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tyler
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# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
from collections import OrderedDict
from datetime import datetime, timezone
from pathlib import Path
import numpy as np
from ..._fiff.meas_info import create_info
from ..._fiff.utils import _mult_cal_one
from ...annotations import Annotations
from ...utils import _check_fname, fill_doc, logger, verbose, warn
from ..base import BaseRaw
def _ensure_path(fname):
out = fname
if not isinstance(out, Path):
out = Path(out)
return out
@fill_doc
def read_raw_nihon(fname, preload=False, verbose=None) -> "RawNihon":
"""Reader for an Nihon Kohden EEG file.
Parameters
----------
fname : path-like
Path to the Nihon Kohden data file (``.EEG``).
preload : bool
If True, all data are loaded at initialization.
%(verbose)s
Returns
-------
raw : instance of RawNihon
A Raw object containing Nihon Kohden data.
See :class:`mne.io.Raw` for documentation of attributes and methods.
See Also
--------
mne.io.Raw : Documentation of attributes and methods of RawNihon.
"""
return RawNihon(fname, preload, verbose)
_valid_headers = [
"EEG-1100A V01.00",
"EEG-1100B V01.00",
"EEG-1100C V01.00",
"QI-403A V01.00",
"QI-403A V02.00",
"EEG-2100 V01.00",
"EEG-2100 V02.00",
"DAE-2100D V01.30",
"DAE-2100D V02.00",
# 'EEG-1200A V01.00', # Not working for the moment.
]
def _read_nihon_metadata(fname):
metadata = {}
fname = _ensure_path(fname)
pnt_fname = fname.with_suffix(".PNT")
if not pnt_fname.exists():
warn("No PNT file exists. Metadata will be blank")
return metadata
logger.info("Found PNT file, reading metadata.")
with open(pnt_fname) as fid:
version = np.fromfile(fid, "|S16", 1).astype("U16")[0]
if version not in _valid_headers:
raise ValueError(f"Not a valid Nihon Kohden PNT file ({version})")
metadata["version"] = version
# Read timestamp
fid.seek(0x40)
meas_str = np.fromfile(fid, "|S14", 1).astype("U14")[0]
meas_date = datetime.strptime(meas_str, "%Y%m%d%H%M%S")
meas_date = meas_date.replace(tzinfo=timezone.utc)
metadata["meas_date"] = meas_date
return metadata
_default_chan_labels = [
"FP1",
"FP2",
"F3",
"F4",
"C3",
"C4",
"P3",
"P4",
"O1",
"O2",
"F7",
"F8",
"T3",
"T4",
"T5",
"T6",
"FZ",
"CZ",
"PZ",
"E",
"PG1",
"PG2",
"A1",
"A2",
"T1",
"T2",
]
_default_chan_labels += [f"X{i}" for i in range(1, 12)]
_default_chan_labels += [f"NA{i}" for i in range(1, 6)]
_default_chan_labels += [f"DC{i:02}" for i in range(1, 33)]
_default_chan_labels += ["BN1", "BN2", "Mark1", "Mark2"]
_default_chan_labels += [f"NA{i}" for i in range(6, 28)]
_default_chan_labels += ["X12/BP1", "X13/BP2", "X14/BP3", "X15/BP4"]
_default_chan_labels += [f"X{i}" for i in range(16, 166)]
_default_chan_labels += ["NA28", "Z"]
_encodings = ("utf-8", "latin1")
def _read_21e_file(fname):
fname = _ensure_path(fname)
e_fname = fname.with_suffix(".21E")
_chan_labels = [x for x in _default_chan_labels]
if e_fname.exists():
# Read the 21E file and update the labels accordingly.
logger.info("Found 21E file, reading channel names.")
for enc in _encodings:
try:
with open(e_fname, encoding=enc) as fid:
keep_parsing = False
for line in fid:
if line.startswith("["):
if "ELECTRODE" in line or "REFERENCE" in line:
keep_parsing = True
else:
keep_parsing = False
elif keep_parsing is True:
idx, name = line.split("=")
idx = int(idx)
if idx >= len(_chan_labels):
n = idx - len(_chan_labels) + 1
_chan_labels.extend(["UNK"] * n)
_chan_labels[idx] = name.strip()
except UnicodeDecodeError:
pass
else:
break
else:
warn(
f"Could not decode 21E file as one of {_encodings}; "
f"Default channel names are chosen."
)
return _chan_labels
def _read_nihon_header(fname):
# Read the Nihon Kohden EEG file header
fname = _ensure_path(fname)
_chan_labels = _read_21e_file(fname)
header = {}
logger.info(f"Reading header from {fname}")
with open(fname) as fid:
version = np.fromfile(fid, "|S16", 1).astype("U16")[0]
if version not in _valid_headers:
raise ValueError(f"Not a valid Nihon Kohden EEG file ({version})")
fid.seek(0x0081)
control_block = np.fromfile(fid, "|S16", 1).astype("U16")[0]
if control_block not in _valid_headers:
raise ValueError(
f"Not a valid Nihon Kohden EEG file (control block {version})"
)
fid.seek(0x17FE)
waveform_sign = np.fromfile(fid, np.uint8, 1)[0]
if waveform_sign != 1:
raise ValueError("Not a valid Nihon Kohden EEG file (waveform block)")
header["version"] = version
fid.seek(0x0091)
n_ctlblocks = np.fromfile(fid, np.uint8, 1)[0]
header["n_ctlblocks"] = n_ctlblocks
controlblocks = []
for i_ctl_block in range(n_ctlblocks):
t_controlblock = {}
fid.seek(0x0092 + i_ctl_block * 20)
t_ctl_address = np.fromfile(fid, np.uint32, 1)[0]
t_controlblock["address"] = t_ctl_address
fid.seek(t_ctl_address + 17)
n_datablocks = np.fromfile(fid, np.uint8, 1)[0]
t_controlblock["n_datablocks"] = n_datablocks
t_controlblock["datablocks"] = []
for i_data_block in range(n_datablocks):
t_datablock = {}
fid.seek(t_ctl_address + i_data_block * 20 + 18)
t_data_address = np.fromfile(fid, np.uint32, 1)[0]
t_datablock["address"] = t_data_address
fid.seek(t_data_address + 0x26)
t_n_channels = np.fromfile(fid, np.uint8, 1)[0].astype(np.int64)
t_datablock["n_channels"] = t_n_channels
t_channels = []
for i_ch in range(t_n_channels):
fid.seek(t_data_address + 0x27 + (i_ch * 10))
t_idx = np.fromfile(fid, np.uint8, 1)[0]
t_channels.append(_chan_labels[t_idx])
t_datablock["channels"] = t_channels
fid.seek(t_data_address + 0x1C)
t_record_duration = np.fromfile(fid, np.uint32, 1)[0].astype(np.int64)
t_datablock["duration"] = t_record_duration
fid.seek(t_data_address + 0x1A)
sfreq = np.fromfile(fid, np.uint16, 1)[0] & 0x3FFF
t_datablock["sfreq"] = sfreq.astype(np.int64)
t_datablock["n_samples"] = np.int64(t_record_duration * sfreq // 10)
t_controlblock["datablocks"].append(t_datablock)
controlblocks.append(t_controlblock)
header["controlblocks"] = controlblocks
# Now check that every data block has the same channels and sfreq
chans = []
sfreqs = []
nsamples = []
for t_ctl in header["controlblocks"]:
for t_dtb in t_ctl["datablocks"]:
chans.append(t_dtb["channels"])
sfreqs.append(t_dtb["sfreq"])
nsamples.append(t_dtb["n_samples"])
for i_elem in range(1, len(chans)):
if chans[0] != chans[i_elem]:
raise ValueError("Channel names in datablocks do not match")
if sfreqs[0] != sfreqs[i_elem]:
raise ValueError("Sample frequency in datablocks do not match")
header["ch_names"] = chans[0]
header["sfreq"] = sfreqs[0]
header["n_samples"] = np.sum(nsamples)
# TODO: Support more than one controlblock and more than one datablock
if header["n_ctlblocks"] != 1:
raise NotImplementedError(
"I dont know how to read more than one "
"control block for this type of file :("
)
if header["controlblocks"][0]["n_datablocks"] > 1:
# Multiple blocks, check that they all have the same kind of data
datablocks = header["controlblocks"][0]["datablocks"]
block_0 = datablocks[0]
for t_block in datablocks[1:]:
if block_0["n_channels"] != t_block["n_channels"]:
raise ValueError(
"Cannot read NK file with different number of channels "
"in each datablock"
)
if block_0["channels"] != t_block["channels"]:
raise ValueError(
"Cannot read NK file with different channels in each datablock"
)
if block_0["sfreq"] != t_block["sfreq"]:
raise ValueError(
"Cannot read NK file with different sfreq in each datablock"
)
return header
def _read_nihon_annotations(fname):
fname = _ensure_path(fname)
log_fname = fname.with_suffix(".LOG")
if not log_fname.exists():
warn("No LOG file exists. Annotations will not be read")
return dict(onset=[], duration=[], description=[])
logger.info("Found LOG file, reading events.")
with open(log_fname) as fid:
version = np.fromfile(fid, "|S16", 1).astype("U16")[0]
if version not in _valid_headers:
raise ValueError(f"Not a valid Nihon Kohden LOG file ({version})")
fid.seek(0x91)
n_logblocks = np.fromfile(fid, np.uint8, 1)[0]
all_onsets = []
all_descriptions = []
for t_block in range(n_logblocks):
fid.seek(0x92 + t_block * 20)
t_blk_address = np.fromfile(fid, np.uint32, 1)[0]
fid.seek(t_blk_address + 0x12)
n_logs = np.fromfile(fid, np.uint8, 1)[0]
fid.seek(t_blk_address + 0x14)
t_logs = np.fromfile(fid, "|S45", n_logs)
for t_log in t_logs:
for enc in _encodings:
try:
t_log = t_log.decode(enc)
except UnicodeDecodeError:
pass
else:
break
else:
warn(f"Could not decode log as one of {_encodings}")
continue
t_desc = t_log[:20].strip("\x00")
t_onset = datetime.strptime(t_log[20:26], "%H%M%S")
t_onset = t_onset.hour * 3600 + t_onset.minute * 60 + t_onset.second
all_onsets.append(t_onset)
all_descriptions.append(t_desc)
annots = dict(
onset=all_onsets,
duration=[0] * len(all_onsets),
description=all_descriptions,
)
return annots
def _map_ch_to_type(ch_name):
ch_type_pattern = OrderedDict(
[("stim", ("Mark",)), ("misc", ("DC", "NA", "Z", "$")), ("bio", ("X",))]
)
for key, kinds in ch_type_pattern.items():
if any(kind in ch_name for kind in kinds):
return key
return "eeg"
def _map_ch_to_specs(ch_name):
unit_mult = 1e-3
phys_min = -12002.9
phys_max = 12002.56
dig_min = -32768
if ch_name.upper() in _default_chan_labels:
idx = _default_chan_labels.index(ch_name.upper())
if (idx < 42 or idx > 73) and idx not in [76, 77]:
unit_mult = 1e-6
phys_min = -3200
phys_max = 3199.902
t_range = phys_max - phys_min
cal = t_range / 65535
offset = phys_min - (dig_min * cal)
out = dict(
unit=unit_mult,
phys_min=phys_min,
phys_max=phys_max,
dig_min=dig_min,
cal=cal,
offset=offset,
)
return out
@fill_doc
class RawNihon(BaseRaw):
"""Raw object from a Nihon Kohden EEG file.
Parameters
----------
fname : path-like
Path to the Nihon Kohden data ``.eeg`` file.
preload : bool
If True, all data are loaded at initialization.
%(verbose)s
See Also
--------
mne.io.Raw : Documentation of attributes and methods.
"""
@verbose
def __init__(self, fname, preload=False, verbose=None):
fname = _check_fname(fname, "read", True, "fname")
data_name = fname.name
logger.info(f"Loading {data_name}")
header = _read_nihon_header(fname)
metadata = _read_nihon_metadata(fname)
# n_chan = len(header['ch_names']) + 1
sfreq = header["sfreq"]
# data are multiplexed int16
ch_names = header["ch_names"]
ch_types = [_map_ch_to_type(x) for x in ch_names]
info = create_info(ch_names, sfreq, ch_types)
n_samples = header["n_samples"]
if "meas_date" in metadata:
with info._unlock():
info["meas_date"] = metadata["meas_date"]
chs = {x: _map_ch_to_specs(x) for x in info["ch_names"]}
cal = np.array([chs[x]["cal"] for x in info["ch_names"]], float)[:, np.newaxis]
offsets = np.array([chs[x]["offset"] for x in info["ch_names"]], float)[
:, np.newaxis
]
gains = np.array([chs[x]["unit"] for x in info["ch_names"]], float)[
:, np.newaxis
]
raw_extras = dict(cal=cal, offsets=offsets, gains=gains, header=header)
for i_ch, ch_name in enumerate(info["ch_names"]):
t_range = chs[ch_name]["phys_max"] - chs[ch_name]["phys_min"]
info["chs"][i_ch]["range"] = t_range
info["chs"][i_ch]["cal"] = 1 / t_range
super().__init__(
info,
preload=preload,
last_samps=(n_samples - 1,),
filenames=[fname.as_posix()],
orig_format="short",
raw_extras=[raw_extras],
)
# Get annotations from LOG file
annots = _read_nihon_annotations(fname)
# Annotate acquisition skips
controlblock = header["controlblocks"][0]
cur_sample = 0
if controlblock["n_datablocks"] > 1:
for i_block in range(controlblock["n_datablocks"] - 1):
t_block = controlblock["datablocks"][i_block]
cur_sample = cur_sample + t_block["n_samples"]
cur_tpoint = (cur_sample - 0.5) / t_block["sfreq"]
# Add annotations as in append raw
annots["onset"].append(cur_tpoint)
annots["duration"].append(0.0)
annots["description"].append("BAD boundary")
annots["onset"].append(cur_tpoint)
annots["duration"].append(0.0)
annots["description"].append("EDGE boundary")
annotations = Annotations(**annots, orig_time=info["meas_date"])
self.set_annotations(annotations)
def _read_segment_file(self, data, idx, fi, start, stop, cals, mult):
"""Read a chunk of raw data."""
# For now we assume one control block
header = self._raw_extras[fi]["header"]
# Get the original cal, offsets and gains
cal = self._raw_extras[fi]["cal"]
offsets = self._raw_extras[fi]["offsets"]
gains = self._raw_extras[fi]["gains"]
# get the right datablock
datablocks = header["controlblocks"][0]["datablocks"]
ends = np.cumsum([t["n_samples"] for t in datablocks])
start_block = np.where(start < ends)[0][0]
stop_block = np.where(stop <= ends)[0][0]
if start_block != stop_block:
# Recursive call for each block independently
new_start = start
sample_start = 0
for t_block_idx in range(start_block, stop_block + 1):
t_block = datablocks[t_block_idx]
if t_block == stop_block:
# If its the last block, we stop on the last sample to read
new_stop = stop
else:
# Otherwise, stop on the last sample of the block
new_stop = t_block["n_samples"] + new_start
samples_to_read = new_stop - new_start
sample_stop = sample_start + samples_to_read
self._read_segment_file(
data[:, sample_start:sample_stop],
idx,
fi,
new_start,
new_stop,
cals,
mult,
)
# Update variables for next loop
sample_start = sample_stop
new_start = new_stop
else:
datablock = datablocks[start_block]
n_channels = datablock["n_channels"] + 1
datastart = datablock["address"] + 0x27 + (datablock["n_channels"] * 10)
# Compute start offset based on the beginning of the block
rel_start = start
if start_block != 0:
rel_start = start - ends[start_block - 1]
start_offset = datastart + rel_start * n_channels * 2
with open(self.filenames[fi], "rb") as fid:
to_read = (stop - start) * n_channels
fid.seek(start_offset)
block_data = np.fromfile(fid, "<u2", to_read) + 0x8000
block_data = block_data.astype(np.int16)
block_data = block_data.reshape(n_channels, -1, order="F")
block_data = block_data[:-1] * cal # cast to float64
block_data += offsets
block_data *= gains
_mult_cal_one(data, block_data, idx, cals, mult)