cosmo interval neighborhoodΒΆ

function nbrhood=cosmo_interval_neighborhood(ds, label, varargin)
% compute neighborhoods stretching intervals
%
% nbrhood=cosmo_interval_neighborhood(ds, label, 'radius', radius)
%
% Inputs:
%   ds            dataset struct
%   label         dimension label in ds.a.fdim.labels
%   'radius', r   neighborhood radius
%
% Returns:
%   nbrhood       struct with fields:
%     .a          } dataset and feature attributes of neighborhood
%     .fa         }
%     .neighbors  If ds has N values in the dimension label, then
%                 neighbors is a Nx1 cell with indices of features
%                 where the indices differ at most radius from each other.
%
% Examples
%     % Illustrate the 'time' dimension in MEEG time-frequency dataset,
%     ds=cosmo_synthetic_dataset('type','timefreq','size','big');
%     %
%     % neighborhoods with bins 5 (=2*1+1) frequency bands wide
%     % (every neighborhood contains all channels and time points)
%     nbrhood=cosmo_interval_neighborhood(ds,'freq','radius',2);
%     cosmo_disp(nbrhood.a.fdim)
%     %|| .labels
%     %||   { 'freq' }
%     %|| .values
%     %||   { [ 2         4         6  ...  10        12        14 ]@1x7 }
%     cosmo_disp(nbrhood.fa.freq)
%     %|| [ 1         2         3  ...  5         6         7 ]@1x7
%     cosmo_disp(nbrhood.neighbors)
%     %|| { [ 1         2         3  ...  9.48e+03  9.48e+03  9.49e+03 ]@1x4590
%     %||   [ 1         2         3  ...  9.79e+03  9.79e+03  9.79e+03 ]@1x6120
%     %||   [ 1         2         3  ...  1.01e+04  1.01e+04  1.01e+04 ]@1x7650
%     %||                                       :
%     %||   [ 613       614       615  ...  1.07e+04  1.07e+04  1.07e+04 ]@1x7650
%     %||   [ 919       920       921  ...  1.07e+04  1.07e+04  1.07e+04 ]@1x6120
%     %||   [ 1.22e+03  1.23e+03  1.23e+03  ...  1.07e+04  1.07e+04  1.07e+04 ]@1x4590 }@7x1
%
%     % ds is an MEEG dataset with a time dimension
%     ds=cosmo_synthetic_dataset('type','timelock','size','big');
%     %
%     % Neighborhoods just the frequency bin itself
%     % (every neighborhood contains all channels)
%     nbrhood=cosmo_interval_neighborhood(ds,'time','radius',2);
%     cosmo_disp(nbrhood.a.fdim)
%     %|| .labels
%     %||   { 'time' }
%     %|| .values
%     %||   { [ -0.2     -0.15      -0.1  ...  0      0.05       0.1 ]@1x7 }
%     cosmo_disp(nbrhood.fa.time)
%     %|| [ 1         2         3  ...  5         6         7 ]@1x7
%     cosmo_disp(nbrhood.neighbors)
%     %|| { [ 1         2         3  ...  916       917       918 ]@1x918
%     %||   [ 1         2         3  ...  1.22e+03  1.22e+03  1.22e+03 ]@1x1224
%     %||   [ 1         2         3  ...  1.53e+03  1.53e+03  1.53e+03 ]@1x1530
%     %||                                      :
%     %||   [ 613       614       615  ...  2.14e+03  2.14e+03  2.14e+03 ]@1x1530
%     %||   [ 919       920       921  ...  2.14e+03  2.14e+03  2.14e+03 ]@1x1224
%     %||   [ 1.22e+03  1.23e+03  1.23e+03  ...  2.14e+03  2.14e+03  2.14e+03 ]@1x918 }@7x1
%
%
% Notes:
%   - to combine neighborhoods from different dimensions (such as
%     time, freq, chan, use cosmo_neighborhood
%   - the output can be used for a searchlight using cosmo_searchlight
%
% See also: cosmo_neighborhood, cosmo_searchlight
%
% #   For CoSMoMVPA's copyright information and license terms,   #
% #   see the COPYING file distributed with CoSMoMVPA.           #

    radius=get_radius(varargin{:});

    cosmo_check_dataset(ds);

    % find dimension index
    [dim,index,attr_name,dim_name]=cosmo_dim_find(ds,label);

    % get dimension values
    dim_values=ds.a.(dim_name).values{index};
    nvalues=numel(dim_values);

    % get feature attribute values
    fa_values=ds.(attr_name).(label);

    % get unique feature attributes
    [fa_idxs,fa_unq]=cosmo_index_unique(fa_values(:));
    nunq=numel(fa_unq);

    % cosmo_index_unique should return a sorted array of values
    assert(issorted(fa_unq));

    % allocate space for output
    neighbors=cell(nvalues,1);

    % mapping from all values to the ones present in fa
    all2unq=zeros(nvalues,1);
    all2unq(fa_unq)=1:nunq;

    for center_id=1:nvalues
        first_pos=max(center_id-radius,1);
        last_pos=min(center_id+radius,nvalues);

        around_unq=all2unq(first_pos:last_pos);
        around_unq=around_unq(around_unq>0); % remove empty ones

        neighbors{center_id}=sort(cat(1,fa_idxs{around_unq}))';
    end

    % store results
    nbrhood=struct();
    nbrhood.a=ds.a;

    a_dim=struct();
    a_dim.labels={label};
    a_dim.values={dim_values(:)'};
    nbrhood.a.(dim_name)=a_dim;

    nbrhood.(attr_name)=struct();

    values=1:nvalues;
    if dim==1
        values=values';
        other_dim_name='fdim';
    else
        other_dim_name='sdim';
    end
    nbrhood.(attr_name).(label)=values;
    if isfield(nbrhood.a,other_dim_name);
        nbrhood.a=rmfield(nbrhood.a,other_dim_name);
    end

    nbrhood.neighbors=neighbors;

    origin=struct();
    origin.a=ds.a;
    origin.(attr_name)=ds.(attr_name);
    nbrhood.origin=origin;

    cosmo_check_neighborhood(nbrhood,ds);


function radius=get_radius(varargin)
    if nargin>=1 && isnumeric(varargin{1})
        error(['Usage: %s(...,''radius'',r)\n',...
                '(Note that as of Jan 2015 the syntax for this '...
                'function has changed)'],...
                mfilename());
    end

    opt=cosmo_structjoin(varargin);

    if ~isfield(opt,'radius')
        error('Missing option ''radius''');
    end

    radius=opt.radius;

    if ~isscalar(radius) || radius<0
        error('radius must be positive scalar');
    end