Merge branch 'main' into fix_annotations_orig_time

doc/changes/devel/13044.newfeature.rst

@@ -0,0 +1 @@
+Add :meth:`mne.Evoked.interpolate_to` to allow interpolating EEG data to other montages, by :newcontrib:`Antoine Collas`.

doc/changes/names.inc

@@ -24,6 +24,7 @@
 .. _Anna Padee: https://github.com/apadee/
 .. _Annalisa Pascarella: https://www.iac.cnr.it/personale/annalisa-pascarella
 .. _Anne-Sophie Dubarry: https://github.com/annesodub
+.. _Antoine Collas: https://www.antoinecollas.fr
 .. _Antoine Gauthier: https://github.com/Okamille
 .. _Antti Rantala: https://github.com/Odingod
 .. _Apoorva Karekal: https://github.com/apoorva6262

doc/references.bib

@@ -2514,3 +2514,11 @@ @article{OyamaEtAl2015
 	year = {2015},
 	pages = {24--36},
 }
+
+@inproceedings{MellotEtAl2024,
+	title = {Physics-informed and Unsupervised Riemannian Domain Adaptation for Machine Learning on Heterogeneous EEG Datasets},
+	author = {Mellot, Apolline and Collas, Antoine and Chevallier, Sylvain and Engemann, Denis and Gramfort, Alexandre},
+	booktitle = {Proceedings of the 32nd European Signal Processing Conference (EUSIPCO)},
+	year = {2024},
+	address = {Lyon, France}
+}

examples/preprocessing/interpolate_to.py

@@ -0,0 +1,81 @@
+"""
+.. _ex-interpolate-to-any-montage:
+
+======================================================
+Interpolate EEG data to any montage
+======================================================
+
+This example demonstrates how to interpolate EEG channels to match a given montage.
+This can be useful for standardizing
+EEG channel layouts across different datasets (see :footcite:`MellotEtAl2024`).
+
+- Using the field interpolation for EEG data.
+- Using the target montage "biosemi16".
+
+In this example, the data from the original EEG channels will be
+interpolated onto the positions defined by the "biosemi16" montage.
+"""
+
+# Authors: Antoine Collas <[email protected]>
+# License: BSD-3-Clause
+# Copyright the MNE-Python contributors.
+
+import matplotlib.pyplot as plt
+
+import mne
+from mne.channels import make_standard_montage
+from mne.datasets import sample
+
+print(__doc__)
+ylim = (-10, 10)
+
+# %%
+# Load EEG data
+data_path = sample.data_path()
+eeg_file_path = data_path / "MEG" / "sample" / "sample_audvis-ave.fif"
+evoked = mne.read_evokeds(eeg_file_path, condition="Left Auditory", baseline=(None, 0))
+
+# Select only EEG channels
+evoked.pick("eeg")
+
+# Plot the original EEG layout
+evoked.plot(exclude=[], picks="eeg", ylim=dict(eeg=ylim))
+
+# %%
+# Define the target montage
+standard_montage = make_standard_montage("biosemi16")
+
+# %%
+# Use interpolate_to to project EEG data to the standard montage
+evoked_interpolated_spline = evoked.copy().interpolate_to(
+    standard_montage, method="spline"
+)
+
+# Plot the interpolated EEG layout
+evoked_interpolated_spline.plot(exclude=[], picks="eeg", ylim=dict(eeg=ylim))
+
+# %%
+# Use interpolate_to to project EEG data to the standard montage
+evoked_interpolated_mne = evoked.copy().interpolate_to(standard_montage, method="MNE")
+
+# Plot the interpolated EEG layout
+evoked_interpolated_mne.plot(exclude=[], picks="eeg", ylim=dict(eeg=ylim))
+
+# %%
+# Comparing before and after interpolation
+fig, axs = plt.subplots(3, 1, figsize=(8, 6), constrained_layout=True)
+evoked.plot(exclude=[], picks="eeg", axes=axs[0], show=False, ylim=dict(eeg=ylim))
+axs[0].set_title("Original EEG Layout")
+evoked_interpolated_spline.plot(
+    exclude=[], picks="eeg", axes=axs[1], show=False, ylim=dict(eeg=ylim)
+)
+axs[1].set_title("Interpolated to Standard 1020 Montage using spline interpolation")
+evoked_interpolated_mne.plot(
+    exclude=[], picks="eeg", axes=axs[2], show=False, ylim=dict(eeg=ylim)
+)
+axs[2].set_title("Interpolated to Standard 1020 Montage using MNE interpolation")
+
+# %%
+# References
+# ----------
+# .. footbibliography::

mne/channels/channels.py

@@ -41,7 +41,7 @@
     pick_info,
     pick_types,
 )
-from .._fiff.proj import setup_proj
+from .._fiff.proj import _has_eeg_average_ref_proj, setup_proj
 from .._fiff.reference import add_reference_channels, set_eeg_reference
 from .._fiff.tag import _rename_list
 from ..bem import _check_origin
@@ -960,6 +960,162 @@ def interpolate_bads(
 
         return self
 
+    def interpolate_to(self, sensors, origin="auto", method="spline", reg=0.0):
+        """Interpolate EEG data onto a new montage.
+
+        .. warning::
+            Be careful, only EEG channels are interpolated. Other channel types are
+            not interpolated.
+
+        Parameters
+        ----------
+        sensors : DigMontage
+            The target montage containing channel positions to interpolate onto.
+        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.
+        method : str
+            Method to use for EEG channels.
+            Supported methods are 'spline' (default) and 'MNE'.
+        reg : float
+            The regularization parameter for the interpolation method
+            (only used when the method is 'spline').
+
+        Returns
+        -------
+        inst : instance of Raw, Epochs, or Evoked
+            The instance with updated channel locations and data.
+
+        Notes
+        -----
+        This method is useful for standardizing EEG layouts across datasets.
+        However, some attributes may be lost after interpolation.
+
+        .. versionadded:: 1.10.0
+        """
+        from ..epochs import BaseEpochs, EpochsArray
+        from ..evoked import Evoked, EvokedArray
+        from ..forward._field_interpolation import _map_meg_or_eeg_channels
+        from ..io import RawArray
+        from ..io.base import BaseRaw
+        from .interpolation import _make_interpolation_matrix
+        from .montage import DigMontage
+
+        # Check that the method option is valid.
+        _check_option("method", method, ["spline", "MNE"])
+        _validate_type(sensors, DigMontage, "sensors")
+
+        # Get target positions from the montage
+        ch_pos = sensors.get_positions().get("ch_pos", {})
+        target_ch_names = list(ch_pos.keys())
+        if not target_ch_names:
+            raise ValueError(
+                "The provided sensors configuration has no channel positions."
+            )
+
+        # Get original channel order
+        orig_names = self.info["ch_names"]
+
+        # Identify EEG channel
+        picks_good_eeg = pick_types(self.info, meg=False, eeg=True, exclude="bads")
+        if len(picks_good_eeg) == 0:
+            raise ValueError("No good EEG channels available for interpolation.")
+        # Also get the full list of EEG channel indices (including bad channels)
+        picks_remove_eeg = pick_types(self.info, meg=False, eeg=True, exclude=[])
+        eeg_names_orig = [orig_names[i] for i in picks_remove_eeg]
+
+        # Identify non-EEG channels in original order
+        non_eeg_names_ordered = [ch for ch in orig_names if ch not in eeg_names_orig]
+
+        # Create destination info for new EEG channels
+        sfreq = self.info["sfreq"]
+        info_interp = create_info(
+            ch_names=target_ch_names,
+            sfreq=sfreq,
+            ch_types=["eeg"] * len(target_ch_names),
+        )
+        info_interp.set_montage(sensors)
+        info_interp["bads"] = [ch for ch in self.info["bads"] if ch in target_ch_names]
+        # Do not assign "projs" directly.
+
+        # Compute the interpolation mapping
+        if method == "spline":
+            origin_val = _check_origin(origin, self.info)
+            pos_from = self.info._get_channel_positions(picks_good_eeg) - origin_val
+            pos_to = np.stack(list(ch_pos.values()), axis=0)
+
+            def _check_pos_sphere(pos):
+                d = np.linalg.norm(pos, axis=-1)
+                d_norm = np.mean(d / np.mean(d))
+                if np.abs(1.0 - d_norm) > 0.1:
+                    warn("Your spherical fit is poor; interpolation may be inaccurate.")
+
+            _check_pos_sphere(pos_from)
+            _check_pos_sphere(pos_to)
+            mapping = _make_interpolation_matrix(pos_from, pos_to, alpha=reg)
+
+        else:
+            assert method == "MNE"
+            info_eeg = pick_info(self.info, picks_good_eeg)
+            # If the original info has an average EEG reference projector but
+            # the destination info does not,
+            # update info_interp via a temporary RawArray.
+            if _has_eeg_average_ref_proj(self.info) and not _has_eeg_average_ref_proj(
+                info_interp
+            ):
+                # Create dummy data: shape (n_channels, 1)
+                temp_data = np.zeros((len(info_interp["ch_names"]), 1))
+                temp_raw = RawArray(temp_data, info_interp, first_samp=0)
+                # Using the public API, add an average reference projector.
+                temp_raw.set_eeg_reference(
+                    ref_channels="average", projection=True, verbose=False
+                )
+                # Extract the updated info.
+                info_interp = temp_raw.info
+            mapping = _map_meg_or_eeg_channels(
+                info_eeg, info_interp, mode="accurate", origin=origin
+            )
+
+        # Interpolate EEG data
+        data_good = self.get_data(picks=picks_good_eeg)
+        data_interp = mapping @ data_good
+
+        # Create a new instance for the interpolated EEG channels
+        # TODO: Creating a new instance leads to a loss of information.
+        #       We should consider updating the existing instance in the future
+        #       by 1) drop channels, 2) add channels, 3) re-order channels.
+        if isinstance(self, BaseRaw):
+            inst_interp = RawArray(data_interp, info_interp, first_samp=self.first_samp)
+        elif isinstance(self, BaseEpochs):
+            inst_interp = EpochsArray(data_interp, info_interp)
+        else:
+            assert isinstance(self, Evoked)
+            inst_interp = EvokedArray(data_interp, info_interp)
+
+        # Merge only if non-EEG channels exist
+        if not non_eeg_names_ordered:
+            return inst_interp
+
+        inst_non_eeg = self.copy().pick(non_eeg_names_ordered).load_data()
+        inst_out = inst_non_eeg.add_channels([inst_interp], force_update_info=True)
+
+        # Reorder channels
+        # Insert the entire new EEG block at the position of the first EEG channel.
+        orig_names_arr = np.array(orig_names)
+        mask_eeg = np.isin(orig_names_arr, eeg_names_orig)
+        if mask_eeg.any():
+            first_eeg_index = np.where(mask_eeg)[0][0]
+            pre = orig_names_arr[:first_eeg_index]
+            new_eeg = np.array(info_interp["ch_names"])
+            post = orig_names_arr[first_eeg_index:]
+            post = post[~np.isin(orig_names_arr[first_eeg_index:], eeg_names_orig)]
+            new_order = np.concatenate((pre, new_eeg, post)).tolist()
+        else:
+            new_order = orig_names
+        inst_out.reorder_channels(new_order)
+        return inst_out
+
 
 @verbose
 def rename_channels(info, mapping, allow_duplicates=False, *, verbose=None):

mne/channels/tests/test_interpolation.py

@@ -12,7 +12,7 @@
 from mne import Epochs, pick_channels, pick_types, read_events
 from mne._fiff.constants import FIFF
 from mne._fiff.proj import _has_eeg_average_ref_proj
-from mne.channels import make_dig_montage
+from mne.channels import make_dig_montage, make_standard_montage
 from mne.channels.interpolation import _make_interpolation_matrix
 from mne.datasets import testing
 from mne.io import RawArray, read_raw_ctf, read_raw_fif, read_raw_nirx
@@ -439,3 +439,85 @@ def test_method_str():
         raw.interpolate_bads(method="spline")
     raw.pick("eeg", exclude=())
     raw.interpolate_bads(method="spline")
+
+
+@pytest.mark.parametrize("montage_name", ["biosemi16", "standard_1020"])
+@pytest.mark.parametrize("method", ["spline", "MNE"])
+@pytest.mark.parametrize("data_type", ["raw", "epochs", "evoked"])
+def test_interpolate_to_eeg(montage_name, method, data_type):
+    """Test the interpolate_to method for EEG for raw, epochs, and evoked."""
+    # Load EEG data
+    raw, epochs_eeg = _load_data("eeg")
+    epochs_eeg = epochs_eeg.copy()
+
+    # Load data for raw
+    raw.load_data()
+
+    # Create a target montage
+    montage = make_standard_montage(montage_name)
+
+    # Prepare data to interpolate to
+    if data_type == "raw":
+        inst = raw.copy()
+    elif data_type == "epochs":
+        inst = epochs_eeg.copy()
+    elif data_type == "evoked":
+        inst = epochs_eeg.average()
+    shape = list(inst._data.shape)
+    orig_total = len(inst.info["ch_names"])
+    n_eeg_orig = len(pick_types(inst.info, eeg=True))
+
+    # Assert first and last channels are not EEG
+    if data_type == "raw":
+        ch_types = inst.get_channel_types()
+        assert ch_types[0] != "eeg"
+        assert ch_types[-1] != "eeg"
+
+    # Record the names and data of the first and last channels.
+    if data_type == "raw":
+        first_name = inst.info["ch_names"][0]
+        last_name = inst.info["ch_names"][-1]
+        data_first = inst._data[..., 0, :].copy()
+        data_last = inst._data[..., -1, :].copy()
+
+    # Interpolate the EEG channels.
+    inst_interp = inst.copy().interpolate_to(montage, method=method)
+
+    # Check that the new channel names include the montage channels.
+    assert set(montage.ch_names).issubset(set(inst_interp.info["ch_names"]))
+    # Check that the overall channel order is changed.
+    assert inst.info["ch_names"] != inst_interp.info["ch_names"]
+
+    # Check that the data shape is as expected.
+    new_nchan_expected = orig_total - n_eeg_orig + len(montage.ch_names)
+    expected_shape = (new_nchan_expected, shape[-1])
+    if len(shape) == 3:
+        expected_shape = (shape[0],) + expected_shape
+    assert inst_interp._data.shape == expected_shape
+
+    # Verify that the first and last channels retain their positions.
+    if data_type == "raw":
+        assert inst_interp.info["ch_names"][0] == first_name
+        assert inst_interp.info["ch_names"][-1] == last_name
+
+    # Verify that the data for the first and last channels is unchanged.
+    if data_type == "raw":
+        np.testing.assert_allclose(
+            inst_interp._data[..., 0, :],
+            data_first,
+            err_msg="Data for the first non-EEG channel has changed.",
+        )
+        np.testing.assert_allclose(
+            inst_interp._data[..., -1, :],
+            data_last,
+            err_msg="Data for the last non-EEG channel has changed.",
+        )
+
+    # Validate that bad channels are carried over.
+    # Mark the first non eeg channel as bad
+    all_ch = inst_interp.info["ch_names"]
+    eeg_ch = [all_ch[i] for i in pick_types(inst_interp.info, eeg=True)]
+    bads = [ch for ch in all_ch if ch not in eeg_ch][:1]
+    inst.info["bads"] = bads
+    inst_interp = inst.copy().interpolate_to(montage, method=method)
+    assert inst_interp.info["bads"] == bads