BUG: Fix bug with MF LCMV rank

doc/changes/latest.inc

@@ -76,6 +76,7 @@ Bugs
 - Fix bug in :func:`mne.concatenate_raws` where two raws could not be merged if the order of the bad channel lists did not match (:gh:`11502` by `Moritz Gerster`_)
 - Fix bug where :meth:`mne.Evoked.plot_topomap` opened an extra figure (:gh:`11607` by `Alex Rockhill`_)
 - Fix bug where :func:`mne.transforms.apply_volume_registration_points` modified info in place (:gh:`11612` by `Alex Rockhill`_)
+- Fix bug where Maxwell-filtered data rank was not handled properly in :func:`mne.beamformer.make_lcmv` (:gh:`11664` by `Eric Larson`_)
 - In :class:`~mne.Report`, custom figures now show up correctly when ``image_format='svg'`` is requested (:gh:`11623` by `Richard Höchenberger`_)
 - Fix bug where providing ``axes`` in `mne.preprocessing.ICA.plot_components` would fail (:gh:`11654` by `Mathieu Scheltienne`_)
 

environment.yml

@@ -31,7 +31,7 @@ dependencies:
 - imageio-ffmpeg>=0.4.1
 - vtk>=9.2
 - traitlets
-- pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5
+- pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6
 - pyvistaqt>=0.4
 - qdarkstyle
 - darkdetect

mne/beamformer/_lcmv.py

@@ -163,7 +163,7 @@ def make_lcmv(
     .. footbibliography::
     """
     # check number of sensor types present in the data and ensure a noise cov
-    info = _simplify_info(info)
+    info = _simplify_info(info, keep=("proc_history",))
     noise_cov, _, allow_mismatch = _check_one_ch_type(
         "lcmv", info, forward, data_cov, noise_cov
     )

mne/beamformer/tests/test_lcmv.py

@@ -1,3 +1,4 @@
+from contextlib import nullcontext
 from copy import deepcopy
 from inspect import signature
 
@@ -1072,9 +1073,9 @@ def test_depth_does_not_matter(bias_params_free, weight_norm, pick_ori):
         assert_allclose(d1, d2, atol=atol)
 
 
-@testing.requires_testing_data
-def test_lcmv_maxfiltered():
-    """Test LCMV on maxfiltered data."""
+@pytest.fixture(scope="session")
+def mf_data():
+    """Produce Maxwell filtered data for beamforming."""
     raw = mne.io.read_raw_fif(fname_raw).fix_mag_coil_types()
     raw_sss = mne.preprocessing.maxwell_filter(raw)
     events = mne.find_events(raw_sss)
@@ -1084,10 +1085,26 @@ def test_lcmv_maxfiltered():
     epochs = mne.Epochs(raw_sss, events)
     data_cov = mne.compute_covariance(epochs, tmin=0)
     fwd = mne.read_forward_solution(fname_fwd)
+    return epochs, data_cov, fwd
+
+
+@testing.requires_testing_data
+@pytest.mark.parametrize("use_rank", ("info", "computed", "full", None))
+def test_lcmv_maxfiltered(mf_data, use_rank):
+    """Test LCMV on maxfiltered data."""
+    epochs, data_cov, fwd = mf_data
     rank = compute_rank(data_cov, info=epochs.info)
     assert rank == {"mag": 71}
-    for use_rank in ("info", rank, "full", None):
-        make_lcmv(epochs.info, fwd, data_cov, rank=use_rank)
+    ctx = nullcontext()
+    if use_rank == "computed":
+        use_rank = rank
+    elif use_rank is None:
+        ctx = pytest.warns(RuntimeWarning, match="rank as it exceeds")
+    with catch_logging() as log, ctx:
+        make_lcmv(epochs.info, fwd, data_cov, rank=use_rank, verbose=True)
+    log = log.getvalue()
+    n = 102 if use_rank == "full" else 71
+    assert f"Making LCMV beamformer with rank {{'mag': {n}}}" in log
 
 
 # To reduce test time, only test combinations that should matter rather than

mne/io/meas_info.py

@@ -1468,19 +1468,16 @@ def save(self, fname):
         write_info(fname, self)
 
 
-def _simplify_info(info):
+def _simplify_info(info, *, keep=()):
     """Return a simplified info structure to speed up picking."""
     chs = [
         {key: ch[key] 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"],
-        custom_ref_applied=info["custom_ref_applied"],
-    )
+    keys = ("bads", "comps", "projs", "custom_ref_applied") + keep
+    sub_info = Info((key, info[key]) for key in keys if key in info)
+    with sub_info._unlock():
+        sub_info["chs"] = chs
     sub_info._update_redundant()
     return sub_info
 

mne/utils/config.py

@@ -202,9 +202,10 @@ def set_memmap_min_size(memmap_min_size):
 
 # These allow for partial matches, e.g. 'MNE_STIM_CHANNEL_1' is okay key
 _known_config_wildcards = (
-    "MNE_STIM_CHANNEL",
-    "MNE_DATASETS_FNIRS",
-    "MNE_NIRS",
+    "MNE_STIM_CHANNEL",  # can have multiple stim channels
+    "MNE_DATASETS_FNIRS",  # mne-nirs
+    "MNE_NIRS",  # mne-nirs
+    "MNE_KIT2FIFF",  # mne-kit-gui
 )
 
 

requirements.txt

@@ -32,7 +32,7 @@ xlrd
 imageio>=2.6.1
 imageio-ffmpeg>=0.4.1
 traitlets
-pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5
+pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6
 pyvistaqt>=0.4
 mffpy>=0.5.7
 ipywidgets

tools/azure_dependencies.sh

@@ -3,20 +3,14 @@
 EXTRA_ARGS=""
 if [ "${TEST_MODE}" == "pip" ]; then
 	python -m pip install --upgrade pip setuptools wheel
-	python -m pip install --upgrade --only-binary ":all:" numpy scipy vtk
-	python -m pip install --upgrade --only-binary="numba,llvmlite" -r requirements.txt
-	# This can be removed once PyVistaQt 0.6 is out (including https://github.com/pyvista/pyvistaqt/pull/127)
-	python -m pip install --upgrade git+https://github.com/pyvista/pyvistaqt
+	python -m pip install --upgrade --only-binary="numba,llvmlite,numpy,scipy,vtk" -r requirements.txt
 elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	python -m pip install --progress-bar off --upgrade pip setuptools wheel
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" python-dateutil pytz joblib threadpoolctl six cycler kiwisolver pyparsing patsy
 	# Broken as of 2022/09/20
 	# python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps --extra-index-url https://www.riverbankcomputing.com/pypi/simple PyQt6 PyQt6-sip PyQt6-Qt6
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps PyQt6 PyQt6-sip PyQt6-Qt6
-	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy
-	# # SciPy<->sklearn problematic, see https://github.com/scipy/scipy/issues/18377
-	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps scipy
-	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" statsmodels pandas scikit-learn dipy matplotlib
+	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy scipy statsmodels pandas scikit-learn dipy matplotlib
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://test.pypi.org/simple" openmeeg
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://wheels.vtk.org" vtk

tools/github_actions_dependencies.sh

@@ -22,10 +22,7 @@ else
 	# pip install $STD_ARGS --pre --only-binary ":all:" --no-deps --extra-index-url https://www.riverbankcomputing.com/pypi/simple PyQt6
 	pip install $STD_ARGS --pre --only-binary ":all:" PyQt6
 	echo "NumPy/SciPy/pandas etc."
-	pip install $STD_ARGS --pre --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy
-	# SciPy<->sklearn problematic, see https://github.com/scipy/scipy/issues/18377
-	pip install $STD_ARGS --pre --only-binary ":all:" scipy
-	pip install $STD_ARGS --pre --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scipy-wheels-nightly/simple" scikit-learn dipy pandas matplotlib pillow statsmodels
+	pip install $STD_ARGS --pre --only-binary ":all:" --default-timeout=60 --extra-index-url "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy scipy scikit-learn dipy pandas matplotlib pillow statsmodels
 	pip install $STD_ARGS --pre --only-binary ":all:" -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py
 	# No Numba because it forces an old NumPy version
 	echo "nilearn and openmeeg"