Merge branch 'main' into enh-opm-grouping-final-fix

Author: PragnyaKhandelwal

doc/changes/dev/13263.newfeature.rst

@@ -0,0 +1 @@
+It is now possible to concatenate raw objects with :func:`mne.concatenate_raws` as long as they inherit from :class:`~mne.io.BaseRaw`, even if their specific types differ (e.g., :class:`~mne.io.Raw` and :class:`~mne.io.RawArray`), by `Clemens Brunner`_.

doc/changes/dev/13855.bugfix.rst

@@ -0,0 +1,3 @@
+Fixed incorrect label orientation for nodes in the 0–90° polar range (the
+12–3 o'clock quadrant) of the connectivity circle plot, by
+:newcontrib:`Pavel Popov`.

doc/changes/dev/13856.bugfix.rst

@@ -0,0 +1 @@
+Fixed an indexing bug in fNIRS support in :meth:`mne.io.BaseRaw.interpolate_bads` (and related methods) that could errantly use incorrect donor channels, by :newcontrib:`Kalle Makela`.

doc/changes/dev/13861.newfeature.rst

@@ -0,0 +1 @@
+Add dark theme support (``theme="light"``, ``"dark"``, or ``"auto"``) to the ``'matplotlib'`` browser backend used by :meth:`mne.io.Raw.plot`, :meth:`mne.Epochs.plot`, and :meth:`mne.preprocessing.ICA.plot_sources`, by `Clemens Brunner`_.

doc/changes/names.inc

@@ -172,6 +172,7 @@
 .. _Jukka Nenonen: https://www.linkedin.com/pub/jukka-nenonen/28/b5a/684
 .. _Jussi Nurminen: https://github.com/jjnurminen
 .. _Kaisu Lankinen: http://bishoplab.berkeley.edu/Kaisu.html
+.. _Kalle Makela: https://github.com/Kallemakela
 .. _Katarina Slama: https://github.com/katarinaslama
 .. _Katia Al-Amir: https://github.com/katia-sentry
 .. _Kay Robbins: https://github.com/VisLab
@@ -257,6 +258,7 @@
 .. _Paul Pasler: https://github.com/ppasler
 .. _Paul Roujansky: https://github.com/paulroujansky
 .. _Pavel Navratil: https://github.com/navrpa13
+.. _Pavel Popov: https://github.com/paavalipopov
 .. _Peter Molfese: https://github.com/pmolfese
 .. _Phillip Alday: https://palday.bitbucket.io
 .. _Pierre Ablin: https://pierreablin.com

doc/conf.py

@@ -27,7 +27,6 @@
 
 import mne
 import mne.html_templates._templates
-from mne.tests.test_docstring_parameters import error_ignores
 from mne.utils import (
     linkcode_resolve,
     run_subprocess,
@@ -432,42 +431,17 @@
     "pooch.HTTPDownloader",
 }
 numpydoc_validate = True
-numpydoc_validation_checks = {"all"} | set(error_ignores)
-numpydoc_validation_exclude = {  # set of regex
-    # dict subclasses
-    r"\.clear",
-    r"\.get$",
-    r"\.copy$",
-    r"\.fromkeys",
-    r"\.items",
-    r"\.keys",
-    r"\.move_to_end",
-    r"\.pop",
-    r"\.popitem",
-    r"\.setdefault",
-    r"\.update",
-    r"\.values",
-    # list subclasses
-    r"\.append",
-    r"\.count",
-    r"\.extend",
-    r"\.index",
-    r"\.insert",
-    r"\.remove",
-    r"\.sort",
-    # we currently don't document these properly (probably okay)
-    r"\.__getitem__",
-    r"\.__contains__",
-    r"\.__hash__",
-    r"\.__mul__",
-    r"\.__sub__",
-    r"\.__add__",
-    r"\.__iter__",
-    r"\.__div__",
-    r"\.__neg__",
-    # copied from sklearn
-    r"mne\.utils\.deprecated",
-}
+try:
+    import tomllib
+    # TODO VERSION: Can be removed once Python 3.11 is required
+except Exception:
+    pass
+else:
+    pyproject_path = Path(__file__).parent.parent / "pyproject.toml"
+    pyproject = tomllib.loads(pyproject_path.read_text("utf-8"))
+    pyproject_nv = pyproject["tool"]["numpydoc_validation"]
+    numpydoc_validation_checks = set(pyproject_nv["checks"])
+    numpydoc_validation_exclude = set(pyproject_nv["exclude"])
 
 
 # -- Sphinx-gallery configuration --------------------------------------------

doc/development/contributing.rst

@@ -607,9 +607,12 @@ dependency
 bugfix
     For bug fixes. Can change code behavior with no deprecation period.
 apichange
-    Code behavior changes that require a deprecation period.
+    Changes to existing code behavior that require a deprecation period. Can include the
+    addition of new features only if existing code behavior is changed alongside this.
 newfeature
-    For new features.
+    For new features that do not change existing code behavior. If existing code
+    behavior is changed alongside the addition of these features, the changes should
+    instead be labelled as ``apichange``.
 other
     For changes that don't fit into any of the above categories, e.g.,
     internal refactorings.

mne/bem.py

@@ -314,7 +314,7 @@ def _check_complete_surface(surf, copy=False, incomplete="raise", extra=""):
         fewer = (fewer[:80] + ["..."]) if len(fewer) > 80 else fewer
         fewer = ", ".join(str(f) for f in fewer)
         msg = (
-            f"Surface {_bem_surf_name[surf['id']]} has topological defects: "
+            f"Surface {_bem_surf_name[surf['id']].strip()} has topological defects: "
             f"{len(fewer)} / {len(surf['rr'])} vertices have fewer than three "
             f"neighboring triangles [{fewer}]{extra}"
         )

mne/channels/interpolation.py

@@ -278,15 +278,19 @@ def _interpolate_bads_nirs(inst, exclude=(), verbose=None):
     dist = pdist(locs3d)
     dist = squareform(dist)
 
-    for bad in picks_bad:
-        dists_to_bad = dist[bad]
+    for bad_raw_idx in picks_bad:
+        # `bad_raw_idx` is the index of the bad channel in `inst`
+        # `bad_dist_idx` is the index of the bad channel in `dist`
+        bad_dist_idx = np.where(picks_nirs == bad_raw_idx)[0][0]
+        dists_to_bad = dist[bad_dist_idx].copy()
         # Ignore distances to self
         dists_to_bad[dists_to_bad == 0] = np.inf
         # Ignore distances to other bad channels
         dists_to_bad[bads_mask] = np.inf
         # Find closest remaining channels for same frequency
-        closest_idx = np.argmin(dists_to_bad) + (bad % 2)
-        inst._data[bad] = inst._data[closest_idx]
+        closest_dist_idx = np.argmin(dists_to_bad) + (bad_dist_idx % 2)
+        closest_raw_idx = picks_nirs[closest_dist_idx]
+        inst._data[bad_raw_idx] = inst._data[closest_raw_idx]
 
     # TODO: this seems like a bug because it does not respect reset_bads
     inst.info["bads"] = [ch for ch in inst.info["bads"] if ch in exclude]

mne/channels/tests/test_interpolation.py

@@ -10,7 +10,7 @@
 from numpy.testing import assert_allclose, assert_array_equal
 
 import mne.channels.channels
-from mne import Epochs, pick_channels, pick_types, read_events
+from mne import Epochs, create_info, pick_channels, pick_types, read_events
 from mne._fiff.constants import FIFF
 from mne._fiff.proj import _has_eeg_average_ref_proj
 from mne.channels import make_dig_montage, make_standard_montage
@@ -333,6 +333,44 @@ def test_interpolation_nirs():
     assert raw_haemo.info["bads"] == []
 
 
+def test_interpolation_nirs_reordered_picks():
+    """Test NIRS interpolation uses the closest donor in raw channel space."""
+    ch_names = [
+        "S1_D1 760",
+        "S1_D1 850",
+        "S2_D2 760",
+        "S2_D2 850",
+        "S3_D3 760",
+        "S3_D3 850",
+        "S10_D10 760",
+        "S10_D10 850",
+    ]
+    info = create_info(ch_names, sfreq=1.0, ch_types=["fnirs_cw_amplitude"] * 8)
+    pair_positions = {
+        "S1_D1": (0.009, 0.0, 0.0),
+        "S2_D2": (0.010, 0.0, 0.0),
+        "S3_D3": (0.030, 0.0, 0.0),
+        "S10_D10": (0.040, 0.0, 0.0),
+    }
+    for idx, ch in enumerate(info["chs"]):
+        pair = ch["ch_name"].rsplit(" ", 1)[0]
+        ch["loc"][:3] = pair_positions[pair]
+        ch["loc"][9] = 760.0 if idx % 2 == 0 else 850.0
+    data = np.arange(len(ch_names), dtype=float).reshape(-1, 1)
+    data = np.repeat(data, 5, axis=1)
+    raw = RawArray(data, info, verbose=False)
+    raw.info["bads"] = ["S2_D2 760", "S2_D2 850"]
+
+    raw.interpolate_bads(
+        method=dict(fnirs="nearest"), origin=(0.0, 0.0, 0.0), verbose=False
+    )
+
+    # Bad S2_D2 should copy from the nearest good pair, S1_D1.
+    picks_bad = pick_channels(raw.ch_names, ["S2_D2 760", "S2_D2 850"], exclude=[])
+    picks_want = pick_channels(raw.ch_names, ["S1_D1 760", "S1_D1 850"], exclude=[])
+    assert_allclose(raw.get_data(picks=picks_bad), raw.get_data(picks=picks_want))
+
+
 @testing.requires_testing_data
 def test_interpolation_ecog():
     """Test interpolation for ECoG."""