Merge remote-tracking branch 'upstream/master' into brain_scraper

* upstream/master:
  MRG, ENH: Automatically fix magnetometers when maxwell filtering (mne-tools#7929)
  MRG: Prepare migration to PyVista 0.25 (mne-tools#7791)
  MAINT: Simpler VTK [circle front] (mne-tools#7931)

.circleci/config.yml

@@ -78,8 +78,7 @@ jobs:
         - run:
             name: Get Python running
             command: |
-              python -m pip install --user --upgrade --progress-bar off pip numpy setuptools
-              python -m pip install --user --upgrade --progress-bar off -f "https://vtk.org/download" "vtk>=9"
+              python -m pip install --user --upgrade --progress-bar off pip setuptools
               python -m pip install --user --upgrade --progress-bar off -r requirements.txt
               python -m pip uninstall -yq pysurfer mayavi
               python -m pip install --user --upgrade --progress-bar off --pre sphinx
@@ -103,7 +102,7 @@ jobs:
                which python
                QT_DEBUG_PLUGINS=1 mne sys_info
                python -c "import numpy; numpy.show_config()"
-               LIBGL_DEBUG=verbose python -c "import pyvista; pyvista.BackgroundPlotter(show=True)"
+               LIBGL_DEBUG=verbose python -c "import pyvistaqt; pyvistaqt.BackgroundPlotter(show=True)"
                python -c "import mne; mne.set_config('MNE_USE_CUDA', 'false')"  # this is needed for the config tutorial
                python -c "import mne; mne.set_config('MNE_LOGGING_LEVEL', 'info')"
                python -c "import mne; level = mne.get_config('MNE_LOGGING_LEVEL'); assert level.lower() == 'info', repr(level)"

.travis.yml

@@ -58,7 +58,6 @@ before_install:
         pip uninstall -yq numpy
         pip install -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" --pre numpy
         pip install -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" scipy pandas scikit-learn matplotlib h5py Pillow
-        pip install -f "https://vtk.org/download" "vtk>=9"
         pip install --upgrade -r requirements.txt
       else
         git clone https://github.com/astropy/ci-helpers.git

doc/changes/latest.inc

@@ -101,6 +101,8 @@ Changelog
 
 - Add generic reader function :func:`mne.io.read_raw` that loads files based on their extensions (it wraps the underlying specific ``read_raw_xxx`` functions) by `Clemens Brunner`_
 
+- Add automatic T3 magnetometer detection and application of :meth:`mne.io.Raw.fix_mag_coil_types` to :func:`mne.preprocessing.maxwell_filter` by `Eric Larson`_
+
 - Add ``'auto'`` option to :meth:`mne.preprocessing.ICA.find_bads_ecg` to automatically determine the threshold for CTPS method by `Yu-Han Luo`_
 
 - Add a ``notebook`` 3d backend for visualization in jupyter notebook with :func:`mne.viz.set_3d_backend` by`Guillaume Favelier`_

doc/conf.py

@@ -456,8 +456,8 @@ def reset_warnings(gallery_conf, fname):
         'ignore', '.*semaphore_tracker: process died unexpectedly.*')
     warnings.filterwarnings(  # needed until SciPy 1.2.0 is released
         'ignore', '.*will be interpreted as an array index.*', module='scipy')
-    warnings.filterwarnings(
-        'ignore', 'VTK 9 no longer accepts an offset array', UserWarning)
+    warnings.filterwarnings(  # PyVista needs to be updated (?)
+        'ignore', '.*VTK 9 no longer accepts an offset array.*')
     for key in ('HasTraits', r'numpy\.testing', 'importlib', r'np\.loads',
                 'Using or importing the ABCs from',  # internal modules on 3.7
                 r"it will be an error for 'np\.bool_'",  # ndimage
@@ -468,7 +468,7 @@ def reset_warnings(gallery_conf, fname):
                 'scipy.* is deprecated and will be removed in',  # dipy
                 r'Converting `np\.character` to a dtype is deprecated',  # vtk
                 r'sphinx\.util\.smartypants is deprecated',
-                'is a deprecated alias',
+               'is a deprecated alias for the builtin',  # NumPy
                 ):
         warnings.filterwarnings(  # deal with other modules having bad imports
             'ignore', message=".*%s.*" % key, category=DeprecationWarning)

doc/install/mne_python.rst

@@ -226,7 +226,7 @@ MNE-Python and its dependencies. Typical output looks like this::
     pandas:        1.0.3
     dipy:          1.1.1
     mayavi:        4.7.2.dev0
-    pyvista:       0.24.1
+    pyvista:       0.25.2 {pyvistaqt=0.1.0}
     vtk:           9.0.0
     PyQt5:         5.14.1
 

environment.yml

@@ -30,13 +30,13 @@ dependencies:
 - traitsui>=6
 - imageio>=2.6.1
 - pip:
-  - -i "https://pypi.org/simple/"
-  - -f "https://vtk.org/download"
   - mne
   - https://github.com/numpy/numpydoc/archive/master.zip
   - imageio-ffmpeg>=0.4.1
-  - vtk
-  - pyvista==0.24.3
+  - vtk<8.2; platform_system == "Darwin"
+  - vtk; platform_system != "Darwin"
+  - pyvista>=0.24
+  - pyvistaqt
   - https://github.com/enthought/mayavi/archive/master.zip
   - PySurfer[save_movie]
   - dipy --only-binary dipy

mne/channels/channels.py

@@ -1357,13 +1357,16 @@ def _compute_ch_adjacency(info, ch_type):
     return ch_adjacency, ch_names
 
 
-def fix_mag_coil_types(info):
+def fix_mag_coil_types(info, use_cal=False):
     """Fix magnetometer coil types.
 
     Parameters
     ----------
     info : dict
         The info dict to correct. Corrections are done in-place.
+    use_cal : bool
+        If True, further refine the check for old coil types by checking
+        ``info['chs'][ii]['cal']``.
 
     Notes
     -----
@@ -1385,24 +1388,31 @@ def fix_mag_coil_types(info):
               current estimates computed by the MNE software is very small.
               Therefore the use of ``fix_mag_coil_types`` is not mandatory.
     """
-    old_mag_inds = _get_T1T2_mag_inds(info)
+    old_mag_inds = _get_T1T2_mag_inds(info, use_cal)
 
     for ii in old_mag_inds:
         info['chs'][ii]['coil_type'] = FIFF.FIFFV_COIL_VV_MAG_T3
-    logger.info('%d of %d T1/T2 magnetometer types replaced with T3.' %
+    logger.info('%d of %d magnetometer types replaced with T3.' %
                 (len(old_mag_inds), len(pick_types(info, meg='mag'))))
     info._check_consistency()
 
 
-def _get_T1T2_mag_inds(info):
+def _get_T1T2_mag_inds(info, use_cal=False):
     """Find T1/T2 magnetometer coil types."""
     picks = pick_types(info, meg='mag')
     old_mag_inds = []
+    # From email exchanges, systems with the larger T2 coil only use the cal
+    # value of 2.09e-11. Newer T3 magnetometers use 4.13e-11 or 1.33e-10
+    # (Triux). So we can use a simple check for > 3e-11.
     for ii in picks:
         ch = info['chs'][ii]
         if ch['coil_type'] in (FIFF.FIFFV_COIL_VV_MAG_T1,
                                FIFF.FIFFV_COIL_VV_MAG_T2):
-            old_mag_inds.append(ii)
+            if use_cal:
+                if ch['cal'] > 3e-11:
+                    old_mag_inds.append(ii)
+            else:
+                old_mag_inds.append(ii)
     return old_mag_inds
 
 

mne/chpi.py

@@ -37,8 +37,8 @@
 from .cov import make_ad_hoc_cov, compute_whitener
 from .dipole import _make_guesses
 from .fixes import jit
-from .preprocessing.maxwell import (_sss_basis, _prep_mf_coils, _get_mf_picks,
-                                    _regularize_out)
+from .preprocessing.maxwell import (_sss_basis, _prep_mf_coils,
+                                    _regularize_out, _get_mf_picks_fix_mags)
 from .transforms import (apply_trans, invert_transform, _angle_between_quats,
                          quat_to_rot, rot_to_quat, _fit_matched_points,
                          _quat_to_affine)
@@ -510,7 +510,7 @@ def _reorder_inv_model(inv_model, n_freqs):
 def _setup_ext_proj(info, ext_order):
     meg_picks = pick_types(info, meg=True, eeg=False, exclude='bads')
     info = pick_info(_simplify_info(info), meg_picks)  # makes a copy
-    _, _, _, _, mag_or_fine = _get_mf_picks(
+    _, _, _, _, mag_or_fine = _get_mf_picks_fix_mags(
         info, int_order=0, ext_order=ext_order, ignore_ref=True,
         verbose='error')
     mf_coils = _prep_mf_coils(info, verbose='error')

mne/conftest.py

@@ -97,6 +97,7 @@ def pytest_configure(config):
     ignore:.*sphinx\.util\.smartypants is deprecated.*:
     ignore:.*pandas\.util\.testing is deprecated.*:
     ignore:.*tostring.*is deprecated.*:DeprecationWarning
+    ignore:VTK 9 no longer accepts an offset array:UserWarning
     always:.*get_data.* is deprecated in favor of.*:DeprecationWarning
     """  # noqa: E501
     for warning_line in warning_lines.split('\n'):

mne/epochs.py

@@ -3149,7 +3149,7 @@ def average_movements(epochs, head_pos=None, orig_sfreq=None, picks=None,
     """  # noqa: E501
     from .preprocessing.maxwell import (_trans_sss_basis, _reset_meg_bads,
                                         _check_usable, _col_norm_pinv,
-                                        _get_n_moments, _get_mf_picks,
+                                        _get_n_moments, _get_mf_picks_fix_mags,
                                         _prep_mf_coils, _check_destination,
                                         _remove_meg_projs, _get_coil_scale)
     if head_pos is None:
@@ -3172,20 +3172,20 @@ def average_movements(epochs, head_pos=None, orig_sfreq=None, picks=None,
                 % (len(epochs.events)))
     if not np.array_equal(epochs.events[:, 0], np.unique(epochs.events[:, 0])):
         raise RuntimeError('Epochs must have monotonically increasing events')
+    info_to = epochs.info.copy()
     meg_picks, mag_picks, grad_picks, good_mask, _ = \
-        _get_mf_picks(epochs.info, int_order, ext_order, ignore_ref)
+        _get_mf_picks_fix_mags(info_to, int_order, ext_order, ignore_ref)
     coil_scale, mag_scale = _get_coil_scale(
-        meg_picks, mag_picks, grad_picks, mag_scale, epochs.info)
+        meg_picks, mag_picks, grad_picks, mag_scale, info_to)
     n_channels, n_times = len(epochs.ch_names), len(epochs.times)
     other_picks = np.setdiff1d(np.arange(n_channels), meg_picks)
     data = np.zeros((n_channels, n_times))
     count = 0
     # keep only MEG w/bad channels marked in "info_from"
-    info_from = pick_info(epochs.info, meg_picks[good_mask], copy=True)
-    all_coils_recon = _prep_mf_coils(epochs.info, ignore_ref=ignore_ref)
+    info_from = pick_info(info_to, meg_picks[good_mask], copy=True)
+    all_coils_recon = _prep_mf_coils(info_to, ignore_ref=ignore_ref)
     all_coils = _prep_mf_coils(info_from, ignore_ref=ignore_ref)
     # remove MEG bads in "to" info
-    info_to = deepcopy(epochs.info)
     _reset_meg_bads(info_to)
     # set up variables
     w_sum = 0.
@@ -3200,7 +3200,7 @@ def average_movements(epochs, head_pos=None, orig_sfreq=None, picks=None,
         event_time = epochs.events[epochs._current - 1, 0] / orig_sfreq
         use_idx = np.where(t <= event_time)[0]
         if len(use_idx) == 0:
-            trans = epochs.info['dev_head_t']['trans']
+            trans = info_to['dev_head_t']['trans']
         else:
             use_idx = use_idx[-1]
             trans = np.vstack([np.hstack([rot[use_idx], trn[[use_idx]].T]),

mne/io/meas_info.py

@@ -816,7 +816,7 @@ def ch_names(self):
 def _simplify_info(info):
     """Return a simplified info structure to speed up picking."""
     chs = [{key: ch[key]
-            for key in ('ch_name', 'kind', 'unit', 'coil_type', 'loc')}
+            for key in ('ch_name', 'kind', 'unit', 'coil_type', 'loc', 'cal')}
            for ch in info['chs']]
     sub_info = Info(chs=chs, bads=info['bads'], comps=info['comps'],
                     projs=info['projs'],

mne/preprocessing/maxwell.py

@@ -33,7 +33,7 @@
 from ..utils import (verbose, logger, _clean_names, warn, _time_mask, _pl,
                      _check_option, _ensure_int, _validate_type, use_log_level)
 from ..fixes import _get_args, _safe_svd, einsum, bincount
-from ..channels.channels import _get_T1T2_mag_inds
+from ..channels.channels import _get_T1T2_mag_inds, fix_mag_coil_types
 
 
 # Note: MF uses single precision and some algorithms might use
@@ -274,7 +274,7 @@ def _prep_maxwell_filter(
     # Now we can actually get moving
     info = raw.info.copy()
     meg_picks, mag_picks, grad_picks, good_mask, mag_or_fine = \
-        _get_mf_picks(info, int_order, ext_order, ignore_ref)
+        _get_mf_picks_fix_mags(info, int_order, ext_order, ignore_ref)
 
     # Magnetometers are scaled to improve numerical stability
     coil_scale, mag_scale = _get_coil_scale(
@@ -417,7 +417,8 @@ def _run_maxwell_filter(
         ctc = ctc[good_mask][:, good_mask]
 
     add_channels = (head_pos[0] is not None) and (not st_only) and copy
-    raw_sss, pos_picks = _copy_preload_add_channels(raw, add_channels, copy)
+    raw_sss, pos_picks = _copy_preload_add_channels(
+        raw, add_channels, copy, info)
     sfreq = info['sfreq']
     del raw
     if not st_only:
@@ -742,10 +743,11 @@ def _do_tSSS(clean_data, orig_in_data, resid, st_correlation,
     clean_data -= np.dot(np.dot(clean_data, t_proj), t_proj.T)
 
 
-def _copy_preload_add_channels(raw, add_channels, copy):
+def _copy_preload_add_channels(raw, add_channels, copy, info):
     """Load data for processing and (maybe) add cHPI pos channels."""
     if copy:
         raw = raw.copy()
+    raw.info['chs'] = info['chs']  # updated coil types
     if add_channels:
         kinds = [FIFF.FIFFV_QUAT_1, FIFF.FIFFV_QUAT_2, FIFF.FIFFV_QUAT_3,
                  FIFF.FIFFV_QUAT_4, FIFF.FIFFV_QUAT_5, FIFF.FIFFV_QUAT_6,
@@ -907,14 +909,13 @@ def _regularize(regularize, exp, S_decomp, mag_or_fine, t, verbose=None):
 
 
 @verbose
-def _get_mf_picks(info, int_order, ext_order, ignore_ref=False, verbose=None):
-    """Pick types for Maxwell filtering."""
+def _get_mf_picks_fix_mags(info, int_order, ext_order, ignore_ref=False,
+                           verbose=None):
+    """Pick types for Maxwell filtering and fix magnetometers."""
     # Check for T1/T2 mag types
-    mag_inds_T1T2 = _get_T1T2_mag_inds(info)
+    mag_inds_T1T2 = _get_T1T2_mag_inds(info, use_cal=True)
     if len(mag_inds_T1T2) > 0:
-        warn('%d T1/T2 magnetometer channel types found. If using SSS, it is '
-             'advised to replace coil types using "fix_mag_coil_types".'
-             % len(mag_inds_T1T2))
+        fix_mag_coil_types(info, use_cal=True)
     # Get indices of channels to use in multipolar moment calculation
     ref = not ignore_ref
     meg_picks = pick_types(info, meg=True, ref_meg=ref, exclude=[])

mne/preprocessing/tests/test_maxwell.py

@@ -20,6 +20,7 @@
 from mne.forward import use_coil_def
 from mne.io import (read_raw_fif, read_info, read_raw_bti, read_raw_kit,
                     BaseRaw, read_raw_ctf)
+from mne.io.constants import FIFF
 from mne.preprocessing.maxwell import (
     maxwell_filter, _get_n_moments, _sss_basis_basic, _sh_complex_to_real,
     _sh_real_to_complex, _sh_negate, _bases_complex_to_real, _trans_sss_basis,
@@ -117,6 +118,13 @@ def _assert_n_free(raw_sss, lower, upper=None):
         'nfree fail: %s <= %s <= %s' % (lower, n_free, upper)
 
 
+def _assert_mag_coil_type(info, coil_type):
+    __tracebackhide__ = True
+    picks = pick_types(info, meg='mag', exclude=())
+    coil_types = set(info['chs'][pick]['coil_type'] for pick in picks)
+    assert coil_types == {coil_type}
+
+
 def read_crop(fname, lims=(0, None)):
     """Read and crop."""
     return read_raw_fif(fname, allow_maxshield='yes').crop(*lims)
@@ -134,8 +142,12 @@ def test_movement_compensation(tmpdir):
     #
     # Movement compensation, no regularization, no tSSS
     #
+    _assert_mag_coil_type(raw.info, FIFF.FIFFV_COIL_VV_MAG_T3)
+    assert_allclose(raw.info['chs'][2]['cal'], 4.14e-11, rtol=1e-6)
+    raw.info['chs'][2]['coil_type'] = FIFF.FIFFV_COIL_VV_MAG_T2
     raw_sss = maxwell_filter(raw, head_pos=head_pos, origin=mf_head_origin,
                              regularize=None, bad_condition='ignore')
+    _assert_mag_coil_type(raw_sss.info, FIFF.FIFFV_COIL_VV_MAG_T3)
     assert_meg_snr(raw_sss, read_crop(sss_movecomp_fname, lims),
                    4.6, 12.4, chpi_med_tol=58)
     # IO
@@ -966,10 +978,12 @@ def test_all():
 def test_triux():
     """Test TRIUX system support."""
     raw = read_crop(tri_fname, (0, 0.999))
-    raw.fix_mag_coil_types()
+    _assert_mag_coil_type(raw.info, FIFF.FIFFV_COIL_VV_MAG_T1)
+    assert_allclose(raw.info['chs'][2]['cal'], 1.33e-10, rtol=1e-6)
     # standard
     with use_coil_def(elekta_def_fname):
         sss_py = maxwell_filter(raw, coord_frame='meg', regularize=None)
+    _assert_mag_coil_type(sss_py.info, FIFF.FIFFV_COIL_VV_MAG_T3)
     assert_meg_snr(sss_py, read_crop(tri_sss_fname), 37, 700)
     # cross-talk
     sss_py = maxwell_filter(raw, coord_frame='meg', regularize=None,

mne/utils/config.py

@@ -479,7 +479,7 @@ def sys_info(fid=None, show_paths=False):
         pandas:        1.0.3
         dipy:          1.1.1
         mayavi:        4.7.2.dev0
-        pyvista:       0.24.1
+        pyvista:       0.25.2 {pyvistaqt=0.1.0}
         vtk:           9.0.0
         PyQt5:         5.14.1
     """  # noqa: E501
@@ -524,9 +524,16 @@ def sys_info(fid=None, show_paths=False):
         else:
             extra = (' (%s)' % op.dirname(mod.__file__)) if show_paths else ''
             if mod_name == 'numpy':
-                extra = ' {%s}%s' % (libs, extra)
+                extra += ' {%s}%s' % (libs, extra)
             elif mod_name == 'matplotlib':
-                extra = ' {backend=%s}%s' % (mod.get_backend(), extra)
+                extra += ' {backend=%s}%s' % (mod.get_backend(), extra)
+            elif mod_name == 'pyvista':
+                try:
+                    from pyvistaqt import __version__
+                except Exception:
+                    pass
+                else:
+                    extra += f' {{pyvistaqt={__version__}}}'
             elif mod_name in ('mayavi', 'vtk'):
                 has_3d = True
             if mod_name == 'vtk':

mne/viz/_brain/_timeviewer.py

@@ -990,6 +990,7 @@ def on_pick(self, vtk_picker, event):
                 self.add_point(hemi, mesh, vertex_id, line, color)
 
     def add_point(self, hemi, mesh, vertex_id, line, color):
+        from ..backends._pyvista import _sphere
         center = mesh.GetPoints().GetPoint(vertex_id)
 
         # from the picked renderer to the subplot coords
@@ -1000,11 +1001,17 @@ def add_point(self, hemi, mesh, vertex_id, line, color):
         spheres = list()
         for ri, view in enumerate(self.brain._views):
             self.plotter.subplot(ri, col)
-            actor, sphere = self.brain._renderer.sphere(
+            # Using _sphere() instead of renderer.sphere() for 2 reasons:
+            # 1) renderer.sphere() fails on Windows in a scenario where a lot
+            #    of picking requests are done in a short span of time (could be
+            #    mitigated with synchronization/delay?)
+            # 2) the glyph filter is used in renderer.sphere() but only one
+            #    sphere is required in this function.
+            actor, sphere = _sphere(
+                plotter=self.plotter,
                 center=np.array(center),
                 color=color,
-                scale=1.0,
-                radius=4.0
+                radius=4.0,
             )
             actors.append(actor)
             spheres.append(sphere)

mne/viz/_brain/tests/test_brain.py

@@ -134,7 +134,8 @@ def test_brain(renderer):
     # screenshot
     brain.show_view(view=dict(azimuth=180., elevation=90.))
     img = brain.screenshot(mode='rgb')
-    assert(img.shape == (size[0], size[1], 3))
+    assert_allclose(img.shape, (size[0], size[1], 3),
+                    atol=50)  # XXX undo once size is fixed
 
     # add annotation
     annots = ['aparc', 'PALS_B12_Lobes']