function [F, dFF] = calcDFoF(masks, video)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Generate the dF/F from a set of masks without doing any sort of background
% subtraction
% Inputs:
%     - masks: MxNx#Neurons matrix containing the ROIs for the identified neurons in the field of view
%     - video: Video from which to calculate the fluorescence
% Output:
%     - F: Mx#Neurons matrix of the raw fluorescence of the neurons from masks
%     - dFF: Mx#Neurons matrix of the normalize fluorescence using the median as Fbar
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

[d1, d2, d3] = size(video);

%Convert to a 2D matrix to increase the speed of the calculation
linvid = reshape(video, [d1*d2 d3]);

%Calculate the value for each ROI
for fn = 1:size(masks, 3)
    mask = masks(:, :, fn);
    ind = find(mask);
    
    F(:, fn) = sum(linvid(ind,:))/length(ind);
    dFF(:, fn) = (F(:, fn)-median(F(:, fn)))/median(F(:, fn));
end