Merge branch 'main' into rescale

doc/changes/devel/13012.bugfix.rst

@@ -0,0 +1 @@
+Fix errant detection of software-rendered vs hardware-rendered MESA GL contexts in 3D rendering on Linux, by `Eric Larson`_.

doc/install/advanced.rst

@@ -281,6 +281,20 @@ of VTK and/or QT are incompatible. This series of commands should fix it:
 If you installed VTK using ``pip`` rather than ``conda``, substitute the first
 line for ``pip uninstall -y vtk``.
 
+3D plotting trouble on Linux
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you are having trouble with 3D plotting on Linux, one possibility is that you
+are using Wayland for graphics. To check, you can do:
+
+.. code-block:: console
+
+    $ echo $XDG_SESSION_TYPE
+    wayland
+
+If so, you will need to tell Qt to use X11 instead of Wayland. You can do this
+by setting ``export QT_QPA_PLATFORM=xcb`` in your terminal session. To make it
+permanent for your logins, you can set it for example in ``~/.profile``.
 
 .. LINKS
 

doc/sphinxext/mne_doc_utils.py

@@ -8,6 +8,7 @@
 import os
 import time
 import warnings
+from pathlib import Path
 
 import numpy as np
 import pyvista
@@ -16,6 +17,7 @@
 import mne
 from mne.utils import (
     _assert_no_instances,
+    _get_extra_data_path,
     sizeof_fmt,
 )
 from mne.viz import Brain
@@ -225,6 +227,7 @@ def reset_modules(gallery_conf, fname, when):
         mne.viz.ui_events._event_channels
     )
 
+    orig_when = when
     when = f"mne/conf.py:Resetter.__call__:{when}:{fname}"
     # Support stuff like
     # MNE_SKIP_INSTANCE_ASSERTIONS="Brain,Plotter,BackgroundPlotter,vtkPolyData,_Renderer" make html-memory  # noqa: E501
@@ -262,6 +265,25 @@ def reset_modules(gallery_conf, fname, when):
         mem = sizeof_fmt(process.memory_info().rss)
         print(f"{prefix}{time.time() - t0:6.1f} s : {mem}".ljust(22))
 
+    if fname == "50_configure_mne.py":
+        # This messes with the config, so let's do so in a temp dir
+        if orig_when == "before":
+            fake_home = Path(_get_extra_data_path()) / "temp"
+            fake_home.mkdir(exist_ok=True, parents=True)
+            os.environ["_MNE_FAKE_HOME_DIR"] = str(fake_home)
+        else:
+            assert orig_when == "after"
+            to_del = Path(os.environ["_MNE_FAKE_HOME_DIR"])
+            try:
+                (to_del / "mne-python.json").unlink()
+            except Exception:
+                pass
+            try:
+                to_del.rmdir()
+            except Exception:
+                pass
+            del os.environ["_MNE_FAKE_HOME_DIR"]
+
 
 report_scraper = mne.report._ReportScraper()
 mne_qt_browser_scraper = mne.viz._scraper._MNEQtBrowserScraper()

examples/preprocessing/otp.py

@@ -72,7 +72,7 @@ def compute_bias(raw):
     idx = epochs.time_as_index(0.036)[0]
     data = epochs.get_data(copy=False)[:, :, idx].T
     evoked = mne.EvokedArray(data, epochs.info, tmin=0.0)
-    dip = fit_dipole(evoked, cov, sphere, n_jobs=None, verbose=False)[0]
+    dip = fit_dipole(evoked, cov, sphere, verbose=False)[0]
     actual_pos = mne.dipole.get_phantom_dipoles()[0][dipole_number - 1]
     misses = 1000 * np.linalg.norm(dip.pos - actual_pos, axis=-1)
     return misses

mne/datasets/utils.py

@@ -356,9 +356,13 @@ def _download_all_example_data(verbose=True):
 
     # If the user has SUBJECTS_DIR, respect it, if not, set it to the EEG one
     # (probably on CircleCI, or otherwise advanced user)
-    fetch_fsaverage(None)
+    fetch_fsaverage(subjects_dir=None)
     logger.info("[done fsaverage]")
 
+    # Now also update the sample dataset path, if not already SUBJECTS_DIR
+    # (some tutorials make use of these files)
+    fetch_fsaverage(subjects_dir=paths["sample"] / "subjects")
+
     fetch_infant_template("6mo")
     logger.info("[done infant_template]")
 

mne/viz/backends/_pyvista.py

@@ -837,7 +837,7 @@ def _toggle_antialias(self):
         """Enable it everywhere except on systems with problematic OpenGL."""
         # MESA can't seem to handle MSAA and depth peeling simultaneously, see
         # https://github.com/pyvista/pyvista/issues/4867
-        bad_system = _is_mesa(self.plotter)
+        bad_system = _is_osmesa(self.plotter)
         for plotter in self._all_plotters:
             if bad_system or not self.antialias:
                 plotter.disable_anti_aliasing()
@@ -1319,10 +1319,11 @@ def _disabled_depth_peeling():
         depth_peeling["enabled"] = depth_peeling_enabled
 
 
-def _is_mesa(plotter):
+def _is_osmesa(plotter):
     # MESA (could use GPUInfo / _get_gpu_info here, but it takes
     # > 700 ms to make a new window + report capabilities!)
     # CircleCI's is: "Mesa 20.0.8 via llvmpipe (LLVM 10.0.0, 256 bits)"
+    # and a working Nouveau is: "Mesa 24.2.3-1ubuntu1 via NVE6"
     if platform.system() == "Darwin":  # segfaults on macOS sometimes
         return False
     gpu_info_full = plotter.ren_win.ReportCapabilities()
@@ -1331,8 +1332,9 @@ def _is_mesa(plotter):
         gpu_info_full,
     )
     gpu_info = " ".join(gpu_info).lower()
-    is_mesa = "mesa" in gpu_info.split()
-    if is_mesa:
+    is_osmesa = "mesa" in gpu_info.split()
+    print(is_osmesa)
+    if is_osmesa:
         # Try to warn if it's ancient
         version = re.findall("mesa ([0-9.]+)[ -].*", gpu_info) or re.findall(
             "OpenGL version string: .* Mesa ([0-9.]+)\n", gpu_info_full
@@ -1345,7 +1347,8 @@ def _is_mesa(plotter):
                     "surface rendering, consider upgrading to 18.3.6 or "
                     "later."
                 )
-    return is_mesa
+        is_osmesa = "via llvmpipe" in gpu_info
+    return is_osmesa
 
 
 class _SafeBackgroundPlotter(BackgroundPlotter):

mne/viz/backends/_qt.py

@@ -102,7 +102,6 @@
     _check_3d_figure,  # noqa: F401
     _close_3d_figure,  # noqa: F401
     _close_all,  # noqa: F401
-    _is_mesa,  # noqa: F401
     _PyVistaRenderer,
     _set_3d_title,  # noqa: F401
     _set_3d_view,  # noqa: F401

mne/viz/backends/tests/test_renderer.py

@@ -217,16 +217,21 @@ def fail(x):
 def test_3d_warning(renderer_pyvistaqt, monkeypatch):
     """Test that warnings are emitted for old Mesa."""
     fig = renderer_pyvistaqt.create_3d_figure((800, 600))
-    _is_mesa = renderer_pyvistaqt.backend._is_mesa
+    from mne.viz.backends._pyvista import _is_osmesa
+
     plotter = fig.plotter
-    good = "OpenGL renderer string: OpenGL 3.3 (Core Profile) Mesa 20.0.8 via llvmpipe (LLVM 10.0.0, 256 bits)\n"  # noqa
-    bad = "OpenGL renderer string: OpenGL 3.3 (Core Profile) Mesa 18.3.4 via llvmpipe (LLVM 7.0, 256 bits)\n"  # noqa
+    pre = "OpenGL renderer string: "
+    good = f"{pre}OpenGL 3.3 (Core Profile) Mesa 20.0.8 via llvmpipe (LLVM 10.0.0, 256 bits)\n"  # noqa
+    bad = f"{pre}OpenGL 3.3 (Core Profile) Mesa 18.3.4 via llvmpipe (LLVM 7.0, 256 bits)\n"  # noqa
     monkeypatch.setattr(platform, "system", lambda: "Linux")  # avoid short-circuit
     monkeypatch.setattr(plotter.ren_win, "ReportCapabilities", lambda: good)
-    assert _is_mesa(plotter)
+    assert _is_osmesa(plotter)
     monkeypatch.setattr(plotter.ren_win, "ReportCapabilities", lambda: bad)
     with pytest.warns(RuntimeWarning, match=r"18\.3\.4 is too old"):
-        assert _is_mesa(plotter)
-    non = "OpenGL 4.1 Metal - 76.3 via Apple M1 Pro\n"
+        assert _is_osmesa(plotter)
+    non = f"{pre}OpenGL 4.1 Metal - 76.3 via Apple M1 Pro\n"
+    monkeypatch.setattr(plotter.ren_win, "ReportCapabilities", lambda: non)
+    assert not _is_osmesa(plotter)
+    non = f"{pre}OpenGL 4.5 (Core Profile) Mesa 24.2.3-1ubuntu1 via NVE6\n"
     monkeypatch.setattr(plotter.ren_win, "ReportCapabilities", lambda: non)
-    assert not _is_mesa(plotter)
+    assert not _is_osmesa(plotter)