[pull] main from mne-tools:main

.github/workflows/tests.yml

@@ -130,7 +130,8 @@ jobs:
             sed -i "/numba/d" environment.yml
           # And on Windows and macOS PySide6.9.0 segfaults
           elif [[ "$RUNNER_OS" == "macOS" ]]; then
-            sed -i "" "s/  - PySide6 .*/  - PySide6 <6.8/g" environment.yml
+            sed -i "" "s/  - PySide6 .*/  - PySide6 =6.7.3/g" environment.yml
+            sed -i "" "s/  - vtk .*/  - vtk =9.3.1/g" environment.yml
           elif [[ "$RUNNER_OS" == "Windows" ]]; then
             sed -i "s/  - PySide6 .*/  - PySide6 <6.8/g" environment.yml
           fi
@@ -139,8 +140,10 @@ jobs:
         with:
           environment-file: ${{ env.CONDA_ENV }}
           environment-name: mne
+          log-level: ${{ runner.debug == '1' && 'debug' || 'info' }}
           create-args: >-
             python=${{ env.PYTHON_VERSION }}
+            -v
         if: ${{ !startswith(matrix.kind, 'pip') }}
         timeout-minutes: 20
       - run: bash ./tools/github_actions_dependencies.sh

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   # Ruff mne
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.12
+    rev: v0.13.0
     hooks:
       - id: ruff-check
         name: ruff lint mne
@@ -58,7 +58,7 @@ repos:
         args: ["--ignore-case"]
 
   - repo: https://github.com/pappasam/toml-sort
-    rev: v0.24.2
+    rev: v0.24.3
     hooks:
       - id: toml-sort-fix
         files: pyproject.toml
@@ -82,7 +82,7 @@ repos:
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.12.1
+    rev: v1.13.0
     hooks:
       - id: zizmor
 

doc/changes/dev/13398.apichange.rst

@@ -0,0 +1 @@
+The default for :func:`mne.make_field_map` will change to ``"auto"`` in MNE-Python 1.12 (from ``(0., 0., 0.04)``), changes by :newcontrib:`Paul Anders`.

doc/changes/names.inc

@@ -231,6 +231,7 @@
 .. _Pablo Mainar: https://github.com/pablomainar
 .. _Pablo-Arias: https://github.com/Pablo-Arias
 .. _Padma Sundaram: https://www.nmr.mgh.harvard.edu/user/8071
+.. _Paul Anders: https://github.com/Mettphysik
 .. _Paul Pasler: https://github.com/ppasler
 .. _Paul Roujansky: https://github.com/paulroujansky
 .. _Pavel Navratil: https://github.com/navrpa13

examples/visualization/mne_helmet.py

@@ -36,6 +36,7 @@
     subject="sample",
     subjects_dir=subjects_dir,
     upsampling=2,
+    origin="auto",
 )
 time = 0.083
 fig = mne.viz.create_3d_figure((512, 512), bgcolor="w", title="MNE helmet")

mne/channels/channels.py

@@ -934,7 +934,7 @@ def interpolate_bads(
             origin = _check_origin(origin, self.info)
         for ch_type, interp in method.items():
             if interp == "nan":
-                _interpolate_bads_nan(self, ch_type, exclude=exclude)
+                _interpolate_bads_nan(self, ch_type=ch_type, exclude=exclude)
         if method.get("eeg", "") == "spline":
             _interpolate_bads_eeg(self, origin=origin, exclude=exclude)
         meg_mne = method.get("meg", "") == "MNE"

mne/channels/interpolation.py

@@ -172,25 +172,25 @@ def _interpolate_bads_eeg(inst, origin, exclude=None, ecog=False, verbose=None):
 
 
 @verbose
-def _interpolate_bads_ecog(inst, origin, exclude=None, verbose=None):
+def _interpolate_bads_ecog(inst, *, origin, exclude=None, verbose=None):
     _interpolate_bads_eeg(inst, origin, exclude=exclude, ecog=True, verbose=verbose)
 
 
 def _interpolate_bads_meg(
-    inst, mode="accurate", origin=(0.0, 0.0, 0.04), verbose=None, ref_meg=False
+    inst, mode="accurate", *, origin, verbose=None, ref_meg=False
 ):
     return _interpolate_bads_meeg(
-        inst, mode, origin, ref_meg=ref_meg, eeg=False, verbose=verbose
+        inst, mode, ref_meg=ref_meg, eeg=False, origin=origin, verbose=verbose
     )
 
 
 @verbose
 def _interpolate_bads_nan(
     inst,
+    *,
     ch_type,
     ref_meg=False,
     exclude=(),
-    *,
     verbose=None,
 ):
     info = _simplify_info(inst.info)
@@ -208,12 +208,12 @@ def _interpolate_bads_nan(
 def _interpolate_bads_meeg(
     inst,
     mode="accurate",
-    origin=(0.0, 0.0, 0.04),
+    *,
     meg=True,
     eeg=True,
     ref_meg=False,
     exclude=(),
-    *,
+    origin,
     method=None,
     verbose=None,
 ):

mne/channels/tests/test_interpolation.py

@@ -264,7 +264,7 @@ def test_interpolation_meg():
 def _this_interpol(inst, ref_meg=False):
     from mne.channels.interpolation import _interpolate_bads_meg
 
-    _interpolate_bads_meg(inst, ref_meg=ref_meg, mode="fast")
+    _interpolate_bads_meg(inst, ref_meg=ref_meg, mode="fast", origin=(0.0, 0.0, 0.04))
     return inst
 
 

mne/conftest.py

@@ -672,6 +672,7 @@ def _check_skip_backend(name):
         assert name == "notebook", name
         pytest.importorskip("jupyter")
         pytest.importorskip("ipympl")
+        pytest.importorskip("ipyevents")
         pytest.importorskip("trame")
         pytest.importorskip("trame_vtk")
         pytest.importorskip("trame_vuetify")

mne/forward/_field_interpolation.py

@@ -22,7 +22,7 @@
 from ..fixes import _safe_svd
 from ..surface import get_head_surf, get_meg_helmet_surf
 from ..transforms import _find_trans, transform_surface_to
-from ..utils import _check_fname, _check_option, _pl, _reg_pinv, logger, verbose
+from ..utils import _check_fname, _check_option, _pl, _reg_pinv, logger, verbose, warn
 from ._lead_dots import (
     _do_cross_dots,
     _do_self_dots,
@@ -116,7 +116,7 @@ def _pinv_tikhonov(x, reg):
     return inv, n
 
 
-def _map_meg_or_eeg_channels(info_from, info_to, mode, origin, miss=None):
+def _map_meg_or_eeg_channels(info_from, info_to, mode, *, origin, miss=None):
     """Find mapping from one set of channels to another.
 
     Parameters
@@ -132,13 +132,15 @@ def _map_meg_or_eeg_channels(info_from, info_to, mode, origin, miss=None):
     origin : array-like, shape (3,) | str
         Origin of the sphere in the head coordinate frame and in meters.
         Can be ``'auto'``, which means a head-digitization-based origin
-        fit. Default is ``(0., 0., 0.04)``.
+        fit.
 
     Returns
     -------
     mapping : array, shape (n_to, n_from)
         A mapping matrix.
     """
+    assert origin is not None  # should be assured elsewhere
+
     # no need to apply trans because both from and to coils are in device
     # coordinates
     info_kinds = set(ch["kind"] for ch in info_to["chs"])
@@ -314,7 +316,8 @@ def _make_surface_mapping(
     trans=None,
     mode="fast",
     n_jobs=None,
-    origin=(0.0, 0.0, 0.04),
+    *,
+    origin,
     verbose=None,
 ):
     """Re-map M/EEG data to a surface.
@@ -337,8 +340,6 @@ def _make_surface_mapping(
     %(n_jobs)s
     origin : array-like, shape (3,) | str
         Origin of the sphere in the head coordinate frame and in meters.
-        The default is ``'auto'``, which means a head-digitization-based
-        origin fit.
     %(verbose)s
 
     Returns
@@ -347,6 +348,8 @@ def _make_surface_mapping(
         A n_vertices x n_sensors array that remaps the MEG or EEG data,
         as `new_data = np.dot(mapping, data)`.
     """
+    assert origin is not None  # should be assured elsewhere
+
     if not all(key in surf for key in ["rr", "nn"]):
         raise KeyError('surf must have both "rr" and "nn"')
     if "coord_frame" not in surf:
@@ -443,7 +446,7 @@ def make_field_map(
     ch_type=None,
     mode="fast",
     meg_surf="helmet",
-    origin=(0.0, 0.0, 0.04),
+    origin=None,
     n_jobs=None,
     *,
     upsampling=1,
@@ -483,6 +486,9 @@ def make_field_map(
         fit. Default is ``(0., 0., 0.04)``.
 
         .. versionadded:: 0.11
+        .. versionchanged:: 1.12
+           In 1.12 the default value is "auto".
+           In 1.11 and prior versions, it is ``(0., 0., 0.04)``.
     %(n_jobs)s
     %(helmet_upsampling)s
 
@@ -498,6 +504,15 @@ def make_field_map(
         The surface maps to be used for field plots. The list contains
         separate ones for MEG and EEG (if both MEG and EEG are present).
     """
+    if origin is None:
+        warn_message = (
+            'Default value for origin is "(0.0, 0.0, 0.04)" in version 1.11 '
+            'but will be changed to "auto" in 1.12. Set the origin parameter '
+            "explicitly to avoid this warning."
+        )
+        warn(warn_message, FutureWarning)
+        origin = (0.0, 0.0, 0.04)
+
     info = evoked.info
 
     if ch_type is None:

mne/forward/tests/test_field_interpolation.py

@@ -50,8 +50,14 @@ def test_field_map_ctf():
     evoked = Epochs(raw, events).average()
     evoked.pick(evoked.ch_names[:50])  # crappy mapping but faster
     # smoke test - passing trans_fname as pathlib.Path as additional check
+    # set origin to "(0.0, 0.0, 0.04)", which was the default until v1.12
+    # estimating origin from "auto" impossible due to missing digitization points
     make_field_map(
-        evoked, trans=Path(trans_fname), subject="sample", subjects_dir=subjects_dir
+        evoked,
+        trans=Path(trans_fname),
+        subject="sample",
+        subjects_dir=subjects_dir,
+        origin=(0.0, 0.0, 0.04),
     )
 
 
@@ -128,11 +134,13 @@ def test_make_field_map_eeg():
     evoked.info["bads"] = ["MEG 2443", "EEG 053"]  # add some bads
     surf = get_head_surf("sample", subjects_dir=subjects_dir)
     # we must have trans if surface is in MRI coords
-    pytest.raises(ValueError, _make_surface_mapping, evoked.info, surf, "eeg")
+    pytest.raises(
+        ValueError, _make_surface_mapping, evoked.info, surf, "eeg", origin="auto"
+    )
 
     evoked.pick(picks="eeg")
     fmd = make_field_map(
-        evoked, trans_fname, subject="sample", subjects_dir=subjects_dir
+        evoked, trans_fname, subject="sample", subjects_dir=subjects_dir, origin="auto"
     )
 
     # trans is necessary for EEG only
@@ -143,10 +151,11 @@ def test_make_field_map_eeg():
         None,
         subject="sample",
         subjects_dir=subjects_dir,
+        origin="auto",
     )
 
     fmd = make_field_map(
-        evoked, trans_fname, subject="sample", subjects_dir=subjects_dir
+        evoked, trans_fname, subject="sample", subjects_dir=subjects_dir, origin="auto"
     )
     assert len(fmd) == 1
     assert_array_equal(fmd[0]["data"].shape, (642, 59))  # maps data onto surf
@@ -163,31 +172,37 @@ def test_make_field_map_meg():
     # let's reduce the number of channels by a bunch to speed it up
     info["bads"] = info["ch_names"][:200]
     # bad ch_type
-    pytest.raises(ValueError, _make_surface_mapping, info, surf, "foo")
+    pytest.raises(ValueError, _make_surface_mapping, info, surf, "foo", origin="auto")
     # bad mode
-    pytest.raises(ValueError, _make_surface_mapping, info, surf, "meg", mode="foo")
+    pytest.raises(
+        ValueError, _make_surface_mapping, info, surf, "meg", mode="foo", origin="auto"
+    )
     # no picks
     evoked_eeg = evoked.copy().pick(picks="eeg")
-    pytest.raises(RuntimeError, _make_surface_mapping, evoked_eeg.info, surf, "meg")
+    pytest.raises(
+        RuntimeError, _make_surface_mapping, evoked_eeg.info, surf, "meg", origin="auto"
+    )
     # bad surface def
     nn = surf["nn"]
     del surf["nn"]
-    pytest.raises(KeyError, _make_surface_mapping, info, surf, "meg")
+    pytest.raises(KeyError, _make_surface_mapping, info, surf, "meg", origin="auto")
     surf["nn"] = nn
     cf = surf["coord_frame"]
     del surf["coord_frame"]
-    pytest.raises(KeyError, _make_surface_mapping, info, surf, "meg")
+    pytest.raises(KeyError, _make_surface_mapping, info, surf, "meg", origin="auto")
     surf["coord_frame"] = cf
 
     # now do it with make_field_map
     evoked.pick(picks="meg")
     evoked.info.normalize_proj()  # avoid projection warnings
-    fmd = make_field_map(evoked, None, subject="sample", subjects_dir=subjects_dir)
+    fmd = make_field_map(
+        evoked, None, subject="sample", subjects_dir=subjects_dir, origin="auto"
+    )
     assert len(fmd) == 1
     assert_array_equal(fmd[0]["data"].shape, (304, 106))  # maps data onto surf
     assert len(fmd[0]["ch_names"]) == 106
 
-    pytest.raises(ValueError, make_field_map, evoked, ch_type="foobar")
+    pytest.raises(ValueError, make_field_map, evoked, ch_type="foobar", origin="auto")
 
     # now test the make_field_map on head surf for MEG
     evoked.pick(picks="meg")
@@ -198,6 +213,7 @@ def test_make_field_map_meg():
         meg_surf="head",
         subject="sample",
         subjects_dir=subjects_dir,
+        origin="auto",
     )
     assert len(fmd) == 1
     assert_array_equal(fmd[0]["data"].shape, (642, 106))  # maps data onto surf
@@ -210,6 +226,7 @@ def test_make_field_map_meg():
         meg_surf="foobar",
         subjects_dir=subjects_dir,
         trans=trans_fname,
+        origin="auto",
     )
 
 
@@ -221,12 +238,15 @@ def test_make_field_map_meeg():
     picks = picks[::10]
     evoked.pick([evoked.ch_names[p] for p in picks])
     evoked.info.normalize_proj()
+    # set origin to "(0.0, 0.0, 0.04)", which was the default until v1.12
+    # estimated origin from "auto" fails the assertions below
     maps = make_field_map(
         evoked,
         trans_fname,
         subject="sample",
         subjects_dir=subjects_dir,
         verbose="debug",
+        origin=(0.0, 0.0, 0.04),
     )
     assert_equal(maps[0]["data"].shape, (642, 6))  # EEG->Head
     assert_equal(maps[1]["data"].shape, (304, 31))  # MEG->Helmet

mne/viz/tests/test_3d.py

@@ -190,6 +190,7 @@ def test_plot_evoked_field(renderer):
                 n_jobs=None,
                 ch_type=t,
                 upsampling=up,
+                origin="auto",
                 verbose=True,
             )
         log = log.getvalue()

tools/install_pre_requirements.sh

@@ -55,9 +55,11 @@ python -m pip install $STD_ARGS \
     git+https://github.com/joblib/joblib \
 	git+https://github.com/h5io/h5io \
 	git+https://github.com/BUNPC/pysnirf2 \
-	git+https://github.com/the-siesta-group/edfio \
 	trame trame-vtk trame-vuetify jupyter ipyevents ipympl openmeeg \
-	imageio-ffmpeg xlrd mffpy traitlets pybv eeglabio defusedxml antio
+	imageio-ffmpeg xlrd mffpy traitlets pybv eeglabio defusedxml antio \
+	edfio
+# https://github.com/the-siesta-group/edfio/issues/78
+# git+https://github.com/the-siesta-group/edfio
 echo "::endgroup::"
 
 echo "::group::Make sure we're on a NumPy 2.0 variant"

tutorials/evoked/20_visualize_evoked.py

@@ -293,7 +293,11 @@ def custom_func(x):
 # <mne.Evoked.plot_field>`:
 
 maps = mne.make_field_map(
-    evks["aud/left"], trans=str(trans_file), subject="sample", subjects_dir=subjects_dir
+    evks["aud/left"],
+    trans=str(trans_file),
+    subject="sample",
+    subjects_dir=subjects_dir,
+    origin="auto",
 )
 evks["aud/left"].plot_field(maps, time=0.1)
 
@@ -310,6 +314,7 @@ def custom_func(x):
         subject="sample",
         subjects_dir=subjects_dir,
         meg_surf="head",
+        origin="auto",
     )
     fig = evk.plot_field(_map, time=0.1)
     mne.viz.set_3d_title(fig, ch_type, size=20)