initial commit

2025-08-19 09:13:22 -07:00
parent 28464811d6
commit 0977a3e14d
820 changed files with 1003358 additions and 2 deletions
--- a/mne/commands/mne_bti2fiff.py
+++ b/mne/commands/mne_bti2fiff.py
@@ -0,0 +1,122 @@
+"""Import BTi / 4D MagnesWH3600 data to fif file.
+
+Notes
+-----
+1. Currently direct inclusion of reference channel weights
+   is not supported. Please use 'mne_create_comp_data' to include
+   the weights or use the low level functions from this module to
+   include them by yourself.
+2. The informed guess for the 4D name is E31 for the ECG channel and
+   E63, E63 for the EOG channels. Please check and adjust if those channels
+   are present in your dataset but 'ECG 01' and 'EOG 01', 'EOG 02' don't
+   appear in the channel names of the raw object.
+
+Examples
+--------
+.. code-block:: console
+
+     $ mne bti2fiff --pdf C,rfDC -o my_raw.fif
+
+"""
+
+# Authors: The MNE-Python contributors.
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import sys
+
+import mne
+from mne.io import read_raw_bti
+
+
+def run():
+    """Run command."""
+    from mne.commands.utils import get_optparser
+
+    parser = get_optparser(__file__)
+
+    parser.add_option(
+        "-p", "--pdf", dest="pdf_fname", help="Input data file name", metavar="FILE"
+    )
+    parser.add_option(
+        "-c",
+        "--config",
+        dest="config_fname",
+        help="Input config file name",
+        metavar="FILE",
+        default="config",
+    )
+    parser.add_option(
+        "--head_shape",
+        dest="head_shape_fname",
+        help="Headshape file name",
+        metavar="FILE",
+        default="hs_file",
+    )
+    parser.add_option(
+        "-o",
+        "--out_fname",
+        dest="out_fname",
+        help="Name of the resulting fiff file",
+        default="as_data_fname",
+    )
+    parser.add_option(
+        "-r",
+        "--rotation_x",
+        dest="rotation_x",
+        type="float",
+        help="Compensatory rotation about Neuromag x axis, deg",
+        default=2.0,
+    )
+    parser.add_option(
+        "-T",
+        "--translation",
+        dest="translation",
+        type="str",
+        help="Default translation, meter",
+        default=(0.00, 0.02, 0.11),
+    )
+    parser.add_option(
+        "--ecg_ch", dest="ecg_ch", type="str", help="4D ECG channel name", default="E31"
+    )
+    parser.add_option(
+        "--eog_ch",
+        dest="eog_ch",
+        type="str",
+        help="4D EOG channel names",
+        default="E63,E64",
+    )
+
+    options, args = parser.parse_args()
+
+    pdf_fname = options.pdf_fname
+    if pdf_fname is None:
+        parser.print_help()
+        sys.exit(1)
+
+    config_fname = options.config_fname
+    head_shape_fname = options.head_shape_fname
+    out_fname = options.out_fname
+    rotation_x = options.rotation_x
+    translation = options.translation
+    ecg_ch = options.ecg_ch
+    eog_ch = options.ecg_ch.split(",")
+
+    if out_fname == "as_data_fname":
+        out_fname = pdf_fname + "_raw.fif"
+
+    raw = read_raw_bti(
+        pdf_fname=pdf_fname,
+        config_fname=config_fname,
+        head_shape_fname=head_shape_fname,
+        rotation_x=rotation_x,
+        translation=translation,
+        ecg_ch=ecg_ch,
+        eog_ch=eog_ch,
+    )
+
+    raw.save(out_fname)
+    raw.close()
+
+
+mne.utils.run_command_if_main()