
dig_ch_pos=dict(zip(ch_names, coords)),
coord_frame="head",
add_missing_fiducials=True,
)
for ch, loc in zip(chs, locs):
ch.update(loc=loc)
cnt_info.update(baselines=np.array(baselines), n_samples=n_samples, n_bytes=n_bytes)
session_label = None if str(session_label) == "" else str(session_label)
info.update(
meas_date=meas_date,
dig=dig,
description=session_label,
subject_info=subject_info,
chs=chs,
)
info._unlocked = False
info._update_redundant()
info["bads"] = bads
return info, cnt_info
@fill_doc
class RawCNT(BaseRaw):
"""Raw object from Neuroscan CNT file.
.. note::
The channel positions are read from the file header. Channels that are
not assigned with keywords ``eog``, ``ecg``, ``emg`` and ``misc`` are
assigned as eeg channels. All the eeg channel locations are fit to a
sphere when computing the z-coordinates for the channels. If channels
assigned as eeg channels have locations far away from the head (i.e.
x and y coordinates don't fit to a sphere), all the channel locations
will be distorted. If you are not sure that the channel locations in
the header are correct, it is probably safer to use a (standard)
montage. See :func:`mne.channels.make_standard_montage`
.. note::
A CNT file can also come from the EEG manufacturer ANT Neuro, in which case the
function :func:`mne.io.read_raw_ant` should be used.
Parameters
----------
input_fname : path-like
Path to the Neuroscan CNT file.
eog : list | tuple
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.
misc : list | tuple
Names of channels or list of indices that should be designated
MISC channels. Defaults to empty tuple.
ecg : list | tuple
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 | tuple
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.
data_format : ``'auto'`` | ``'int16'`` | ``'int32'``
Defines the data format the data is read in. If ``'auto'``, it is
determined from the file header using ``numsamples`` field.
Defaults to ``'auto'``.
date_format : ``'mm/dd/yy'`` | ``'dd/mm/yy'``
Format of date in the header. Defaults to ``'mm/dd/yy'``.
header : ``'auto'`` | ``'new'`` | ``'old'``
Defines the header format. Used to describe how bad channels
are formatted. If auto, reads using old and new header and
if either contain a bad channel make channel bad.
Defaults to ``'auto'``.
%(preload)s
%(verbose)s
See Also
--------
mne.io.Raw : Documentation of attributes and methods.
"""
def __init__(
self,
input_fname,
eog=(),
misc=(),
ecg=(),
emg=(),
data_format="auto",
date_format="mm/dd/yy",
*,
header="auto",
preload=False,
verbose=None,
):
_check_option("date_format", date_format, ["mm/dd/yy", "dd/mm/yy"])
if date_format == "dd/mm/yy":
_date_format = "%d/%m/%y %H:%M:%S"
else:
_date_format = "%m/%d/%y %H:%M:%S"
input_fname = path.abspath(input_fname)
try:
info, cnt_info = _get_cnt_info(
input_fname, eog, ecg, emg, misc, data_format, _date_format, header
)
except Exception:
raise RuntimeError(
f"{_explain_exception()}\n"
"WARNING: mne.io.read_raw_cnt "
"supports Neuroscan CNT files only. If this file is an ANT Neuro CNT, "
"please use mne.io.read_raw_ant instead."
)
last_samps = [cnt_info["n_samples"] - 1]
super().__init__(
info,
preload,
filenames=[input_fname],
raw_extras=[cnt_info],
last_samps=last_samps,
orig_format="int",
verbose=verbose,
)
data_format = "int32" if cnt_info["n_bytes"] == 4 else "int16"
self.set_annotations(
_read_annotations_cnt(input_fname, data_format=data_format)
)
def _read_segment_file(self, data, idx, fi, start, stop, cals, mult):
"""Take a chunk of raw data, multiply by mult or cals, and store."""
n_channels = self._raw_extras[fi]["orig_nchan"]
if "stim_channel" in self._raw_extras[fi]:
f_channels = n_channels - 1 # Stim channel already read.
stim_ch = self._raw_extras[fi]["stim_channel"]
else:
f_channels = n_channels
stim_ch = None
channel_offset = self._raw_extras[fi]["channel_offset"]
baselines = self._raw_extras[fi]["baselines"]
n_bytes = self._raw_extras[fi]["n_bytes"]
n_samples = self._raw_extras[fi]["n_samples"]
dtype = "<i4" if n_bytes == 4 else "<i2"
chunk_size = channel_offset * f_channels # Size of chunks in file.
# The data is divided into blocks of samples / channel.
# channel_offset determines the amount of successive samples.
# Here we use sample offset to align the data because start can be in
# the middle of these blocks.
data_left = (stop - start) * f_channels
# Read up to 100 MB of data at a time, block_size is in data samples
block_size = ((int(100e6) // n_bytes) // chunk_size) * chunk_size
block_size = min(data_left, block_size)
s_offset = start % channel_offset
with open(self.filenames[fi], "rb", buffering=0) as fid:
fid.seek(900 + f_channels * (75 + (start - s_offset) * n_bytes))
for sample_start in np.arange(0, data_left, block_size) // f_channels:
# Earlier comment says n_samples is unreliable, but I think it
# is because it needed to be changed to unsigned int
# See: PR #12393
sample_stop = sample_start + min(
(
n_samples,
block_size // f_channels,
data_left // f_channels - sample_start,
)
)
n_samps = sample_stop - sample_start
one = np.zeros((n_channels, n_samps))
# In case channel offset and start time do not align perfectly,
# extra sample sets are read here to cover the desired time
# window. The whole (up to 100 MB) block is read at once and
# then reshaped to (n_channels, n_samples).
extra_samps = (
chunk_size
if (s_offset != 0 or n_samps % channel_offset != 0)
else 0
)
if s_offset >= (channel_offset / 2): # Extend at the end.
extra_samps += chunk_size
count = n_samps // channel_offset * chunk_size + extra_samps
n_chunks = count // chunk_size
samps = np.fromfile(fid, dtype=dtype, count=count)
samps = samps.reshape((n_chunks, f_channels, channel_offset), order="C")
# Intermediate shaping to chunk sizes.
block = np.zeros((n_channels, channel_offset * n_chunks))
for set_idx, row in enumerate(samps): # Final shape.
block_slice = slice(
set_idx * channel_offset, (set_idx + 1) * channel_offset
)
block[:f_channels, block_slice] = row
if "stim_channel" in self._raw_extras[fi]:
_data_start = start + sample_start
_data_stop = start + sample_stop
block[-1] = stim_ch[_data_start:_data_stop]
one[idx] = block[idx, s_offset : n_samps + s_offset]
one[idx] -= baselines[idx][:, None]
_mult_cal_one(data[:, sample_start:sample_stop], one, idx, cals, mult)