# Authors: Matti Hämäläinen # Alexandre Gramfort # Martin Luessi # # License: BSD-3-Clause # The computations in this code were primarily derived from Matti Hämäläinen's # C code. from time import time from copy import deepcopy import re import numpy as np import shutil import os from os import path as op import tempfile from ..io import RawArray, Info from ..io.constants import FIFF from ..io.open import fiff_open from ..io.tree import dir_tree_find from ..io.tag import find_tag, read_tag from ..io.matrix import (_read_named_matrix, _transpose_named_matrix, write_named_matrix) from ..io.meas_info import (_read_bad_channels, write_info, _write_ch_infos, _read_extended_ch_info, _make_ch_names_mapping, _rename_list) from ..io.pick import (pick_channels_forward, pick_info, pick_channels, pick_types) from ..io.write import (write_int, start_block, end_block, write_coord_trans, write_name_list, write_string, start_and_end_file, write_id) from ..io.base import BaseRaw from ..evoked import Evoked, EvokedArray from ..epochs import BaseEpochs from ..source_space import (_read_source_spaces_from_tree, find_source_space_hemi, _set_source_space_vertices, _write_source_spaces_to_fid, _get_src_nn, _src_kind_dict) from ..source_estimate import _BaseVectorSourceEstimate, _BaseSourceEstimate from ..surface import _normal_orth from ..transforms import (transform_surface_to, invert_transform, write_trans) from ..utils import (_check_fname, get_subjects_dir, has_mne_c, warn, run_subprocess, check_fname, logger, verbose, fill_doc, _validate_type, _check_compensation_grade, _check_option, _check_stc_units, _stamp_to_dt, _on_missing, repr_html) from ..label import Label class Forward(dict): """Forward class to represent info from forward solution. Like :class:`mne.Info`, this data structure behaves like a dictionary. It contains all metadata necessary for a forward solution. .. warning:: This class should not be modified or created by users. Forward objects should be obtained using :func:`mne.make_forward_solution` or :func:`mne.read_forward_solution`. Attributes ---------- ch_names : list of str A convenience wrapper accessible as ``fwd.ch_names`` which wraps ``fwd['info']['ch_names']``. See Also -------- mne.make_forward_solution mne.read_forward_solution Notes ----- Forward data is accessible via string keys using standard :class:`python:dict` access (e.g., ``fwd['nsource'] == 4096``): source_ori : int The source orientation, either ``FIFF.FIFFV_MNE_FIXED_ORI`` or ``FIFF.FIFFV_MNE_FREE_ORI``. coord_frame : int The coordinate frame of the forward solution, usually ``FIFF.FIFFV_COORD_HEAD``. nsource : int The number of source locations. nchan : int The number of channels. sol : dict The forward solution, with entries: ``'data'`` : ndarray, shape (n_channels, nsource * n_ori) The forward solution data. The shape will be ``(n_channels, nsource)`` for a fixed-orientation forward and ``(n_channels, nsource * 3)`` for a free-orientation forward. ``'row_names'`` : list of str The channel names. mri_head_t : instance of Transform The mri ↔ head transformation that was used. info : instance of :class:`~mne.Info` The measurement information (with contents reduced compared to that of the original data). src : instance of :class:`~mne.SourceSpaces` The source space used during forward computation. This can differ from the original source space as: 1. Source points are removed due to proximity to (or existing outside) the inner skull surface. 2. The source space will be converted to the ``coord_frame`` of the forward solution, which typically means it gets converted from MRI to head coordinates. source_rr : ndarray, shape (n_sources, 3) The source locations. source_nn : ndarray, shape (n_sources, 3) The source normals. Will be all +Z (``(0, 0, 1.)``) for volume source spaces. For surface source spaces, these are normal to the cortical surface. surf_ori : int Whether ``sol`` is surface-oriented with the surface normal in the Z component (``FIFF.FIFFV_MNE_FIXED_ORI``) or +Z in the given ``coord_frame`` in the Z component (``FIFF.FIFFV_MNE_FREE_ORI``). Forward objects also have some attributes that are accessible via ``.`` access, like ``fwd.ch_names``. """ def copy(self): """Copy the Forward instance.""" return Forward(deepcopy(self)) def _get_src_type_and_ori_for_repr(self): src_types = np.array([src['type'] for src in self['src']]) if (src_types == 'surf').all(): src_type = 'Surface with %d vertices' % self['nsource'] elif (src_types == 'vol').all(): src_type = 'Volume with %d grid points' % self['nsource'] elif (src_types == 'discrete').all(): src_type = 'Discrete with %d dipoles' % self['nsource'] else: count_string = '' if (src_types == 'surf').any(): count_string += '%d surface, ' % (src_types == 'surf').sum() if (src_types == 'vol').any(): count_string += '%d volume, ' % (src_types == 'vol').sum() if (src_types == 'discrete').any(): count_string += '%d discrete, ' \ % (src_types == 'discrete').sum() count_string = count_string.rstrip(', ') src_type = ('Mixed (%s) with %d vertices' % (count_string, self['nsource'])) if self['source_ori'] == FIFF.FIFFV_MNE_UNKNOWN_ORI: src_ori = 'Unknown' elif self['source_ori'] == FIFF.FIFFV_MNE_FIXED_ORI: src_ori = 'Fixed' elif self['source_ori'] == FIFF.FIFFV_MNE_FREE_ORI: src_ori = 'Free' return src_type, src_ori def __repr__(self): """Summarize forward info instead of printing all.""" entr = ' 0: raise ValueError('Width of matrix must be a multiple of n') tmp = np.arange(ma * bdn, dtype=np.int64).reshape(bdn, ma) tmp = np.tile(tmp, (1, n)) ii = tmp.ravel() jj = np.arange(na, dtype=np.int64)[None, :] jj = jj * np.ones(ma, dtype=np.int64)[:, None] jj = jj.T.ravel() # column indices foreach sparse bd bd = sparse.coo_matrix((A.T.ravel(), np.c_[ii, jj].T)).tocsc() return bd def _get_tag_int(fid, node, name, id_): """Check we have an appropriate tag.""" tag = find_tag(fid, node, id_) if tag is None: fid.close() raise ValueError(name + ' tag not found') return int(tag.data) def _read_one(fid, node): """Read all interesting stuff for one forward solution.""" # This function assumes the fid is open as a context manager if node is None: return None one = Forward() one['source_ori'] = _get_tag_int(fid, node, 'Source orientation', FIFF.FIFF_MNE_SOURCE_ORIENTATION) one['coord_frame'] = _get_tag_int(fid, node, 'Coordinate frame', FIFF.FIFF_MNE_COORD_FRAME) one['nsource'] = _get_tag_int(fid, node, 'Number of sources', FIFF.FIFF_MNE_SOURCE_SPACE_NPOINTS) one['nchan'] = _get_tag_int(fid, node, 'Number of channels', FIFF.FIFF_NCHAN) try: one['sol'] = _read_named_matrix(fid, node, FIFF.FIFF_MNE_FORWARD_SOLUTION, transpose=True) one['_orig_sol'] = one['sol']['data'].copy() except Exception: logger.error('Forward solution data not found') raise try: fwd_type = FIFF.FIFF_MNE_FORWARD_SOLUTION_GRAD one['sol_grad'] = _read_named_matrix(fid, node, fwd_type, transpose=True) one['_orig_sol_grad'] = one['sol_grad']['data'].copy() except Exception: one['sol_grad'] = None if one['sol']['data'].shape[0] != one['nchan'] or \ (one['sol']['data'].shape[1] != one['nsource'] and one['sol']['data'].shape[1] != 3 * one['nsource']): raise ValueError('Forward solution matrix has wrong dimensions') if one['sol_grad'] is not None: if one['sol_grad']['data'].shape[0] != one['nchan'] or \ (one['sol_grad']['data'].shape[1] != 3 * one['nsource'] and one['sol_grad']['data'].shape[1] != 3 * 3 * one['nsource']): raise ValueError('Forward solution gradient matrix has ' 'wrong dimensions') return one @fill_doc def _read_forward_meas_info(tree, fid): """Read light measurement info from forward operator. Parameters ---------- tree : tree FIF tree structure. fid : file id The file id. Returns ------- %(info_not_none)s """ # This function assumes fid is being used as a context manager info = Info() info._unlocked = True # Information from the MRI file parent_mri = dir_tree_find(tree, FIFF.FIFFB_MNE_PARENT_MRI_FILE) if len(parent_mri) == 0: raise ValueError('No parent MEG information found in operator') parent_mri = parent_mri[0] tag = find_tag(fid, parent_mri, FIFF.FIFF_MNE_FILE_NAME) info['mri_file'] = tag.data if tag is not None else None tag = find_tag(fid, parent_mri, FIFF.FIFF_PARENT_FILE_ID) info['mri_id'] = tag.data if tag is not None else None # Information from the MEG file parent_meg = dir_tree_find(tree, FIFF.FIFFB_MNE_PARENT_MEAS_FILE) if len(parent_meg) == 0: raise ValueError('No parent MEG information found in operator') parent_meg = parent_meg[0] tag = find_tag(fid, parent_meg, FIFF.FIFF_MNE_FILE_NAME) info['meas_file'] = tag.data if tag is not None else None tag = find_tag(fid, parent_meg, FIFF.FIFF_PARENT_FILE_ID) info['meas_id'] = tag.data if tag is not None else None # Add channel information info['chs'] = chs = list() for k in range(parent_meg['nent']): kind = parent_meg['directory'][k].kind pos = parent_meg['directory'][k].pos if kind == FIFF.FIFF_CH_INFO: tag = read_tag(fid, pos) chs.append(tag.data) ch_names_mapping = _read_extended_ch_info(chs, parent_meg, fid) info._update_redundant() # Get the MRI <-> head coordinate transformation tag = find_tag(fid, parent_mri, FIFF.FIFF_COORD_TRANS) coord_head = FIFF.FIFFV_COORD_HEAD coord_mri = FIFF.FIFFV_COORD_MRI coord_device = FIFF.FIFFV_COORD_DEVICE coord_ctf_head = FIFF.FIFFV_MNE_COORD_CTF_HEAD if tag is None: raise ValueError('MRI/head coordinate transformation not found') cand = tag.data if cand['from'] == coord_mri and cand['to'] == coord_head: info['mri_head_t'] = cand else: raise ValueError('MRI/head coordinate transformation not found') # Get the MEG device <-> head coordinate transformation tag = find_tag(fid, parent_meg, FIFF.FIFF_COORD_TRANS) if tag is None: raise ValueError('MEG/head coordinate transformation not found') cand = tag.data if cand['from'] == coord_device and cand['to'] == coord_head: info['dev_head_t'] = cand elif cand['from'] == coord_ctf_head and cand['to'] == coord_head: info['ctf_head_t'] = cand else: raise ValueError('MEG/head coordinate transformation not found') info['bads'] = _read_bad_channels( fid, parent_meg, ch_names_mapping=ch_names_mapping) # clean up our bad list, old versions could have non-existent bads info['bads'] = [bad for bad in info['bads'] if bad in info['ch_names']] # Check if a custom reference has been applied tag = find_tag(fid, parent_mri, FIFF.FIFF_MNE_CUSTOM_REF) if tag is None: tag = find_tag(fid, parent_mri, 236) # Constant 236 used before v0.11 info['custom_ref_applied'] = int(tag.data) if tag is not None else False info._unlocked = False return info def _subject_from_forward(forward): """Get subject id from inverse operator.""" return forward['src']._subject # This sets the forward solution order (and gives human-readable names) _FWD_ORDER = dict( meg='MEG', eeg='EEG', ) @verbose def _merge_fwds(fwds, *, verbose=None): """Merge loaded forward dicts into one dict.""" fwd = None first_key = None combined = list() for key in _FWD_ORDER: if key not in fwds: continue if fwd is None: # assign fwd = fwds[key] first_key = key combined.append(_FWD_ORDER[key]) continue a = fwd b = fwds[key] a_kind, b_kind = _FWD_ORDER[first_key], _FWD_ORDER[key] combined.append(b_kind) if (a['sol']['data'].shape[1] != b['sol']['data'].shape[1] or a['source_ori'] != b['source_ori'] or a['nsource'] != b['nsource'] or a['coord_frame'] != b['coord_frame']): raise ValueError( f'The {a_kind} and {b_kind} forward solutions do not match') for k in ('sol', 'sol_grad'): if a[k] is None: continue a[k]['data'] = np.r_[a[k]['data'], b[k]['data']] a[f'_orig_{k}'] = np.r_[a[f'_orig_{k}'], b[f'_orig_{k}']] a[k]['nrow'] = a[k]['nrow'] + b[k]['nrow'] a[k]['row_names'] = a[k]['row_names'] + b[k]['row_names'] a['nchan'] = a['nchan'] + b['nchan'] if len(fwds) > 1: logger.info(f' Forward solutions combined: {", ".join(combined)}') return fwd @verbose def read_forward_solution(fname, include=(), exclude=(), verbose=None): """Read a forward solution a.k.a. lead field. Parameters ---------- fname : str The file name, which should end with -fwd.fif or -fwd.fif.gz. include : list, optional List of names of channels to include. If empty all channels are included. exclude : list, optional List of names of channels to exclude. If empty include all channels. %(verbose)s Returns ------- fwd : instance of Forward The forward solution. See Also -------- write_forward_solution, make_forward_solution Notes ----- Forward solutions, which are derived from an original forward solution with free orientation, are always stored on disk as forward solution with free orientation in X/Y/Z RAS coordinates. To apply any transformation to the forward operator (surface orientation, fixed orientation) please apply :func:`convert_forward_solution` after reading the forward solution with :func:`read_forward_solution`. Forward solutions, which are derived from an original forward solution with fixed orientation, are stored on disk as forward solution with fixed surface-based orientations. Please note that the transformation to surface-based, fixed orientation cannot be reverted after loading the forward solution with :func:`read_forward_solution`. """ check_fname(fname, 'forward', ('-fwd.fif', '-fwd.fif.gz', '_fwd.fif', '_fwd.fif.gz')) fname = _check_fname(fname=fname, must_exist=True, overwrite='read') # Open the file, create directory logger.info('Reading forward solution from %s...' % fname) f, tree, _ = fiff_open(fname) with f as fid: # Find all forward solutions fwds = dir_tree_find(tree, FIFF.FIFFB_MNE_FORWARD_SOLUTION) if len(fwds) == 0: raise ValueError('No forward solutions in %s' % fname) # Parent MRI data parent_mri = dir_tree_find(tree, FIFF.FIFFB_MNE_PARENT_MRI_FILE) if len(parent_mri) == 0: raise ValueError('No parent MRI information in %s' % fname) parent_mri = parent_mri[0] src = _read_source_spaces_from_tree(fid, tree, patch_stats=False) for s in src: s['id'] = find_source_space_hemi(s) fwd = None # Locate and read the forward solutions megnode = None eegnode = None for k in range(len(fwds)): tag = find_tag(fid, fwds[k], FIFF.FIFF_MNE_INCLUDED_METHODS) if tag is None: raise ValueError('Methods not listed for one of the forward ' 'solutions') if tag.data == FIFF.FIFFV_MNE_MEG: megnode = fwds[k] elif tag.data == FIFF.FIFFV_MNE_EEG: eegnode = fwds[k] fwds = dict() megfwd = _read_one(fid, megnode) if megfwd is not None: fwds['meg'] = megfwd if is_fixed_orient(megfwd): ori = 'fixed' else: ori = 'free' logger.info(' Read MEG forward solution (%d sources, ' '%d channels, %s orientations)' % (megfwd['nsource'], megfwd['nchan'], ori)) del megfwd eegfwd = _read_one(fid, eegnode) if eegfwd is not None: fwds['eeg'] = eegfwd if is_fixed_orient(eegfwd): ori = 'fixed' else: ori = 'free' logger.info(' Read EEG forward solution (%d sources, ' '%d channels, %s orientations)' % (eegfwd['nsource'], eegfwd['nchan'], ori)) del eegfwd fwd = _merge_fwds(fwds) del fwds # Get the MRI <-> head coordinate transformation tag = find_tag(fid, parent_mri, FIFF.FIFF_COORD_TRANS) if tag is None: raise ValueError('MRI/head coordinate transformation not found') mri_head_t = tag.data if (mri_head_t['from'] != FIFF.FIFFV_COORD_MRI or mri_head_t['to'] != FIFF.FIFFV_COORD_HEAD): mri_head_t = invert_transform(mri_head_t) if (mri_head_t['from'] != FIFF.FIFFV_COORD_MRI or mri_head_t['to'] != FIFF.FIFFV_COORD_HEAD): fid.close() raise ValueError('MRI/head coordinate transformation not ' 'found') fwd['mri_head_t'] = mri_head_t # # get parent MEG info # fwd['info'] = _read_forward_meas_info(tree, fid) # MNE environment parent_env = dir_tree_find(tree, FIFF.FIFFB_MNE_ENV) if len(parent_env) > 0: parent_env = parent_env[0] tag = find_tag(fid, parent_env, FIFF.FIFF_MNE_ENV_WORKING_DIR) if tag is not None: with fwd['info']._unlock(): fwd['info']['working_dir'] = tag.data tag = find_tag(fid, parent_env, FIFF.FIFF_MNE_ENV_COMMAND_LINE) if tag is not None: with fwd['info']._unlock(): fwd['info']['command_line'] = tag.data # Transform the source spaces to the correct coordinate frame # if necessary # Make sure forward solution is in either the MRI or HEAD coordinate frame if fwd['coord_frame'] not in (FIFF.FIFFV_COORD_MRI, FIFF.FIFFV_COORD_HEAD): raise ValueError('Only forward solutions computed in MRI or head ' 'coordinates are acceptable') # Transform each source space to the HEAD or MRI coordinate frame, # depending on the coordinate frame of the forward solution # NOTE: the function transform_surface_to will also work on discrete and # volume sources nuse = 0 for s in src: try: s = transform_surface_to(s, fwd['coord_frame'], mri_head_t) except Exception as inst: raise ValueError('Could not transform source space (%s)' % inst) nuse += s['nuse'] # Make sure the number of sources match after transformation if nuse != fwd['nsource']: raise ValueError('Source spaces do not match the forward solution.') logger.info(' Source spaces transformed to the forward solution ' 'coordinate frame') fwd['src'] = src # Handle the source locations and orientations fwd['source_rr'] = np.concatenate([ss['rr'][ss['vertno'], :] for ss in src], axis=0) # Store original source orientations fwd['_orig_source_ori'] = fwd['source_ori'] # Deal with include and exclude pick_channels_forward(fwd, include=include, exclude=exclude, copy=False) if is_fixed_orient(fwd, orig=True): fwd['source_nn'] = np.concatenate([_src['nn'][_src['vertno'], :] for _src in fwd['src']], axis=0) fwd['source_ori'] = FIFF.FIFFV_MNE_FIXED_ORI fwd['surf_ori'] = True else: fwd['source_nn'] = np.kron(np.ones((fwd['nsource'], 1)), np.eye(3)) fwd['source_ori'] = FIFF.FIFFV_MNE_FREE_ORI fwd['surf_ori'] = False return Forward(fwd) @verbose def convert_forward_solution(fwd, surf_ori=False, force_fixed=False, copy=True, use_cps=True, verbose=None): """Convert forward solution between different source orientations. Parameters ---------- fwd : Forward The forward solution to modify. surf_ori : bool, optional (default False) Use surface-based source coordinate system? Note that force_fixed=True implies surf_ori=True. force_fixed : bool, optional (default False) If True, force fixed source orientation mode. copy : bool Whether to return a new instance or modify in place. %(use_cps)s %(verbose)s Returns ------- fwd : Forward The modified forward solution. """ from scipy import sparse fwd = fwd.copy() if copy else fwd if force_fixed is True: surf_ori = True if any([src['type'] == 'vol' for src in fwd['src']]) and force_fixed: raise ValueError( 'Forward operator was generated with sources from a ' 'volume source space. Conversion to fixed orientation is not ' 'possible. Consider using a discrete source space if you have ' 'meaningful normal orientations.') if surf_ori and use_cps: if any(s.get('patch_inds') is not None for s in fwd['src']): logger.info(' Average patch normals will be employed in ' 'the rotation to the local surface coordinates..' '..') else: use_cps = False logger.info(' No patch info available. The standard source ' 'space normals will be employed in the rotation ' 'to the local surface coordinates....') # We need to change these entries (only): # 1. source_nn # 2. sol['data'] # 3. sol['ncol'] # 4. sol_grad['data'] # 5. sol_grad['ncol'] # 6. source_ori if is_fixed_orient(fwd, orig=True) or (force_fixed and not use_cps): # Fixed fwd['source_nn'] = np.concatenate([_get_src_nn(s, use_cps) for s in fwd['src']], axis=0) if not is_fixed_orient(fwd, orig=True): logger.info(' Changing to fixed-orientation forward ' 'solution with surface-based source orientations...') fix_rot = _block_diag(fwd['source_nn'].T, 1) # newer versions of numpy require explicit casting here, so *= no # longer works fwd['sol']['data'] = (fwd['_orig_sol'] * fix_rot).astype('float32') fwd['sol']['ncol'] = fwd['nsource'] if fwd['sol_grad'] is not None: x = sparse.block_diag([fix_rot] * 3) fwd['sol_grad']['data'] = fwd['_orig_sol_grad'] * x # dot prod fwd['sol_grad']['ncol'] = 3 * fwd['nsource'] fwd['source_ori'] = FIFF.FIFFV_MNE_FIXED_ORI fwd['surf_ori'] = True elif surf_ori: # Free, surf-oriented # Rotate the local source coordinate systems fwd['source_nn'] = np.kron(np.ones((fwd['nsource'], 1)), np.eye(3)) logger.info(' Converting to surface-based source orientations...') # Actually determine the source orientations pp = 0 for s in fwd['src']: if s['type'] in ['surf', 'discrete']: nn = _get_src_nn(s, use_cps) stop = pp + 3 * s['nuse'] fwd['source_nn'][pp:stop] = _normal_orth(nn).reshape(-1, 3) pp = stop del nn else: pp += 3 * s['nuse'] # Rotate the solution components as well if force_fixed: fwd['source_nn'] = fwd['source_nn'][2::3, :] fix_rot = _block_diag(fwd['source_nn'].T, 1) # newer versions of numpy require explicit casting here, so *= no # longer works fwd['sol']['data'] = (fwd['_orig_sol'] * fix_rot).astype('float32') fwd['sol']['ncol'] = fwd['nsource'] if fwd['sol_grad'] is not None: x = sparse.block_diag([fix_rot] * 3) fwd['sol_grad']['data'] = fwd['_orig_sol_grad'] * x # dot prod fwd['sol_grad']['ncol'] = 3 * fwd['nsource'] fwd['source_ori'] = FIFF.FIFFV_MNE_FIXED_ORI fwd['surf_ori'] = True else: surf_rot = _block_diag(fwd['source_nn'].T, 3) fwd['sol']['data'] = fwd['_orig_sol'] * surf_rot fwd['sol']['ncol'] = 3 * fwd['nsource'] if fwd['sol_grad'] is not None: x = sparse.block_diag([surf_rot] * 3) fwd['sol_grad']['data'] = fwd['_orig_sol_grad'] * x # dot prod fwd['sol_grad']['ncol'] = 9 * fwd['nsource'] fwd['source_ori'] = FIFF.FIFFV_MNE_FREE_ORI fwd['surf_ori'] = True else: # Free, cartesian logger.info(' Cartesian source orientations...') fwd['source_nn'] = np.tile(np.eye(3), (fwd['nsource'], 1)) fwd['sol']['data'] = fwd['_orig_sol'].copy() fwd['sol']['ncol'] = 3 * fwd['nsource'] if fwd['sol_grad'] is not None: fwd['sol_grad']['data'] = fwd['_orig_sol_grad'].copy() fwd['sol_grad']['ncol'] = 9 * fwd['nsource'] fwd['source_ori'] = FIFF.FIFFV_MNE_FREE_ORI fwd['surf_ori'] = False logger.info(' [done]') return fwd @verbose def write_forward_solution(fname, fwd, overwrite=False, verbose=None): """Write forward solution to a file. Parameters ---------- fname : str File name to save the forward solution to. It should end with ``-fwd.fif`` or ``-fwd.fif.gz``. fwd : Forward Forward solution. %(overwrite)s %(verbose)s See Also -------- read_forward_solution Notes ----- Forward solutions, which are derived from an original forward solution with free orientation, are always stored on disk as forward solution with free orientation in X/Y/Z RAS coordinates. Transformations (surface orientation, fixed orientation) will be reverted. To reapply any transformation to the forward operator please apply :func:`convert_forward_solution` after reading the forward solution with :func:`read_forward_solution`. Forward solutions, which are derived from an original forward solution with fixed orientation, are stored on disk as forward solution with fixed surface-based orientations. Please note that the transformation to surface-based, fixed orientation cannot be reverted after loading the forward solution with :func:`read_forward_solution`. """ check_fname(fname, 'forward', ('-fwd.fif', '-fwd.fif.gz', '_fwd.fif', '_fwd.fif.gz')) # check for file existence and expand `~` if present fname = _check_fname(fname, overwrite) with start_and_end_file(fname) as fid: _write_forward_solution(fid, fwd) def _write_forward_solution(fid, fwd): start_block(fid, FIFF.FIFFB_MNE) # # MNE env # start_block(fid, FIFF.FIFFB_MNE_ENV) write_id(fid, FIFF.FIFF_BLOCK_ID) data = fwd['info'].get('working_dir', None) if data is not None: write_string(fid, FIFF.FIFF_MNE_ENV_WORKING_DIR, data) data = fwd['info'].get('command_line', None) if data is not None: write_string(fid, FIFF.FIFF_MNE_ENV_COMMAND_LINE, data) end_block(fid, FIFF.FIFFB_MNE_ENV) # # Information from the MRI file # start_block(fid, FIFF.FIFFB_MNE_PARENT_MRI_FILE) write_string(fid, FIFF.FIFF_MNE_FILE_NAME, fwd['info']['mri_file']) if fwd['info']['mri_id'] is not None: write_id(fid, FIFF.FIFF_PARENT_FILE_ID, fwd['info']['mri_id']) # store the MRI to HEAD transform in MRI file write_coord_trans(fid, fwd['info']['mri_head_t']) end_block(fid, FIFF.FIFFB_MNE_PARENT_MRI_FILE) # write measurement info write_forward_meas_info(fid, fwd['info']) # invert our original source space transform src = list() for s in fwd['src']: s = deepcopy(s) try: # returns source space to original coordinate frame # usually MRI s = transform_surface_to(s, fwd['mri_head_t']['from'], fwd['mri_head_t']) except Exception as inst: raise ValueError('Could not transform source space (%s)' % inst) src.append(s) # # Write the source spaces (again) # _write_source_spaces_to_fid(fid, src) n_vert = sum([ss['nuse'] for ss in src]) if fwd['_orig_source_ori'] == FIFF.FIFFV_MNE_FIXED_ORI: n_col = n_vert else: n_col = 3 * n_vert # Undo transformations sol = fwd['_orig_sol'].copy() if fwd['sol_grad'] is not None: sol_grad = fwd['_orig_sol_grad'].copy() else: sol_grad = None if fwd['surf_ori'] is True: if fwd['_orig_source_ori'] == FIFF.FIFFV_MNE_FIXED_ORI: warn('The forward solution, which is stored on disk now, is based ' 'on a forward solution with fixed orientation. Please note ' 'that the transformation to surface-based, fixed orientation ' 'cannot be reverted after loading the forward solution with ' 'read_forward_solution.', RuntimeWarning) else: warn('This forward solution is based on a forward solution with ' 'free orientation. The original forward solution is stored ' 'on disk in X/Y/Z RAS coordinates. Any transformation ' '(surface orientation or fixed orientation) will be ' 'reverted. To reapply any transformation to the forward ' 'operator please apply convert_forward_solution after ' 'reading the forward solution with read_forward_solution.', RuntimeWarning) # # MEG forward solution # picks_meg = pick_types(fwd['info'], meg=True, eeg=False, ref_meg=False, exclude=[]) picks_eeg = pick_types(fwd['info'], meg=False, eeg=True, ref_meg=False, exclude=[]) n_meg = len(picks_meg) n_eeg = len(picks_eeg) row_names_meg = [fwd['sol']['row_names'][p] for p in picks_meg] row_names_eeg = [fwd['sol']['row_names'][p] for p in picks_eeg] if n_meg > 0: meg_solution = dict(data=sol[picks_meg], nrow=n_meg, ncol=n_col, row_names=row_names_meg, col_names=[]) _transpose_named_matrix(meg_solution) start_block(fid, FIFF.FIFFB_MNE_FORWARD_SOLUTION) write_int(fid, FIFF.FIFF_MNE_INCLUDED_METHODS, FIFF.FIFFV_MNE_MEG) write_int(fid, FIFF.FIFF_MNE_COORD_FRAME, fwd['coord_frame']) write_int(fid, FIFF.FIFF_MNE_SOURCE_ORIENTATION, fwd['_orig_source_ori']) write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NPOINTS, n_vert) write_int(fid, FIFF.FIFF_NCHAN, n_meg) write_named_matrix(fid, FIFF.FIFF_MNE_FORWARD_SOLUTION, meg_solution) if sol_grad is not None: meg_solution_grad = dict(data=sol_grad[picks_meg], nrow=n_meg, ncol=n_col * 3, row_names=row_names_meg, col_names=[]) _transpose_named_matrix(meg_solution_grad) write_named_matrix(fid, FIFF.FIFF_MNE_FORWARD_SOLUTION_GRAD, meg_solution_grad) end_block(fid, FIFF.FIFFB_MNE_FORWARD_SOLUTION) # # EEG forward solution # if n_eeg > 0: eeg_solution = dict(data=sol[picks_eeg], nrow=n_eeg, ncol=n_col, row_names=row_names_eeg, col_names=[]) _transpose_named_matrix(eeg_solution) start_block(fid, FIFF.FIFFB_MNE_FORWARD_SOLUTION) write_int(fid, FIFF.FIFF_MNE_INCLUDED_METHODS, FIFF.FIFFV_MNE_EEG) write_int(fid, FIFF.FIFF_MNE_COORD_FRAME, fwd['coord_frame']) write_int(fid, FIFF.FIFF_MNE_SOURCE_ORIENTATION, fwd['_orig_source_ori']) write_int(fid, FIFF.FIFF_NCHAN, n_eeg) write_int(fid, FIFF.FIFF_MNE_SOURCE_SPACE_NPOINTS, n_vert) write_named_matrix(fid, FIFF.FIFF_MNE_FORWARD_SOLUTION, eeg_solution) if sol_grad is not None: eeg_solution_grad = dict(data=sol_grad[picks_eeg], nrow=n_eeg, ncol=n_col * 3, row_names=row_names_eeg, col_names=[]) _transpose_named_matrix(eeg_solution_grad) write_named_matrix(fid, FIFF.FIFF_MNE_FORWARD_SOLUTION_GRAD, eeg_solution_grad) end_block(fid, FIFF.FIFFB_MNE_FORWARD_SOLUTION) end_block(fid, FIFF.FIFFB_MNE) def is_fixed_orient(forward, orig=False): """Check if the forward operator is fixed orientation. Parameters ---------- forward : instance of Forward The forward. orig : bool If True, consider the original source orientation. If False (default), consider the current source orientation. Returns ------- fixed_ori : bool Whether or not it is fixed orientation. """ if orig: # if we want to know about the original version fixed_ori = (forward['_orig_source_ori'] == FIFF.FIFFV_MNE_FIXED_ORI) else: # most of the time we want to know about the current version fixed_ori = (forward['source_ori'] == FIFF.FIFFV_MNE_FIXED_ORI) return fixed_ori @fill_doc def write_forward_meas_info(fid, info): """Write measurement info stored in forward solution. Parameters ---------- fid : file id The file id %(info_not_none)s """ info._check_consistency() # # Information from the MEG file # start_block(fid, FIFF.FIFFB_MNE_PARENT_MEAS_FILE) write_string(fid, FIFF.FIFF_MNE_FILE_NAME, info['meas_file']) if info['meas_id'] is not None: write_id(fid, FIFF.FIFF_PARENT_BLOCK_ID, info['meas_id']) # get transformation from CTF and DEVICE to HEAD coordinate frame meg_head_t = info.get('dev_head_t', info.get('ctf_head_t')) if meg_head_t is None: fid.close() raise ValueError('Head<-->sensor transform not found') write_coord_trans(fid, meg_head_t) ch_names_mapping = dict() if 'chs' in info: # Channel information ch_names_mapping = _make_ch_names_mapping(info['chs']) write_int(fid, FIFF.FIFF_NCHAN, len(info['chs'])) _write_ch_infos(fid, info['chs'], False, ch_names_mapping) if 'bads' in info and len(info['bads']) > 0: # Bad channels bads = _rename_list(info['bads'], ch_names_mapping) start_block(fid, FIFF.FIFFB_MNE_BAD_CHANNELS) write_name_list(fid, FIFF.FIFF_MNE_CH_NAME_LIST, bads) end_block(fid, FIFF.FIFFB_MNE_BAD_CHANNELS) end_block(fid, FIFF.FIFFB_MNE_PARENT_MEAS_FILE) def _select_orient_forward(forward, info, noise_cov=None, copy=True): """Prepare forward solution for inverse solvers.""" # fwd['sol']['row_names'] may be different order from fwd['info']['chs'] fwd_sol_ch_names = forward['sol']['row_names'] all_ch_names = set(fwd_sol_ch_names) all_bads = set(info['bads']) if noise_cov is not None: all_ch_names &= set(noise_cov['names']) all_bads |= set(noise_cov['bads']) else: noise_cov = dict(bads=info['bads']) ch_names = [c['ch_name'] for c in info['chs'] if c['ch_name'] not in all_bads and c['ch_name'] in all_ch_names] if not len(info['bads']) == len(noise_cov['bads']) or \ not all(b in noise_cov['bads'] for b in info['bads']): logger.info('info["bads"] and noise_cov["bads"] do not match, ' 'excluding bad channels from both') # check the compensation grade _check_compensation_grade(forward['info'], info, 'forward') n_chan = len(ch_names) logger.info("Computing inverse operator with %d channels." % n_chan) forward = pick_channels_forward(forward, ch_names, ordered=True, copy=copy) info_idx = [info['ch_names'].index(name) for name in ch_names] info_picked = pick_info(info, info_idx) forward['info']._check_consistency() info_picked._check_consistency() return forward, info_picked def _triage_loose(src, loose, fixed='auto'): _validate_type(loose, (str, dict, 'numeric'), 'loose') _validate_type(fixed, (str, bool), 'fixed') orig_loose = loose if isinstance(loose, str): _check_option('loose', loose, ('auto',)) if fixed is True: loose = 0. else: # False or auto loose = 0.2 if src.kind == 'surface' else 1. src_types = set(_src_kind_dict[s['type']] for s in src) if not isinstance(loose, dict): loose = float(loose) loose = {key: loose for key in src_types} loose_keys = set(loose.keys()) if loose_keys != src_types: raise ValueError( f'loose, if dict, must have keys {sorted(src_types)} to match the ' f'source space, got {sorted(loose_keys)}') # if fixed is auto it can be ignored, if it's False it can be ignored, # only really need to care about fixed=True if fixed is True: if not all(v == 0. for v in loose.values()): raise ValueError( 'When using fixed=True, loose must be 0. or "auto", ' f'got {orig_loose}') elif fixed is False: if any(v == 0. for v in loose.values()): raise ValueError( 'If loose==0., then fixed must be True or "auto", got False') del fixed for key, this_loose in loose.items(): if key not in ('surface', 'discrete') and this_loose != 1: raise ValueError( 'loose parameter has to be 1 or "auto" for non-surface/' f'discrete source spaces, got loose["{key}"] = {this_loose}') if not 0 <= this_loose <= 1: raise ValueError( f'loose ({key}) must be between 0 and 1, got {this_loose}') return loose @verbose def compute_orient_prior(forward, loose='auto', verbose=None): """Compute orientation prior. Parameters ---------- forward : instance of Forward Forward operator. %(loose)s %(verbose)s Returns ------- orient_prior : ndarray, shape (n_sources,) Orientation priors. See Also -------- compute_depth_prior """ _validate_type(forward, Forward, 'forward') n_sources = forward['sol']['data'].shape[1] loose = _triage_loose(forward['src'], loose) orient_prior = np.ones(n_sources, dtype=np.float64) if is_fixed_orient(forward): if any(v > 0. for v in loose.values()): raise ValueError('loose must be 0. with forward operator ' 'with fixed orientation, got %s' % (loose,)) return orient_prior if all(v == 1. for v in loose.values()): return orient_prior # We actually need non-unity prior, compute it for each source space # separately if not forward['surf_ori']: raise ValueError('Forward operator is not oriented in surface ' 'coordinates. loose parameter should be 1. ' 'not %s.' % (loose,)) start = 0 logged = dict() for s in forward['src']: this_type = _src_kind_dict[s['type']] use_loose = loose[this_type] if not logged.get(this_type): if use_loose == 1.: name = 'free' else: name = 'fixed' if use_loose == 0. else 'loose' logger.info(f'Applying {name.ljust(5)} dipole orientations to ' f'{this_type.ljust(7)} source spaces: {use_loose}') logged[this_type] = True stop = start + 3 * s['nuse'] orient_prior[start:stop:3] *= use_loose orient_prior[start + 1:stop:3] *= use_loose start = stop return orient_prior def _restrict_gain_matrix(G, info): """Restrict gain matrix entries for optimal depth weighting.""" # Figure out which ones have been used if len(info['chs']) != G.shape[0]: raise ValueError('G.shape[0] (%d) and length of info["chs"] (%d) ' 'do not match' % (G.shape[0], len(info['chs']))) for meg, eeg, kind in ( ('grad', False, 'planar'), ('mag', False, 'magnetometer or axial gradiometer'), (False, True, 'EEG')): sel = pick_types(info, meg=meg, eeg=eeg, ref_meg=False, exclude=[]) if len(sel) > 0: logger.info(' %d %s channels' % (len(sel), kind)) break else: warn('Could not find MEG or EEG channels to limit depth channels') sel = slice(None) return G[sel] @verbose def compute_depth_prior(forward, info, exp=0.8, limit=10.0, limit_depth_chs=False, combine_xyz='spectral', noise_cov=None, rank=None, verbose=None): """Compute depth prior for depth weighting. Parameters ---------- forward : instance of Forward The forward solution. %(info_not_none)s exp : float Exponent for the depth weighting, must be between 0 and 1. limit : float | None The upper bound on depth weighting. Can be None to be bounded by the largest finite prior. limit_depth_chs : bool | 'whiten' How to deal with multiple channel types in depth weighting. The default is True, which whitens based on the source sensitivity of the highest-SNR channel type. See Notes for details. .. versionchanged:: 0.18 Added the "whiten" option. combine_xyz : 'spectral' | 'fro' When a loose (or free) orientation is used, how the depth weighting for each triplet should be calculated. If 'spectral', use the squared spectral norm of Gk. If 'fro', use the squared Frobenius norm of Gk. .. versionadded:: 0.18 noise_cov : instance of Covariance | None The noise covariance to use to whiten the gain matrix when ``limit_depth_chs='whiten'``. .. versionadded:: 0.18 %(rank_none)s .. versionadded:: 0.18 %(verbose)s Returns ------- depth_prior : ndarray, shape (n_vertices,) The depth prior. See Also -------- compute_orient_prior Notes ----- The defaults used by the minimum norm code and sparse solvers differ. In particular, the values for MNE are:: compute_depth_prior(..., limit=10., limit_depth_chs=True, combine_xyz='spectral') In sparse solvers and LCMV, the values are:: compute_depth_prior(..., limit=None, limit_depth_chs='whiten', combine_xyz='fro') The ``limit_depth_chs`` argument can take the following values: * :data:`python:True` (default) Use only grad channels in depth weighting (equivalent to MNE C minimum-norm code). If grad channels aren't present, only mag channels will be used (if no mag, then eeg). This makes the depth prior dependent only on the sensor geometry (and relationship to the sources). * ``'whiten'`` Compute a whitener and apply it to the gain matirx before computing the depth prior. In this case ``noise_cov`` must not be None. Whitening the gain matrix makes the depth prior depend on both sensor geometry and the data of interest captured by the noise covariance (e.g., projections, SNR). .. versionadded:: 0.18 * :data:`python:False` Use all channels. Not recommended since the depth weighting will be biased toward whichever channel type has the largest values in SI units (such as EEG being orders of magnitude larger than MEG). """ from ..cov import Covariance, compute_whitener _validate_type(forward, Forward, 'forward') patch_areas = forward.get('patch_areas', None) is_fixed_ori = is_fixed_orient(forward) G = forward['sol']['data'] logger.info('Creating the depth weighting matrix...') _validate_type(noise_cov, (Covariance, None), 'noise_cov', 'Covariance or None') _validate_type(limit_depth_chs, (str, bool), 'limit_depth_chs') if isinstance(limit_depth_chs, str): if limit_depth_chs != 'whiten': raise ValueError('limit_depth_chs, if str, must be "whiten", got ' '%s' % (limit_depth_chs,)) if not isinstance(noise_cov, Covariance): raise ValueError('With limit_depth_chs="whiten", noise_cov must be' ' a Covariance, got %s' % (type(noise_cov),)) if combine_xyz is not False: # private / expert option _check_option('combine_xyz', combine_xyz, ('fro', 'spectral')) # If possible, pick best depth-weighting channels if limit_depth_chs is True: G = _restrict_gain_matrix(G, info) elif limit_depth_chs == 'whiten': whitener, _ = compute_whitener(noise_cov, info, pca=True, rank=rank, verbose=False) G = np.dot(whitener, G) # Compute the gain matrix if is_fixed_ori or combine_xyz in ('fro', False): d = np.sum(G ** 2, axis=0) if not (is_fixed_ori or combine_xyz is False): d = d.reshape(-1, 3).sum(axis=1) # Spherical leadfield can be zero at the center d[d == 0.] = np.min(d[d != 0.]) else: # 'spectral' # n_pos = G.shape[1] // 3 # The following is equivalent to this, but 4-10x faster # d = np.zeros(n_pos) # for k in range(n_pos): # Gk = G[:, 3 * k:3 * (k + 1)] # x = np.dot(Gk.T, Gk) # d[k] = linalg.svdvals(x)[0] G.shape = (G.shape[0], -1, 3) d = np.linalg.norm(np.einsum('svj,svk->vjk', G, G), # vector dot prods ord=2, axis=(1, 2)) # ord=2 spectral (largest s.v.) G.shape = (G.shape[0], -1) # XXX Currently the fwd solns never have "patch_areas" defined if patch_areas is not None: if not is_fixed_ori and combine_xyz is False: patch_areas = np.repeat(patch_areas, 3) d /= patch_areas ** 2 logger.info(' Patch areas taken into account in the depth ' 'weighting') w = 1.0 / d if limit is not None: ws = np.sort(w) weight_limit = limit ** 2 if limit_depth_chs is False: # match old mne-python behavior # we used to do ind = np.argmin(ws), but this is 0 by sort above n_limit = 0 limit = ws[0] * weight_limit else: # match C code behavior limit = ws[-1] n_limit = len(d) if ws[-1] > weight_limit * ws[0]: ind = np.where(ws > weight_limit * ws[0])[0][0] limit = ws[ind] n_limit = ind logger.info(' limit = %d/%d = %f' % (n_limit + 1, len(d), np.sqrt(limit / ws[0]))) scale = 1.0 / limit logger.info(' scale = %g exp = %g' % (scale, exp)) w = np.minimum(w / limit, 1) depth_prior = w ** exp if not (is_fixed_ori or combine_xyz is False): depth_prior = np.repeat(depth_prior, 3) return depth_prior def _stc_src_sel(src, stc, on_missing='raise', extra=', likely due to forward calculations'): """Select the vertex indices of a source space using a source estimate.""" if isinstance(stc, list): vertices = stc else: assert isinstance(stc, _BaseSourceEstimate) vertices = stc.vertices del stc if not len(src) == len(vertices): raise RuntimeError('Mismatch between number of source spaces (%s) and ' 'STC vertices (%s)' % (len(src), len(vertices))) src_sels, stc_sels, out_vertices = [], [], [] src_offset = stc_offset = 0 for s, v in zip(src, vertices): joint_sel = np.intersect1d(s['vertno'], v) src_sels.append(np.searchsorted(s['vertno'], joint_sel) + src_offset) src_offset += len(s['vertno']) idx = np.searchsorted(v, joint_sel) stc_sels.append(idx + stc_offset) stc_offset += len(v) out_vertices.append(np.array(v)[idx]) src_sel = np.concatenate(src_sels) stc_sel = np.concatenate(stc_sels) assert len(src_sel) == len(stc_sel) == sum(len(v) for v in out_vertices) n_stc = sum(len(v) for v in vertices) n_joint = len(src_sel) if n_joint != n_stc: msg = ('Only %i of %i SourceEstimate %s found in ' 'source space%s' % (n_joint, n_stc, 'vertex' if n_stc == 1 else 'vertices', extra)) _on_missing(on_missing, msg) return src_sel, stc_sel, out_vertices def _fill_measurement_info(info, fwd, sfreq, data): """Fill the measurement info of a Raw or Evoked object.""" sel = pick_channels(info['ch_names'], fwd['sol']['row_names']) info = pick_info(info, sel) info['bads'] = [] now = time() sec = np.floor(now) usec = 1e6 * (now - sec) # this is probably correct based on what's done in meas_info.py... with info._unlock(check_after=True): info.update(meas_id=fwd['info']['meas_id'], file_id=info['meas_id'], meas_date=_stamp_to_dt((int(sec), int(usec))), highpass=0., lowpass=sfreq / 2., sfreq=sfreq, projs=[]) # reorder data (which is in fwd order) to match that of info order = [fwd['sol']['row_names'].index(name) for name in info['ch_names']] data = data[order] return info, data @verbose def _apply_forward(fwd, stc, start=None, stop=None, on_missing='raise', use_cps=True, verbose=None): """Apply forward model and return data, times, ch_names.""" _validate_type(stc, _BaseSourceEstimate, 'stc', 'SourceEstimate') _validate_type(fwd, Forward, 'fwd') if isinstance(stc, _BaseVectorSourceEstimate): vector = True fwd = convert_forward_solution(fwd, force_fixed=False, surf_ori=False) else: vector = False if not is_fixed_orient(fwd): fwd = convert_forward_solution(fwd, force_fixed=True, use_cps=use_cps) if np.all(stc.data > 0): warn('Source estimate only contains currents with positive values. ' 'Use pick_ori="normal" when computing the inverse to compute ' 'currents not current magnitudes.') _check_stc_units(stc) src_sel, stc_sel, _ = _stc_src_sel(fwd['src'], stc, on_missing=on_missing) gain = fwd['sol']['data'] stc_sel = slice(None) if len(stc_sel) == len(stc.data) else stc_sel times = stc.times[start:stop].copy() stc_data = stc.data[stc_sel, ..., start:stop].reshape(-1, len(times)) del stc if vector: gain = gain.reshape(len(gain), gain.shape[1] // 3, 3) gain = gain[:, src_sel].reshape(len(gain), -1) # save some memory if possible logger.info('Projecting source estimate to sensor space...') data = np.dot(gain, stc_data) logger.info('[done]') return data, times @verbose def apply_forward(fwd, stc, info, start=None, stop=None, use_cps=True, on_missing='raise', verbose=None): """Project source space currents to sensor space using a forward operator. The sensor space data is computed for all channels present in fwd. Use pick_channels_forward or pick_types_forward to restrict the solution to a subset of channels. The function returns an Evoked object, which is constructed from evoked_template. The evoked_template should be from the same MEG system on which the original data was acquired. An exception will be raised if the forward operator contains channels that are not present in the template. Parameters ---------- fwd : Forward Forward operator to use. stc : SourceEstimate The source estimate from which the sensor space data is computed. %(info_not_none)s start : int, optional Index of first time sample (index not time is seconds). stop : int, optional Index of first time sample not to include (index not time is seconds). %(use_cps)s .. versionadded:: 0.15 %(on_missing_fwd)s Default is "raise". .. versionadded:: 0.18 %(verbose)s Returns ------- evoked : Evoked Evoked object with computed sensor space data. See Also -------- apply_forward_raw: Compute sensor space data and return a Raw object. """ _validate_type(info, Info, 'info') _validate_type(fwd, Forward, 'forward') info._check_consistency() # make sure evoked_template contains all channels in fwd for ch_name in fwd['sol']['row_names']: if ch_name not in info['ch_names']: raise ValueError('Channel %s of forward operator not present in ' 'evoked_template.' % ch_name) # project the source estimate to the sensor space data, times = _apply_forward(fwd, stc, start, stop, on_missing=on_missing, use_cps=use_cps) # fill the measurement info sfreq = float(1.0 / stc.tstep) info, data = _fill_measurement_info(info, fwd, sfreq, data) evoked = EvokedArray(data, info, times[0], nave=1) evoked._set_times(times) evoked._update_first_last() return evoked @verbose def apply_forward_raw(fwd, stc, info, start=None, stop=None, on_missing='raise', use_cps=True, verbose=None): """Project source space currents to sensor space using a forward operator. The sensor space data is computed for all channels present in fwd. Use pick_channels_forward or pick_types_forward to restrict the solution to a subset of channels. The function returns a Raw object, which is constructed using provided info. The info object should be from the same MEG system on which the original data was acquired. An exception will be raised if the forward operator contains channels that are not present in the info. Parameters ---------- fwd : Forward Forward operator to use. stc : SourceEstimate The source estimate from which the sensor space data is computed. %(info_not_none)s start : int, optional Index of first time sample (index not time is seconds). stop : int, optional Index of first time sample not to include (index not time is seconds). %(on_missing_fwd)s Default is "raise". .. versionadded:: 0.18 %(use_cps)s .. versionadded:: 0.21 %(verbose)s Returns ------- raw : Raw object Raw object with computed sensor space data. See Also -------- apply_forward: Compute sensor space data and return an Evoked object. """ # make sure info contains all channels in fwd for ch_name in fwd['sol']['row_names']: if ch_name not in info['ch_names']: raise ValueError('Channel %s of forward operator not present in ' 'info.' % ch_name) # project the source estimate to the sensor space data, times = _apply_forward(fwd, stc, start, stop, on_missing=on_missing, use_cps=use_cps) sfreq = 1.0 / stc.tstep info, data = _fill_measurement_info(info, fwd, sfreq, data) with info._unlock(): info['projs'] = [] # store sensor data in Raw object using the info raw = RawArray(data, info, first_samp=int(np.round(times[0] * sfreq))) raw._projector = None return raw @fill_doc def restrict_forward_to_stc(fwd, stc, on_missing='ignore'): """Restrict forward operator to active sources in a source estimate. Parameters ---------- fwd : instance of Forward Forward operator. stc : instance of SourceEstimate Source estimate. %(on_missing_fwd)s Default is "ignore". .. versionadded:: 0.18 Returns ------- fwd_out : instance of Forward Restricted forward operator. See Also -------- restrict_forward_to_label """ _validate_type(on_missing, str, 'on_missing') _check_option('on_missing', on_missing, ('ignore', 'warn', 'raise')) src_sel, _, vertices = _stc_src_sel(fwd['src'], stc, on_missing=on_missing) del stc return _restrict_forward_to_src_sel(fwd, src_sel) def _restrict_forward_to_src_sel(fwd, src_sel): fwd_out = deepcopy(fwd) # figure out the vertno we are keeping idx_sel = np.concatenate([[[si] * len(s['vertno']), s['vertno']] for si, s in enumerate(fwd['src'])], axis=-1) assert idx_sel.ndim == 2 and idx_sel.shape[0] == 2 assert idx_sel.shape[1] == fwd['nsource'] idx_sel = idx_sel[:, src_sel] fwd_out['source_rr'] = fwd['source_rr'][src_sel] fwd_out['nsource'] = len(src_sel) if is_fixed_orient(fwd): idx = src_sel if fwd['sol_grad'] is not None: idx_grad = (3 * src_sel[:, None] + np.arange(3)).ravel() else: idx = (3 * src_sel[:, None] + np.arange(3)).ravel() if fwd['sol_grad'] is not None: idx_grad = (9 * src_sel[:, None] + np.arange(9)).ravel() fwd_out['source_nn'] = fwd['source_nn'][idx] fwd_out['sol']['data'] = fwd['sol']['data'][:, idx] if fwd['sol_grad'] is not None: fwd_out['sol_grad']['data'] = fwd['sol_grad']['data'][:, idx_grad] fwd_out['sol']['ncol'] = len(idx) if is_fixed_orient(fwd, orig=True): idx = src_sel if fwd['sol_grad'] is not None: idx_grad = (3 * src_sel[:, None] + np.arange(3)).ravel() else: idx = (3 * src_sel[:, None] + np.arange(3)).ravel() if fwd['sol_grad'] is not None: idx_grad = (9 * src_sel[:, None] + np.arange(9)).ravel() fwd_out['_orig_sol'] = fwd['_orig_sol'][:, idx] if fwd['sol_grad'] is not None: fwd_out['_orig_sol_grad'] = fwd['_orig_sol_grad'][:, idx_grad] vertices = [idx_sel[1][idx_sel[0] == si] for si in range(len(fwd_out['src']))] _set_source_space_vertices(fwd_out['src'], vertices) return fwd_out def restrict_forward_to_label(fwd, labels): """Restrict forward operator to labels. Parameters ---------- fwd : Forward Forward operator. labels : instance of Label | list Label object or list of label objects. Returns ------- fwd_out : dict Restricted forward operator. See Also -------- restrict_forward_to_stc """ vertices = [np.array([], int), np.array([], int)] if not isinstance(labels, list): labels = [labels] # Get vertices separately of each hemisphere from all label for label in labels: _validate_type(label, Label, "label", "Label or list") i = 0 if label.hemi == 'lh' else 1 vertices[i] = np.append(vertices[i], label.vertices) # Remove duplicates and sort vertices = [np.unique(vert_hemi) for vert_hemi in vertices] fwd_out = deepcopy(fwd) fwd_out['source_rr'] = np.zeros((0, 3)) fwd_out['nsource'] = 0 fwd_out['source_nn'] = np.zeros((0, 3)) fwd_out['sol']['data'] = np.zeros((fwd['sol']['data'].shape[0], 0)) fwd_out['_orig_sol'] = np.zeros((fwd['_orig_sol'].shape[0], 0)) if fwd['sol_grad'] is not None: fwd_out['sol_grad']['data'] = np.zeros( (fwd['sol_grad']['data'].shape[0], 0)) fwd_out['_orig_sol_grad'] = np.zeros( (fwd['_orig_sol_grad'].shape[0], 0)) fwd_out['sol']['ncol'] = 0 nuse_lh = fwd['src'][0]['nuse'] for i in range(2): fwd_out['src'][i]['vertno'] = np.array([], int) fwd_out['src'][i]['nuse'] = 0 fwd_out['src'][i]['inuse'] = fwd['src'][i]['inuse'].copy() fwd_out['src'][i]['inuse'].fill(0) fwd_out['src'][i]['use_tris'] = np.array([[]], int) fwd_out['src'][i]['nuse_tri'] = np.array([0]) # src_sel is idx to cols in fwd that are in any label per hemi src_sel = np.intersect1d(fwd['src'][i]['vertno'], vertices[i]) src_sel = np.searchsorted(fwd['src'][i]['vertno'], src_sel) # Reconstruct each src vertno = fwd['src'][i]['vertno'][src_sel] fwd_out['src'][i]['inuse'][vertno] = 1 fwd_out['src'][i]['nuse'] += len(vertno) fwd_out['src'][i]['vertno'] = np.where(fwd_out['src'][i]['inuse'])[0] # Reconstruct part of fwd that is not sol data src_sel += i * nuse_lh # Add column shift to right hemi fwd_out['source_rr'] = np.vstack([fwd_out['source_rr'], fwd['source_rr'][src_sel]]) fwd_out['nsource'] += len(src_sel) if is_fixed_orient(fwd): idx = src_sel if fwd['sol_grad'] is not None: idx_grad = (3 * src_sel[:, None] + np.arange(3)).ravel() else: idx = (3 * src_sel[:, None] + np.arange(3)).ravel() if fwd['sol_grad'] is not None: idx_grad = (9 * src_sel[:, None] + np.arange(9)).ravel() fwd_out['source_nn'] = np.vstack( [fwd_out['source_nn'], fwd['source_nn'][idx]]) fwd_out['sol']['data'] = np.hstack( [fwd_out['sol']['data'], fwd['sol']['data'][:, idx]]) if fwd['sol_grad'] is not None: fwd_out['sol_grad']['data'] = np.hstack( [fwd_out['sol_grad']['data'], fwd['sol_rad']['data'][:, idx_grad]]) fwd_out['sol']['ncol'] += len(idx) if is_fixed_orient(fwd, orig=True): idx = src_sel if fwd['sol_grad'] is not None: idx_grad = (3 * src_sel[:, None] + np.arange(3)).ravel() else: idx = (3 * src_sel[:, None] + np.arange(3)).ravel() if fwd['sol_grad'] is not None: idx_grad = (9 * src_sel[:, None] + np.arange(9)).ravel() fwd_out['_orig_sol'] = np.hstack( [fwd_out['_orig_sol'], fwd['_orig_sol'][:, idx]]) if fwd['sol_grad'] is not None: fwd_out['_orig_sol_grad'] = np.hstack( [fwd_out['_orig_sol_grad'], fwd['_orig_sol_grad'][:, idx_grad]]) return fwd_out def _do_forward_solution(subject, meas, fname=None, src=None, spacing=None, mindist=None, bem=None, mri=None, trans=None, eeg=True, meg=True, fixed=False, grad=False, mricoord=False, overwrite=False, subjects_dir=None, verbose=None): """Calculate a forward solution for a subject using MNE-C routines. This is kept around for testing purposes. This function wraps to mne_do_forward_solution, so the mne command-line tools must be installed and accessible from Python. Parameters ---------- subject : str Name of the subject. meas : Raw | Epochs | Evoked | str If Raw or Epochs, a temporary evoked file will be created and saved to a temporary directory. If str, then it should be a filename to a file with measurement information the mne command-line tools can understand (i.e., raw or evoked). fname : str | None Destination forward solution filename. If None, the solution will be created in a temporary directory, loaded, and deleted. src : str | None Source space name. If None, the MNE default is used. spacing : str The spacing to use. Can be ``'#'`` for spacing in mm, ``'ico#'`` for a recursively subdivided icosahedron, or ``'oct#'`` for a recursively subdivided octahedron (e.g., ``spacing='ico4'``). Default is 7 mm. mindist : float | str | None Minimum distance of sources from inner skull surface (in mm). If None, the MNE default value is used. If string, 'all' indicates to include all points. bem : str | None Name of the BEM to use (e.g., "sample-5120-5120-5120"). If None (Default), the MNE default will be used. mri : str | None The name of the trans file in FIF format. If None, trans must not be None. trans : dict | str | None File name of the trans file in text format. If None, mri must not be None. eeg : bool If True (Default), include EEG computations. meg : bool If True (Default), include MEG computations. fixed : bool If True, make a fixed-orientation forward solution (Default: False). Note that fixed-orientation inverses can still be created from free-orientation forward solutions. grad : bool If True, compute the gradient of the field with respect to the dipole coordinates as well (Default: False). mricoord : bool If True, calculate in MRI coordinates (Default: False) %(overwrite)s %(subjects_dir)s %(verbose)s See Also -------- make_forward_solution Returns ------- fwd : Forward The generated forward solution. """ if not has_mne_c(): raise RuntimeError('mne command line tools could not be found') # check for file existence temp_dir = tempfile.mkdtemp() if fname is None: fname = op.join(temp_dir, 'temp-fwd.fif') _check_fname(fname, overwrite) _validate_type(subject, "str", "subject") # check for meas to exist as string, or try to make evoked _validate_type(meas, ('path-like', BaseRaw, BaseEpochs, Evoked), 'meas') if isinstance(meas, (BaseRaw, BaseEpochs, Evoked)): meas_file = op.join(temp_dir, 'info.fif') write_info(meas_file, meas.info) meas = meas_file else: meas = _check_fname(meas, overwrite='read', must_exist=True) # deal with trans/mri if mri is not None and trans is not None: raise ValueError('trans and mri cannot both be specified') if mri is None and trans is None: # MNE allows this to default to a trans/mri in the subject's dir, # but let's be safe here and force the user to pass us a trans/mri raise ValueError('Either trans or mri must be specified') if trans is not None: _validate_type(trans, "str", "trans") if not op.isfile(trans): raise IOError('trans file "%s" not found' % trans) if mri is not None: # deal with trans if not isinstance(mri, str): if isinstance(mri, dict): mri_data = deepcopy(mri) mri = op.join(temp_dir, 'mri-trans.fif') try: write_trans(mri, mri_data) except Exception: raise IOError('mri was a dict, but could not be ' 'written to disk as a transform file') else: raise ValueError('trans must be a string or dict (trans)') if not op.isfile(mri): raise IOError('trans file "%s" could not be found' % trans) # deal with meg/eeg if not meg and not eeg: raise ValueError('meg or eeg (or both) must be True') path, fname = op.split(fname) if not op.splitext(fname)[1] == '.fif': raise ValueError('Forward name does not end with .fif') path = op.abspath(path) # deal with mindist if mindist is not None: if isinstance(mindist, str): if not mindist.lower() == 'all': raise ValueError('mindist, if string, must be "all"') mindist = ['--all'] else: mindist = ['--mindist', '%g' % mindist] # src, spacing, bem for element, name, kind in zip((src, spacing, bem), ("src", "spacing", "bem"), ('path-like', 'str', 'path-like')): if element is not None: _validate_type(element, kind, name, "%s or None" % kind) # put together the actual call cmd = ['mne_do_forward_solution', '--subject', subject, '--meas', meas, '--fwd', fname, '--destdir', path] if src is not None: cmd += ['--src', src] if spacing is not None: if spacing.isdigit(): pass # spacing in mm else: # allow both "ico4" and "ico-4" style values match = re.match(r"(oct|ico)-?(\d+)$", spacing) if match is None: raise ValueError("Invalid spacing parameter: %r" % spacing) spacing = '-'.join(match.groups()) cmd += ['--spacing', spacing] if mindist is not None: cmd += mindist if bem is not None: cmd += ['--bem', bem] if mri is not None: cmd += ['--mri', '%s' % mri] if trans is not None: cmd += ['--trans', '%s' % trans] if not meg: cmd.append('--eegonly') if not eeg: cmd.append('--megonly') if fixed: cmd.append('--fixed') if grad: cmd.append('--grad') if mricoord: cmd.append('--mricoord') if overwrite: cmd.append('--overwrite') env = os.environ.copy() subjects_dir = get_subjects_dir(subjects_dir, raise_error=True) env['SUBJECTS_DIR'] = subjects_dir try: logger.info('Running forward solution generation command with ' 'subjects_dir %s' % subjects_dir) run_subprocess(cmd, env=env) except Exception: raise else: fwd = read_forward_solution(op.join(path, fname), verbose=False) finally: shutil.rmtree(temp_dir, ignore_errors=True) return fwd @verbose def average_forward_solutions(fwds, weights=None, verbose=None): """Average forward solutions. Parameters ---------- fwds : list of Forward Forward solutions to average. Each entry (dict) should be a forward solution. weights : array | None Weights to apply to each forward solution in averaging. If None, forward solutions will be equally weighted. Weights must be non-negative, and will be adjusted to sum to one. %(verbose)s Returns ------- fwd : Forward The averaged forward solution. """ # check for fwds being a list _validate_type(fwds, list, "fwds") if not len(fwds) > 0: raise ValueError('fwds must not be empty') # check weights if weights is None: weights = np.ones(len(fwds)) weights = np.asanyarray(weights) # in case it's a list, convert it if not np.all(weights >= 0): raise ValueError('weights must be non-negative') if not len(weights) == len(fwds): raise ValueError('weights must be None or the same length as fwds') w_sum = np.sum(weights) if not w_sum > 0: raise ValueError('weights cannot all be zero') weights /= w_sum # check our forward solutions for fwd in fwds: # check to make sure it's a forward solution _validate_type(fwd, dict, "each entry in fwds", "dict") # check to make sure the dict is actually a fwd check_keys = ['info', 'sol_grad', 'nchan', 'src', 'source_nn', 'sol', 'source_rr', 'source_ori', 'surf_ori', 'coord_frame', 'mri_head_t', 'nsource'] if not all(key in fwd for key in check_keys): raise KeyError('forward solution dict does not have all standard ' 'entries, cannot compute average.') # check forward solution compatibility if any(fwd['sol'][k] != fwds[0]['sol'][k] for fwd in fwds[1:] for k in ['nrow', 'ncol']): raise ValueError('Forward solutions have incompatible dimensions') if any(fwd[k] != fwds[0][k] for fwd in fwds[1:] for k in ['source_ori', 'surf_ori', 'coord_frame']): raise ValueError('Forward solutions have incompatible orientations') # actually average them (solutions and gradients) fwd_ave = deepcopy(fwds[0]) fwd_ave['sol']['data'] *= weights[0] fwd_ave['_orig_sol'] *= weights[0] for fwd, w in zip(fwds[1:], weights[1:]): fwd_ave['sol']['data'] += w * fwd['sol']['data'] fwd_ave['_orig_sol'] += w * fwd['_orig_sol'] if fwd_ave['sol_grad'] is not None: fwd_ave['sol_grad']['data'] *= weights[0] fwd_ave['_orig_sol_grad'] *= weights[0] for fwd, w in zip(fwds[1:], weights[1:]): fwd_ave['sol_grad']['data'] += w * fwd['sol_grad']['data'] fwd_ave['_orig_sol_grad'] += w * fwd['_orig_sol_grad'] return fwd_ave