New function for preprocessing

for ii=1:length(intensity)

    dod(ii) = DataClass();

    d = intensity(ii).GetDataTimeSeries();

    % Optional (user prompt): Adding dc offset if intensity (d) has negative values

    if ~isempty(d(d<=0))

        quest = {'Intensity signal has negative values. If you would like to add a dc offset, please click YES. If you would like to proceed with negative values, hit CANCEL.'};

        dlgtitle = 'Warning';

        btn1 = 'YES';

        btn2 = 'CANCEL';

        detbtn = btn1;

        answer = questdlg(quest,dlgtitle,btn1,btn2,detbtn)

        switch answer

            case 'YES'

                for j = 1:size(d,2)

                    foo = d(:,j);

                    if ~isempty(find(foo<0))

                        d(:,j) = foo + abs(min(foo));

                        foo = d(:,j);

                    end

                    if ~isempty(find(foo == 0))

                        d(:,j) = foo + min(foo(foo > 0));

                    end

                end

        end

    end

    dm = mean(abs(d),1);

    nTpts = size(d,1);

    dod(ii).SetTime(intensity(ii).GetTime());

% SYNTAX:

% intensity = hmrR_PreprocessIntensity_Negative( intensity )

%

% UI NAME:

% hmrR_PreprocessIntensity_Negative

%

% DESCRIPTION:

% Fix negative values in intensity by either adding an offset to make all

% numbers positive (+eps)(option 1) or just set values <=0 to +eps (option

% 2)

%

% INPUT:

% intensity - SNIRF data type where the d matrix is intensity

%

% OUTPUT:

% intensity - SNIRF data type where the d matrix is intensity

%

% USAGE OPTIONS:

% Intensity_to_Intensity: d = hmrR_PreprocessIntensity_Negative(data)

%

function d = hmrR_PreprocessIntensity_Negative( intensity )

for ii=1:length(intensity)

    d = intensity(ii).GetDataTimeSeries();

    if ~isempty(d(d<=0))

        quest = {'Intensity signal has negative values.'};

        dlgtitle = 'Warning';

        btn1 = 'OPTION1: Add a dc offset';

        btn2 = 'OPTION2: Set values <=0 to eps';

        btn3 = 'CANCEL';

        detbtn = btn3;

        answer = questdlg(quest,dlgtitle,btn1,btn2,btn3, detbtn);

        switch answer  

            case 'OPTION1: Add a dc offset'

                for j = 1:size(d,2)

                    foo = d(:,j);

                    if ~isempty(find(foo<0))

                        d(:,j) = foo + abs(min(foo)) + eps;

                    end

                end

            case 'OPTION2: Set values <=0 to eps'

                for j = 1:size(d,2)

                    foo = d(:,j);

                    if ~isempty(find(foo<0))

                        d(find(foo<=0),j) = eps;

                    end

                end

        end

    end

    intensity(ii).SetDataTimeSeries(d);

end