def copyfile_brainvision(vhdr_src, vhdr_dest, anonymize=None, verbose=False):
"""Copy a BrainVision file triplet to a new location and repair links.
The BrainVision file format consists of three files: .vhdr, .eeg, and .vmrk
The .eeg and .vmrk files associated with the .vhdr file will be given names
as in `vhdr_dest` with adjusted extensions. Internal file pointers will be
fixed.
Parameters
----------
vhdr_src : str
The src path of the .vhdr file to be copied.
vhdr_dest : str
The destination path of the .vhdr file.
anonymize : dict | None
If None (default), no anonymization is performed.
If dict, data will be anonymized depending on the keys provided with
the dict: `daysback` is a required key, `keep_his` is an optional key.
`daysback` : int
Number of days by which to move back the recording date in time.
In studies with multiple subjects the relative recording date
differences between subjects can be kept by using the same number
of `daysback` for all subject anonymizations. `daysback` should be
great enough to shift the date prior to 1925 to conform with BIDS
anonymization rules.
`keep_his` : bool
By default (False), all subject information next to the recording
date will be overwritten as well. If True, keep subject information
apart from the recording date.
verbose : bool
Determine whether results should be logged. Defaults to False.
See Also
--------
mne.io.anonymize_info
"""
# Get extenstion of the brainvision file
fname_src, ext_src = _parse_ext(vhdr_src)
fname_dest, ext_dest = _parse_ext(vhdr_dest)
if ext_src != ext_dest:
raise ValueError(f'Need to move data with same extension'
f' but got "{ext_src}", "{ext_dest}"')
eeg_file_path, vmrk_file_path = _get_brainvision_paths(vhdr_src)
# extract encoding from brainvision header file, or default to utf-8
enc = _get_brainvision_encoding(vhdr_src, verbose)
# Copy data .eeg ... no links to repair
sh.copyfile(eeg_file_path, fname_dest + '.eeg')
# Write new header and marker files, fixing the file pointer links
# For that, we need to replace an old "basename" with a new one
# assuming that all .eeg, .vhdr, .vmrk share one basename
__, basename_src = op.split(fname_src)
assert basename_src + '.eeg' == op.split(eeg_file_path)[-1]
assert basename_src + '.vmrk' == op.split(vmrk_file_path)[-1]
__, basename_dest = op.split(fname_dest)
search_lines = ['DataFile=' + basename_src + '.eeg',
'MarkerFile=' + basename_src + '.vmrk']
with open(vhdr_src, 'r', encoding=enc) as fin:
with open(vhdr_dest, 'w', encoding=enc) as fout:
for line in fin.readlines():
if line.strip() in search_lines:
line = line.replace(basename_src, basename_dest)
fout.write(line)
with open(vmrk_file_path, 'r', encoding=enc) as fin:
with open(fname_dest + '.vmrk', 'w', encoding=enc) as fout:
for line in fin.readlines():
if line.strip() in search_lines:
line = line.replace(basename_src, basename_dest)
fout.write(line)
if anonymize is not None:
raw = read_raw_brainvision(vhdr_src, preload=False, verbose=0)
daysback, keep_his = _check_anonymize(anonymize, raw, '.vhdr')
raw.info = anonymize_info(raw.info, daysback=daysback,
keep_his=keep_his)
_anonymize_brainvision(fname_dest + '.vhdr',
date=raw.info['meas_date'])
if verbose:
for ext in ['.eeg', '.vhdr', '.vmrk']:
_, fname = os.path.split(fname_dest + ext)
dirname = op.dirname(op.realpath(vhdr_dest))
print(f'Created "{fname}" in "{dirname}".')
if anonymize:
print('Anonymized all dates in VHDR and VMRK.')
def copyfile_edf(src, dest, anonymize=None):
"""Copy an EDF, EDF+, or BDF file to a new location, optionally anonymize.
.. warning:: EDF/EDF+/BDF files contain two fields for recording dates:
A generic "startdate" field that supports only 2-digit years,
and a "Startdate" field as part of the "local recording
identification", which supports 4-digit years.
If you want to anonymize your file, MNE-BIDS will set the
"startdate" field to 85 (i.e., 1985), the earliest possible
date for that field. However, the "Startdate" field in the
file's "local recording identification" and the date in the
session's corresponding ``scans.tsv`` will be set correctly
according to the argument provided to the ``anonymize``
parameter. Note that it is possible that not all EDF/EDF+/BDF
reading software parses the accurate recording date, and
that for some reading software, the wrong year (1985) may
be parsed.
Parameters
----------
src : str | pathlib.Path
The source path of the .edf or .bdf file to be copied.
dest : str | pathlib.Path
The destination path of the .edf or .bdf file.
anonymize : dict | None
If None (default), no anonymization is performed.
If dict, data will be anonymized depending on the keys provided with
the dict: `daysback` is a required key, `keep_his` is an optional key.
`daysback` : int
Number of days by which to move back the recording date in time.
In studies with multiple subjects the relative recording date
differences between subjects can be kept by using the same number
of `daysback` for all subject anonymizations. `daysback` should be
great enough to shift the date prior to 1925 to conform with BIDS
anonymization rules. Due to limitations of the EDF/BDF format, the
year of the anonymized date will always be set to 1985 in the
'startdate' field of the file. The correctly-shifted year will be
written to the 'local recording identification' region of the
file header, which may not be parsed by all EDF/EDF+/BDF reader
softwares.
`keep_his` : bool
By default (False), all subject information next to the recording
date will be overwritten as well. If True, keep subject information
apart from the recording date. Participant names and birthdates
will always be anonymized if present, regardless of this setting.
See Also
--------
mne.io.anonymize_info
copyfile_brainvision
copyfile_bti
copyfile_ctf
copyfile_eeglab
copyfile_kit
"""
# Ensure source & destination extensions are the same
fname_src, ext_src = _parse_ext(src)
fname_dest, ext_dest = _parse_ext(dest)
if ext_src != ext_dest:
raise ValueError(f'Need to move data with same extension, '
f' but got "{ext_src}" and "{ext_dest}"')
# Copy data prior to any anonymization
sh.copyfile(src, dest)
# Anonymize EDF/BDF data, if requested
if anonymize is not None:
if ext_src == '.bdf':
raw = read_raw_bdf(dest, preload=False, verbose=0)
elif ext_src == '.edf':
raw = read_raw_edf(dest, preload=False, verbose=0)
else:
raise ValueError('Unsupported file type ({0})'.format(ext_src))
# Get subject info, recording info, and recording date
with open(dest, 'rb') as f:
f.seek(8) # id_info field starts 8 bytes in
id_info = f.read(80).decode('ascii').rstrip()
rec_info = f.read(80).decode('ascii').rstrip()
# Parse metadata from file
if len(id_info) == 0 or len(id_info.split(' ')) != 4:
id_info = "X X X X"
if len(rec_info) == 0 or len(rec_info.split(' ')) != 5:
rec_info = "Startdate X X X X"
pid, sex, birthdate, name = id_info.split(' ')
start_date, admin_code, tech, equip = rec_info.split(' ')[1:5]
# Try to anonymize the recording date
daysback, keep_his = _check_anonymize(anonymize, raw, '.edf')
anonymize_info(raw.info, daysback=daysback, keep_his=keep_his)
start_date = '01-JAN-1985'
meas_date = '01.01.85'
# Anonymize ID info and write to file
if keep_his:
# Always remove participant birthdate and name to be safe
id_info = [pid, sex, "X", "X"]
rec_info = ["Startdate", start_date, admin_code, tech, equip]
else:
id_info = ["0", "X", "X", "X"]
rec_info = ["Startdate", start_date, "X",
"mne-bids_anonymize", "X"]
with open(dest, 'r+b') as f:
f.seek(8) # id_info field starts 8 bytes in
f.write(bytes(" ".join(id_info).ljust(80), 'ascii'))
f.write(bytes(" ".join(rec_info).ljust(80), 'ascii'))
f.write(bytes(meas_date, 'ascii'))