diff --git a/examples/preprocessing/interpolate_to.py b/examples/preprocessing/interpolate_to.py index b97a7251cbb..711b24190a5 100644 --- a/examples/preprocessing/interpolate_to.py +++ b/examples/preprocessing/interpolate_to.py @@ -2,21 +2,30 @@ .. _ex-interpolate-to-any-montage: ====================================================== -Interpolate EEG data to any montage +Interpolate MEG or EEG data to any montage ====================================================== -This example demonstrates how to interpolate EEG channels to match a given montage. -This can be useful for standardizing +This example demonstrates both EEG montage interpolation and MEG system +transformation. + +For EEG, 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". +- Using the MNE interpolation for MEG data to transform from Neuromag + (planar gradiometers and magnetometers) to CTF (axial gradiometers). + -In this example, the data from the original EEG channels will be +In the first example, the data from the original EEG channels will be interpolated onto the positions defined by the "biosemi16" montage. + +In the second example, we will interpolate MEG data from a 306-sensor Neuromag +to 275-sensor CTF system. """ # Authors: Antoine Collas +# Konstantinos Tsilimparis # License: BSD-3-Clause # Copyright the MNE-Python contributors. @@ -30,6 +39,9 @@ ylim = (-10, 10) # %% +# Part 1: EEG System Transformation +# ================================== + # Load EEG data data_path = sample.data_path() eeg_file_path = data_path / "MEG" / "sample" / "sample_audvis-ave.fif" @@ -75,6 +87,63 @@ ) axs[2].set_title("Interpolated to Standard 1020 Montage using MNE interpolation") +# %% +# Part 2: MEG System Transformation +# ================================== +# We demonstrate transforming MEG data from Neuromag (planar gradiometers +# and magnetometers) to CTF (axial gradiometers) sensor configuration. + +# Load the full evoked data with MEG channels +evoked_meg = mne.read_evokeds( + eeg_file_path, condition="Left Auditory", baseline=(None, 0) +) +evoked_meg.pick("meg") + +print("Original Neuromag system:") +print(f" Number of magnetometers: {len(mne.pick_types(evoked_meg.info, meg='mag'))}") +print(f" Number of gradiometers: {len(mne.pick_types(evoked_meg.info, meg='grad'))}") + +# %% +# Transform to CTF sensor configuration +# ====================================== + +# Interpolate Neuromag to CTF +evoked_ctf = evoked_meg.copy().interpolate_to("ctf275", mode="accurate") + +print("\nTransformed to CTF system:") +print(f" Number of MEG channels: {len(mne.pick_types(evoked_ctf.info, meg=True))}") +print(f" Bad channels in original: {evoked_meg.info['bads']}") + +# %% +# Compare evoked responses: Original Neuromag vs Transformed CTF +# The data should be similar but projected onto different sensor arrays + +# Set consistent y-limits for comparison +ylim_meg = dict(grad=[-300, 300], mag=[-600, 600], meg=[-300, 300]) + +fig, axes = plt.subplots(3, 1, figsize=(10, 8), layout="constrained") + +# Plot original Neuromag gradiometers +evoked_meg.copy().pick("grad").plot( + axes=axes[0], show=False, spatial_colors=True, ylim=ylim_meg, time_unit="s" +) +axes[0].set_title("Original Neuromag Planar Gradiometers", fontsize=14) + + +# Plot original Neuromag magnetometers +evoked_meg.copy().pick("mag").plot( + axes=axes[1], show=False, spatial_colors=True, ylim=ylim_meg, time_unit="s" +) +axes[1].set_title("Original Neuromag Magnetometers", fontsize=14) + +# Plot transformed CTF gradiometers +evoked_ctf.plot( + axes=axes[2], show=False, spatial_colors=True, ylim=ylim_meg, time_unit="s" +) +axes[2].set_title("Transformed to CTF275 Axial Gradiometers", fontsize=14) + +plt.show() + # %% # References # ---------- diff --git a/mne/channels/__init__.pyi b/mne/channels/__init__.pyi index 470bc0cfd0b..628e092dcf4 100644 --- a/mne/channels/__init__.pyi +++ b/mne/channels/__init__.pyi @@ -30,6 +30,7 @@ __all__ = [ "read_dig_localite", "read_dig_polhemus_isotrak", "read_layout", + "read_meg_montage", "read_polhemus_fastscan", "read_vectorview_selection", "rename_channels", @@ -75,6 +76,7 @@ from .montage import ( read_dig_hpts, read_dig_localite, read_dig_polhemus_isotrak, + read_meg_montage, read_polhemus_fastscan, transform_to_head, ) diff --git a/mne/channels/channels.py b/mne/channels/channels.py index ef98efd1731..8d7c5a25805 100644 --- a/mne/channels/channels.py +++ b/mne/channels/channels.py @@ -41,7 +41,7 @@ pick_info, pick_types, ) -from .._fiff.proj import _has_eeg_average_ref_proj, setup_proj +from .._fiff.proj import setup_proj from .._fiff.reference import add_reference_channels, set_eeg_reference from .._fiff.tag import _rename_list from ..bem import _check_origin @@ -968,161 +968,110 @@ def interpolate_bads( return self - def interpolate_to(self, sensors, origin="auto", method="spline", reg=0.0): - """Interpolate EEG data onto a new montage. + def interpolate_to( + self, sensors, origin="auto", method="MNE", mode="accurate", reg=0.0 + ): + """Interpolate data onto a new sensor configuration. - .. warning:: - Be careful, only EEG channels are interpolated. Other channel types are - not interpolated. + This method can interpolate EEG data onto a new montage or transform + MEG data to a different sensor configuration (e.g., Neuromag to CTF). Parameters ---------- - sensors : DigMontage - The target montage containing channel positions to interpolate onto. + sensors : DigMontage | str + For EEG: A DigMontage object containing target channel positions. + For MEG: A string specifying the target MEG system. Currently + supported: ``'neuromag'``, ``'ctf151'`` or ``'ctf275'``. 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. + origin fit. Used for both EEG and MEG interpolation. method : str - Method to use for EEG channels. - Supported methods are 'spline' (default) and 'MNE'. + Interpolation method to use. + For EEG: ``'MNE'`` (default) or ``'spline'``. + For MEG: ``'MNE'`` (default). + mode : str + Either ``'accurate'`` (default) or ``'fast'``, determines the + quality of the Legendre polynomial expansion used for + interpolation of MEG channels using the minimum-norm method. + Only used for MEG interpolation. reg : float - The regularization parameter for the interpolation method - (only used when the method is 'spline'). + The regularization parameter for the interpolation method. + Only used when ``method='spline'`` for EEG channels. Returns ------- inst : instance of Raw, Epochs, or Evoked - The instance with updated channel locations and data. + A new instance with interpolated data and updated channel + information. Notes ----- - This method is useful for standardizing EEG layouts across datasets. - However, some attributes may be lost after interpolation. + **For EEG data:** - .. 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 + This method interpolates EEG channels onto a new montage using + spherical splines or minimum-norm estimation. Non-EEG channels + are preserved without modification. - # Check that the method option is valid. - _check_option("method", method, ["spline", "MNE"]) - _validate_type(sensors, DigMontage, "sensors") + **For MEG data:** - # 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." - ) + This method transforms MEG data to a different sensor configuration + using field interpolation. - # 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) + Common use cases for MEG transformation: - 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 - ) + - Transform Neuromag data to CTF sensor layout for comparison + - Transform CTF data to Neuromag sensor layout + - Simulate what data would look like on a different MEG system - # Interpolate EEG data - data_good = self.get_data(picks=picks_good_eeg) - data_interp = mapping @ data_good + .. warning:: + MEG field interpolation assumes that the head position relative + to the sensors is similar between systems. Large differences in + head position may affect interpolation accuracy. - # 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 + .. versionadded:: 1.10.0 + """ + from .interpolation import _interpolate_to_eeg, _interpolate_to_meg + from .montage import DigMontage + + _check_preload(self, "interpolation") + + # Determine if we're doing EEG or MEG interpolation + is_meg_interpolation = isinstance(sensors, str) + is_eeg_interpolation = isinstance(sensors, DigMontage) + + if is_eeg_interpolation: + # Check that the method option is valid. + _validate_type(sensors, DigMontage, "sensors") + + method = _handle_default("interpolation_method", method) + + # Filter method to only include 'eeg' and 'meg' + supported_ch_types = ["eeg", "meg"] + keys_to_delete = [key for key in method if key not in supported_ch_types] + for key in keys_to_delete: + del method[key] + + # Force MEG to always use MNE method, + # otherwise when method = "spline", the _handle_default function + # forces all channel types to use that method + if "meg" in method: + method["meg"] = "MNE" + valids = {"eeg": ("spline", "MNE"), "meg": ("MNE")} + for key in method: + _check_option("method[key]", key, tuple(valids)) + _check_option(f"method['{key}']", method[key], valids[key]) + logger.info("Setting channel interpolation method to %s.", method) + + return _interpolate_to_eeg(self, sensors, origin, method, reg) + + elif is_meg_interpolation: + # MEG interpolation to canonical sensor configuration + _check_option("sensors", sensors, ["neuromag", "ctf151", "ctf275"]) + _check_option("method", method, ["MNE"]) + _check_option("mode", mode, ["accurate", "fast"]) + + return _interpolate_to_meg(self, sensors, origin, mode) @verbose diff --git a/mne/channels/data/montages/ctf151.csv b/mne/channels/data/montages/ctf151.csv new file mode 100644 index 00000000000..40c42b0b2e8 --- /dev/null +++ b/mne/channels/data/montages/ctf151.csv @@ -0,0 +1,152 @@ +name,coil_type,x,y,z,ex_x,ex_y,ex_z,ey_x,ey_y,ey_z,ez_x,ez_y,ez_z +MLC11-606,5001,-0.014323,0.048909,0.083084,0.728954,0.665674,-0.159696,-0.680884,0.680884,-0.269802,-0.070866,0.305408,0.949581 +MLC12-606,5001,-0.040601,0.042758,0.079940,0.708622,0.705572,-0.004790,-0.644792,0.644792,-0.410470,-0.286528,0.293956,0.911862 +MLC13-606,5001,-0.073375,0.034411,0.064147,0.561962,0.806275,0.184715,-0.516439,0.516439,-0.683068,-0.646135,0.288465,0.706610 +MLC14-606,5001,-0.090027,0.012140,0.050707,0.289690,0.900312,0.324835,-0.425104,0.425104,-0.799107,-0.857535,0.093405,0.505875 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2312,3012,0.051300,-0.086100,0.039700,0.153007,-0.302213,-0.940940,0.880738,0.473520,-0.008900,0.448244,-0.827360,0.338622 +MEG 2313,3012,0.051300,-0.086100,0.039700,0.880738,0.473520,-0.008900,-0.153007,0.302213,0.940940,0.448244,-0.827360,0.338622 +MEG 2311,3024,0.051300,-0.086100,0.039700,0.153007,-0.302213,-0.940940,0.880738,0.473520,-0.008900,0.448244,-0.827360,0.338622 +MEG 2323,3012,0.063700,-0.088400,0.006200,0.056398,-0.071297,-0.995860,0.798667,0.601776,0.002200,0.599127,-0.795485,0.090881 +MEG 2322,3012,0.063700,-0.088400,0.006200,0.798667,0.601776,0.002200,-0.056398,0.071297,0.995860,0.599127,-0.795485,0.090881 +MEG 2321,3024,0.063700,-0.088400,0.006200,0.056398,-0.071297,-0.995860,0.798667,0.601776,0.002200,0.599127,-0.795485,0.090881 +MEG 2332,3012,0.033000,-0.105100,-0.027700,-0.004900,0.023300,-0.999715,0.951414,0.307905,0.002500,0.307875,-0.951130,-0.023677 +MEG 2333,3012,0.033000,-0.105100,-0.027700,0.951414,0.307905,0.002500,0.004900,-0.023300,0.999715,0.307875,-0.951130,-0.023677 +MEG 2331,3024,0.033000,-0.105100,-0.027700,-0.004900,0.023300,-0.999715,0.951414,0.307905,0.002500,0.307875,-0.951130,-0.023677 +MEG 2343,3012,0.033300,-0.103400,0.006300,0.041500,-0.123300,-0.991501,0.948001,0.318300,0.000100,0.315583,-0.939949,0.130098 +MEG 2342,3012,0.033300,-0.103400,0.006300,0.948001,0.318300,0.000100,-0.041500,0.123300,0.991501,0.315583,-0.939949,0.130098 +MEG 2341,3024,0.033300,-0.103400,0.006300,0.041500,-0.123300,-0.991501,0.948001,0.318300,0.000100,0.315583,-0.939949,0.130098 +MEG 2412,3012,0.095200,-0.030600,0.039200,0.323999,-0.063600,-0.943897,0.309099,0.950098,0.042100,0.894117,-0.305398,0.327489 +MEG 2413,3012,0.095200,-0.030600,0.039200,0.309099,0.950098,0.042100,-0.323999,0.063600,0.943897,0.894117,-0.305398,0.327489 +MEG 2411,3024,0.095200,-0.030600,0.039200,0.323999,-0.063600,-0.943897,0.309099,0.950098,0.042100,0.894117,-0.305398,0.327489 +MEG 2423,3012,0.101700,-0.033800,0.005800,0.066101,-0.028300,-0.997412,0.314004,0.949411,-0.006100,0.947126,-0.312788,0.071643 +MEG 2422,3012,0.101700,-0.033800,0.005800,0.314004,0.949411,-0.006100,-0.066101,0.028300,0.997412,0.947126,-0.312788,0.071643 +MEG 2421,3024,0.101700,-0.033800,0.005800,0.066101,-0.028300,-0.997412,0.314004,0.949411,-0.006100,0.947126,-0.312788,0.071643 +MEG 2433,3012,0.086600,-0.063900,0.005600,0.060099,-0.044799,-0.997187,0.549293,0.835589,-0.004400,0.833435,-0.547483,0.074826 +MEG 2432,3012,0.086600,-0.063900,0.005600,0.549293,0.835589,-0.004400,-0.060099,0.044799,0.997187,0.833435,-0.547483,0.074826 +MEG 2431,3024,0.086600,-0.063900,0.005600,0.060099,-0.044799,-0.997187,0.549293,0.835589,-0.004400,0.833435,-0.547483,0.074826 +MEG 2442,3012,0.078100,-0.062900,0.039400,0.259507,-0.203505,-0.944125,0.598716,0.800921,-0.008000,0.757798,-0.563187,0.329687 +MEG 2443,3012,0.078100,-0.062900,0.039400,0.598716,0.800921,-0.008000,-0.259507,0.203505,0.944125,0.757798,-0.563187,0.329687 +MEG 2441,3024,0.078100,-0.062900,0.039400,0.259507,-0.203505,-0.944125,0.598716,0.800921,-0.008000,0.757798,-0.563187,0.329687 +MEG 2512,3012,0.063000,-0.090600,-0.027600,-0.013600,0.025200,-0.999598,0.808198,0.588899,0.003800,0.588757,-0.807821,-0.028376 +MEG 2513,3012,0.063000,-0.090600,-0.027600,0.808198,0.588899,0.003800,0.013600,-0.025200,0.999598,0.588757,-0.807821,-0.028376 +MEG 2511,3024,0.063000,-0.090600,-0.027600,-0.013600,0.025200,-0.999598,0.808198,0.588899,0.003800,0.588757,-0.807821,-0.028376 +MEG 2522,3012,0.086100,-0.066100,-0.028000,-0.021299,0.011700,-0.999673,0.571385,0.820678,-0.002600,0.820380,-0.571254,-0.024165 +MEG 2523,3012,0.086100,-0.066100,-0.028000,0.571385,0.820678,-0.002600,0.021299,-0.011700,0.999673,0.820380,-0.571254,-0.024165 +MEG 2521,3024,0.086100,-0.066100,-0.028000,-0.021299,0.011700,-0.999673,0.571385,0.820678,-0.002600,0.820380,-0.571254,-0.024165 +MEG 2533,3012,0.075700,-0.079800,-0.062000,0.014300,-0.000900,-0.999897,0.690798,0.722998,0.009300,0.722916,-0.690860,0.010961 +MEG 2532,3012,0.075700,-0.079800,-0.062000,0.690798,0.722998,0.009300,-0.014300,0.000900,0.999897,0.722916,-0.690860,0.010961 +MEG 2531,3024,0.075700,-0.079800,-0.062000,0.014300,-0.000900,-0.999897,0.690798,0.722998,0.009300,0.722916,-0.690860,0.010961 +MEG 2543,3012,0.048800,-0.099400,-0.062100,0.011000,-0.007000,-0.999915,0.903014,0.429706,0.007000,0.429621,-0.903014,0.011048 +MEG 2542,3012,0.048800,-0.099400,-0.062100,0.903014,0.429706,0.007000,-0.011000,0.007000,0.999915,0.429621,-0.903014,0.011048 +MEG 2541,3024,0.048800,-0.099400,-0.062100,0.011000,-0.007000,-0.999915,0.903014,0.429706,0.007000,0.429621,-0.903014,0.011048 +MEG 2612,3012,0.108700,-0.003300,-0.028000,-0.020500,0.003400,-0.999813,0.081001,0.996713,0.001700,0.996532,-0.080951,-0.020708 +MEG 2613,3012,0.108700,-0.003300,-0.028000,0.081001,0.996713,0.001700,0.020500,-0.003400,0.999813,0.996532,-0.080951,-0.020708 +MEG 2611,3024,0.108700,-0.003300,-0.028000,-0.020500,0.003400,-0.999813,0.081001,0.996713,0.001700,0.996532,-0.080951,-0.020708 +MEG 2623,3012,0.106800,-0.020600,-0.062100,0.013100,0.004500,-0.999904,0.215701,0.976404,0.007200,0.976343,-0.215775,0.011820 +MEG 2622,3012,0.106800,-0.020600,-0.062100,0.215701,0.976404,0.007200,-0.013100,-0.004500,0.999904,0.976343,-0.215775,0.011820 +MEG 2621,3024,0.106800,-0.020600,-0.062100,0.013100,0.004500,-0.999904,0.215701,0.976404,0.007200,0.976343,-0.215775,0.011820 +MEG 2633,3012,0.095100,-0.052400,-0.062000,0.015200,0.003300,-0.999879,0.476590,0.879082,0.010100,0.879009,-0.476686,0.011789 +MEG 2632,3012,0.095100,-0.052400,-0.062000,0.476590,0.879082,0.010100,-0.015200,-0.003300,0.999879,0.879009,-0.476686,0.011789 +MEG 2631,3024,0.095100,-0.052400,-0.062000,0.015200,0.003300,-0.999879,0.476590,0.879082,0.010100,0.879009,-0.476686,0.011789 +MEG 2642,3012,0.101700,-0.036100,-0.027800,-0.027699,0.005300,-0.999573,0.341491,0.939874,-0.004500,0.939449,-0.341469,-0.027844 +MEG 2643,3012,0.101700,-0.036100,-0.027800,0.341491,0.939874,-0.004500,0.027699,-0.005300,0.999573,0.939449,-0.341469,-0.027844 +MEG 2641,3024,0.101700,-0.036100,-0.027800,-0.027699,0.005300,-0.999573,0.341491,0.939874,-0.004500,0.939449,-0.341469,-0.027844 diff --git a/mne/channels/interpolation.py b/mne/channels/interpolation.py index c0a70a7d6ed..896e47f3846 100644 --- a/mne/channels/interpolation.py +++ b/mne/channels/interpolation.py @@ -415,3 +415,207 @@ def _interpolate_bads_seeg( out = out.reshape(bads_shaft.size, inst._data.shape[0], -1) out = out.swapaxes(0, 1) inst._data[..., bads_shaft, :] = out + + +def _interpolate_to_eeg(inst, sensors, origin, method, reg): + """Interpolate EEG data to a new montage. + + Parameters + ---------- + inst : instance of Raw, Epochs, or Evoked + The instance to interpolate. + sensors : DigMontage + Target montage with channel positions. + origin : array-like, shape (3,) | str + Origin of the sphere in head coordinate frame. + method : dict + Dictionary with 'eeg' key specifying interpolation method. + reg : float + Regularization parameter for spline interpolation. + + Returns + ------- + inst : instance of Raw, Epochs, or Evoked + A new instance with interpolated data. + """ + from .._fiff.meas_info import create_info + from .._fiff.proj import _has_eeg_average_ref_proj + from ..bem import _check_origin + 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 ..utils import warn + + # 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 = inst.info["ch_names"] + + # Identify EEG channel + picks_good_eeg = pick_types(inst.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(inst.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 = inst.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 inst.info["bads"] if ch in target_ch_names] + + # Compute the interpolation mapping + if method["eeg"] == "spline": + origin_val = _check_origin(origin, inst.info) + pos_from = inst.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["eeg"] == "MNE" + info_eeg = pick_info(inst.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(inst.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 = inst.get_data(picks=picks_good_eeg) + data_interp = mapping @ data_good + + # Create a new instance for the interpolated EEG channels + if isinstance(inst, BaseRaw): + inst_interp = RawArray(data_interp, info_interp, first_samp=inst.first_samp) + elif isinstance(inst, BaseEpochs): + inst_interp = EpochsArray(data_interp, info_interp) + else: + assert isinstance(inst, 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 = inst.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 + + +def _interpolate_to_meg(inst, sensors, origin, mode): + """Interpolate MEG data to a canonical sensor configuration. + + Parameters + ---------- + inst : instance of Raw, Epochs, or Evoked + The instance to interpolate. + sensors : str + Target MEG system name ('neuromag', 'ctf151', or 'ctf275'). + origin : array-like, shape (3,) | str + Origin of the sphere in head coordinate frame. + mode : str + Either 'accurate' or 'fast'. + + Returns + ------- + inst : instance of Raw, Epochs, or Evoked + A new instance with interpolated data. + """ + from ..bem import _check_origin + 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 .montage import read_meg_montage + + # Get MEG channels from source + picks_meg = pick_types(inst.info, meg=True, ref_meg=False, exclude="bads") + if len(picks_meg) == 0: + raise ValueError("No good MEG channels available for interpolation.") + + # Load target sensor configuration + info_to = read_meg_montage(sensors) + + # Update dev_head_t from source data + if inst.info["dev_head_t"] is not None: + info_to["dev_head_t"] = inst.info["dev_head_t"].copy() + + # Get source MEG info + info_from = pick_info(inst.info, picks_meg) + + # Compute field interpolation mapping + origin_val = _check_origin(origin, inst.info) + mapping = _map_meg_or_eeg_channels(info_from, info_to, mode=mode, origin=origin_val) + + # Apply mapping to MEG data + data_meg = inst.get_data(picks=picks_meg) + data_interp = mapping @ data_meg + + # Create new instance with interpolated MEG data + if isinstance(inst, BaseRaw): + inst_out = RawArray(data_interp, info_to, first_samp=inst.first_samp) + elif isinstance(inst, BaseEpochs): + inst_out = EpochsArray(data_interp, info_to) + else: + assert isinstance(inst, Evoked) + inst_out = EvokedArray(data_interp, info_to) + + # Add non-MEG channels if they exist + non_meg_picks = pick_types(inst.info, meg=False, exclude=[], ref_meg=False) + if len(non_meg_picks) > 0: + non_meg_names = [inst.info["ch_names"][i] for i in non_meg_picks] + inst_non_meg = inst.copy().pick(non_meg_names).load_data() + inst_out = inst_out.add_channels([inst_non_meg], force_update_info=True) + + return inst_out diff --git a/mne/channels/montage.py b/mne/channels/montage.py index 35fdbce917c..7881fb49346 100644 --- a/mne/channels/montage.py +++ b/mne/channels/montage.py @@ -7,6 +7,7 @@ from collections import OrderedDict from copy import deepcopy from dataclasses import dataclass +from pathlib import Path import numpy as np @@ -1737,6 +1738,124 @@ def read_custom_montage( return montage +@verbose +def read_meg_montage(system, *, verbose=None): + """Load canonical MEG sensor definitions from CSV files. + + Parameters + ---------- + system : str + The MEG system name. Currently supported: 'neuromag', 'ctf151' or + 'ctf275'. + %(verbose)s + + Returns + ------- + info : Info + An Info object containing the canonical sensor definitions. + + Notes + ----- + This function loads pre-defined canonical sensor positions and + orientations from CSV files stored in mne/channels/data/montages/. + + .. versionadded:: 1.11 + """ + # Validate system input + _check_option("system", system, ["neuromag", "ctf151", "ctf275"]) + + # Map system names to CSV filenames + system_files = { + "neuromag": "neuromag306.csv", + "ctf151": "ctf151.csv", + "ctf275": "ctf275.csv", + } + + # Load the CSV file + montage_dir = Path(__file__).parent / "data" / "montages" + csv_file = montage_dir / system_files[system] + + if not csv_file.exists(): + raise FileNotFoundError(f"Canonical sensor file not found: {csv_file}. ") + + # Read sensor definitions manually + ch_names = [] + rows = [] + with open(csv_file) as fid: + # Read header to get column names + header = fid.readline().strip().split(",") + # Create a mapping from column name to index + col_idx = {name: i for i, name in enumerate(header)} + + # Read data rows + for line in fid: + values = line.strip().split(",") + if not values[0]: # skip empty lines + continue + rows.append(values) + ch_names.append(values[col_idx["name"]]) + + # Create base info structure + # Use a dummy sample rate; it won't matter for field interpolation + info = create_info(ch_names=ch_names, sfreq=1000.0, ch_types="mag") + + # Update each channel with full coil information + for idx, row in enumerate(rows): + ch = info["chs"][idx] + + # Set coil type + ch["coil_type"] = int(row[col_idx["coil_type"]]) + + # Set position and orientation in loc field + # loc[0:3] = position + ch["loc"][:3] = [ + float(row[col_idx["x"]]), + float(row[col_idx["y"]]), + float(row[col_idx["z"]]), + ] + + # loc[3:6] = ex (first orientation vector) + ch["loc"][3:6] = [ + float(row[col_idx["ex_x"]]), + float(row[col_idx["ex_y"]]), + float(row[col_idx["ex_z"]]), + ] + + # loc[6:9] = ey (second orientation vector) + ch["loc"][6:9] = [ + float(row[col_idx["ey_x"]]), + float(row[col_idx["ey_y"]]), + float(row[col_idx["ey_z"]]), + ] + + # loc[9:12] = ez (third orientation vector / normal) + ch["loc"][9:12] = [ + float(row[col_idx["ez_x"]]), + float(row[col_idx["ez_y"]]), + float(row[col_idx["ez_z"]]), + ] + + # Set coordinate frame to device coordinates + ch["coord_frame"] = FIFF.FIFFV_COORD_DEVICE + + # Set channel kind to MEG + ch["kind"] = FIFF.FIFFV_MEG_CH + + # Set unit based on coil type + # Neuromag gradiometers (3012) use T/m, magnetometers (3024) use T + # CTF gradiometers (5001) use T + if ch["coil_type"] == 3012: # Neuromag planar gradiometer + ch["unit"] = FIFF.FIFF_UNIT_T_M + else: # Magnetometers and CTF gradiometers + ch["unit"] = FIFF.FIFF_UNIT_T + + # Set device to head transform to identity (canonical positions) + # This will be updated based on the actual data being interpolated + info["dev_head_t"] = Transform("meg", "head", np.eye(4)) + + return info + + def compute_dev_head_t(montage): """Compute device to head transform from a DigMontage. diff --git a/mne/channels/tests/test_montage.py b/mne/channels/tests/test_montage.py index 0294cbe9d16..1dff6d0d990 100644 --- a/mne/channels/tests/test_montage.py +++ b/mne/channels/tests/test_montage.py @@ -1989,7 +1989,7 @@ def test_read_dig_hpts(): def test_get_builtin_montages(): """Test help function to obtain builtin montages.""" - EXPECTED_COUNT = 28 + EXPECTED_COUNT = 31 montages = get_builtin_montages() assert len(montages) == EXPECTED_COUNT