function [] = mergeFocusSegmentation(focusfolder, segmentationfolder)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Merges the fields of view for the focus and segmentation videos/data since
% the two were taken from different iterations of the registration. Saves
% the quadrant focus data to the segmented data into the segmentation folder
% Inputs:
%     - focusfolder: the directory that contains the annotated focus data
%     - segmentationfolder: the directory that contains the masks
% Outputs: (none)
%     - 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

cd(focusfolder)
A = dir('*associated.mat');

for fn = 1:length(A) 
    cd(focusfolder)
    load(A(fn).name, 'maxmove');
    focusmax = maxmove;
    tmove = sum(focusmax(1:3, :));
    greenind = strfind(A(fn).name, 'Green')+4;
    quads = zeros(600, 600);
    quads = quads(tmove(3)+1:end-tmove(4), tmove(1)+1:end-tmove(2));
    [d1, d2] = size(quads);
    quads(1:floor(d1/2), (floor(d2/2)+1):end) = 1;
    quads(1:floor(d1/2), 1:floor(d2/2)) = 2;
    quads((floor(d1/2)+1):end, 1:floor(d2/2)) = 3;
    quads((floor(d1/2)+1):end, (floor(d2/2)+1):end) = 4;
    cd(segmentationfolder)
    B = dir(strcat(A(fn).name(1:greenind), '*associated.mat'));
    load(B(1).name);
    segmaxmove = maxmove;
    C = dir(strcat(A(fn).name(1:greenind), '*projection.tif'));
    segproj = imread(C(1).name);
    [quadrants, vid2, ~, focuscrop, segmentationcrop] = convergeMaxMove(quads, segproj, focusmax, segmaxmove);
    if size(quadrants) ~= size(vid2)
        break
    end
    save(strcat(A(fn).name(1:greenind), '_matchFocusSegmentation.mat'), 'quadrants', 'focuscrop', 'segmentationcrop');
    
end