cosmo meeg senstype2layout mappingΒΆ

function senstype2layout=cosmo_meeg_senstype2layout_mapping(varargin)
% return mapping from MEEG sensor types to sensor layouts
%
% senstype2layout=cosmo_meeg_senstype2layout_mapping()
%
% Output:
%   senstype2layout       struct where the fieldnames (keys) are senstypes
%                         (acquisition systems with a possible suffix
%                         indicating a type of channel)
%                         If a senstype does not have an associated layout
%                         then the corresponding value is set to [].
%                         Otherwise each value has fields:
%                         .pos     Nx2 x and y coordinates (for N channels)
%                         .width   Nx1 channel widths
%                         .height  Nx1 channel heights
%                         .label   Nx1 cell with channel labels
%                         .name    string with name of layout
%
% Examples:
%     % (This example requires FieldTrip)
%     cosmo_skip_test_if_no_external('fieldtrip');
%     %
%     senstype2layout=cosmo_meeg_senstype2layout_mapping();
%     % get layout for neuromag306 MEG planar (gradiometers)
%     layout=senstype2layout.neuromag306alt_planar;
%     cosmo_disp(layout.label)
%     %|| { 'MEG0113'
%     %||   'MEG0112'
%     %||   'MEG0122'
%     %||      :
%     %||   'MEG2643'
%     %||   'COMNT'
%     %||   'SCALE'   }@206x1
%     cosmo_disp([layout.pos layout.width layout.height])
%     %|| [ -0.408     0.253    0.0323    0.0332
%     %||   -0.408     0.284    0.0323    0.0332
%     %||   -0.328     0.285    0.0323    0.0332
%     %||      :         :         :         :
%     %||    0.373    -0.082    0.0323    0.0332
%     %||    -0.45     -0.45    0.0323    0.0332
%     %||     0.45     -0.45    0.0323    0.0332 ]@206x4
%     layout.name
%     %|| 'neuromag306planar.lay'
%
%     % (This example requires FieldTrip)
%     cosmo_skip_test_if_no_external('fieldtrip');
%     %
%     senstype2layout=cosmo_meeg_senstype2layout_mapping();
%     % get layout for neuromag306 MEG combined planar
%     % (combined gradiometers)
%     layout=senstype2layout.neuromag306alt_planar_combined;
%     cosmo_disp(layout.label)
%     %|| { 'MEG0112+0113'
%     %||   'MEG0122+0123'
%     %||   'MEG0132+0133'
%     %||         :
%     %||   'MEG2642+2643'
%     %||   'COMNT'
%     %||   'SCALE'        }@104x1
%     cosmo_disp([layout.pos layout.width layout.height])
%     %|| [ -0.408     0.273    0.0645    0.0712
%     %||   -0.328     0.306    0.0645    0.0712
%     %||   -0.377     0.179    0.0645    0.0712
%     %||      :         :         :         :
%     %||    0.373    -0.104    0.0645    0.0712
%     %||    -0.45     -0.45    0.0645    0.0712
%     %||     0.45     -0.45    0.0645    0.0712 ]@104x4
%     layout.name
%     %|| 'neuromag306cmb.lay'
%
%     % (This example requires FieldTrip)
%     cosmo_skip_test_if_no_external('fieldtrip');
%     %
%     senstype2layout=cosmo_meeg_senstype2layout_mapping();
%     % get layout for EEG elec1020
%     layout=senstype2layout.eeg1020;
%     cosmo_disp(layout.label)
%     %|| { 'Fp1'
%     %||   'Fpz'
%     %||   'Fp2'
%     %||     :
%     %||   'O2'
%     %||   'COMNT'
%     %||   'SCALE' }@23x1
%     cosmo_disp([layout.pos layout.width layout.height])
%     %|| [ -0.139     0.428     0.125    0.0938
%     %||        0      0.45     0.125    0.0938
%     %||    0.139     0.428     0.125    0.0938
%     %||      :         :         :         :
%     %||    0.139    -0.428     0.125    0.0938
%     %||    -0.45      0.45     0.125    0.0938
%     %||     0.45      0.45     0.125    0.0938 ]@23x4
%     layout.name
%     %|| 'EEG1020.lay'
%
% Notes:
%   - this function requires FieldTrip, as it uses its collection of
%     layouts
%   - the output from this function is similar to FieldTrip's
%     ft_prepare_layout, but positions are not scaled as in FieldTrip
%   - this function caches previously read layouts, for optimization
%     reasons. run "clear functions" to reset the cache.
%   - this function uses cosmo_meeg_layout_collection and
%     cosmo_meeg_senstype_collection to match sensor types with layouts
%   - this function does not provide layouts for all sensor types; if you
%     find a layout of interest is missing, please get in touch with the
%     developers
%
% See also: cosmo_meeg_layout_collection, cosmo_meeg_senstype_collection
%
% #   For CoSMoMVPA's copyright information and license terms,   #
% #   see the COPYING file distributed with CoSMoMVPA.           #

    % 'secret' options with thresholds to find best matching layout
    defaults=struct();
    defaults.thr_layout=.7;
    defaults.thr_senstype=.8;
    opt=cosmo_structjoin(defaults,varargin);

    senstype2layout=get_mapping(opt);

function senstype2layout=get_mapping(opt)
    % helper function to actually compute the mapping
    persistent cached_opt;
    persistent cached_senstype2layout;

    if ~isequal(opt,cached_opt) || isempty(cached_senstype2layout)
        sc=cosmo_meeg_senstype_collection();
        names=fieldnames(sc);
        n=numel(names);

        senstype2layout=struct();

        for k=1:n
            name=names{k};
            lay=find_layout(name,opt);
            senstype2layout.(name)=lay;
        end

        cached_opt=opt;
        cached_senstype2layout=senstype2layout;
    end

    senstype2layout=cached_senstype2layout;


function pairs=senstypes_alt_names()
    % return pairs of sensor types with and without the 'alt' name, e.g.
    % neuromag306alt_planar and neuromag306_planar
    sc=cosmo_meeg_senstype_collection();
    names=fieldnames(sc);

    names_without_alt=strrep(names,'alt','');
    msk_with_alt=~cosmo_match(names, names_without_alt);
    idxs_with_alt=find(msk_with_alt);
    ncandidates=numel(idxs_with_alt);

    pairs=cell(ncandidates,2);
    pos=0;
    for k=1:ncandidates
        idx_with_alt=idxs_with_alt(k);
        name_without_alt=names_without_alt{idx_with_alt};
        idx_all=find(cosmo_match(names_without_alt,name_without_alt));
        idx_without_alt=setdiff(idx_all,idx_with_alt);
        switch numel(idx_without_alt)
            case 0
                continue
            case 1
                pos=pos+1;
                name_with_alt=names{idx_with_alt};
                pairs(pos,:)={name_without_alt,name_with_alt};
            otherwise
                assert(false);
        end
    end

    pairs=pairs(1:pos,:);

function alt_name=find_alt_name(name)
    alt_name=[];

    pairs=senstypes_alt_names();
    for col=1:2
        msk=cosmo_match(pairs(:,col),name);
        if any(msk)
            assert(sum(msk)==1)
            alt_name=pairs{msk,3-col};
            return
        end
    end



function lay=find_layout(name,opt)
    % find layout based on sensname
    % if no layout is found, lay is returned as []
    lay=find_layout_helper(name,opt);

    if ~isempty(lay)
        return
    end

    % not found, try to use the alternative name
    alt_name=find_alt_name(name);
    if ~isempty(alt_name)
        lay=find_layout_helper(alt_name,opt);
    end

function lay=find_layout_helper(name,opt)
    % helper function: first tries to get the layout directly, if that does
    % not work, try to infer planar channels from the combined channels
    sc=cosmo_meeg_senstype_collection();
    label=sc.(name).label;
    lay=find_layout_from_label(label,opt);

    if ~isempty(lay)
        return
    end

    lay=infer_planar_layout_from_combined(name,opt);

function planar_lay=infer_planar_layout_from_combined(planar_name,opt)
    % helper function in case no planar layout is found (e.g. ctf151)
    planar_lay=[];

    combined_name=[planar_name '_combined'];

    sc=cosmo_meeg_senstype_collection();
    if all(cosmo_isfield(sc,{planar_name,combined_name}))
        planar_label=sc.(planar_name).label;
        combined_label=sc.(combined_name).label;
        combined_lay=find_layout_from_label(combined_label,opt);
        if isempty(combined_lay)
            return;
        end

        % get rid of COMNT and SCALE labels
        keep=cosmo_match(combined_lay.label,combined_label);
        combined_lay=slice_layout(combined_lay,keep);

        if ~isequal(combined_lay.label,combined_label)
            return
        end

        % ensure mapping between number of labels
        nlabels=size(combined_lay.pos,1);
        combined2planar_idxs=reshape(repmat(1:nlabels,2,1),[],1);

        planar_lay=slice_layout(combined_lay,combined2planar_idxs);

        planar_lay.label=reshape(planar_label',[],1);
        planar_lay.name=[];
    end

function lay=slice_layout(lay, to_select)
    % helper function to select a subset of channels
    nrows=size(lay.pos,1);
    keys=fieldnames(lay);
    for k=1:numel(keys)
        key=keys{k};
        value=lay.(key);
        if size(value,1)==nrows
            lay.(key)=value(to_select,:);
        end
    end


function lay=find_layout_from_label(label,opt)
    % use labels from the layout to identify it
    lay_coll=cosmo_meeg_layout_collection();
    lay_label=cellfun(@(x)x.label,lay_coll,'UniformOutput',false);
    [in_lay, in_label]=cosmo_overlap(lay_label,{label});
    [coverage,i]=max(mean([in_lay, in_label],2));

    % try to be smart and use decent thresholds
    if in_lay(i)<opt.thr_layout || coverage<opt.thr_senstype
        lay=[];
    else
        lay=lay_coll{i};
    end