From b9a4acae708ee58a0a6256e15e03ec8ed59c581c Mon Sep 17 00:00:00 2001
From: Alex Rockhill <aprockhill@mailbox.org>
Date: Wed, 3 Jan 2024 16:04:41 -0800
Subject: [PATCH 1/8] [ENH, MRG] Add interpolation per epoch [skip ci]

---
 .../preprocessing/interpolate_bad_channels.py | 21 ++++++++
 mne/channels/channels.py                      | 26 ++--------
 mne/epochs.py                                 | 51 +++++++++++++++++++
 mne/tests/test_epochs.py                      | 34 +++++++++++++
 mne/utils/docs.py                             | 31 +++++++++++
 5 files changed, 141 insertions(+), 22 deletions(-)

diff --git a/examples/preprocessing/interpolate_bad_channels.py b/examples/preprocessing/interpolate_bad_channels.py
index a56aec7d8f7..75a53bc8fab 100644
--- a/examples/preprocessing/interpolate_bad_channels.py
+++ b/examples/preprocessing/interpolate_bad_channels.py
@@ -23,6 +23,7 @@
 
 # sphinx_gallery_thumbnail_number = 2
 
+import numpy as np
 import mne
 from mne.datasets import sample
 
@@ -48,6 +49,26 @@
 )
 evoked_interp_mne.plot(exclude=[], picks=("grad", "eeg"))
 
+# %%
+# You can also interpolate bad channels per epoch
+raw = mne.io.read_raw(meg_path / "sample_audvis_raw.fif")
+events = mne.read_events(meg_path / "sample_audvis_raw-eve.fif")
+epochs = mne.Epochs(raw, events=events)
+
+# try to only remove bad channels on some epochs to save EEG 053
+epochs.drop_bad(reject=dict(grad=4000e-13, mag=4e-12, eeg=100e-6))
+
+interpolate_channels = [entry if len(entry) < 5 else tuple()
+                        for entry in epochs.drop_log]
+drop_epochs = np.array([len(entry) >= 5 for entry in epochs.drop_log])
+del epochs
+
+epochs = mne.Epochs(raw, events=events)
+epochs.interpolate_bads_per_epoch(interpolate_channels)
+epochs = epochs[~drop_epochs]
+epochs.average().plot()
+
+
 # %%
 # References
 # ----------
diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 325be7350a6..2b7aac3df92 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -823,36 +823,18 @@ def interpolate_bads(
         ----------
         reset_bads : bool
             If True, remove the bads from info.
-        mode : str
-            Either ``'accurate'`` or ``'fast'``, determines the quality of the
-            Legendre polynomial expansion used for interpolation of channels
-            using the minimum-norm method.
-        origin : array-like, shape (3,) | str
-            Origin of the sphere in the head coordinate frame and in meters.
-            Can be ``'auto'`` (default), which means a head-digitization-based
-            origin fit.
+        %(mode_interp)s
+        %(origin_interp)s
 
             .. versionadded:: 0.17
-        method : dict | str | None
-            Method to use for each channel type.
-
-            - ``"meg"`` channels support ``"MNE"`` (default) and ``"nan"``
-            - ``"eeg"`` channels support ``"spline"`` (default), ``"MNE"`` and ``"nan"``
-            - ``"fnirs"`` channels support ``"nearest"`` (default) and ``"nan"``
-
-            None is an alias for::
-
-                method=dict(meg="MNE", eeg="spline", fnirs="nearest")
-
-            If a :class:`str` is provided, the method will be applied to all channel
-            types supported and available in the instance. The method ``"nan"`` will
-            replace the channel data with ``np.nan``.
+        %(method_interp)s
 
             .. warning::
                 Be careful when using ``method="nan"``; the default value
                 ``reset_bads=True`` may not be what you want.
 
             .. versionadded:: 0.21
+
         exclude : list | tuple
             The channels to exclude from interpolation. If excluded a bad
             channel will stay in bads.
diff --git a/mne/epochs.py b/mne/epochs.py
index 34d942536bd..3b45e6f9897 100644
--- a/mne/epochs.py
+++ b/mne/epochs.py
@@ -1410,6 +1410,57 @@ def drop_bad(self, reject="existing", flat="existing", verbose=None):
         self._get_data(out=False, verbose=verbose)
         return self
 
+    @verbose
+    def interpolate_bads_per_epoch(
+        self,
+        interp_chs,
+        mode="accurate",
+        origin="auto",
+        method=None,
+        verbose=None,
+    ):
+        """Interpolate bad channels per epoch.
+
+        Parameters
+        ----------
+        interp_chs : list
+            A list containing channels to interpolate for each epoch.
+        %(mode_interp)s
+        %(origin_interp)s
+        %(method_interp)s
+        %(verbose)s
+
+        Returns
+        -------
+        epochs : instance of Epochs
+            The epochs with bad channels interpolated per epoch. Operates in-place.
+
+        Notes
+        -----
+        .. versionadded:: 1.7
+        """
+        _check_preload(self, "epochs.interpolate_bads_per_epoch")
+        if len(interp_chs) != len(self):
+            raise ValueError(
+                "The length of ``interp_chs`` must be "
+                f"the same as the the number of epochs ({len(self)}), "
+                f"got {len(interp_chs)}"
+            )
+        for i, this_interp_ch in enumerate(interp_chs):
+            chs_not_found = [ch for ch in this_interp_ch if ch not in self.ch_names]
+            if chs_not_found:
+                raise ValueError(
+                    f"Channels {chs_not_found} not found " f"for interp_chs[{i}]"
+                )
+        for epoch_idx, this_interp_chs in enumerate(interp_chs):
+            if this_interp_chs:
+                logger.debug(f"Interpolating {this_interp_chs} on epoch {epoch_idx}")
+                epoch = self[epoch_idx]
+                epoch.info["bads"] = list(this_interp_chs)
+                epoch.interpolate_bads(mode=mode, origin=origin, method=method)
+                self._data[epoch_idx] = epoch._data
+        return self
+
     def drop_log_stats(self, ignore=("IGNORED",)):
         """Compute the channel stats based on a drop_log from Epochs.
 
diff --git a/mne/tests/test_epochs.py b/mne/tests/test_epochs.py
index c68fc7ce6bd..362f0cc67e4 100644
--- a/mne/tests/test_epochs.py
+++ b/mne/tests/test_epochs.py
@@ -720,6 +720,40 @@ def test_reject():
         assert "is a noop" in log
 
 
+def test_interpolate_bads_per_epochs():
+    raw, events, _ = _get_data()
+    names = raw.ch_names[::5]
+    assert "MEG 2443" in names
+    raw.pick(names).load_data()
+    assert "eog" in raw
+    raw.info.normalize_proj()
+    picks = np.arange(len(raw.ch_names))
+    # cull the list just to contain the relevant event
+    events = events[events[:, 2] == event_id, :]
+    assert len(events) == 7
+    # test interpolate bads per epoch
+    epochs = Epochs(
+        raw,
+        events,
+        event_id,
+        tmin,
+        tmax,
+        picks=picks,
+        preload=True,
+    )
+    with pytest.raises(ValueError, match="length of ``interp_chs``"):
+        epochs.interpolate_bads_per_epoch([])
+    interp_chs = [tuple() for _ in range(len(epochs))]
+    interp_chs[0] = ("foo",)
+    with pytest.raises(ValueError, match="Channels .* not found"):
+        epochs.interpolate_bads_per_epoch(interp_chs)
+
+    interp_chs[0] = (epochs.ch_names[0],)
+    data_before = epochs.get_data().copy()
+    data_after = epochs.interpolate_bads_per_epoch(interp_chs).get_data()
+    assert not np.array_equal(data_before[0], data_after[0])
+
+
 def test_reject_by_annotations_reject_tmin_reject_tmax():
     """Test reject_by_annotations with reject_tmin and reject_tmax defined."""
     # 10 seconds of data, event at 2s, bad segment from 1s to 1.5s
diff --git a/mne/utils/docs.py b/mne/utils/docs.py
index 1fa26fa16dd..c667b20c13c 100644
--- a/mne/utils/docs.py
+++ b/mne/utils/docs.py
@@ -2221,6 +2221,23 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
     forward-backward filtering (via :func:`~scipy.signal.filtfilt`).
 """
 
+docdict["method_interp"] = """
+method : dict | str | None
+    Method to use for each channel type.
+
+    - ``"meg"`` channels support ``"MNE"`` (default) and ``"nan"``
+    - ``"eeg"`` channels support ``"spline"`` (default), ``"MNE"`` and ``"nan"``
+    - ``"fnirs"`` channels support ``"nearest"`` (default) and ``"nan"``
+
+    None is an alias for::
+
+        method=dict(meg="MNE", eeg="spline", fnirs="nearest")
+
+    If a :class:`str` is provided, the method will be applied to all channel
+    types supported and available in the instance. The method ``"nan"`` will
+    replace the channel data with ``np.nan``.
+"""
+
 docdict["method_kw_psd"] = """\
 **method_kw
     Additional keyword arguments passed to the spectral estimation
@@ -2259,6 +2276,13 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
     Extraction mode, see Notes.
 """
 
+docdict["mode_interp"] = """
+mode : str
+    Either ``'accurate'`` or ``'fast'``, determines the quality of the
+    Legendre polynomial expansion used for interpolation of channels
+    using the minimum-norm method.
+"""
+
 docdict["mode_pctf"] = """
 mode : None | 'mean' | 'max' | 'svd'
     Compute summary of PSFs/CTFs across all indices specified in 'idx'.
@@ -2658,6 +2682,13 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
         The default changed from False in 1.4 to True in 1.5.
 """
 
+docdict["origin_interp"] = """
+origin : array-like, shape (3,) | str
+    Origin of the sphere in the head coordinate frame and in meters.
+    Can be ``'auto'`` (default), which means a head-digitization-based
+    origin fit.
+"""
+
 docdict["origin_maxwell"] = """
 origin : array-like, shape (3,) | str
     Origin of internal and external multipolar moment space in meters.

From a8976a4d143ef41d77afde7584b45df30dae3303 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Thu, 4 Jan 2024 00:09:04 +0000
Subject: [PATCH 2/8] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 examples/preprocessing/interpolate_bad_channels.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/examples/preprocessing/interpolate_bad_channels.py b/examples/preprocessing/interpolate_bad_channels.py
index 75a53bc8fab..fe730907105 100644
--- a/examples/preprocessing/interpolate_bad_channels.py
+++ b/examples/preprocessing/interpolate_bad_channels.py
@@ -24,6 +24,7 @@
 # sphinx_gallery_thumbnail_number = 2
 
 import numpy as np
+
 import mne
 from mne.datasets import sample
 
@@ -58,8 +59,9 @@
 # try to only remove bad channels on some epochs to save EEG 053
 epochs.drop_bad(reject=dict(grad=4000e-13, mag=4e-12, eeg=100e-6))
 
-interpolate_channels = [entry if len(entry) < 5 else tuple()
-                        for entry in epochs.drop_log]
+interpolate_channels = [
+    entry if len(entry) < 5 else tuple() for entry in epochs.drop_log
+]
 drop_epochs = np.array([len(entry) >= 5 for entry in epochs.drop_log])
 del epochs
 

From 24a25e5eeb74039b07ccfab21ce752143da3f062 Mon Sep 17 00:00:00 2001
From: Alex Rockhill <aprockhill@mailbox.org>
Date: Wed, 3 Jan 2024 16:10:55 -0800
Subject: [PATCH 3/8] add changelog entry

---
 doc/changes/devel/12334.newfeature.rst | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 doc/changes/devel/12334.newfeature.rst

diff --git a/doc/changes/devel/12334.newfeature.rst b/doc/changes/devel/12334.newfeature.rst
new file mode 100644
index 00000000000..23a330ce6ce
--- /dev/null
+++ b/doc/changes/devel/12334.newfeature.rst
@@ -0,0 +1 @@
+Add :meth:`mne.Epochs.interpolate_bads_per_channel` to interpolate channels only on selected epochs for which they are bad, by `Alex Rockhill`_
\ No newline at end of file

From 9cf13b344b24f0eb536c9c2cbca7cb1500131d82 Mon Sep 17 00:00:00 2001
From: Alex Rockhill <aprockhill@mailbox.org>
Date: Wed, 3 Jan 2024 16:11:29 -0800
Subject: [PATCH 4/8] style

---
 examples/preprocessing/interpolate_bad_channels.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/examples/preprocessing/interpolate_bad_channels.py b/examples/preprocessing/interpolate_bad_channels.py
index 75a53bc8fab..f9741c5675c 100644
--- a/examples/preprocessing/interpolate_bad_channels.py
+++ b/examples/preprocessing/interpolate_bad_channels.py
@@ -58,8 +58,9 @@
 # try to only remove bad channels on some epochs to save EEG 053
 epochs.drop_bad(reject=dict(grad=4000e-13, mag=4e-12, eeg=100e-6))
 
-interpolate_channels = [entry if len(entry) < 5 else tuple()
-                        for entry in epochs.drop_log]
+interpolate_channels = [
+    entry if len(entry) < 5 else tuple() for entry in epochs.drop_log
+]
 drop_epochs = np.array([len(entry) >= 5 for entry in epochs.drop_log])
 del epochs
 

From 37c5acd674583ff714e59e1fcdadff322c0d071c Mon Sep 17 00:00:00 2001
From: Alex Rockhill <aprockhill@mailbox.org>
Date: Wed, 3 Jan 2024 16:16:02 -0800
Subject: [PATCH 5/8] add docstring

---
 mne/tests/test_epochs.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mne/tests/test_epochs.py b/mne/tests/test_epochs.py
index 362f0cc67e4..c0782852919 100644
--- a/mne/tests/test_epochs.py
+++ b/mne/tests/test_epochs.py
@@ -721,6 +721,7 @@ def test_reject():
 
 
 def test_interpolate_bads_per_epochs():
+    """Test interpolating bad channels per epoch."""
     raw, events, _ = _get_data()
     names = raw.ch_names[::5]
     assert "MEG 2443" in names

From df27b947ccc4f4ec55eacdef56be16124d7e860a Mon Sep 17 00:00:00 2001
From: Alex Rockhill <aprockhill@mailbox.org>
Date: Wed, 3 Jan 2024 17:53:52 -0800
Subject: [PATCH 6/8] fix circle, speed up example

---
 examples/preprocessing/interpolate_bad_channels.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/examples/preprocessing/interpolate_bad_channels.py b/examples/preprocessing/interpolate_bad_channels.py
index fe730907105..b189e7ae011 100644
--- a/examples/preprocessing/interpolate_bad_channels.py
+++ b/examples/preprocessing/interpolate_bad_channels.py
@@ -53,11 +53,12 @@
 # %%
 # You can also interpolate bad channels per epoch
 raw = mne.io.read_raw(meg_path / "sample_audvis_raw.fif")
+raw.pick("eeg")  # just to speed up execution
 events = mne.read_events(meg_path / "sample_audvis_raw-eve.fif")
 epochs = mne.Epochs(raw, events=events)
 
 # try to only remove bad channels on some epochs to save EEG 053
-epochs.drop_bad(reject=dict(grad=4000e-13, mag=4e-12, eeg=100e-6))
+epochs.drop_bad(reject=dict(eeg=100e-6))
 
 interpolate_channels = [
     entry if len(entry) < 5 else tuple() for entry in epochs.drop_log
@@ -65,12 +66,11 @@
 drop_epochs = np.array([len(entry) >= 5 for entry in epochs.drop_log])
 del epochs
 
-epochs = mne.Epochs(raw, events=events)
+epochs = mne.Epochs(raw, events=events, preload=True)
 epochs.interpolate_bads_per_epoch(interpolate_channels)
 epochs = epochs[~drop_epochs]
 epochs.average().plot()
 
-
 # %%
 # References
 # ----------

From d9b4b83950e2eab419f1b4c6832db50ca453994a Mon Sep 17 00:00:00 2001
From: Alex Rockhill <aprockhill@mailbox.org>
Date: Thu, 4 Jan 2024 08:36:21 -0800
Subject: [PATCH 7/8] saved version roundtrip to disk

---
 doc/changes/devel/12334.newfeature.rst        |  2 +-
 .../preprocessing/interpolate_bad_channels.py |  3 +-
 mne/_fiff/meas_info.py                        | 18 +++++++--
 mne/_fiff/pick.py                             |  9 ++++-
 mne/_fiff/tag.py                              |  9 ++++-
 mne/_fiff/write.py                            | 38 +++++++++++++++++--
 mne/channels/channels.py                      |  3 +-
 mne/epochs.py                                 | 14 +++++--
 mne/utils/docs.py                             |  5 +++
 9 files changed, 83 insertions(+), 18 deletions(-)

diff --git a/doc/changes/devel/12334.newfeature.rst b/doc/changes/devel/12334.newfeature.rst
index 23a330ce6ce..107b8fe8c30 100644
--- a/doc/changes/devel/12334.newfeature.rst
+++ b/doc/changes/devel/12334.newfeature.rst
@@ -1 +1 @@
-Add :meth:`mne.Epochs.interpolate_bads_per_channel` to interpolate channels only on selected epochs for which they are bad, by `Alex Rockhill`_
\ No newline at end of file
+Allow :meth:`mne.Epochs.interpolate_bads` to interpolate channels only on selected epochs for which they are bad, by `Alex Rockhill`_
\ No newline at end of file
diff --git a/examples/preprocessing/interpolate_bad_channels.py b/examples/preprocessing/interpolate_bad_channels.py
index b189e7ae011..1059408ec55 100644
--- a/examples/preprocessing/interpolate_bad_channels.py
+++ b/examples/preprocessing/interpolate_bad_channels.py
@@ -67,7 +67,8 @@
 del epochs
 
 epochs = mne.Epochs(raw, events=events, preload=True)
-epochs.interpolate_bads_per_epoch(interpolate_channels)
+epochs.info["bads"] = interpolate_channels
+epochs.interpolate_bads()
 epochs = epochs[~drop_epochs]
 epochs.average().plot()
 
diff --git a/mne/_fiff/meas_info.py b/mne/_fiff/meas_info.py
index 483ddc34b52..4d31bfa6915 100644
--- a/mne/_fiff/meas_info.py
+++ b/mne/_fiff/meas_info.py
@@ -951,10 +951,15 @@ def _check_bads_info_compat(bads, info):
     if not len(bads):
         return  # e.g. in empty_info
     for bi, bad in enumerate(bads):
-        _validate_type(bad, str, f"bads[{bi}]")
+        _validate_type(bad, (str, list, tuple), f"bads[{bi}]")
     if "ch_names" not in info:  # somewhere in init, or deepcopy, or _empty_info, etc.
         return
-    missing = [bad for bad in bads if bad not in info["ch_names"]]
+    missing = [
+        bad
+        for bads_list in bads
+        for bad in ([bads_list] if isinstance(bads_list, str) else bads_list)
+        if bad not in info["ch_names"]
+    ]
     if len(missing) > 0:
         raise ValueError(f"bad channel(s) {missing} marked do not exist in info")
 
@@ -2569,8 +2574,13 @@ def read_meas_info(fid, tree, clean_bads=False, verbose=None):
     info["dig"] = _format_dig_points(dig)
     info["bads"] = bads
     info._update_redundant()
-    if clean_bads:
-        info["bads"] = [b for b in bads if b in info["ch_names"]]
+    if clean_bads and info["bads"]:
+        if isinstance(info["bads"][0], str):
+            info["bads"] = [b for b in bads if b in info["ch_names"]]
+        else:
+            info["bads"] = [
+                [b for b in bads_list if b in info["ch_names"]] for bads_list in bads
+            ]
     info["projs"] = projs
     info["comps"] = comps
     info["acq_pars"] = acq_pars
diff --git a/mne/_fiff/pick.py b/mne/_fiff/pick.py
index 4c5854f36fe..269211603ad 100644
--- a/mne/_fiff/pick.py
+++ b/mne/_fiff/pick.py
@@ -670,7 +670,14 @@ def pick_info(info, sel=(), copy=True, verbose=None):
     with info._unlock():
         info["chs"] = [info["chs"][k] for k in sel]
     info._update_redundant()
-    info["bads"] = [ch for ch in info["bads"] if ch in info["ch_names"]]
+    if info["bads"]:
+        if isinstance(info["bads"][0], str):
+            info["bads"] = [ch for ch in info["bads"] if ch in info["ch_names"]]
+        else:
+            info["bads"] = [
+                [ch for ch in bads_list if ch in info["ch_names"]]
+                for bads_list in info["bads"]
+            ]
     if "comps" in info:
         comps = deepcopy(info["comps"])
         for c in comps:
diff --git a/mne/_fiff/tag.py b/mne/_fiff/tag.py
index 81ed12baf6f..6b7848a2bbc 100644
--- a/mne/_fiff/tag.py
+++ b/mne/_fiff/tag.py
@@ -517,7 +517,14 @@ def has_tag(node, kind):
 
 
 def _rename_list(bads, ch_names_mapping):
-    return [ch_names_mapping.get(bad, bad) for bad in bads]
+    if not bads:
+        return bads
+    if isinstance(bads[0], str):
+        return [ch_names_mapping.get(bad, bad) for bad in bads]
+    else:
+        return [
+            [ch_names_mapping.get(bad, bad) for bad in bads_list] for bads_list in bads
+        ]
 
 
 def _int_item(x):
diff --git a/mne/_fiff/write.py b/mne/_fiff/write.py
index 3e6621d0069..a35cbd4c82c 100644
--- a/mne/_fiff/write.py
+++ b/mne/_fiff/write.py
@@ -156,16 +156,46 @@ def write_name_list_sanitized(fid, kind, lst, name):
 def _safe_name_list(lst, operation, name):
     if operation == "write":
         assert isinstance(lst, (list, tuple, np.ndarray)), type(lst)
-        if any("{COLON}" in val for val in lst):
-            raise ValueError(f'The substring "{{COLON}}" in {name} not supported.')
-        return ":".join(val.replace(":", "{COLON}") for val in lst)
+        if any(
+            "{COLON}" in val or "{COMMA}" in val
+            for val2 in lst
+            for val in ([val2] if isinstance(val2, str) else val2)
+        ):
+            raise ValueError(
+                f'The substring "{{COLON}}" or "{{COMMA}}" in {name} not supported.'
+            )
+        if not lst:
+            return ""
+        if isinstance(lst[0], str):
+            return ":".join(val.replace(":", "{COLON}") for val in lst)
+        return ",".join(
+            ":".join(
+                val.replace(":", "{COLON}").replace(",", "{COMMA}") for val in val2
+            )
+            for val2 in lst
+        )
     else:
         # take a sanitized string and return a list of strings
         assert operation == "read"
         assert lst is None or isinstance(lst, str)
         if not lst:  # None or empty string
             return []
-        return [val.replace("{COLON}", ":") for val in lst.split(":")]
+        if "," in lst:
+            return [
+                (
+                    [
+                        val.replace("{COLON}", ":").replace("{COMMA}", ",")
+                        for val in val2.split(":")
+                    ]
+                    if val2
+                    else list()
+                )
+                for val2 in lst.split(",")
+            ]
+        return [
+            val.replace("{COLON}", ":").replace("{COMMA}", ",")
+            for val in lst.split(":")
+        ]
 
 
 def write_float_matrix(fid, kind, mat):
diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 2b7aac3df92..5ed3a8967b3 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -821,8 +821,7 @@ def interpolate_bads(
 
         Parameters
         ----------
-        reset_bads : bool
-            If True, remove the bads from info.
+        %(reset_bads)s
         %(mode_interp)s
         %(origin_interp)s
 
diff --git a/mne/epochs.py b/mne/epochs.py
index 3b45e6f9897..f65b3e87e19 100644
--- a/mne/epochs.py
+++ b/mne/epochs.py
@@ -66,7 +66,12 @@
 )
 from .baseline import _check_baseline, _log_rescale, rescale
 from .bem import _check_origin
-from .channels.channels import InterpolationMixin, ReferenceMixin, UpdateChannelsMixin
+from .channels.channels import (
+    InterpolationMixin,
+    ReferenceMixin,
+    UpdateChannelsMixin,
+    interpolate_bads,
+)
 from .event import _read_events_fif, make_fixed_length_events, match_event_names
 from .evoked import EvokedArray
 from .filter import FilterMixin, _check_fun, detrend
@@ -1410,13 +1415,14 @@ def drop_bad(self, reject="existing", flat="existing", verbose=None):
         self._get_data(out=False, verbose=verbose)
         return self
 
-    @verbose
-    def interpolate_bads_per_epoch(
+    @copy_function_doc_to_method_doc(interpolate_bads)
+    def interpolate_bads(
         self,
-        interp_chs,
+        reset_bads=True,
         mode="accurate",
         origin="auto",
         method=None,
+        exclude=(),
         verbose=None,
     ):
         """Interpolate bad channels per epoch.
diff --git a/mne/utils/docs.py b/mne/utils/docs.py
index c667b20c13c..d90acbc3a17 100644
--- a/mne/utils/docs.py
+++ b/mne/utils/docs.py
@@ -3357,6 +3357,11 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
     The resolution of the topomap image (number of pixels along each side).
 """
 
+docdict["reset_bads"] = """
+reset_bads : bool
+    If True, remove the bads from info.
+"""
+
 docdict["return_pca_vars_pctf"] = """
 return_pca_vars : bool
     Whether or not to return the explained variances across the specified

From ab01496aa5d45d2dfe0bfc925d68271ed3c30e31 Mon Sep 17 00:00:00 2001
From: Alex Rockhill <aprockhill@mailbox.org>
Date: Thu, 4 Jan 2024 09:07:47 -0800
Subject: [PATCH 8/8] revert info bads changes, overload

---
 doc/changes/devel/12334.newfeature.rst        |  2 +-
 .../preprocessing/interpolate_bad_channels.py |  3 +-
 mne/_fiff/meas_info.py                        | 18 ++------
 mne/_fiff/pick.py                             |  9 +---
 mne/_fiff/tag.py                              |  9 +---
 mne/_fiff/write.py                            | 38 ++--------------
 mne/channels/channels.py                      |  5 +--
 mne/epochs.py                                 | 44 ++++++++++++++-----
 mne/tests/test_epochs.py                      |  8 ++--
 mne/utils/docs.py                             |  6 +++
 10 files changed, 56 insertions(+), 86 deletions(-)

diff --git a/doc/changes/devel/12334.newfeature.rst b/doc/changes/devel/12334.newfeature.rst
index 107b8fe8c30..da738a25838 100644
--- a/doc/changes/devel/12334.newfeature.rst
+++ b/doc/changes/devel/12334.newfeature.rst
@@ -1 +1 @@
-Allow :meth:`mne.Epochs.interpolate_bads` to interpolate channels only on selected epochs for which they are bad, by `Alex Rockhill`_
\ No newline at end of file
+Allow :meth:`mne.Epochs.interpolate_bads` to interpolate channels only on selected epochs for which they are bad using ``interp_chs``, by `Alex Rockhill`_
\ No newline at end of file
diff --git a/examples/preprocessing/interpolate_bad_channels.py b/examples/preprocessing/interpolate_bad_channels.py
index 1059408ec55..969b090d03d 100644
--- a/examples/preprocessing/interpolate_bad_channels.py
+++ b/examples/preprocessing/interpolate_bad_channels.py
@@ -67,8 +67,7 @@
 del epochs
 
 epochs = mne.Epochs(raw, events=events, preload=True)
-epochs.info["bads"] = interpolate_channels
-epochs.interpolate_bads()
+epochs.interpolate_bads(interp_chs=interpolate_channels)
 epochs = epochs[~drop_epochs]
 epochs.average().plot()
 
diff --git a/mne/_fiff/meas_info.py b/mne/_fiff/meas_info.py
index 4d31bfa6915..483ddc34b52 100644
--- a/mne/_fiff/meas_info.py
+++ b/mne/_fiff/meas_info.py
@@ -951,15 +951,10 @@ def _check_bads_info_compat(bads, info):
     if not len(bads):
         return  # e.g. in empty_info
     for bi, bad in enumerate(bads):
-        _validate_type(bad, (str, list, tuple), f"bads[{bi}]")
+        _validate_type(bad, str, f"bads[{bi}]")
     if "ch_names" not in info:  # somewhere in init, or deepcopy, or _empty_info, etc.
         return
-    missing = [
-        bad
-        for bads_list in bads
-        for bad in ([bads_list] if isinstance(bads_list, str) else bads_list)
-        if bad not in info["ch_names"]
-    ]
+    missing = [bad for bad in bads if bad not in info["ch_names"]]
     if len(missing) > 0:
         raise ValueError(f"bad channel(s) {missing} marked do not exist in info")
 
@@ -2574,13 +2569,8 @@ def read_meas_info(fid, tree, clean_bads=False, verbose=None):
     info["dig"] = _format_dig_points(dig)
     info["bads"] = bads
     info._update_redundant()
-    if clean_bads and info["bads"]:
-        if isinstance(info["bads"][0], str):
-            info["bads"] = [b for b in bads if b in info["ch_names"]]
-        else:
-            info["bads"] = [
-                [b for b in bads_list if b in info["ch_names"]] for bads_list in bads
-            ]
+    if clean_bads:
+        info["bads"] = [b for b in bads if b in info["ch_names"]]
     info["projs"] = projs
     info["comps"] = comps
     info["acq_pars"] = acq_pars
diff --git a/mne/_fiff/pick.py b/mne/_fiff/pick.py
index 269211603ad..4c5854f36fe 100644
--- a/mne/_fiff/pick.py
+++ b/mne/_fiff/pick.py
@@ -670,14 +670,7 @@ def pick_info(info, sel=(), copy=True, verbose=None):
     with info._unlock():
         info["chs"] = [info["chs"][k] for k in sel]
     info._update_redundant()
-    if info["bads"]:
-        if isinstance(info["bads"][0], str):
-            info["bads"] = [ch for ch in info["bads"] if ch in info["ch_names"]]
-        else:
-            info["bads"] = [
-                [ch for ch in bads_list if ch in info["ch_names"]]
-                for bads_list in info["bads"]
-            ]
+    info["bads"] = [ch for ch in info["bads"] if ch in info["ch_names"]]
     if "comps" in info:
         comps = deepcopy(info["comps"])
         for c in comps:
diff --git a/mne/_fiff/tag.py b/mne/_fiff/tag.py
index 6b7848a2bbc..81ed12baf6f 100644
--- a/mne/_fiff/tag.py
+++ b/mne/_fiff/tag.py
@@ -517,14 +517,7 @@ def has_tag(node, kind):
 
 
 def _rename_list(bads, ch_names_mapping):
-    if not bads:
-        return bads
-    if isinstance(bads[0], str):
-        return [ch_names_mapping.get(bad, bad) for bad in bads]
-    else:
-        return [
-            [ch_names_mapping.get(bad, bad) for bad in bads_list] for bads_list in bads
-        ]
+    return [ch_names_mapping.get(bad, bad) for bad in bads]
 
 
 def _int_item(x):
diff --git a/mne/_fiff/write.py b/mne/_fiff/write.py
index a35cbd4c82c..3e6621d0069 100644
--- a/mne/_fiff/write.py
+++ b/mne/_fiff/write.py
@@ -156,46 +156,16 @@ def write_name_list_sanitized(fid, kind, lst, name):
 def _safe_name_list(lst, operation, name):
     if operation == "write":
         assert isinstance(lst, (list, tuple, np.ndarray)), type(lst)
-        if any(
-            "{COLON}" in val or "{COMMA}" in val
-            for val2 in lst
-            for val in ([val2] if isinstance(val2, str) else val2)
-        ):
-            raise ValueError(
-                f'The substring "{{COLON}}" or "{{COMMA}}" in {name} not supported.'
-            )
-        if not lst:
-            return ""
-        if isinstance(lst[0], str):
-            return ":".join(val.replace(":", "{COLON}") for val in lst)
-        return ",".join(
-            ":".join(
-                val.replace(":", "{COLON}").replace(",", "{COMMA}") for val in val2
-            )
-            for val2 in lst
-        )
+        if any("{COLON}" in val for val in lst):
+            raise ValueError(f'The substring "{{COLON}}" in {name} not supported.')
+        return ":".join(val.replace(":", "{COLON}") for val in lst)
     else:
         # take a sanitized string and return a list of strings
         assert operation == "read"
         assert lst is None or isinstance(lst, str)
         if not lst:  # None or empty string
             return []
-        if "," in lst:
-            return [
-                (
-                    [
-                        val.replace("{COLON}", ":").replace("{COMMA}", ",")
-                        for val in val2.split(":")
-                    ]
-                    if val2
-                    else list()
-                )
-                for val2 in lst.split(",")
-            ]
-        return [
-            val.replace("{COLON}", ":").replace("{COMMA}", ",")
-            for val in lst.split(":")
-        ]
+        return [val.replace("{COLON}", ":") for val in lst.split(":")]
 
 
 def write_float_matrix(fid, kind, mat):
diff --git a/mne/channels/channels.py b/mne/channels/channels.py
index 5ed3a8967b3..25eca7ce65a 100644
--- a/mne/channels/channels.py
+++ b/mne/channels/channels.py
@@ -813,6 +813,7 @@ def interpolate_bads(
         origin="auto",
         method=None,
         exclude=(),
+        *,
         verbose=None,
     ):
         """Interpolate bad MEG and EEG channels.
@@ -834,9 +835,7 @@ def interpolate_bads(
 
             .. versionadded:: 0.21
 
-        exclude : list | tuple
-            The channels to exclude from interpolation. If excluded a bad
-            channel will stay in bads.
+        %(exclude_interp)s
         %(verbose)s
 
         Returns
diff --git a/mne/epochs.py b/mne/epochs.py
index f65b3e87e19..bd2b0c31dab 100644
--- a/mne/epochs.py
+++ b/mne/epochs.py
@@ -66,12 +66,7 @@
 )
 from .baseline import _check_baseline, _log_rescale, rescale
 from .bem import _check_origin
-from .channels.channels import (
-    InterpolationMixin,
-    ReferenceMixin,
-    UpdateChannelsMixin,
-    interpolate_bads,
-)
+from .channels.channels import InterpolationMixin, ReferenceMixin, UpdateChannelsMixin
 from .event import _read_events_fif, make_fixed_length_events, match_event_names
 from .evoked import EvokedArray
 from .filter import FilterMixin, _check_fun, detrend
@@ -1415,7 +1410,6 @@ def drop_bad(self, reject="existing", flat="existing", verbose=None):
         self._get_data(out=False, verbose=verbose)
         return self
 
-    @copy_function_doc_to_method_doc(interpolate_bads)
     def interpolate_bads(
         self,
         reset_bads=True,
@@ -1423,17 +1417,25 @@ def interpolate_bads(
         origin="auto",
         method=None,
         exclude=(),
+        *,
+        interp_chs=None,
         verbose=None,
     ):
-        """Interpolate bad channels per epoch.
+        """Interpolate bad channels, optionally different channels on each epoch.
+
+        Operates in-place.
 
         Parameters
         ----------
-        interp_chs : list
-            A list containing channels to interpolate for each epoch.
+        %(reset_bads)s
         %(mode_interp)s
         %(origin_interp)s
         %(method_interp)s
+        %(exclude_interp)s
+        interp_chs : list | None
+            The channels to interpolate on each epoch. Must be the same
+            length as the epochs and each list entry must be a list of channels
+            to interpolate for each epoch.
         %(verbose)s
 
         Returns
@@ -1443,9 +1445,19 @@ def interpolate_bads(
 
         Notes
         -----
+        The ``"MNE"`` method uses minimum-norm projection to a sphere and back.
+
         .. versionadded:: 1.7
         """
-        _check_preload(self, "epochs.interpolate_bads_per_epoch")
+        if interp_chs is None:
+            return super().interpolate_bads(
+                reset_bads=reset_bads,
+                mode=mode,
+                origin=origin,
+                method=method,
+                exclude=exclude,
+            )
+        _check_preload(self, "epochs.interpolate_bads")
         if len(interp_chs) != len(self):
             raise ValueError(
                 "The length of ``interp_chs`` must be "
@@ -1463,8 +1475,16 @@ def interpolate_bads(
                 logger.debug(f"Interpolating {this_interp_chs} on epoch {epoch_idx}")
                 epoch = self[epoch_idx]
                 epoch.info["bads"] = list(this_interp_chs)
-                epoch.interpolate_bads(mode=mode, origin=origin, method=method)
+                epoch.interpolate_bads(
+                    reset_bads=epoch_idx == 0,  # check once for warning
+                    mode=mode,
+                    origin=origin,
+                    method=method,
+                    exclude=exclude,
+                )
                 self._data[epoch_idx] = epoch._data
+                if epoch_idx == 0:
+                    self.info["bads"] = epoch.info["bads"]
         return self
 
     def drop_log_stats(self, ignore=("IGNORED",)):
diff --git a/mne/tests/test_epochs.py b/mne/tests/test_epochs.py
index c0782852919..f339c8fe9ca 100644
--- a/mne/tests/test_epochs.py
+++ b/mne/tests/test_epochs.py
@@ -720,7 +720,7 @@ def test_reject():
         assert "is a noop" in log
 
 
-def test_interpolate_bads_per_epochs():
+def test_interpolate_bads_per_epoch():
     """Test interpolating bad channels per epoch."""
     raw, events, _ = _get_data()
     names = raw.ch_names[::5]
@@ -743,15 +743,15 @@ def test_interpolate_bads_per_epochs():
         preload=True,
     )
     with pytest.raises(ValueError, match="length of ``interp_chs``"):
-        epochs.interpolate_bads_per_epoch([])
+        epochs.interpolate_bads(interp_chs=[])
     interp_chs = [tuple() for _ in range(len(epochs))]
     interp_chs[0] = ("foo",)
     with pytest.raises(ValueError, match="Channels .* not found"):
-        epochs.interpolate_bads_per_epoch(interp_chs)
+        epochs.interpolate_bads(interp_chs=interp_chs)
 
     interp_chs[0] = (epochs.ch_names[0],)
     data_before = epochs.get_data().copy()
-    data_after = epochs.interpolate_bads_per_epoch(interp_chs).get_data()
+    data_after = epochs.interpolate_bads(interp_chs=interp_chs).get_data()
     assert not np.array_equal(data_before[0], data_after[0])
 
 
diff --git a/mne/utils/docs.py b/mne/utils/docs.py
index d90acbc3a17..27d1b1d1c58 100644
--- a/mne/utils/docs.py
+++ b/mne/utils/docs.py
@@ -1168,6 +1168,12 @@ def _reflow_param_docstring(docstring, has_first_line=True, width=75):
     (below the nasion) and positive Y values (in front of the LPA/RPA).
 """
 
+docdict["exclude_interp"] = """
+exclude : list | tuple
+    The channels to exclude from interpolation. If excluded a bad
+    channel will stay in bads.
+"""
+
 _exclude_spectrum = """\
 exclude : list of str | 'bads'
     Channel names to exclude{}. If ``'bads'``, channels