Merge branch 'main' into xfit

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.3
+    rev: v0.9.7
     hooks:
       - id: ruff
         name: ruff lint mne
@@ -23,7 +23,7 @@ repos:
 
   # Codespell
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.4.0
+    rev: v2.4.1
     hooks:
       - id: codespell
         additional_dependencies:
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.2.2
+    rev: v1.3.1
     hooks:
       - id: zizmor
 

azure-pipelines.yml

@@ -89,6 +89,7 @@ stages:
           DISPLAY: ':99'
           OPENBLAS_NUM_THREADS: '1'
           MNE_TEST_ALLOW_SKIP: '^.*(PySide6 causes segfaults).*$'
+          MNE_BROWSER_PRECOMPUTE: 'false'
         steps:
           - bash: |
               set -e
@@ -243,7 +244,7 @@ stages:
           PYTHONIOENCODING: 'utf-8'
           AZURE_CI_WINDOWS: 'true'
           PYTHON_ARCH: 'x64'
-        timeoutInMinutes: 80
+        timeoutInMinutes: 90
         strategy:
           maxParallel: 4
           matrix:

doc/changes/devel/13044.newfeature.rst

@@ -0,0 +1 @@
+Add :meth:`mne.Evoked.interpolate_to` to allow interpolating EEG data to other montages, by :newcontrib:`Antoine Collas`.

doc/changes/devel/13083.bugfix.rst

@@ -0,0 +1 @@
+Fix bug with reading digitization points from digitization strings with newer MEGIN systems, by `Eric Larson`_.

doc/changes/devel/13100.bugfix.rst

@@ -0,0 +1 @@
+Do not convert the first "New Segment" marker in a BrainVision file to an annotation, as it only contains the recording date (which is already available in ``info["meas_date"]``), by `Clemens Brunner`_.

doc/changes/devel/13107.newfeature.rst

@@ -0,0 +1 @@
+The :meth:`mne.Info.save` method now has an ``overwrite`` and a ``verbose`` parameter, by `Stefan Appelhoff`_.

doc/changes/devel/13113.bugfix.rst

@@ -0,0 +1 @@
+Fix bug in :func:`mne.io.read_raw_gdf`, by :newcontrib:`Rongfei Jin`.

doc/changes/names.inc

@@ -24,6 +24,7 @@
 .. _Anna Padee: https://github.com/apadee/
 .. _Annalisa Pascarella: https://www.iac.cnr.it/personale/annalisa-pascarella
 .. _Anne-Sophie Dubarry: https://github.com/annesodub
+.. _Antoine Collas: https://www.antoinecollas.fr
 .. _Antoine Gauthier: https://github.com/Okamille
 .. _Antti Rantala: https://github.com/Odingod
 .. _Apoorva Karekal: https://github.com/apoorva6262
@@ -256,6 +257,7 @@
 .. _Romain Derollepot: https://github.com/rderollepot
 .. _Romain Trachel: https://fr.linkedin.com/in/trachelr
 .. _Roman Goj: https://romanmne.blogspot.co.uk
+.. _Rongfei Jin: https://github.com/greasycat
 .. _Ross Maddox: https://medicine.umich.edu/dept/khri/ross-maddox-phd
 .. _Rotem Falach: https://github.com/Falach
 .. _Roy Eric Wieske: https://github.com/Randomidous

doc/development/governance.rst

@@ -46,7 +46,9 @@ Governance Model
 Leadership Roles
 ^^^^^^^^^^^^^^^^
 
-The MNE-Python leadership structure shall consist of:
+The MNE-Python leadership structure shall consist of the following groups.
+A list of the current members of the respective groups is maintained at the
+page :ref:`governance-people`.
 
 Maintainer Team
 ---------------

doc/references.bib

@@ -2514,3 +2514,11 @@ @article{OyamaEtAl2015
 	year = {2015},
 	pages = {24--36},
 }
+
+@inproceedings{MellotEtAl2024,
+	title = {Physics-informed and Unsupervised Riemannian Domain Adaptation for Machine Learning on Heterogeneous EEG Datasets},
+	author = {Mellot, Apolline and Collas, Antoine and Chevallier, Sylvain and Engemann, Denis and Gramfort, Alexandre},
+	booktitle = {Proceedings of the 32nd European Signal Processing Conference (EUSIPCO)},
+	year = {2024},
+	address = {Lyon, France}
+}

doc/sphinxext/related_software.py

@@ -85,6 +85,10 @@
         "Home-page": "https://eeg-positions.readthedocs.io",
         "Summary": "Compute and plot standard EEG electrode positions.",
     },
+    "mne-faster": {
+        "Home-page": "https://github.com/wmvanvliet/mne-faster",
+        "Summary": "MNE-FASTER: automatic bad channel/epoch/component detection.",  # noqa: E501
+    },
     "mne-features": {
         "Home-page": "https://mne.tools/mne-features",
         "Summary": "MNE-Features software for extracting features from multivariate time series",  # noqa: E501

examples/preprocessing/interpolate_to.py

@@ -0,0 +1,81 @@
+"""
+.. _ex-interpolate-to-any-montage:
+
+======================================================
+Interpolate EEG data to any montage
+======================================================
+
+This example demonstrates how to interpolate EEG channels to match a given montage.
+This can be useful for standardizing
+EEG channel layouts across different datasets (see :footcite:`MellotEtAl2024`).
+
+- Using the field interpolation for EEG data.
+- Using the target montage "biosemi16".
+
+In this example, the data from the original EEG channels will be
+interpolated onto the positions defined by the "biosemi16" montage.
+"""
+
+# Authors: Antoine Collas <[email protected]>
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import matplotlib.pyplot as plt
+
+import mne
+from mne.channels import make_standard_montage
+from mne.datasets import sample
+
+print(__doc__)
+ylim = (-10, 10)
+
+# %%
+# Load EEG data
+data_path = sample.data_path()
+eeg_file_path = data_path / "MEG" / "sample" / "sample_audvis-ave.fif"
+evoked = mne.read_evokeds(eeg_file_path, condition="Left Auditory", baseline=(None, 0))
+
+# Select only EEG channels
+evoked.pick("eeg")
+
+# Plot the original EEG layout
+evoked.plot(exclude=[], picks="eeg", ylim=dict(eeg=ylim))
+
+# %%
+# Define the target montage
+standard_montage = make_standard_montage("biosemi16")
+
+# %%
+# Use interpolate_to to project EEG data to the standard montage
+evoked_interpolated_spline = evoked.copy().interpolate_to(
+    standard_montage, method="spline"
+)
+
+# Plot the interpolated EEG layout
+evoked_interpolated_spline.plot(exclude=[], picks="eeg", ylim=dict(eeg=ylim))
+
+# %%
+# Use interpolate_to to project EEG data to the standard montage
+evoked_interpolated_mne = evoked.copy().interpolate_to(standard_montage, method="MNE")
+
+# Plot the interpolated EEG layout
+evoked_interpolated_mne.plot(exclude=[], picks="eeg", ylim=dict(eeg=ylim))
+
+# %%
+# Comparing before and after interpolation
+fig, axs = plt.subplots(3, 1, figsize=(8, 6), constrained_layout=True)
+evoked.plot(exclude=[], picks="eeg", axes=axs[0], show=False, ylim=dict(eeg=ylim))
+axs[0].set_title("Original EEG Layout")
+evoked_interpolated_spline.plot(
+    exclude=[], picks="eeg", axes=axs[1], show=False, ylim=dict(eeg=ylim)
+)
+axs[1].set_title("Interpolated to Standard 1020 Montage using spline interpolation")
+evoked_interpolated_mne.plot(
+    exclude=[], picks="eeg", axes=axs[2], show=False, ylim=dict(eeg=ylim)
+)
+axs[2].set_title("Interpolated to Standard 1020 Montage using MNE interpolation")
+
+# %%
+# References
+# ----------
+# .. footbibliography::

mne/_fiff/_digitization.py

@@ -181,6 +181,9 @@ def _read_dig_fif(fid, meas_info, *, return_ch_names=False):
             if kind == FIFF.FIFF_DIG_POINT:
                 tag = read_tag(fid, pos)
                 dig.append(tag.data)
+            elif kind == FIFF.FIFF_DIG_STRING:
+                tag = read_tag(fid, pos)
+                dig.extend(tag.data)
             elif kind == FIFF.FIFF_MNE_COORD_FRAME:
                 tag = read_tag(fid, pos)
                 coord_frame = _coord_frame_named.get(int(tag.data.item()))

mne/_fiff/meas_info.py

@@ -46,7 +46,7 @@
     write_dig,
 )
 from .compensator import get_current_comp
-from .constants import FIFF, _ch_unit_mul_named, _coord_frame_named
+from .constants import FIFF, _ch_unit_mul_named
 from .ctf_comp import _read_ctf_comp, write_ctf_comp
 from .open import fiff_open
 from .pick import (
@@ -1935,15 +1935,24 @@ def _repr_html_(self):
         info_template = _get_html_template("repr", "info.html.jinja")
         return info_template.render(info=self)
 
-    def save(self, fname):
+    @verbose
+    def save(self, fname, *, overwrite=False, verbose=None):
         """Write measurement info in fif file.
 
         Parameters
         ----------
         fname : path-like
             The name of the file. Should end by ``'-info.fif'``.
+        %(overwrite)s
+
+            .. versionadded:: 1.10
+        %(verbose)s
+
+        See Also
+        --------
+        mne.io.write_info
         """
-        write_info(fname, self)
+        write_info(fname, self, overwrite=overwrite)
 
 
 def _simplify_info(info, *, keep=()):
@@ -1961,7 +1970,7 @@ def _simplify_info(info, *, keep=()):
 
 
 @verbose
-def read_fiducials(fname, verbose=None):
+def read_fiducials(fname, *, verbose=None):
     """Read fiducials from a fiff file.
 
     Parameters
@@ -1981,26 +1990,8 @@ def read_fiducials(fname, verbose=None):
     fname = _check_fname(fname=fname, overwrite="read", must_exist=True)
     fid, tree, _ = fiff_open(fname)
     with fid:
-        isotrak = dir_tree_find(tree, FIFF.FIFFB_ISOTRAK)
-        isotrak = isotrak[0]
-        pts = []
-        coord_frame = FIFF.FIFFV_COORD_HEAD
-        for k in range(isotrak["nent"]):
-            kind = isotrak["directory"][k].kind
-            pos = isotrak["directory"][k].pos
-            if kind == FIFF.FIFF_DIG_POINT:
-                tag = read_tag(fid, pos)
-                pts.append(DigPoint(tag.data))
-            elif kind == FIFF.FIFF_MNE_COORD_FRAME:
-                tag = read_tag(fid, pos)
-                coord_frame = tag.data[0]
-                coord_frame = _coord_frame_named.get(coord_frame, coord_frame)
-
-    # coord_frame is not stored in the tag
-    for pt in pts:
-        pt["coord_frame"] = coord_frame
-
-    return pts, coord_frame
+        pts = _read_dig_fif(fid, tree)
+    return pts, pts[0]["coord_frame"]
 
 
 @verbose

mne/_fiff/open.py

@@ -348,7 +348,7 @@ def _show_tree(
                         postpend += " ... list len=" + str(len(tag.data))
                     elif issparse(tag.data):
                         postpend += (
-                            f" ... sparse ({tag.data.getformat()}) shape="
+                            f" ... sparse ({tag.data.__class__.__name__}) shape="
                             f"{tag.data.shape}"
                         )
                     else:

mne/_fiff/tag.py

@@ -270,19 +270,26 @@ def _read_id_struct(fid, tag, shape, rlims):
     )
 
 
-def _read_dig_point_struct(fid, tag, shape, rlims):
+def _read_dig_point_struct(fid, tag, shape, rlims, *, string=False):
     """Read dig point struct tag."""
     kind = int(np.frombuffer(fid.read(4), dtype=">i4").item())
     kind = _dig_kind_named.get(kind, kind)
     ident = int(np.frombuffer(fid.read(4), dtype=">i4").item())
     if kind == FIFF.FIFFV_POINT_CARDINAL:
         ident = _dig_cardinal_named.get(ident, ident)
-    return dict(
-        kind=kind,
-        ident=ident,
-        r=np.frombuffer(fid.read(12), dtype=">f4"),
-        coord_frame=FIFF.FIFFV_COORD_UNKNOWN,
-    )
+    n = 1 if not string else int(np.frombuffer(fid.read(4), dtype=">i4").item())
+    out = [
+        dict(
+            kind=kind,
+            ident=ident,
+            r=np.frombuffer(fid.read(12), dtype=">f4"),
+            coord_frame=FIFF.FIFFV_COORD_UNKNOWN,
+        )
+        for _ in range(n)
+    ]
+    if not string:
+        out = out[0]
+    return out
 
 
 def _read_coord_trans_struct(fid, tag, shape, rlims):
@@ -378,18 +385,21 @@ def _read_julian(fid, tag, shape, rlims):
     FIFF.FIFFT_COMPLEX_DOUBLE: _read_complex_double,
     FIFF.FIFFT_ID_STRUCT: _read_id_struct,
     FIFF.FIFFT_DIG_POINT_STRUCT: _read_dig_point_struct,
+    FIFF.FIFFT_DIG_STRING_STRUCT: partial(_read_dig_point_struct, string=True),
     FIFF.FIFFT_COORD_TRANS_STRUCT: _read_coord_trans_struct,
     FIFF.FIFFT_CH_INFO_STRUCT: _read_ch_info_struct,
     FIFF.FIFFT_OLD_PACK: _read_old_pack,
     FIFF.FIFFT_DIR_ENTRY_STRUCT: _read_dir_entry_struct,
     FIFF.FIFFT_JULIAN: _read_julian,
+    FIFF.FIFFT_VOID: lambda fid, tag, shape, rlims: None,
 }
 _call_dict_names = {
     FIFF.FIFFT_STRING: "str",
     FIFF.FIFFT_COMPLEX_FLOAT: "c8",
     FIFF.FIFFT_COMPLEX_DOUBLE: "c16",
     FIFF.FIFFT_ID_STRUCT: "ids",
     FIFF.FIFFT_DIG_POINT_STRUCT: "dps",
+    FIFF.FIFFT_DIG_STRING_STRUCT: "dss",
     FIFF.FIFFT_COORD_TRANS_STRUCT: "cts",
     FIFF.FIFFT_CH_INFO_STRUCT: "cis",
     FIFF.FIFFT_OLD_PACK: "op_",

mne/_fiff/tests/test_meas_info.py

@@ -29,7 +29,7 @@
     write_cov,
     write_forward_solution,
 )
-from mne._fiff import meas_info
+from mne._fiff import meas_info, tag
 from mne._fiff._digitization import DigPoint, _make_dig_points
 from mne._fiff.constants import FIFF
 from mne._fiff.meas_info import (
@@ -975,7 +975,7 @@ def test_field_round_trip(tmp_path):
             meas_date=_stamp_to_dt((1, 2)),
         )
     fname = tmp_path / "temp-info.fif"
-    write_info(fname, info)
+    info.save(fname)
     info_read = read_info(fname)
     assert_object_equal(info, info_read)
     with pytest.raises(TypeError, match="datetime"):
@@ -1268,3 +1268,12 @@ def test_get_montage():
     assert len(raw.info.get_montage().ch_names) == len(ch_names)
     raw.info["bads"] = [ch_names[0]]
     assert len(raw.info.get_montage().ch_names) == len(ch_names)
+
+
+def test_tag_consistency():
+    """Test that structures for tag reading are consistent."""
+    call_set = set(tag._call_dict)
+    call_names = set(tag._call_dict_names)
+    assert call_set == call_names, "Mismatch between _call_dict and _call_dict_names"
+    # TODO: This was inspired by FIFF_DIG_STRING gh-13083, we should ideally add a test
+    # that those dig points can actually be read in correctly at some point.