MRG: Backport #10619 and #10620 (#10621)

* Drop EEG rejection thresholds when replacing EEG with CSD channels (#10619)

* Drop EEG rejection thresholds when replacing EEG with CSD channels

This is an attempt to fix the issue reported at
https://mne.discourse.group/t/saving-epoch-error-no-eeg-channel-found

* fix, working version

* Update doc/changes/latest.inc

Co-authored-by: Richard Höchenberger <[email protected]>

Co-authored-by: Alex <[email protected]>

* Simplify #10619 (#10620)

* MAINT: Fix

* FIX: Fix for regression

* FIX: Fix for pandas

* FIX: Better fix

* FIX: Adjust

Co-authored-by: Alex <[email protected]>
Co-authored-by: Eric Larson <[email protected]>

Author: 3 people

azure-pipelines.yml

@@ -111,7 +111,7 @@ stages:
     - bash: |
         set -e
         python -m pip install --progress-bar off --upgrade pip setuptools wheel codecov
-        python -m pip install --progress-bar off mne-qt-browser[opengl] vtk scikit-learn pytest-error-for-skips python-picard
+        python -m pip install --progress-bar off mne-qt-browser[opengl] vtk scikit-learn pytest-error-for-skips python-picard "pyqt5>=5.10,!=5.15.3"
         python -m pip uninstall -yq mne
         python -m pip install --progress-bar off --upgrade -e .[test]
       displayName: 'Install dependencies with pip'

doc/changes/1.0.inc

@@ -24,6 +24,8 @@ Version 1.0.X
 
 - Retain epochs metadata when using :func:`mne.channels.combine_channels` (:gh:`10504` by `Clemens Brunner`_)
 
+- Fix issue with saving epochs once :func:`~mne.preprocessing.compute_current_source_density` has been used if a rejection threshold was used first (:gh:`10619` by `Alex Rockhill`_ and `Richard Höchenberger`_)
+
 Version 1.0.2 (2022-04-15)
 --------------------------
 - Fix bug where ``theme`` was not handled properly in :meth:`mne.io.Raw.plot` (:gh:`10500` by `Eric Larson`_)

mne/beamformer/tests/test_lcmv.py

@@ -677,8 +677,8 @@ def test_localization_bias_fixed(bias_params_fixed, reg, weight_norm, use_cov,
         # no reg
         (0.00, 'vector', None, True, None, 23, 24, 0.96, 0.97),
         (0.00, 'vector', 'unit-noise-gain-invariant', True, None, 52, 54, 0.95, 0.96),  # noqa: E501
-        (0.00, 'vector', 'unit-noise-gain', True, None, 44, 46, 0.97, 0.98),
-        (0.00, 'vector', 'nai', True, None, 44, 46, 0.97, 0.98),
+        (0.00, 'vector', 'unit-noise-gain', True, None, 44, 48, 0.97, 0.99),
+        (0.00, 'vector', 'nai', True, None, 44, 48, 0.97, 0.99),
         (0.00, 'max-power', None, True, None, 14, 15, 0, 0),
         (0.00, 'max-power', 'unit-noise-gain-invariant', True, None, 35, 37, 0, 0),  # noqa: E501
         (0.00, 'max-power', 'unit-noise-gain', True, None, 35, 37, 0, 0),

mne/preprocessing/_csd.py

@@ -172,4 +172,12 @@ def compute_current_source_density(inst, sphere='auto', lambda2=1e-5,
     for pick in picks:
         inst.info['chs'][pick].update(coil_type=FIFF.FIFFV_COIL_EEG_CSD,
                                       unit=FIFF.FIFF_UNIT_V_M2)
+
+    # Remove rejection thresholds for EEG
+    if isinstance(inst, BaseEpochs):
+        if inst.reject and 'eeg' in inst.reject:
+            del inst.reject['eeg']
+        if inst.flat and 'eeg' in inst.flat:
+            del inst.flat['eeg']
+
     return inst

mne/preprocessing/tests/test_csd.py

@@ -17,7 +17,8 @@
 from scipy import linalg
 
 from mne.channels import make_dig_montage
-from mne import create_info, EvokedArray, pick_types, Epochs
+from mne import (create_info, EvokedArray, pick_types, Epochs, find_events,
+                 read_epochs)
 from mne.io import read_raw_fif, RawArray
 from mne.io.constants import FIFF
 from mne.utils import object_diff
@@ -183,3 +184,16 @@ def test_csd_fif():
         ch.update(coil_type=FIFF.FIFFV_COIL_EEG, unit=FIFF.FIFF_UNIT_V)
         raw_csd._data[pick] = raw._data[pick]
     assert object_diff(raw.info, raw_csd.info) == ''
+
+
+def test_csd_epochs(tmp_path):
+    """Test making epochs, saving to disk and loading."""
+    raw = read_raw_fif(raw_fname)
+    raw.pick_types(eeg=True, stim=True).load_data()
+    events = find_events(raw)
+    epochs = Epochs(raw, events, reject=dict(eeg=1e-4), preload=True)
+    epochs = compute_current_source_density(epochs)
+    epo_fname = tmp_path / 'test_csd_epo.fif'
+    epochs.save(epo_fname)
+    epochs2 = read_epochs(epo_fname, preload=True)
+    assert_allclose(epochs._data, epochs2._data)

mne/viz/backends/_utils.py

@@ -232,7 +232,6 @@ def _qt_get_stylesheet(theme):
                 # but it's easy enough just to set it transparent and inherit
                 # the bgcolor of the window (which is the same). We also take
                 # the separator images from QDarkStyle (MIT).
-                icons_path = _qt_init_icons()
                 stylesheet = """\
 QStatusBar {
   border: 1px solid rgb(76, 76, 75);
@@ -245,23 +244,7 @@ def _qt_get_stylesheet(theme):
   background-color: transparent;
   border-bottom: 1px solid rgb(99, 99, 99);
 }
-QToolBar::separator:horizontal {
-  width: 16px;
-  image: url("%(icons_path)s/[email protected]");
-}
-QToolBar::separator:vertical {
-  height: 16px;
-  image: url("%(icons_path)s/[email protected]");
-}
-QToolBar::handle:horizontal {
-  width: 16px;
-  image: url("%(icons_path)s/[email protected]");
-}
-QToolBar::handle:vertical {
-  height: 16px;
-  image: url("%(icons_path)s/[email protected]");
-}
-""" % dict(icons_path=icons_path)
+"""
             else:
                 stylesheet = ''
         else:

tools/azure_dependencies.sh

@@ -14,7 +14,7 @@ elif [ "${TEST_MODE}" == "pip-pre" ]; then
 	# SciPy Windows build is missing from conda nightly builds
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy
 	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" pandas scikit-learn dipy statsmodels
+	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps --default-timeout=60 -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" pandas scikit-learn dipy statsmodels
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" --no-deps -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py Pillow matplotlib
 	# Until VTK comes out with a 3.10 wheel, we need to use PyVista's
 	python -m pip install --progress-bar off --upgrade --pre --only-binary ":all:" https://github.com/pyvista/pyvista-wheels/raw/3b70f3933bc246b035354b172a0459ffc96b0343/vtk-9.1.0.dev0-cp310-cp310-win_amd64.whl

tools/github_actions_dependencies.sh

@@ -17,7 +17,7 @@ else
 	echo "PyQt5"
 	pip install $STD_ARGS --pre --only-binary ":all:" --no-deps --extra-index-url https://www.riverbankcomputing.com/pypi/simple PyQt5 PyQt5-sip PyQt5-Qt5
 	echo "NumPy/SciPy/pandas etc."
-	pip install $STD_ARGS --pre --only-binary ":all:" --no-deps -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy scipy pandas scikit-learn statsmodels dipy
+	pip install $STD_ARGS --pre --only-binary ":all:" --no-deps --default-timeout=60 -i "https://pypi.anaconda.org/scipy-wheels-nightly/simple" numpy scipy pandas scikit-learn statsmodels dipy
 	echo "H5py, pillow, matplotlib"
 	pip install $STD_ARGS --pre --only-binary ":all:" --no-deps -f "https://7933911d6844c6c53a7d-47bd50c35cd79bd838daf386af554a83.ssl.cf2.rackcdn.com" h5py pillow matplotlib
 	# We don't install Numba here because it forces an old NumPy version