cosmo sphere offsetsΒΆ

function [offsets,distances]=cosmo_sphere_offsets(radius)
% computes sub index offsets for voxels in a sphere
%
% [offsets,distances]=cosmo_sphere_offsets(radius)
%
% Input:
%  radius      radius of the sphere (in voxel units)
%
% Output
%  offsets     Px3 sub indices relative to the origin (0,0,0).
%              offsets(p,:)=[i, j, k] means that the euclidian distance
%              between points at (i,j,k) and the origin is less than or
%              or equal to radius
%  distances   Px1 distances from the origin (in voxel units).
%
% Example:
%     % compute offsets for voxels that share a side or edge, but not those
%     % that only share a corner (because sqrt(2) < 1.5 < sqrt(3)).
%     [o, d]=cosmo_sphere_offsets(1.5);
%     cosmo_disp(o);
%     %|| [  0         0         0
%     %||   -1         0         0
%     %||    0        -1         0
%     %||    :         :         :
%     %||    1         0        -1
%     %||    1         0         1
%     %||    1         1         0 ]@19x3
%     cosmo_disp(d)
%     %|| [    0
%     %||      1
%     %||      1
%     %||     :
%     %||   1.41
%     %||   1.41
%     %||   1.41 ]@19x1
%
% Notes:
%   - this function computes distances in voxel space, not in world space.
%     If voxels have the same size sof  mm along all dimensions (i.e. are
%     of size s x s x s mm^2 for some value of s; this property is known as
%     "isotropic") then using radius=d/s will select voxels within
%     distance d mm. This function is less suitable for spherical offsets
%     in world space when voxels are non-isotropic.
%   - offsets and distances are sorted by distance.
%
% See also sub2ind, ind2sub, cosmo_spherical_neighborhood
%
% #   For CoSMoMVPA's copyright information and license terms,   #
% #   see the COPYING file distributed with CoSMoMVPA.           #

    % how big a box should be to contain all voxels with the given radius
    side=ceil(radius)*2+1;

    % make an array that is sufficienly large (actually too big)
    offsets=zeros(side^3,3);

    % keep track of where we store indices in offsets:
    % for every location within the sphere (in the code below),
    % add one to row_pos and then store the locations
    row_pos=0;

    % the grid positions (relative to the origin) to consider
    single_dimension_candidates=floor(-radius):ceil(radius);

    % Consider the candidates in all three spatial dimensions using
    % nested for loops and an if statement.
    % For each position:
    % - see if it is at most at distance 'radius' from the origin
    % - if that is the case, increase row_pos and store the position in
    %   'offsets'
    %
    for x=single_dimension_candidates
        for y=single_dimension_candidates
            for z=single_dimension_candidates
                if x^2+y^2+z^2<=radius^2
                    row_pos=row_pos+1;
                    offsets(row_pos,:)=[x y z];
                end
            end
        end
    end

    % cut off empty values at the end
    offsets=offsets(1:row_pos,:);

    % compute distances
    unsorted_distances=sqrt(sum(offsets.^2,2));

    % sort distances and apply to offsets
    [distances,idxs]=sort(unsorted_distances);
    offsets=offsets(idxs,:);