spatial_resolution.py

# -*- coding: utf-8 -*-
# Authors: Olaf Hauk <olaf.hauk@mrc-cbu.cam.ac.uk>
#
# License: BSD (3-clause)
"""Compute resolution metrics from resolution matrix.

Resolution metrics: localisation error, spatial extent, relative amplitude.
Metrics can be computed for point-spread and cross-talk functions (PSFs/CTFs).
"""
import numpy as np

from mne import SourceEstimate
from mne.utils import logger, verbose


@verbose
def resolution_metrics(resmat, src, function='psf', metric='peak_err',
                       threshold=0.5, verbose=None):
    """Compute spatial resolution metrics for linear solvers.

    Parameters
    ----------
    resmat : array, shape (n_orient * n_vertices, n_vertices)
        The resolution matrix.
        If not a square matrix and if the number of rows is a multiple of
        number of columns (e.g. free or loose orientations), then the Euclidean
        length per source location is computed (e.g. if inverse operator with
        free orientations was applied to forward solution with fixed
        orientations).
    src : instance of SourceSpaces
        Source space object from forward or inverse operator.
    function : 'psf' | 'ctf'
        Whether to compute metrics for columns (point-spread functions, PSFs)
        or rows (cross-talk functions, CTFs) of the resolution matrix.
    metric : str
        The resolution metric to compute. Allowed options are:

        Localization-based metrics:

        - ``'peak_err'`` Peak localization error (PLE), Euclidean distance
          between peak and true source location.
        - ``'cog_err'`` Centre-of-gravity localisation error (CoG), Euclidean
          distance between CoG and true source location.

        Spatial-extent-based metrics:

        - ``'sd_ext'`` spatial deviation (e.g. [1,2]_).
        - ``'maxrad_ext'`` maximum radius to 50%% of max amplitude.

        Amplitude-based metrics:

        - ``'peak_amp'`` Ratio between absolute maximum amplitudes of peaks per
            location and maximum peak across locations.
        - ``'sum_amp'`` Ratio between sums of absolute amplitudes.

    threshold : float
        Amplitude fraction threshold for spatial extent metric 'maxrad_ext'.
        Defaults to 0.5.
    %(verbose)s

    Returns
    -------
    resolution_metric : instance of SourceEstimate
        The resolution metric.

    Notes
    -----
    For details, see [1]_ [2]_.

    .. versionadded:: 0.20

    References
    ----------
    .. [1] Molins A, Stufflebeam S M, Brown E N, Hämäläinen M S (2008).
           Quantification of the benefit from integrating MEG and EEG data in
           minimum l2-norm estimation. Neuroimage, 42(3):1069-77.
    .. [2] Hauk O, Stenroos M, Treder M (2019). "Towards an Objective
           Evaluation of EEG/MEG Source Estimation Methods: The Linear Tool
           Kit", bioRxiv, doi: https://doi.org/10.1101/672956.
    """
    # Check if input options are valid
    metrics = ('peak_err', 'cog_err', 'sd_ext', 'maxrad_ext', 'peak_amp',
               'sum_amp')
    if metric not in metrics:
        raise ValueError('"%s" is not a recognized metric.' % metric)

    if function not in ['psf', 'ctf']:
        raise ValueError('Not a recognised resolution function: %s.'
                         % function)

    if metric in ('peak_err', 'cog_err'):
        resolution_metric = _localisation_error(resmat, src, function=function,
                                                metric=metric)

    elif metric in ('sd_ext', 'maxrad_ext'):
        resolution_metric = _spatial_extent(resmat, src, function=function,
                                            metric=metric, threshold=threshold)

    elif metric in ('peak_amp', 'sum_amp'):
        resolution_metric = _relative_amplitude(resmat, src, function=function,
                                                metric=metric)

    # get vertices from source space
    vertno_lh = src[0]['vertno']
    vertno_rh = src[1]['vertno']
    vertno = [vertno_lh, vertno_rh]

    # Convert array to source estimate
    resolution_metric = SourceEstimate(resolution_metric, vertno, tmin=0.,
                                       tstep=1.)

    return resolution_metric


def _localisation_error(resmat, src, function, metric):
    """Compute localisation error metrics for resolution matrix.

    Parameters
    ----------
    resmat : array, shape (n_orient * n_locations, n_locations)
        The resolution matrix.
        If not a square matrix and if the number of rows is a multiple of
        number of columns (i.e. n_orient>1), then the Euclidean length per
        source location is computed (e.g. if inverse operator with free
        orientations was applied to forward solution with fixed orientations).
    src : Source Space
        Source space object from forward or inverse operator.
    function : 'psf' | 'ctf'
        Whether to compute metrics for columns (point-spread functions, PSFs)
        or rows (cross-talk functions, CTFs).
    metric : str
        What type of localisation error to compute.

        - 'peak_err': Peak localisation error (PLE), Euclidean distance between
          peak and true source location, in centimeters.
        - 'cog_err': Centre-of-gravity localisation error (CoG), Euclidean
          distance between CoG and true source location, in centimeters.

    Returns
    -------
    locerr : array, shape (n_locations,)
        Localisation error per location (in cm).
    """
    # ensure resolution matrix is square
    # combine rows (Euclidean length) if necessary
    resmat = _rectify_resolution_matrix(resmat)
    locations = _get_src_locations(src)  # locs used in forw. and inv. operator
    locations = 100. * locations  # convert to cm (more common)
    resmat = np.absolute(resmat)  # only use absolute values

    # The code below will operate on columns, so transpose if you want CTFs
    if function == 'ctf':
        resmat = resmat.T

    # Euclidean distance between true location and maximum
    if metric == 'peak_err':
        resmax = resmat.argmax(axis=0)  # find indices of maxima along columns
        maxloc = locations[resmax, :]   # locations of maxima
        diffloc = locations - maxloc    # diff btw true locs and maxima locs
        locerr = np.sqrt(np.sum(diffloc ** 2, 1))  # Euclidean distance

    # centre of gravity
    elif metric == 'cog_err':
        locerr = np.empty(locations.shape[0])  # initialise result array
        for ii, rr in enumerate(locations):
            resvec = resmat[:, ii].T  # corresponding column of resmat
            cog = resvec.dot(locations) / np.sum(resvec)   # centre of gravity
            locerr[ii] = np.sqrt(np.sum((rr - cog) ** 2))  # Euclidean distance

    return locerr


def _spatial_extent(resmat, src, function, metric, threshold=0.5):
    """Compute spatial width metrics for resolution matrix.

    Parameters
    ----------
    resmat : array, shape (n_orient * n_dipoles, n_dipoles)
        The resolution matrix.
        If not a square matrix and if the number of rows is a multiple of
        number of columns (i.e. n_orient>1), then the Euclidean length per
        source location is computed (e.g. if inverse operator with free
        orientations was applied to forward solution with fixed orientations).
    src : Source Space
        Source space object from forward or inverse operator.
    function : 'psf' | 'ctf'
        Whether to compute metrics for columns (PSFs) or rows (CTFs).
    metric : str
        What type of width metric to compute.

        - 'sd_ext': spatial deviation (e.g. Molins et al.), in centimeters.
        - 'maxrad_ext': maximum radius to fraction threshold of max amplitude,
          in centimeters.

    threshold : float
        Amplitude fraction threshold for metric 'maxrad'. Defaults to 0.5.

    Returns
    -------
    width : array, shape (n_dipoles,)
        Spatial width metric per location.
    """
    locations = _get_src_locations(src)  # locs used in forw. and inv. operator
    locations = 100. * locations  # convert to cm (more common)
    resmat = np.absolute(resmat)  # only use absolute values

    # The code below will operate on columns, so transpose if you want CTFs
    if function == 'ctf':
        resmat = resmat.T

    resmax = resmat.argmax(axis=0)  # find indices of maxima along rows
    width = np.empty(len(resmax))   # initialise output array

    # spatial deviation as in Molins et al.
    if metric == 'sd_ext':
        for ii in range(locations.shape[0]):

            diffloc = locations - locations[ii, :]  # locs w/r/t true source
            locerr = np.sum(diffloc**2, 1)  # squared Eucl dists to true source
            resvec = resmat[:, ii]**2       # pick current row
            # spatial deviation (Molins et al, NI 2008, eq. 12)
            width[ii] = np.sqrt(np.sum(np.multiply(locerr, resvec)) /
                                np.sum(resvec))

    # maximum radius to 50% of max amplitude
    elif metric == 'maxrad_ext':
        maxamp = resmat.max(axis=0)  # peak ampl. per location across columns
        for ii, amps in enumerate(maxamp):  # for all locations
            resvec = resmat[:, ii]  # pick current column
            # indices of elements with values larger than fraction threshold
            # of peak amplitude
            thresh_idx = np.where(resvec > threshold * amps)
            # get distances for those indices from true source position
            locs_thresh = locations[thresh_idx, :] - locations[ii, :]
            # get maximum distance
            width[ii] = np.sqrt(np.sum(locs_thresh**2, 1).max())

    return width


def _relative_amplitude(resmat, src, function, metric):
    """Compute relative amplitude metrics for resolution matrix.

    Parameters
    ----------
    resmat : array, shape (n_orient * n_dipoles, n_dipoles)
        The resolution matrix.
        If not a square matrix and if the number of rows is a multiple of
        number of columns (i.e. n_orient>1), then the Euclidean length per
        source location is computed (e.g. if inverse operator with free
        orientations was applied to forward solution with fixed orientations).
    src : Source Space
        Source space object from forward or inverse operator.
    function : 'psf' | 'ctf'
        Whether to compute metrics for columns (PSFs) or rows (CTFs).
    metric : str
        Which amplitudes to use.

        - 'peak_amp': Ratio between absolute maximum amplitudes of peaks per
          location and maximum peak across locations.
        - 'sum_amp': Ratio between sums of absolute amplitudes.

    Returns
    -------
    relamp : array, shape (n_dipoles,)
        Relative amplitude metric per location.
    """
    # The code below will operate on columns, so transpose if you want CTFs
    if function == 'ctf':
        resmat = resmat.T

    resmat = np.absolute(resmat)  # only use absolute values

    # Ratio between amplitude at peak and global peak maximum
    if metric == 'peak_amp':
        maxamps = resmat.max(axis=0)  # maximum amplitudes per column
        maxmaxamps = maxamps.max()    # global absolute maximum
        relamp = maxamps / maxmaxamps

    # ratio between sums of absolute amplitudes
    elif metric == 'sum_amp':
        sumamps = np.sum(resmat, axis=0)  # sum of amplitudes per column
        sumampsmax = sumamps.max()        # maximum of summed amplitudes
        relamp = sumamps / sumampsmax

    return relamp


def _get_src_locations(src):
    """Get source positions from src object."""
    # vertices used in forward and inverse operator
    vertno_lh = src[0]['vertno']
    vertno_rh = src[1]['vertno']

    # locations corresponding to vertices for both hemispheres
    locations_lh = src[0]['rr'][vertno_lh, :]
    locations_rh = src[1]['rr'][vertno_rh, :]
    locations = np.vstack([locations_lh, locations_rh])

    return locations


def _rectify_resolution_matrix(resmat):
    """
    Ensure resolution matrix is square matrix.

    If resmat is not a square matrix, it is assumed that the inverse operator
    had free or loose orientation constraint, i.e. multiple values per source
    location. The Euclidean length for values at each location is computed to
    make resmat a square matrix.
    """
    shape = resmat.shape
    if not shape[0] == shape[1]:
        if shape[0] < shape[1]:
            raise ValueError('Number of target sources (%d) cannot be lower '
                             'than number of input sources (%d)' % shape[0],
                             shape[1])

        if np.mod(shape[0], shape[1]):  # if ratio not integer
            raise ValueError('Number of target sources (%d) must be a '
                             'multiple of the number of input sources (%d)'
                             % shape[0], shape[1])

        ns = shape[0] // shape[1]  # number of source components per vertex

        # Combine rows of resolution matrix
        resmatl = [np.sqrt((resmat[ns * i:ns * (i + 1), :]**2).sum(axis=0))
                   for i in np.arange(0, shape[1], dtype=int)]

        resmat = np.array(resmatl)

        logger.info('Rectified resolution matrix from (%d, %d) to (%d, %d).' %
                    (shape[0], shape[1], resmat.shape[0], resmat.shape[1]))

    return resmat