Source code for mne_bids.copyfiles

"""Utility functions to copy raw data files.

When writing BIDS datasets, we often move and/or rename raw data files. several
original data formats have properties that restrict such operations. That is,
moving/renaming raw data files naively might lead to broken files, for example
due to internal pointers that are not being updated.

"""

# Authors: Mainak Jas <mainak.jas@telecom-paristech.fr>
#          Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#          Teon Brooks <teon.brooks@gmail.com>
#          Chris Holdgraf <choldgraf@berkeley.edu>
#          Stefan Appelhoff <stefan.appelhoff@mailbox.org>
#          Matt Sanderson <matt.sanderson@mq.edu.au>
#
# License: BSD-3-Clause
import os
import os.path as op
import re
import shutil as sh
from pathlib import Path

import numpy as np
from mne.io import anonymize_info, read_raw_bdf, read_raw_brainvision, read_raw_edf
from mne.utils import logger, verbose
from scipy.io import loadmat, savemat

from mne_bids.path import BIDSPath, _mkdir_p, _parse_ext
from mne_bids.utils import _check_anonymize, _get_mrk_meas_date, warn


def _copytree(src, dst, **kwargs):
    """See: https://github.com/jupyterlab/jupyterlab/pull/5150."""
    try:
        sh.copytree(src, dst, **kwargs)
    except sh.Error as error:
        # `copytree` throws an error if copying to + from NFS even though
        # the copy is successful (see https://bugs.python.org/issue24564)
        if "[Errno 22]" not in str(error) or not op.exists(dst):
            raise


def _get_brainvision_encoding(vhdr_file):
    """Get the encoding of .vhdr and .vmrk files.

    Parameters
    ----------
    vhdr_file : str
        Path to the header file.

    Returns
    -------
    enc : str
        Encoding of the .vhdr file to pass it on to open() function
        either 'UTF-8' (default) or whatever encoding scheme is specified
        in the header.

    """
    with open(vhdr_file, "rb") as ef:
        enc = ef.read()
        if enc.find(b"Codepage=") != -1:
            enc = enc[enc.find(b"Codepage=") + 9 :]
            enc = enc.split()[0]
            enc = enc.decode()
            src = "(read from header)"
        else:
            enc = "UTF-8"
            src = "(default)"
        logger.debug(f"Detected file encoding: {enc} {src}.")
    return enc


def _get_brainvision_paths(vhdr_path):
    """Get the .eeg/.dat and .vmrk file paths from a BrainVision header file.

    Parameters
    ----------
    vhdr_path : str
        Path to the header file.

    Returns
    -------
    paths : tuple
        Paths to the .eeg/.dat file at index 0 and the .vmrk file at index 1 of
        the returned tuple.

    """
    fname, ext = _parse_ext(vhdr_path)
    if ext != ".vhdr":
        raise ValueError(f'Expecting file ending in ".vhdr",' f" but got {ext}")

    # Header file seems fine
    # extract encoding from brainvision header file, or default to utf-8
    enc = _get_brainvision_encoding(vhdr_path)

    # ..and read it
    with open(vhdr_path, encoding=enc) as f:
        lines = f.readlines()

    # Try to find data file .eeg/.dat
    eeg_file_match = re.search(r"DataFile=(.*\.(eeg|dat))", " ".join(lines))

    if not eeg_file_match:
        raise ValueError("Could not find a .eeg or .dat file link in" f" {vhdr_path}")
    else:
        eeg_file = eeg_file_match.groups()[0]

    # Try to find marker file .vmrk
    vmrk_file_match = re.search(r"MarkerFile=(.*\.vmrk)", " ".join(lines))
    if not vmrk_file_match:
        raise ValueError("Could not find a .vmrk file link in" f" {vhdr_path}")
    else:
        vmrk_file = vmrk_file_match.groups()[0]

    # Make sure we are dealing with file names as is customary, not paths
    # Paths are problematic when copying the files to another system. Instead,
    # always use the file name and keep the file triplet in the same directory
    assert os.sep not in eeg_file
    assert os.sep not in vmrk_file

    # Assert the paths exist
    head, tail = op.split(vhdr_path)
    eeg_file_path = op.join(head, eeg_file)
    vmrk_file_path = op.join(head, vmrk_file)
    assert op.exists(eeg_file_path)
    assert op.exists(vmrk_file_path)

    # Return the paths
    return (eeg_file_path, vmrk_file_path)


[docs] def copyfile_ctf(src, dest): """Copy and rename CTF files to a new location. Parameters ---------- src : path-like Path to the source raw .ds folder. dest : path-like Path to the destination of the new bids folder. See Also -------- copyfile_brainvision copyfile_bti copyfile_edf copyfile_eeglab copyfile_kit """ _copytree(src, dest) # list of file types to rename file_types = ( ".acq", ".eeg", ".dat", ".hc", ".hist", ".infods", ".bak", ".meg4", ".newds", ".res4", ) # Consider CTF files that are split having consecutively numbered extensions extra_ctf_file_types = tuple( f".{i}_meg4" for i in range(1, 21) ) # cap at 20 is arbitrary file_types += extra_ctf_file_types # Rename files in dest with the name of the dest directory fnames = [f for f in os.listdir(dest) if f.endswith(file_types)] bids_folder_name = op.splitext(op.split(dest)[-1])[0] for fname in fnames: ext = op.splitext(fname)[-1] os.replace(op.join(dest, fname), op.join(dest, bids_folder_name + ext))
[docs] def copyfile_kit(src, dest, subject_id, session_id, task, run, _init_kwargs): """Copy and rename KIT files to a new location. Parameters ---------- src : path-like Path to the source raw .con or .sqd folder. dest : path-like Path to the destination of the new bids folder. subject_id : str | None The subject ID. Corresponds to "sub". session_id : str | None The session identifier. Corresponds to "ses". task : str | None The task identifier. Corresponds to "task". run : int | None The run number. Corresponds to "run". _init_kwargs : dict Extract information of marker and headpoints See Also -------- copyfile_brainvision copyfile_bti copyfile_ctf copyfile_edf copyfile_eeglab """ # create parent directories in case it does not exist yet _mkdir_p(op.dirname(dest)) # KIT data requires the marker file to be copied over too sh.copyfile(src, dest) data_path = op.split(dest)[0] datatype = "meg" if "mrk" in _init_kwargs and _init_kwargs["mrk"] is not None: hpi = _init_kwargs["mrk"] acq_map = dict() if isinstance(hpi, list): if _get_mrk_meas_date(hpi[0]) > _get_mrk_meas_date(hpi[1]): raise ValueError("Markers provided in incorrect order.") _, marker_ext = _parse_ext(hpi[0]) acq_map = dict(zip(["pre", "post"], hpi)) else: _, marker_ext = _parse_ext(hpi) acq_map[None] = hpi for key, value in acq_map.items(): marker_path = BIDSPath( subject=subject_id, session=session_id, task=task, run=run, acquisition=key, suffix="markers", extension=marker_ext, datatype=datatype, ) sh.copyfile(value, op.join(data_path, marker_path.basename)) for acq in ["elp", "hsp"]: if acq in _init_kwargs and _init_kwargs[acq] is not None: position_file = _init_kwargs[acq] task, run, acq = None, None, acq.upper() position_ext = ".pos" position_path = BIDSPath( subject=subject_id, session=session_id, task=task, run=run, acquisition=acq, suffix="headshape", extension=position_ext, datatype=datatype, ) sh.copyfile(position_file, op.join(data_path, position_path.basename))
def _replace_file(fname, pattern, replace): """Overwrite file, replacing end of lines matching pattern with replace.""" new_content = [] for line in open(fname): match = re.match(pattern, line) if match: line = match.group()[: -len(replace)] + replace + "\n" new_content.append(line) with open(fname, "w", encoding="utf-8") as fout: fout.writelines(new_content) def _anonymize_brainvision(vhdr_file, date): """Anonymize vmrk and vhdr files in place using `date` datetime object.""" _, vmrk_file = _get_brainvision_paths(vhdr_file) # Go through VMRK pattern = re.compile(r"^Mk\d+=New Segment,.*,\d+,\d+,\d+,\d{20}$") replace = date.strftime("%Y%m%d%H%M%S%f") _replace_file(vmrk_file, pattern, replace) # Go through VHDR pattern = re.compile(r"^Impedance \[kOhm\] at \d\d:\d\d:\d\d :$") replace = f'at {date.strftime("%H:%M:%S")} :' _replace_file(vhdr_file, pattern, replace)
[docs] @verbose def copyfile_brainvision(vhdr_src, vhdr_dest, anonymize=None, verbose=None): """Copy a BrainVision file triplet to a new location and repair links. The BrainVision file format consists of three files: .vhdr, .eeg/.dat, and .vmrk The .eeg/.dat 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 : path-like The source path of the .vhdr file to be copied. vhdr_dest : path-like 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)s See Also -------- mne.io.anonymize_info copyfile_bti copyfile_ctf copyfile_edf copyfile_eeglab copyfile_kit """ # Get extension 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}" and "{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) # raise warning if binary file has .dat extension if ".dat" in eeg_file_path: warn( "The file extension of your binary EEG data file is .dat, while " "the expected extension for raw data is .eeg. " "This might imply it's preprocessed or processed data: " "We copied the files and changed the extension to .eeg, " "but please ensure that this is actually BIDS compatible data!" ) # Copy data .eeg/.dat ... 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/.dat, .vhdr, .vmrk share one basename __, basename_src = op.split(fname_src) assert op.split(eeg_file_path)[-1] in [basename_src + ".eeg", basename_src + ".dat"] assert basename_src + ".vmrk" == op.split(vmrk_file_path)[-1] __, basename_dest = op.split(fname_dest) search_lines = [ "DataFile=" + basename_src + ".eeg", "DataFile=" + basename_src + ".dat", "MarkerFile=" + basename_src + ".vmrk", ] with open(vhdr_src, 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, 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"]) for ext in [".eeg", ".vhdr", ".vmrk"]: _, fname = os.path.split(fname_dest + ext) dirname = op.dirname(op.realpath(vhdr_dest)) logger.info(f'Created "{fname}" in "{dirname}".') if anonymize: logger.info("Anonymized all dates in VHDR and VMRK.")
[docs] 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 : path-like The source path of the .edf or .bdf file to be copied. dest : path-like 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 software. `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.lower() != ext_dest.lower(): raise ValueError( f"Need to move data with same extension, " f' but got "{ext_src}" and "{ext_dest}"' ) if ext_dest in [".EDF", ".BDF"]: warn( "Upper-case extension for EDF/BDF files is not supported " "in BIDS. Converting destination extension to lower-case." ) ext_dest = ext_dest.lower() dest = Path(dest).with_suffix(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 in [".bdf", ".BDF"]: raw = read_raw_bdf(dest, preload=False, verbose=0) elif ext_src in [".edf", ".EDF"]: raw = read_raw_edf(dest, preload=False, verbose=0) else: raise ValueError(f"Unsupported file type ({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"))
[docs] def copyfile_eeglab(src, dest): """Copy an EEGLAB file to a new location. If the EEGLAB ``.set`` file comes with an accompanying ``.fdt`` binary file that contains the actual data, this function will copy this file, too, and update all internal pointers in the new ``.set`` file. Parameters ---------- src : path-like Path to the source raw .set file. dest : path-like Path to the destination of the new .set file. See Also -------- copyfile_brainvision copyfile_bti copyfile_ctf copyfile_edf copyfile_kit """ # Get extension of the EEGLAB file _, 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}, {ext_dest}" ) # Load the EEG struct # NOTE: do *not* simplify cells, because this changes the underlying # structure and potentially breaks re-reading of the file uint16_codec = None eeg = loadmat( file_name=src, simplify_cells=False, appendmat=False, uint16_codec=uint16_codec, mat_dtype=True, ) oldstyle = False if "EEG" in eeg: eeg = eeg["EEG"] oldstyle = True has_fdt_link = False try: # If the data field is a string, it points to a .fdt file in src dir if isinstance(eeg["data"][0, 0][0], str): has_fdt_link = True except IndexError: pass if has_fdt_link: fdt_fname = eeg["data"][0, 0][0] assert fdt_fname.endswith(".fdt"), f"Unexpected fdt name: {fdt_fname}" head, _ = op.split(src) fdt_path = op.join(head, fdt_fname) # Copy the .fdt file and give it a new name fdt_name_new = fname_dest + ".fdt" sh.copyfile(fdt_path, fdt_name_new) # Now adjust the pointer in the .set file # NOTE: Clunky numpy code is to match MATLAB structure for "savemat" _, tail = op.split(fdt_name_new) new_value = np.empty((1, 1), dtype=object) new_value[0, 0] = np.atleast_1d(np.array(tail)) eeg["data"] = new_value # Save the EEG dictionary as a Matlab struct again mdict = dict(EEG=eeg) if oldstyle else eeg savemat(file_name=dest, mdict=mdict, appendmat=False) else: # If no .fdt file, simply copy the .set file, no modifications # necessary sh.copyfile(src, dest)
[docs] def copyfile_bti(raw, dest): """Copy BTi data. Parameters ---------- raw : mne.io.Raw An MNE-Python raw object of BTi data. dest : path-like Destination to copy the BTi data to. See Also -------- copyfile_brainvision copyfile_ctf copyfile_edf copyfile_eeglab copyfile_kit """ os.makedirs(dest, exist_ok=True) for key, val in ( ("pdf_fname", None), ("config_fname", "config"), ("head_shape_fname", "hs_file"), ): keyfile = raw._raw_extras[0].get(key) # Keep name of pdf file if key == "pdf_fname": val = op.basename(keyfile) # If no headshape file present, cannot copy it if key == "head_shape_fname" and keyfile is None: continue sh.copyfile(keyfile, op.join(dest, val))