Fix write_fine_calibration mangling Neuromag channel names (mne-tools#13999)

Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com>

Author: apoorva-01

doc/changes/dev/13999.bugfix.rst

@@ -0,0 +1 @@
+Fix bug where :func:`mne.preprocessing.write_fine_calibration` wrote internal ``MEG`` channel names (e.g. ``MEG0113``) instead of the bare channel numbers (e.g. ``113``) that MaxFilter expects, breaking round trips of Neuromag calibration files, by :newcontrib:`Apoorva Verma`.

doc/changes/names.inc

@@ -30,6 +30,7 @@
 .. _Antoine Gauthier: https://github.com/Okamille
 .. _Antti Rantala: https://github.com/Odingod
 .. _Apoorva Karekal: https://github.com/apoorva6262
+.. _Apoorva Verma: https://github.com/apoorva-01
 .. _Archit Singhal: https://github.com/architsinghal-mriirs
 .. _Arne Pelzer: https://github.com/aplzr
 .. _Ashley Drew: https://github.com/ashdrew

mne/preprocessing/_fine_cal.py

@@ -595,6 +595,15 @@ def write_fine_calibration(fname, calibration):
     keys = ("ch_names", "locs", "imb_cals")
     with open(fname, "wb") as cal_file:
         for ch_name, loc, imb_cal in zip(*(calibration[key] for key in keys)):
+            # MaxFilter expects bare channel numbers, so undo the "MEG%04d"
+            # renaming that read_fine_calibration applies to Neuromag channels.
+            # Match only that 4-digit form, leaving e.g. KIT "MEG001" untouched.
+            if (
+                ch_name.startswith("MEG")
+                and len(ch_name) == 7
+                and ch_name[3:].isdigit()
+            ):
+                ch_name = str(int(ch_name[3:]))
             cal_line = np.concatenate([loc, imb_cal]).round(6)
             cal_line = " ".join(f"{c:0.6f}" for c in cal_line)
             cal_file.write(f"{ch_name} {cal_line}\n".encode("ASCII"))

mne/preprocessing/tests/test_fine_cal.py

@@ -59,6 +59,37 @@ def test_fine_cal_io(tmp_path, fname):
     assert object_diff(fine_cal_dict, fine_cal_dict_reload) == ""
 
 
+def test_fine_cal_io_preserves_channel_numbers(tmp_path):
+    """Test that writing keeps bare channel numbers MaxFilter expects (#13859)."""
+    loc = " ".join(["0.000000"] * 12)
+    src = tmp_path / "sss_cal.dat"
+    # both 3-digit (zero-padded on read) and 4-digit channel numbers
+    src.write_text(f"113\t{loc} -0.008282\n2643\t{loc} -0.005429\n")
+
+    cal = read_fine_calibration(src)
+    # read_fine_calibration renames Neuromag channels to match raw.info
+    assert cal["ch_names"] == ["MEG0113", "MEG2643"]
+
+    out = tmp_path / "out.dat"
+    write_fine_calibration(out, cal)
+    written_numbers = [line.split()[0] for line in out.read_text().splitlines()]
+    assert written_numbers == ["113", "2643"]
+
+
+def test_fine_cal_io_keeps_non_neuromag_names(tmp_path):
+    """Test that writing leaves non-Neuromag channel names untouched."""
+    loc = " ".join(["0.000000"] * 12)
+    src = tmp_path / "sss_cal.dat"
+    src.write_text(f"MLC11\t{loc} -0.008282\n")
+
+    cal = read_fine_calibration(src)
+    assert cal["ch_names"] == ["MLC11"]
+
+    out = tmp_path / "out.dat"
+    write_fine_calibration(out, cal)
+    assert out.read_text().split()[0] == "MLC11"
+
+
 @testing.requires_testing_data
 @pytest.mark.parametrize(
     "kind",