Merge branch 'main' into cnt_bug

doc/changes/devel/12195.newfeature.rst

@@ -0,0 +1 @@
+Add ability reject :class:`mne.Epochs` using callables, by `Jacob Woessner`_.

doc/changes/devel/12410.bugfix.rst

@@ -0,0 +1 @@
+In :func:`~mne.viz.plot_compare_evokeds`, actually plot GFP (not RMS amplitude) for EEG channels when global field power is requested by `Daniel McCloy`_.

mne/epochs.py

@@ -787,7 +787,7 @@ def apply_baseline(self, baseline=(None, 0), *, verbose=None):
         self.baseline = baseline
         return self
 
-    def _reject_setup(self, reject, flat):
+    def _reject_setup(self, reject, flat, *, allow_callable=False):
         """Set self._reject_time and self._channel_type_idx."""
         idx = channel_indices_by_type(self.info)
         reject = deepcopy(reject) if reject is not None else dict()
@@ -814,11 +814,21 @@ def _reject_setup(self, reject, flat):
                     f"{key.upper()}."
                 )
 
-        # check for invalid values
-        for rej, kind in zip((reject, flat), ("Rejection", "Flat")):
-            for key, val in rej.items():
-                if val is None or val < 0:
-                    raise ValueError(f'{kind} value must be a number >= 0, not "{val}"')
+            # check for invalid values
+            for rej, kind in zip((reject, flat), ("Rejection", "Flat")):
+                for key, val in rej.items():
+                    name = f"{kind} dict value for {key}"
+                    if callable(val) and allow_callable:
+                        continue
+                    extra_str = ""
+                    if allow_callable:
+                        extra_str = "or callable"
+                    _validate_type(val, "numeric", name, extra=extra_str)
+                    if val is None or val < 0:
+                        raise ValueError(
+                            f"If using numerical {name} criteria, the value "
+                            f"must be >= 0, not {repr(val)}"
+                        )
 
         # now check to see if our rejection and flat are getting more
         # restrictive
@@ -836,6 +846,9 @@ def _reject_setup(self, reject, flat):
             reject[key] = old_reject[key]
         # make sure new thresholds are at least as stringent as the old ones
         for key in reject:
+            # Skip this check if old_reject and reject are callables
+            if callable(reject[key]) and allow_callable:
+                continue
             if key in old_reject and reject[key] > old_reject[key]:
                 raise ValueError(
                     bad_msg.format(
@@ -851,6 +864,8 @@ def _reject_setup(self, reject, flat):
         for key in set(old_flat) - set(flat):
             flat[key] = old_flat[key]
         for key in flat:
+            if callable(flat[key]) and allow_callable:
+                continue
             if key in old_flat and flat[key] < old_flat[key]:
                 raise ValueError(
                     bad_msg.format(
@@ -1404,7 +1419,7 @@ def drop_bad(self, reject="existing", flat="existing", verbose=None):
             flat = self.flat
         if any(isinstance(rej, str) and rej != "existing" for rej in (reject, flat)):
             raise ValueError('reject and flat, if strings, must be "existing"')
-        self._reject_setup(reject, flat)
+        self._reject_setup(reject, flat, allow_callable=True)
         self._get_data(out=False, verbose=verbose)
         return self
 
@@ -1520,8 +1535,9 @@ def drop(self, indices, reason="USER", verbose=None):
             Set epochs to remove by specifying indices to remove or a boolean
             mask to apply (where True values get removed). Events are
             correspondingly modified.
-        reason : str
-            Reason for dropping the epochs ('ECG', 'timeout', 'blink' etc).
+        reason : list | tuple | str
+            Reason(s) for dropping the epochs ('ECG', 'timeout', 'blink' etc).
+            Reason(s) are applied to all indices specified.
             Default: 'USER'.
         %(verbose)s
 
@@ -1533,7 +1549,9 @@ def drop(self, indices, reason="USER", verbose=None):
         indices = np.atleast_1d(indices)
 
         if indices.ndim > 1:
-            raise ValueError("indices must be a scalar or a 1-d array")
+            raise TypeError("indices must be a scalar or a 1-d array")
+        # Check if indices and reasons are of the same length
+        # if using collection to drop epochs
 
         if indices.dtype == np.dtype(bool):
             indices = np.where(indices)[0]
@@ -3199,6 +3217,10 @@ class Epochs(BaseEpochs):
             See :meth:`~mne.Epochs.equalize_event_counts`
         - 'USER'
             For user-defined reasons (see :meth:`~mne.Epochs.drop`).
+
+        When dropping based on flat or reject parameters the tuple of
+        reasons contains a tuple of channels that satisfied the rejection
+        criteria.
     filename : str
         The filename of the object.
     times :  ndarray
@@ -3667,37 +3689,69 @@ def _is_good(
 ):
     """Test if data segment e is good according to reject and flat.
 
+    The reject and flat parameters can accept functions as values.
+
     If full_report=True, it will give True/False as well as a list of all
     offending channels.
     """
     bad_tuple = tuple()
     has_printed = False
     checkable = np.ones(len(ch_names), dtype=bool)
     checkable[np.array([c in ignore_chs for c in ch_names], dtype=bool)] = False
+
     for refl, f, t in zip([reject, flat], [np.greater, np.less], ["", "flat"]):
         if refl is not None:
-            for key, thresh in refl.items():
+            for key, refl in refl.items():
+                criterion = refl
                 idx = channel_type_idx[key]
                 name = key.upper()
                 if len(idx) > 0:
                     e_idx = e[idx]
-                    deltas = np.max(e_idx, axis=1) - np.min(e_idx, axis=1)
                     checkable_idx = checkable[idx]
-                    idx_deltas = np.where(
-                        np.logical_and(f(deltas, thresh), checkable_idx)
-                    )[0]
+                    # Check if criterion is a function and apply it
+                    if callable(criterion):
+                        result = criterion(e_idx)
+                        _validate_type(result, tuple, "reject/flat output")
+                        if len(result) != 2:
+                            raise TypeError(
+                                "Function criterion must return a tuple of length 2"
+                            )
+                        cri_truth, reasons = result
+                        _validate_type(cri_truth, (bool, np.bool_), cri_truth, "bool")
+                        _validate_type(
+                            reasons, (str, list, tuple), reasons, "str, list, or tuple"
+                        )
+                        idx_deltas = np.where(np.logical_and(cri_truth, checkable_idx))[
+                            0
+                        ]
+                    else:
+                        deltas = np.max(e_idx, axis=1) - np.min(e_idx, axis=1)
+                        idx_deltas = np.where(
+                            np.logical_and(f(deltas, criterion), checkable_idx)
+                        )[0]
 
                     if len(idx_deltas) > 0:
-                        bad_names = [ch_names[idx[i]] for i in idx_deltas]
-                        if not has_printed:
-                            logger.info(
-                                f"    Rejecting {t} epoch based on {name} : {bad_names}"
-                            )
-                            has_printed = True
-                        if not full_report:
-                            return False
+                        # Check to verify that refl is a callable that returns
+                        # (bool, reason). Reason must be a str/list/tuple.
+                        # If using tuple
+                        if callable(refl):
+                            if isinstance(reasons, str):
+                                reasons = (reasons,)
+                            for idx, reason in enumerate(reasons):
+                                _validate_type(reason, str, reason)
+                            bad_tuple += tuple(reasons)
                         else:
-                            bad_tuple += tuple(bad_names)
+                            bad_names = [ch_names[idx[i]] for i in idx_deltas]
+                            if not has_printed:
+                                logger.info(
+                                    "    Rejecting %s epoch based on %s : "
+                                    "%s" % (t, name, bad_names)
+                                )
+                                has_printed = True
+                            if not full_report:
+                                return False
+                            else:
+                                bad_tuple += tuple(bad_names)
 
     if not full_report:
         return True

mne/tests/test_epochs.py

@@ -550,7 +550,20 @@ def test_reject():
         preload=False,
         reject=dict(eeg=np.inf),
     )
-    for val in (None, -1):  # protect against older MNE-C types
+
+    # Good function
+    def my_reject_1(epoch_data):
+        bad_idxs = np.where(np.percentile(epoch_data, 90, axis=1) > 1e-35)
+        reasons = "a" * len(bad_idxs[0])
+        return len(bad_idxs) > 0, reasons
+
+    # Bad function
+    def my_reject_2(epoch_data):
+        bad_idxs = np.where(np.percentile(epoch_data, 90, axis=1) > 1e-35)
+        reasons = "a" * len(bad_idxs[0])
+        return len(bad_idxs), reasons
+
+    for val in (-1, -2):  # protect against older MNE-C types
         for kwarg in ("reject", "flat"):
             pytest.raises(
                 ValueError,
@@ -564,6 +577,44 @@ def test_reject():
                 preload=False,
                 **{kwarg: dict(grad=val)},
             )
+
+    # Check that reject and flat in constructor are not callables
+    val = my_reject_1
+    for kwarg in ("reject", "flat"):
+        with pytest.raises(
+            TypeError,
+            match=r".* must be an instance of numeric, got <class 'function'> instead.",
+        ):
+            Epochs(
+                raw,
+                events,
+                event_id,
+                tmin,
+                tmax,
+                picks=picks_meg,
+                preload=False,
+                **{kwarg: dict(grad=val)},
+            )
+
+    # Check if callable returns a tuple with reasons
+    bad_types = [my_reject_2, ("Hi" "Hi"), (1, 1), None]
+    for val in bad_types:  # protect against bad types
+        for kwarg in ("reject", "flat"):
+            with pytest.raises(
+                TypeError,
+                match=r".* must be an instance of .* got <class '.*'> instead.",
+            ):
+                epochs = Epochs(
+                    raw,
+                    events,
+                    event_id,
+                    tmin,
+                    tmax,
+                    picks=picks_meg,
+                    preload=True,
+                )
+                epochs.drop_bad(**{kwarg: dict(grad=val)})
+
     pytest.raises(
         KeyError,
         Epochs,
@@ -2149,6 +2200,93 @@ def test_reject_epochs(tmp_path):
     assert epochs_cleaned.flat == dict(grad=new_flat["grad"], mag=flat["mag"])
 
 
+@testing.requires_testing_data
+def test_callable_reject():
+    """Test using a callable for rejection."""
+    raw = read_raw_fif(fname_raw_testing, preload=True)
+    raw.crop(0, 5)
+    raw.del_proj()
+    chans = raw.info["ch_names"][-6:-1]
+    raw.pick(chans)
+    data = raw.get_data()
+
+    # Add some artifacts
+    new_data = data
+    new_data[0, 180:200] *= 1e7
+    new_data[0, 610:880] += 1e-3
+    edit_raw = mne.io.RawArray(new_data, raw.info)
+
+    events = mne.make_fixed_length_events(edit_raw, id=1, duration=1.0, start=0)
+    epochs = mne.Epochs(edit_raw, events, tmin=0, tmax=1, baseline=None, preload=True)
+    assert len(epochs) == 5
+
+    epochs = mne.Epochs(
+        edit_raw,
+        events,
+        tmin=0,
+        tmax=1,
+        baseline=None,
+        preload=True,
+    )
+    epochs.drop_bad(
+        reject=dict(eeg=lambda x: ((np.median(x, axis=1) > 1e-3).any(), "eeg median"))
+    )
+
+    assert epochs.drop_log[2] == ("eeg median",)
+
+    epochs = mne.Epochs(
+        edit_raw,
+        events,
+        tmin=0,
+        tmax=1,
+        baseline=None,
+        preload=True,
+    )
+    epochs.drop_bad(
+        reject=dict(eeg=lambda x: ((np.max(x, axis=1) > 1).any(), ("eeg max",)))
+    )
+
+    assert epochs.drop_log[0] == ("eeg max",)
+
+    def reject_criteria(x):
+        max_condition = np.max(x, axis=1) > 1e-2
+        median_condition = np.median(x, axis=1) > 1e-4
+        return (max_condition.any() or median_condition.any()), "eeg max or median"
+
+    epochs = mne.Epochs(
+        edit_raw,
+        events,
+        tmin=0,
+        tmax=1,
+        baseline=None,
+        preload=True,
+    )
+    epochs.drop_bad(reject=dict(eeg=reject_criteria))
+
+    assert epochs.drop_log[0] == ("eeg max or median",) and epochs.drop_log[2] == (
+        "eeg max or median",
+    )
+
+    # Test reasons must be str or tuple of str
+    with pytest.raises(
+        TypeError,
+        match=r".* must be an instance of str, got <class 'int'> instead.",
+    ):
+        epochs = mne.Epochs(
+            edit_raw,
+            events,
+            tmin=0,
+            tmax=1,
+            baseline=None,
+            preload=True,
+        )
+        epochs.drop_bad(
+            reject=dict(
+                eeg=lambda x: ((np.median(x, axis=1) > 1e-3).any(), ("eeg median", 2))
+            )
+        )
+
+
 def test_preload_epochs():
     """Test preload of epochs."""
     raw, events, picks = _get_data()
@@ -3180,9 +3318,16 @@ def test_drop_epochs():
     events1 = events[events[:, 2] == event_id]
 
     # Bound checks
-    pytest.raises(IndexError, epochs.drop, [len(epochs.events)])
-    pytest.raises(IndexError, epochs.drop, [-len(epochs.events) - 1])
-    pytest.raises(ValueError, epochs.drop, [[1, 2], [3, 4]])
+    with pytest.raises(IndexError, match=r"Epoch index .* is out of bounds"):
+        epochs.drop([len(epochs.events)])
+    with pytest.raises(IndexError, match=r"Epoch index .* is out of bounds"):
+        epochs.drop([-len(epochs.events) - 1])
+    with pytest.raises(TypeError, match="indices must be a scalar or a 1-d array"):
+        epochs.drop([[1, 2], [3, 4]])
+    with pytest.raises(
+        TypeError, match=r".* must be an instance of .* got <class '.*'> instead."
+    ):
+        epochs.drop([1], reason=("a", "b", 2))
 
     # Test selection attribute
     assert_array_equal(epochs.selection, np.where(events[:, 2] == event_id)[0])
@@ -3202,6 +3347,18 @@ def test_drop_epochs():
     assert_array_equal(events[epochs[3:].selection], events1[[5, 6]])
     assert_array_equal(events[epochs["1"].selection], events1[[0, 1, 3, 5, 6]])
 
+    # Test using tuple to drop epochs
+    raw, events, picks = _get_data()
+    epochs_tuple = Epochs(raw, events, event_id, tmin, tmax, picks=picks, preload=True)
+    selection_tuple = epochs_tuple.selection.copy()
+    epochs_tuple.drop((2, 3, 4), reason=("a", "b"))
+    n_events = len(epochs.events)
+    assert [epochs_tuple.drop_log[k] for k in selection_tuple[[2, 3, 4]]] == [
+        ("a", "b"),
+        ("a", "b"),
+        ("a", "b"),
+    ]
+
 
 @pytest.mark.parametrize("preload", (True, False))
 def test_drop_epochs_mult(preload):