# Authors: Alexandre Gramfort # Matti Hämäläinen # Denis Engemann # Teon Brooks # # License: BSD-3-Clause from copy import deepcopy from itertools import count import re import numpy as np from .constants import FIFF from .pick import pick_types, pick_info, _electrode_types, _ELECTRODE_CH_TYPES from .tag import find_tag, _rename_list from .tree import dir_tree_find from .write import (write_int, write_float, write_string, write_name_list, write_float_matrix, end_block, start_block) from ..defaults import (_INTERPOLATION_DEFAULT, _BORDER_DEFAULT, _EXTRAPOLATE_DEFAULT) from ..utils import (logger, verbose, warn, fill_doc, _validate_type, object_diff, _check_option) class Projection(dict): """Projection vector. A basic class to proj a meaningful print for projection vectors. .. warning:: This class is generally not meant to be instantiated directly, use ``compute_proj_*`` functions instead. Parameters ---------- data : dict The data dictionary. desc : str The projector description. kind : int The projector kind. active : bool Whether or not the projector has been applied. explained_var : float | None The explained variance (proportion). """ def __init__(self, *, data, desc='', kind=FIFF.FIFFV_PROJ_ITEM_FIELD, active=False, explained_var=None): super().__init__(desc=desc, kind=kind, active=active, data=data, explained_var=explained_var) def __repr__(self): # noqa: D105 s = "%s" % self['desc'] s += ", active : %s" % self['active'] s += f", n_channels : {len(self['data']['col_names'])}" if self['explained_var'] is not None: s += f', exp. var : {self["explained_var"] * 100:0.2f}%' return "" % s # speed up info copy by taking advantage of mutability def __deepcopy__(self, memodict): """Make a deepcopy.""" cls = self.__class__ result = cls.__new__(cls) for k, v in self.items(): if k == 'data': v = v.copy() v['data'] = v['data'].copy() result[k] = v else: result[k] = v # kind, active, desc, explained_var immutable return result def __eq__(self, other): """Equality == method.""" return True if len(object_diff(self, other)) == 0 else False def __ne__(self, other): """Different != method.""" return not self.__eq__(other) @fill_doc def plot_topomap( self, info, *, sensors=True, show_names=False, contours=6, outlines='head', sphere=None, image_interp=_INTERPOLATION_DEFAULT, extrapolate=_EXTRAPOLATE_DEFAULT, border=_BORDER_DEFAULT, res=64, size=1, cmap=None, vlim=(None, None), cnorm=None, colorbar=False, cbar_fmt='%3.1f', units=None, axes=None, show=True): """Plot topographic maps of SSP projections. Parameters ---------- %(info_not_none)s Used to determine the layout. %(sensors_topomap)s %(show_names_topomap)s .. versionadded:: 1.2 %(contours_topomap)s %(outlines_topomap)s %(sphere_topomap_auto)s %(image_interp_topomap)s %(extrapolate_topomap)s .. versionadded:: 1.2 %(border_topomap)s %(res_topomap)s %(size_topomap)s %(cmap_topomap)s %(vlim_plot_topomap_proj)s %(cnorm)s .. versionadded:: 1.2 %(colorbar_topomap)s %(cbar_fmt_topomap)s .. versionadded:: 1.2 %(units_topomap)s .. versionadded:: 1.2 %(axes_plot_projs_topomap)s %(show)s Returns ------- fig : instance of Figure Figure distributing one image per channel across sensor topography. Notes ----- .. versionadded:: 0.15.0 """ # noqa: E501 from ..viz.topomap import plot_projs_topomap return plot_projs_topomap( self, info, sensors=sensors, show_names=show_names, contours=contours, outlines=outlines, sphere=sphere, image_interp=image_interp, extrapolate=extrapolate, border=border, res=res, size=size, cmap=cmap, vlim=vlim, cnorm=cnorm, colorbar=colorbar, cbar_fmt=cbar_fmt, units=units, axes=axes, show=show) class ProjMixin(object): """Mixin class for Raw, Evoked, Epochs. Notes ----- This mixin adds a proj attribute as a property to data containers. It is True if at least one proj is present and all of them are active. The projs might not be applied yet if data are not preloaded. In this case it's the _projector attribute that does the job. If a private _data attribute is present then the projs applied to it are the ones marked as active. A proj parameter passed in constructor of raw or epochs calls apply_proj and hence after the .proj attribute is True. As soon as you've applied the projs it will stay active in the remaining pipeline. The suggested pipeline is proj=True in epochs (it's cheaper than for raw). When you use delayed SSP in Epochs, projs are applied when you call get_data() method. They are not applied to the evoked._data unless you call apply_proj(). The reason is that you want to reject with projs although it's not stored in proj mode. """ @property def proj(self): """Whether or not projections are active.""" return (len(self.info['projs']) > 0 and all(p['active'] for p in self.info['projs'])) @verbose def add_proj(self, projs, remove_existing=False, verbose=None): """Add SSP projection vectors. Parameters ---------- projs : list List with projection vectors. remove_existing : bool Remove the projection vectors currently in the file. %(verbose)s Returns ------- self : instance of Raw | Epochs | Evoked The data container. """ if isinstance(projs, Projection): projs = [projs] if (not isinstance(projs, list) and not all(isinstance(p, Projection) for p in projs)): raise ValueError('Only projs can be added. You supplied ' 'something else.') # mark proj as inactive, as they have not been applied projs = deactivate_proj(projs, copy=True) if remove_existing: # we cannot remove the proj if they are active if any(p['active'] for p in self.info['projs']): raise ValueError('Cannot remove projectors that have ' 'already been applied') with self.info._unlock(): self.info['projs'] = projs else: self.info['projs'].extend(projs) # We don't want to add projectors that are activated again. with self.info._unlock(): self.info['projs'] = _uniquify_projs(self.info['projs'], check_active=False, sort=False) return self @verbose def apply_proj(self, verbose=None): """Apply the signal space projection (SSP) operators to the data. Parameters ---------- %(verbose)s Returns ------- self : instance of Raw | Epochs | Evoked The instance. Notes ----- Once the projectors have been applied, they can no longer be removed. It is usually not recommended to apply the projectors at too early stages, as they are applied automatically later on (e.g. when computing inverse solutions). Hint: using the copy method individual projection vectors can be tested without affecting the original data. With evoked data, consider the following example:: projs_a = mne.read_proj('proj_a.fif') projs_b = mne.read_proj('proj_b.fif') # add the first, copy, apply and see ... evoked.add_proj(a).copy().apply_proj().plot() # add the second, copy, apply and see ... evoked.add_proj(b).copy().apply_proj().plot() # drop the first and see again evoked.copy().del_proj(0).apply_proj().plot() evoked.apply_proj() # finally keep both """ from ..epochs import BaseEpochs from ..evoked import Evoked from .base import BaseRaw if self.info['projs'] is None or len(self.info['projs']) == 0: logger.info('No projector specified for this dataset. ' 'Please consider the method self.add_proj.') return self # Exit delayed mode if you apply proj if isinstance(self, BaseEpochs) and self._do_delayed_proj: logger.info('Leaving delayed SSP mode.') self._do_delayed_proj = False if all(p['active'] for p in self.info['projs']): logger.info('Projections have already been applied. ' 'Setting proj attribute to True.') return self _projector, info = setup_proj(deepcopy(self.info), add_eeg_ref=False, activate=True) # let's not raise a RuntimeError here, otherwise interactive plotting if _projector is None: # won't be fun. logger.info('The projections don\'t apply to these data.' ' Doing nothing.') return self self._projector, self.info = _projector, info if isinstance(self, (BaseRaw, Evoked)): if self.preload: self._data = np.dot(self._projector, self._data) else: # BaseEpochs if self.preload: for ii, e in enumerate(self._data): self._data[ii] = self._project_epoch(e) else: self.load_data() # will automatically apply logger.info('SSP projectors applied...') return self def del_proj(self, idx='all'): """Remove SSP projection vector. .. note:: The projection vector can only be removed if it is inactive (has not been applied to the data). Parameters ---------- idx : int | list of int | str Index of the projector to remove. Can also be "all" (default) to remove all projectors. Returns ------- self : instance of Raw | Epochs | Evoked The instance. """ if isinstance(idx, str) and idx == 'all': idx = list(range(len(self.info['projs']))) idx = np.atleast_1d(np.array(idx, int)).ravel() for ii in idx: proj = self.info['projs'][ii] if (proj['active'] and set(self.info['ch_names']) & set(proj['data']['col_names'])): msg = (f'Cannot remove projector that has already been ' f'applied, unless you first remove all channels it ' f'applies to. The problematic projector is: {proj}') raise ValueError(msg) keep = np.ones(len(self.info['projs'])) keep[idx] = False # works with negative indexing and does checks with self.info._unlock(): self.info['projs'] = [p for p, k in zip(self.info['projs'], keep) if k] return self @fill_doc def plot_projs_topomap( self, ch_type=None, *, sensors=True, show_names=False, contours=6, outlines='head', sphere=None, image_interp=_INTERPOLATION_DEFAULT, extrapolate=_EXTRAPOLATE_DEFAULT, border=_BORDER_DEFAULT, res=64, size=1, cmap=None, vlim=(None, None), cnorm=None, colorbar=False, cbar_fmt='%3.1f', units=None, axes=None, show=True): """Plot SSP vector. Parameters ---------- %(ch_type_topomap_proj)s %(sensors_topomap)s %(show_names_topomap)s .. versionadded:: 1.2 %(contours_topomap)s %(outlines_topomap)s %(sphere_topomap_auto)s %(image_interp_topomap)s %(extrapolate_topomap)s .. versionadded:: 0.20 %(border_topomap)s %(res_topomap)s %(size_topomap)s Only applies when plotting multiple topomaps at a time. %(cmap_topomap)s %(vlim_plot_topomap_proj)s %(cnorm)s .. versionadded:: 1.2 %(colorbar_topomap)s %(cbar_fmt_topomap)s .. versionadded:: 1.2 %(units_topomap)s .. versionadded:: 1.2 %(axes_plot_projs_topomap)s %(show)s Returns ------- fig : instance of Figure Figure distributing one image per channel across sensor topography. """ _projs = [deepcopy(_proj) for _proj in self.info['projs']] if _projs is None or len(_projs) == 0: raise ValueError('No projectors in Info; nothing to plot.') if ch_type is not None: # make sure the requested channel type(s) exist _validate_type(ch_type, (str, list, tuple), 'ch_type') if isinstance(ch_type, str): ch_type = [ch_type] bad_ch_types = [_type not in self for _type in ch_type] if any(bad_ch_types): raise ValueError(f'ch_type {ch_type[bad_ch_types]} not ' f'present in {self.__class__.__name__}.') # remove projs from unrequested channel types. This is a bit # convoluted because Projection objects don't store channel types, # only channel names available_ch_types = np.array(self.get_channel_types()) for _proj in _projs[::-1]: idx = np.isin(self.ch_names, _proj['data']['col_names']) proj_ch_type = np.unique(available_ch_types[idx]) err_msg = 'Projector contains multiple channel types' assert len(proj_ch_type) == 1, err_msg if proj_ch_type[0] != ch_type: _projs.remove(_proj) if len(_projs) == 0: raise ValueError('Nothing to plot (no projectors for channel ' f'type {ch_type}).') # now we have non-empty _projs list with correct channel type(s) from ..viz.topomap import plot_projs_topomap fig = plot_projs_topomap( _projs, self.info, sensors=sensors, show_names=show_names, contours=contours, outlines=outlines, sphere=sphere, image_interp=image_interp, extrapolate=extrapolate, border=border, res=res, size=size, cmap=cmap, vlim=vlim, cnorm=cnorm, colorbar=colorbar, cbar_fmt=cbar_fmt, units=units, axes=axes, show=show) return fig def _reconstruct_proj(self, mode='accurate', origin='auto'): from ..forward import _map_meg_or_eeg_channels if len(self.info['projs']) == 0: return self self.apply_proj() for kind in ('meg', 'eeg'): kwargs = dict(meg=False) kwargs[kind] = True picks = pick_types(self.info, **kwargs) if len(picks) == 0: continue info_from = pick_info(self.info, picks) info_to = info_from.copy() with info_to._unlock(): info_to['projs'] = [] if kind == 'eeg' and _has_eeg_average_ref_proj(info_from): info_to['projs'] = [ make_eeg_average_ref_proj(info_to, verbose=False)] mapping = _map_meg_or_eeg_channels( info_from, info_to, mode=mode, origin=origin) self.data[..., picks, :] = np.matmul( mapping, self.data[..., picks, :]) return self def _proj_equal(a, b, check_active=True): """Test if two projectors are equal.""" equal = ((a['active'] == b['active'] or not check_active) and a['kind'] == b['kind'] and a['desc'] == b['desc'] and a['data']['col_names'] == b['data']['col_names'] and a['data']['row_names'] == b['data']['row_names'] and a['data']['ncol'] == b['data']['ncol'] and a['data']['nrow'] == b['data']['nrow'] and np.all(a['data']['data'] == b['data']['data'])) return equal @verbose def _read_proj(fid, node, *, ch_names_mapping=None, verbose=None): ch_names_mapping = {} if ch_names_mapping is None else ch_names_mapping projs = list() # Locate the projection data nodes = dir_tree_find(node, FIFF.FIFFB_PROJ) if len(nodes) == 0: return projs # This might exist but we won't use it: # global_nchan = None # tag = find_tag(fid, nodes[0], FIFF.FIFF_NCHAN) # if tag is not None: # global_nchan = int(tag.data) items = dir_tree_find(nodes[0], FIFF.FIFFB_PROJ_ITEM) for item in items: # Find all desired tags in one item # This probably also exists but used to be written incorrectly # sometimes # tag = find_tag(fid, item, FIFF.FIFF_NCHAN) # if tag is not None: # nchan = int(tag.data) # else: # nchan = global_nchan tag = find_tag(fid, item, FIFF.FIFF_DESCRIPTION) if tag is not None: desc = tag.data else: tag = find_tag(fid, item, FIFF.FIFF_NAME) if tag is not None: desc = tag.data else: raise ValueError('Projection item description missing') tag = find_tag(fid, item, FIFF.FIFF_PROJ_ITEM_KIND) if tag is not None: kind = int(tag.data) else: raise ValueError('Projection item kind missing') tag = find_tag(fid, item, FIFF.FIFF_PROJ_ITEM_NVEC) if tag is not None: nvec = int(tag.data) else: raise ValueError('Number of projection vectors not specified') tag = find_tag(fid, item, FIFF.FIFF_PROJ_ITEM_CH_NAME_LIST) if tag is not None: names = tag.data.split(':') else: raise ValueError('Projection item channel list missing') tag = find_tag(fid, item, FIFF.FIFF_PROJ_ITEM_VECTORS) if tag is not None: data = tag.data else: raise ValueError('Projection item data missing') tag = find_tag(fid, item, FIFF.FIFF_MNE_PROJ_ITEM_ACTIVE) if tag is not None: active = bool(tag.data) else: active = False tag = find_tag(fid, item, FIFF.FIFF_MNE_ICA_PCA_EXPLAINED_VAR) if tag is not None: explained_var = float(tag.data) else: explained_var = None # handle the case when data is transposed for some reason if data.shape[0] == len(names) and data.shape[1] == nvec: data = data.T if data.shape[1] != len(names): raise ValueError('Number of channel names does not match the ' 'size of data matrix') # just always use this, we used to have bugs with writing the # number correctly... nchan = len(names) names[:] = _rename_list(names, ch_names_mapping) # Use exactly the same fields in data as in a named matrix one = Projection(kind=kind, active=active, desc=desc, data=dict(nrow=nvec, ncol=nchan, row_names=None, col_names=names, data=data), explained_var=explained_var) projs.append(one) if len(projs) > 0: logger.info(' Read a total of %d projection items:' % len(projs)) for proj in projs: misc = 'active' if proj['active'] else ' idle' logger.info(f' {proj["desc"]} ' f'({proj["data"]["nrow"]} x ' f'{len(proj["data"]["col_names"])}) {misc}') return projs ############################################################################### # Write def _write_proj(fid, projs, *, ch_names_mapping=None): """Write a projection operator to a file. Parameters ---------- fid : file The file descriptor of the open file. projs : dict The projection operator. """ if len(projs) == 0: return ch_names_mapping = dict() if ch_names_mapping is None else ch_names_mapping # validation _validate_type(projs, (list, tuple), 'projs') for pi, proj in enumerate(projs): _validate_type(proj, Projection, f'projs[{pi}]') start_block(fid, FIFF.FIFFB_PROJ) for proj in projs: start_block(fid, FIFF.FIFFB_PROJ_ITEM) write_int(fid, FIFF.FIFF_NCHAN, len(proj['data']['col_names'])) names = _rename_list(proj['data']['col_names'], ch_names_mapping) write_name_list(fid, FIFF.FIFF_PROJ_ITEM_CH_NAME_LIST, names) write_string(fid, FIFF.FIFF_NAME, proj['desc']) write_int(fid, FIFF.FIFF_PROJ_ITEM_KIND, proj['kind']) if proj['kind'] == FIFF.FIFFV_PROJ_ITEM_FIELD: write_float(fid, FIFF.FIFF_PROJ_ITEM_TIME, 0.0) write_int(fid, FIFF.FIFF_PROJ_ITEM_NVEC, proj['data']['nrow']) write_int(fid, FIFF.FIFF_MNE_PROJ_ITEM_ACTIVE, proj['active']) write_float_matrix(fid, FIFF.FIFF_PROJ_ITEM_VECTORS, proj['data']['data']) if proj['explained_var'] is not None: write_float(fid, FIFF.FIFF_MNE_ICA_PCA_EXPLAINED_VAR, proj['explained_var']) end_block(fid, FIFF.FIFFB_PROJ_ITEM) end_block(fid, FIFF.FIFFB_PROJ) ############################################################################### # Utils def _check_projs(projs, copy=True): """Check that projs is a list of Projection.""" if not isinstance(projs, (list, tuple)): raise TypeError('projs must be a list or tuple, got %s' % (type(projs),)) for pi, p in enumerate(projs): if not isinstance(p, Projection): raise TypeError('All entries in projs list must be Projection ' 'instances, but projs[%d] is type %s' % (pi, type(p))) return deepcopy(projs) if copy else projs def make_projector(projs, ch_names, bads=(), include_active=True): """Create an SSP operator from SSP projection vectors. Parameters ---------- projs : list List of projection vectors. ch_names : list of str List of channels to include in the projection matrix. bads : list of str Some bad channels to exclude. If bad channels were marked in the raw file when projs were calculated using mne-python, they should not need to be included here as they will have been automatically omitted from the projectors. include_active : bool Also include projectors that are already active. Returns ------- proj : array of shape [n_channels, n_channels] The projection operator to apply to the data. nproj : int How many items in the projector. U : array The orthogonal basis of the projection vectors. """ return _make_projector(projs, ch_names, bads, include_active) def _make_projector(projs, ch_names, bads=(), include_active=True, inplace=False): """Subselect projs based on ch_names and bads. Use inplace=True mode to modify ``projs`` inplace so that no warning will be raised next time projectors are constructed with the given inputs. If inplace=True, no meaningful data are returned. """ from scipy import linalg nchan = len(ch_names) if nchan == 0: raise ValueError('No channel names specified') default_return = (np.eye(nchan, nchan), 0, np.empty((nchan, 0))) # Check trivial cases first if projs is None: return default_return nvec = 0 nproj = 0 for p in projs: if not p['active'] or include_active: nproj += 1 nvec += p['data']['nrow'] if nproj == 0: return default_return # Pick the appropriate entries vecs = np.zeros((nchan, nvec)) nvec = 0 nonzero = 0 bads = set(bads) for k, p in enumerate(projs): if not p['active'] or include_active: if (len(p['data']['col_names']) != len(np.unique(p['data']['col_names']))): raise ValueError('Channel name list in projection item %d' ' contains duplicate items' % k) # Get the two selection vectors to pick correct elements from # the projection vectors omitting bad channels sel = [] vecsel = [] p_set = set(p['data']['col_names']) # faster membership access for c, name in enumerate(ch_names): if name not in bads and name in p_set: sel.append(c) vecsel.append(p['data']['col_names'].index(name)) # If there is something to pick, pickit nrow = p['data']['nrow'] this_vecs = vecs[:, nvec:nvec + nrow] if len(sel) > 0: this_vecs[sel] = p['data']['data'][:, vecsel].T # Rescale for better detection of small singular values for v in range(p['data']['nrow']): psize = np.linalg.norm(this_vecs[:, v]) if psize > 0: orig_n = p['data']['data'].any(axis=0).sum() # Average ref still works if channels are removed # Use relative power to determine if we're in trouble. # 10% loss is hopefully a reasonable threshold. if psize < 0.9 and not inplace and \ (p['kind'] != FIFF.FIFFV_PROJ_ITEM_EEG_AVREF or len(vecsel) == 1): warn( f'Projection vector {repr(p["desc"])} has been ' f'reduced to {100 * psize:0.2f}% of its ' 'original magnitude by subselecting ' f'{len(vecsel)}/{orig_n} of the original ' 'channels. If the ignored channels were bad ' 'during SSP computation, we recommend ' 'recomputing proj (via compute_proj_raw ' 'or related functions) with the bad channels ' 'properly marked, because computing SSP with bad ' 'channels present in the data but unmarked is ' 'dangerous (it can bias the PCA used by SSP). ' 'On the other hand, if you know that all channels ' 'were good during SSP computation, you can safely ' 'use info.normalize_proj() to suppress this ' 'warning during projection.') this_vecs[:, v] /= psize nonzero += 1 # If doing "inplace" mode, "fix" the projectors to only operate # on this subset of channels. if inplace: p['data']['data'] = this_vecs[sel].T p['data']['col_names'] = [p['data']['col_names'][ii] for ii in vecsel] p['data']['ncol'] = len(p['data']['col_names']) nvec += p['data']['nrow'] # Check whether all of the vectors are exactly zero if nonzero == 0 or inplace: return default_return # Reorthogonalize the vectors U, S, _ = linalg.svd(vecs[:, :nvec], full_matrices=False) # Throw away the linearly dependent guys nproj = np.sum((S / S[0]) > 1e-2) U = U[:, :nproj] # Here is the celebrated result proj = np.eye(nchan, nchan) - np.dot(U, U.T) if nproj >= nchan: # e.g., 3 channels and 3 projectors raise RuntimeError('Application of %d projectors for %d channels ' 'will yield no components.' % (nproj, nchan)) return proj, nproj, U def _normalize_proj(info): """Normalize proj after subselection to avoid warnings. This is really only useful for tests, and might not be needed eventually if we change or improve our handling of projectors with picks. """ # Here we do info.get b/c info can actually be a noise cov _make_projector(info['projs'], info.get('ch_names', info.get('names')), info['bads'], include_active=True, inplace=True) @fill_doc def make_projector_info(info, include_active=True): """Make an SSP operator using the measurement info. Calls make_projector on good channels. Parameters ---------- %(info_not_none)s include_active : bool Also include projectors that are already active. Returns ------- proj : array of shape [n_channels, n_channels] The projection operator to apply to the data. nproj : int How many items in the projector. """ proj, nproj, _ = make_projector(info['projs'], info['ch_names'], info['bads'], include_active) return proj, nproj @verbose def activate_proj(projs, copy=True, verbose=None): """Set all projections to active. Useful before passing them to make_projector. Parameters ---------- projs : list The projectors. copy : bool Modify projs in place or operate on a copy. %(verbose)s Returns ------- projs : list The projectors. """ if copy: projs = deepcopy(projs) # Activate the projection items for proj in projs: proj['active'] = True logger.info('%d projection items activated' % len(projs)) return projs @verbose def deactivate_proj(projs, copy=True, verbose=None): """Set all projections to inactive. Useful before saving raw data without projectors applied. Parameters ---------- projs : list The projectors. copy : bool Modify projs in place or operate on a copy. %(verbose)s Returns ------- projs : list The projectors. """ if copy: projs = deepcopy(projs) # Deactivate the projection items for proj in projs: proj['active'] = False logger.info('%d projection items deactivated' % len(projs)) return projs # Keep in sync with doc below _EEG_AVREF_PICK_DICT = {k: True for k in _ELECTRODE_CH_TYPES} @verbose def make_eeg_average_ref_proj(info, activate=True, *, ch_type='eeg', verbose=None): """Create an EEG average reference SSP projection vector. Parameters ---------- %(info_not_none)s activate : bool If True projections are activated. ch_type : str The channel type to use for reference projection. Valid types are 'eeg', 'ecog', 'seeg' and 'dbs'. .. versionadded:: 1.2 %(verbose)s Returns ------- proj: instance of Projection The SSP/PCA projector. """ if info.get('custom_ref_applied', False): raise RuntimeError('A custom reference has been applied to the ' 'data earlier. Please use the ' 'mne.io.set_eeg_reference function to move from ' 'one EEG reference to another.') _validate_type(ch_type, (list, tuple, str), 'ch_type') singleton = False if isinstance(ch_type, str): ch_type = [ch_type] singleton = True for ci, this_ch_type in enumerate(ch_type): _check_option('ch_type' + ('' if singleton else f'[{ci}]'), this_ch_type, list(_EEG_AVREF_PICK_DICT)) ch_type_name = '/'.join(c.upper() for c in ch_type) logger.info(f"Adding average {ch_type_name} reference projection.") ch_dict = {c: True for c in ch_type} for c in ch_type: one_picks = pick_types(info, exclude='bads', **{c: True}) if len(one_picks) == 0: raise ValueError(f'Cannot create {ch_type_name} average reference ' f'projector (no {c.upper()} data found)') del ch_type ch_sel = pick_types(info, **ch_dict, exclude='bads') ch_names = info['ch_names'] ch_names = [ch_names[k] for k in ch_sel] n_chs = len(ch_sel) vec = np.ones((1, n_chs)) vec /= np.sqrt(n_chs) explained_var = None proj_data = dict(col_names=ch_names, row_names=None, data=vec, nrow=1, ncol=n_chs) proj = Projection( active=activate, data=proj_data, explained_var=explained_var, desc=f'Average {ch_type_name} reference', kind=FIFF.FIFFV_PROJ_ITEM_EEG_AVREF) return proj @verbose def _has_eeg_average_ref_proj( info, *, projs=None, check_active=False, ch_type=None, verbose=None): """Determine if a list of projectors has an average EEG ref. Optionally, set check_active=True to additionally check if the CAR has already been applied. """ from .meas_info import Info _validate_type(info, Info, 'info') projs = info.get('projs', []) if projs is None else projs if ch_type is None: pick_kwargs = _EEG_AVREF_PICK_DICT else: ch_type = [ch_type] if isinstance(ch_type, str) else ch_type pick_kwargs = {ch_type: True for ch_type in ch_type} ch_type = '/'.join(c.upper() for c in pick_kwargs) want_names = [ info['ch_names'][pick] for pick in pick_types( info, exclude='bads', **pick_kwargs)] if not want_names: return False found_names = list() for proj in projs: if (proj['kind'] == FIFF.FIFFV_PROJ_ITEM_EEG_AVREF or re.match('^Average .* reference$', proj['desc'])): if not check_active or proj['active']: found_names.extend(proj['data']['col_names']) # If some are missing we have a problem (keep order for the message, # otherwise we could use set logic) missing = [name for name in want_names if name not in found_names] if missing: if found_names: # found some but not all: warn warn(f'Incomplete {ch_type} projector, ' f'missing channel(s) {missing}') return False return True def _needs_eeg_average_ref_proj(info): """Determine if the EEG needs an averge EEG reference. This returns True if no custom reference has been applied and no average reference projection is present in the list of projections. """ if info['custom_ref_applied']: return False if not _electrode_types(info): return False if _has_eeg_average_ref_proj(info): return False return True @verbose def setup_proj(info, add_eeg_ref=True, activate=True, *, eeg_ref_ch_type='eeg', verbose=None): """Set up projection for Raw and Epochs. Parameters ---------- %(info_not_none)s Warning: will be modified in-place. add_eeg_ref : bool If True, an EEG average reference will be added (unless one already exists). activate : bool If True projections are activated. eeg_ref_ch_type : str The channel type to use for reference projection. Valid types are 'eeg', 'ecog', 'seeg' and 'dbs'. .. versionadded:: 1.2 %(verbose)s Returns ------- projector : array of shape [n_channels, n_channels] The projection operator to apply to the data. info : mne.Info The modified measurement info. """ # Add EEG ref reference proj if necessary if add_eeg_ref and _needs_eeg_average_ref_proj(info): eeg_proj = make_eeg_average_ref_proj( info, activate=activate, ch_type=eeg_ref_ch_type) info['projs'].append(eeg_proj) # Create the projector projector, nproj = make_projector_info(info) if nproj == 0: if verbose: logger.info('The projection vectors do not apply to these ' 'channels') projector = None else: logger.info('Created an SSP operator (subspace dimension = %d)' % nproj) # The projection items have been activated if activate: with info._unlock(): info['projs'] = activate_proj(info['projs'], copy=False) return projector, info def _uniquify_projs(projs, check_active=True, sort=True): """Make unique projs.""" final_projs = [] for proj in projs: # flatten if not any(_proj_equal(p, proj, check_active) for p in final_projs): final_projs.append(proj) my_count = count(len(final_projs)) def sorter(x): """Sort in a nice way.""" digits = [s for s in x['desc'] if s.isdigit()] if digits: sort_idx = int(digits[-1]) else: sort_idx = next(my_count) return (sort_idx, x['desc']) return sorted(final_projs, key=sorter) if sort else final_projs