generateElecMask.m

function vol_elec = generateElecMask(elec_allCoord,coordRange,elec,doWarn)
% vol_elec = generateElecMask(elec_allCoord,coordRange,elec,doWarn)
% 
% Convert point clouds of electrodes into 3D masks.
% 
% (c) Yu (Andy) Huang, Parra Lab at CCNY
% yhuang16@citymail.cuny.edu
% April 2018

vol_elec = zeros(coordRange);
vol_isElec = zeros(coordRange); % for detecting electrodes overlap
% vol_elecLabel = zeros(coordRange);
% rnge = cell(length(elec_allCoord),1);

for i = 1:length(elec_allCoord)
    temp = elec_allCoord{i};
    if isempty(temp)
        error(['Electrode ' elec{i} ' goes out of image boundary. ROAST cannot proceed without a properly placed electrode. Please expand the input MRI by specifying the ''zeroPadding'' option.']);
    else
        ind = find(temp(:,1)>0 & temp(:,1)<=coordRange(1)...
            & temp(:,2)>0 & temp(:,2)<=coordRange(2)...
            & temp(:,3)>0 & temp(:,3)<=coordRange(3));
        if isempty(ind)
            error(['Electrode ' elec{i} ' goes out of image boundary. ROAST cannot proceed without a properly placed electrode. Please expand the input MRI by specifying the ''zeroPadding'' option.']);
%             elec_allCoord{i} = [];
%             rnge{i} = [];
        else
            if length(ind)<size(temp,1)
                if doWarn
                    warning(['Part of the electrode ' elec{i} ' goes out of image boundary. ROAST can continue but results may not be accurate. It is recommended that you expand the input MRI by specifying the ''zeroPadding'' option.']);
                end
            end
            temp = temp(ind,:);
            indElec = sub2ind(size(vol_elec),temp(:,1),temp(:,2),temp(:,3));
            if any(vol_isElec(indElec))
                error(['Electrode ' elec{i} ' overlaps with Electrode ' elec{i-1} '. ROAST cannot continue as overlapping electrodes will confuse ROAST when setting up the boundary conditions for the model. To avoid overlapping, please do not place two electrodes too close to each other, or reduce the size of any neighboring electrodes.']);
            end
%             vol_elec(indElec) = 1;
            vol_elec(indElec) = i; % individual mask/color for each elec & gel
            vol_isElec(indElec) = 1;            
%             vol_elecLabel(indElec) = i;
%             elec_allCoord{i} = temp;
%             rnge{i} = [max(temp);min(temp)];
        end
    end
end

% allCoord = cell2mat(elec_allCoord);
% vol_elec(sub2ind(size(vol_elec),allCoord(:,1),allCoord(:,2),allCoord(:,3)))=1;