BUG: Evoked.get_data() should exclude bad channels when explicit picks are given

doc/changes/dev/14013.bugfix.rst

@@ -0,0 +1 @@
+Fix :meth:`mne.Evoked.get_data` so that explicit ``picks`` (e.g. ``picks="eeg"``) exclude channels marked as bad by default, matching the existing behavior of :meth:`mne.Epochs.get_data`, and clarify the ``picks`` docstring to describe this conditional bad-channel behavior, by :newcontrib:`Eva Safi`.

doc/changes/names.inc

@@ -100,6 +100,7 @@
 .. _Erica Peterson: https://github.com/nordme
 .. _Erkka Heinila: https://github.com/Teekuningas
 .. _Etienne de Montalivet: https://github.com/etiennedemontalivet
+.. _Eva Safi: https://github.com/evasafi 
 .. _Evan Hathaway: https://github.com/ephathaway
 .. _Evgenii Kalenkovich: https://github.com/kalenkovich
 .. _Evgeny Goldstein: https://github.com/evgenygoldstein

mne/evoked.py

@@ -233,7 +233,7 @@ def get_data(self, picks=None, units=None, tmin=None, tmax=None):
 
         Parameters
         ----------
-        %(picks_all)s
+        %(picks_all_get_data)s
         %(units)s
         tmin : float | None
             Start time of data to get in seconds.
@@ -252,7 +252,14 @@ def get_data(self, picks=None, units=None, tmin=None, tmax=None):
         # Avoid circular import
         from .io.base import _get_ch_factors
 
-        picks = _picks_to_idx(self.info, picks, "all", exclude=())
+        # When no picks are given, keep prior behavior of including bads.
+        # When explicit picks are given (e.g. picks="eeg"), exclude bads by
+        # default, matching the behavior of Epochs.get_data().
+        orig_picks = picks
+        if orig_picks is None:
+            picks = _picks_to_idx(self.info, picks, "all", exclude=())
+        else:
+            picks = _picks_to_idx(self.info, picks)
 
         start, stop = self._handle_tmin_tmax(tmin, tmax)
 

mne/tests/test_evoked.py

@@ -71,6 +71,22 @@ def test_get_data():
     d2 = evoked.get_data(picks="eeg", units="V")
     assert_array_equal(d1, d2)
 
+    # Regression test for gh-12577: explicit picks should exclude bad
+    # channels in Evoked.get_data(), matching Epochs.get_data().
+    evoked_bads = evoked.copy()
+    eeg_ch_names = [
+        ch
+        for ch, kind in zip(evoked_bads.ch_names, evoked_bads.get_channel_types())
+        if kind == "eeg"
+    ]
+    evoked_bads.info["bads"] = [eeg_ch_names[0]]
+    n_eeg_with_bads = len(pick_types(evoked_bads.info, eeg=True, exclude=()))
+    n_eeg_without_bads = len(pick_types(evoked_bads.info, eeg=True, exclude="bads"))
+    assert n_eeg_without_bads < n_eeg_with_bads  # sanity check the fixture
+    assert evoked_bads.get_data(picks="eeg").shape[0] == n_eeg_without_bads
+    # picks=None should still keep prior behavior (bads included)
+    assert evoked_bads.get_data().shape[0] == len(evoked_bads.ch_names)
+
     # Convert to µV
     d3 = evoked.get_data(picks="eeg", units="µV")
     assert_array_equal(d1 * 1e6, d3)

mne/utils/docs.py

@@ -3547,6 +3547,12 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
 docdict["picks_all_data_noref"] = _reflow_param_docstring(
     f"{picks_base} all data channels {noref}"
 )
+docdict["picks_all_get_data"] = _reflow_param_docstring(
+    f"{picks_base} all channels, and bad channels are included by default "
+    f"when picks is None. If picks are given as channel type(s) (e.g., "
+    f"``'eeg'``), bad channels of those types are excluded by default. "
+    f"{reminder}"
+)
 docdict["picks_all_notypes"] = _reflow_param_docstring(
     f"{picks_base_notypes} all channels. {reminder}"
 )