function[obj] = remove_blinks(obj, settings)

eyes = fieldnames(obj.data);
for e = 1:length(eyes)
    eye = eyes{e};
    signal = obj.data.(eye).uncorrected.raw;

    %no data available for eye
    if isempty(signal)
        continue
    end
    
    %% Kill the missing datapoints
    missing = find(obj.time == signal);
    signal(missing) = NaN;    
    
    %% store original signal for reference
    obj.data.(eye).uncorrected.raw = signal;
    obj.blink_count.(eye) = 0;
    obj.missing_data_count.(eye) = 0;
    %% Kill the blinks (pupil dilation dip)
    nans = find(isnan(signal));

    %% Count the NaNs before extending them.
    nans=find(isnan(signal));
    dnans = diff(nans);

    missing_data_list = find(dnans>1);
    missing_data_count = 0;
    if ~isempty(missing_data_list)
        blink_list(:,1)   = nans(missing_data_list);
        blink_list(:,2)   = dnans(missing_data_list);
        blink_list(:,3)   = dnans(missing_data_list) < settings.MaximumBlinkSize;

        obj.blink_count.(eye) = length(find(blink_list(:,3)));
        obj.missing_data_count.(eye) = length(missing_data_list);

        obj.blinks.(eye) = blink_list;
    end

    %% Extend the NaNs
    for n = 1:length(nans)
        window = [nans(n)-settings.BlinkExtension(1):nans(n)+settings.BlinkExtension(2)];
        window(find(window<1)) = []; %% kill the negative indices for early blinks
        signal(window) = NaN;
    end

    if isempty(obj.blink_count.(eye))
        obj.blink_count.(eye) = 0;
    end

    if isempty(obj.missing_data_count.(eye))
        obj.missing_data_count.(eye) = 0;
    end
    
    %% determine quality;
    obj.quality.(eye) =  100 - (length(find(isnan(signal))) / length(signal)*100);
    obj.valid = 1;
  
    if (obj.quality.(eye) < settings.QualityThreshold)
        obj.display_and_log(sprintf('\t*) %2d blinks filtered (%2d missing data events); quality : %2d percent -> Trial excluded\n', obj.blink_count.(eye), obj.missing_data_count.(eye),round(obj.quality.(eye))));
        obj.valid.(eye) = 0;
    else
        obj.display_and_log(sprintf('\t*) %2d blinks filtered (%2d missing data events); quality : %2d percent', obj.blink_count.(eye), obj.missing_data_count.(eye),round(obj.quality.(eye))));    
    end

    %% Interpolate NaNs
    signal= obj.inpaint_nans(signal);

    obj.data.(eye).uncorrected.interpolated = signal;

end