initial commit

mne/commands/mne_anonymize.py

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+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+"""Anonymize raw fif file.
+
+To anonymize other file types call :func:`mne.io.anonymize_info` on their
+:class:`~mne.Info` objects and resave to disk.
+
+Examples
+--------
+.. code-block:: console
+
+    $ mne anonymize -f sample_audvis_raw.fif
+
+"""
+
+import os.path as op
+import sys
+
+import mne
+
+ANONYMIZE_FILE_PREFIX = "anon"
+
+
+def mne_anonymize(fif_fname, out_fname, keep_his, daysback, overwrite):
+    """Call *anonymize_info* on fif file and save.
+
+    Parameters
+    ----------
+    fif_fname : path-like
+        Raw fif File
+    out_fname : path-like | None
+        Output file name
+        relative paths are saved relative to parent dir of fif_fname
+        None will save to parent dir of fif_fname with default prefix
+    daysback : int | None
+        Number of days to subtract from all dates.
+        If None will default to move date of service to Jan 1 2000
+    keep_his : bool
+        If True his_id of subject_info will NOT be overwritten.
+        defaults to False
+    overwrite : bool
+        Overwrite output file if it already exists
+    """
+    raw = mne.io.read_raw_fif(fif_fname, allow_maxshield=True)
+    raw.anonymize(daysback=daysback, keep_his=keep_his)
+
+    # determine out_fname
+    dir_name = op.split(fif_fname)[0]
+    if out_fname is None:
+        fif_bname = op.basename(fif_fname)
+        out_fname = op.join(dir_name, f"{ANONYMIZE_FILE_PREFIX}-{fif_bname}")
+    elif not op.isabs(out_fname):
+        out_fname = op.join(dir_name, out_fname)
+
+    raw.save(out_fname, overwrite=overwrite)
+
+
+def run():
+    """Run *mne_anonymize* command."""
+    from mne.commands.utils import get_optparser
+
+    parser = get_optparser(__file__)
+
+    parser.add_option(
+        "-f",
+        "--file",
+        type="string",
+        dest="file",
+        help="Name of file to modify.",
+        metavar="FILE",
+        default=None,
+    )
+    parser.add_option(
+        "-o",
+        "--output",
+        type="string",
+        dest="output",
+        help="Name of anonymized output file."
+        "`anon-` prefix is added to FILE if not given",
+        metavar="OUTFILE",
+        default=None,
+    )
+    parser.add_option(
+        "--keep_his",
+        dest="keep_his",
+        action="store_true",
+        help="Keep the HIS tag (not advised)",
+        default=False,
+    )
+    parser.add_option(
+        "-d",
+        "--daysback",
+        type="int",
+        dest="daysback",
+        help="Move dates in file backwards by this many days.",
+        metavar="N_DAYS",
+        default=None,
+    )
+    parser.add_option(
+        "--overwrite",
+        dest="overwrite",
+        action="store_true",
+        help="Overwrite input file.",
+        default=False,
+    )
+
+    options, args = parser.parse_args()
+    if options.file is None:
+        parser.print_help()
+        sys.exit(1)
+
+    fname = options.file
+    out_fname = options.output
+    keep_his = options.keep_his
+    daysback = options.daysback
+    overwrite = options.overwrite
+    if not fname.endswith(".fif"):
+        raise ValueError(f"{fname} does not seem to be a .fif file.")
+
+    mne_anonymize(fname, out_fname, keep_his, daysback, overwrite)
+
+
+is_main = __name__ == "__main__"
+if is_main:
+    run()