[074d3d]: / mne / io / egi / general.py

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#
# Authors: The MNE-Python contributors.
# License: BSD-3-Clause
# Copyright the MNE-Python contributors.
import os
import re
import numpy as np
from ...utils import _pl, _soft_import
def _extract(tags, filepath=None, obj=None):
"""Extract info from XML."""
_soft_import("defusedxml", "reading EGI MFF data")
from defusedxml.minidom import parse
if obj is not None:
fileobj = obj
elif filepath is not None:
fileobj = parse(filepath)
else:
raise ValueError("There is not object or file to extract data")
infoxml = dict()
for tag in tags:
value = fileobj.getElementsByTagName(tag)
infoxml[tag] = []
for i in range(len(value)):
infoxml[tag].append(value[i].firstChild.data)
return infoxml
def _get_gains(filepath):
"""Parse gains."""
_soft_import("defusedxml", "reading EGI MFF data")
from defusedxml.minidom import parse
file_obj = parse(filepath)
objects = file_obj.getElementsByTagName("calibration")
gains = dict()
for ob in objects:
value = ob.getElementsByTagName("type")
if value[0].firstChild.data == "GCAL":
data_g = _extract(["ch"], obj=ob)["ch"]
gains.update(gcal=np.asarray(data_g, dtype=np.float64))
elif value[0].firstChild.data == "ICAL":
data_g = _extract(["ch"], obj=ob)["ch"]
gains.update(ical=np.asarray(data_g, dtype=np.float64))
return gains
def _get_ep_info(filepath):
"""Get epoch info."""
_soft_import("defusedxml", "reading EGI MFF data")
from defusedxml.minidom import parse
epochfile = filepath + "/epochs.xml"
epochlist = parse(epochfile)
epochs = epochlist.getElementsByTagName("epoch")
keys = ("first_samps", "last_samps", "first_blocks", "last_blocks")
epoch_info = {key: list() for key in keys}
for epoch in epochs:
ep_begin = int(epoch.getElementsByTagName("beginTime")[0].firstChild.data)
ep_end = int(epoch.getElementsByTagName("endTime")[0].firstChild.data)
first_block = int(epoch.getElementsByTagName("firstBlock")[0].firstChild.data)
last_block = int(epoch.getElementsByTagName("lastBlock")[0].firstChild.data)
epoch_info["first_samps"].append(ep_begin)
epoch_info["last_samps"].append(ep_end)
epoch_info["first_blocks"].append(first_block)
epoch_info["last_blocks"].append(last_block)
# Don't turn into ndarray here, keep native int because it can deal with
# huge numbers (could use np.uint64 but it's more work)
return epoch_info
def _get_blocks(filepath):
"""Get info from meta data blocks."""
binfile = os.path.join(filepath)
n_blocks = 0
samples_block = []
header_sizes = []
n_channels = []
sfreq = []
# Meta data consists of:
# * 1 byte of flag (1 for meta data, 0 for data)
# * 1 byte of header size
# * 1 byte of block size
# * 1 byte of n_channels
# * n_channels bytes of offsets
# * n_channels bytes of sigfreqs?
with open(binfile, "rb") as fid:
fid.seek(0, 2) # go to end of file
file_length = fid.tell()
block_size = file_length
fid.seek(0)
position = 0
while position < file_length:
block = _block_r(fid)
if block is None:
samples_block.append(samples_block[n_blocks - 1])
n_blocks += 1
fid.seek(block_size, 1)
position = fid.tell()
continue
block_size = block["block_size"]
header_size = block["header_size"]
header_sizes.append(header_size)
samples_block.append(block["nsamples"])
n_blocks += 1
fid.seek(block_size, 1)
sfreq.append(block["sfreq"])
n_channels.append(block["nc"])
position = fid.tell()
if any([n != n_channels[0] for n in n_channels]):
raise RuntimeError("All the blocks don't have the same amount of channels.")
if any([f != sfreq[0] for f in sfreq]):
raise RuntimeError("All the blocks don't have the same sampling frequency.")
if len(samples_block) < 1:
raise RuntimeError("There seems to be no data")
samples_block = np.array(samples_block)
signal_blocks = dict(
n_channels=n_channels[0],
sfreq=sfreq[0],
n_blocks=n_blocks,
samples_block=samples_block,
header_sizes=header_sizes,
)
return signal_blocks
def _get_signalfname(filepath):
"""Get filenames."""
_soft_import("defusedxml", "reading EGI MFF data")
from defusedxml.minidom import parse
listfiles = os.listdir(filepath)
binfiles = list(
f for f in listfiles if "signal" in f and f[-4:] == ".bin" and f[0] != "."
)
all_files = {}
infofiles = list()
for binfile in binfiles:
bin_num_str = re.search(r"\d+", binfile).group()
infofile = "info" + bin_num_str + ".xml"
infofiles.append(infofile)
infobjfile = os.path.join(filepath, infofile)
infobj = parse(infobjfile)
if len(infobj.getElementsByTagName("EEG")):
signal_type = "EEG"
elif len(infobj.getElementsByTagName("PNSData")):
signal_type = "PNS"
all_files[signal_type] = {
"signal": f"signal{bin_num_str}.bin",
"info": infofile,
}
if "EEG" not in all_files:
infofiles_str = "\n".join(infofiles)
raise FileNotFoundError(
f"Could not find any EEG data in the {len(infofiles)} file{_pl(infofiles)} "
f"found in {filepath}:\n{infofiles_str}"
)
return all_files
def _block_r(fid):
"""Read meta data."""
if np.fromfile(fid, dtype=np.dtype("i4"), count=1).item() != 1: # not meta
return None
header_size = np.fromfile(fid, dtype=np.dtype("i4"), count=1).item()
block_size = np.fromfile(fid, dtype=np.dtype("i4"), count=1).item()
hl = int(block_size / 4)
nc = np.fromfile(fid, dtype=np.dtype("i4"), count=1).item()
nsamples = int(hl / nc)
np.fromfile(fid, dtype=np.dtype("i4"), count=nc) # sigoffset
sigfreq = np.fromfile(fid, dtype=np.dtype("i4"), count=nc)
depth = sigfreq[0] & 0xFF
if depth != 32:
raise ValueError("I do not know how to read this MFF (depth != 32)")
sfreq = sigfreq[0] >> 8
count = int(header_size / 4 - (4 + 2 * nc))
np.fromfile(fid, dtype=np.dtype("i4"), count=count) # sigoffset
block = dict(
nc=nc,
hl=hl,
nsamples=nsamples,
block_size=block_size,
header_size=header_size,
sfreq=sfreq,
)
return block