function [] = allCorrCompare(locArray)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Calculate the correlation for the 6 way comparison between registrations
% with and without memory and under different filtering conditions. This is 
% a time intesntive process. To account for the differences in FOV size
% between different registrations, the correlation is performed on a
% fixed field of view from the unregistered video where registered pixels
% are replaced with the registered video.
% Inputs:
%     - locArray: string array of 7 file paths:
%           1.  raw video [filepath]
%           2.  unfiltered without memory [filepath]
%           3.  bandpass filtered without memory [filepath]
%           4.  bandpass & Okada filtered without memory [filepath]
%           5.  unfiltered with memory [filepath]
%           6.  bandpass filtered with memory [filepath]
%           7.  bandpass & Okada filtered with memory [filepath]
% Output: (none)
%     -
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% Parse folder locations from locArray
%Folder names with the different conditions.

origvidfolder   = locArray(1);   % raw video [filepath]
unomem          = locArray(2);   % unfiltered without memory [filepath]
bpnomem         = locArray(3);   % bandpass filtered without memory [filepath]
oknomem         = locArray(4);   % bandpass & Okada filtered without memory [filepath]
unfiltfolder    = locArray(5);   % unfiltered with memory [filepath]
bandpassfolder  = locArray(6);   % bandpass filtered with memory [filepath]
okadafolder     = locArray(7);   % bandpass & Okada filtered with memory [filepath]

cd(unomem)

%% Identify and calculate correlation for all registered videos
A = dir('*egis*.h5');
for fn = 1:length(A)
    vidname = A(fn).name;
    gind = strfind(vidname, 'Green');
    cd(origvidfolder)
        v = dir(strcat(vidname(1:gind), '*okada1.h5'));
        ov = h5read(v(1).name, '/video');
    for it = 1:3
        % Obtains the FOV for that iteration of the registration
        [unmFOV unmmax unmvid1] = finalFOV(unomem, vidname, it); 
        [bpnmFOV bpnmmax bpnmvid1] = finalFOV(bpnomem, vidname, it);
        [oknmFOV oknmmax oknmvid1] = finalFOV(oknomem, vidname, it);
        [okadaFOV okadamax okvid1] = finalFOV(okadafolder, vidname, it);
        [bpFOV bpmax bpvid1] = finalFOV(bandpassfolder, vidname, it);
        [uFOV umax uvid1] = finalFOV(unfiltfolder, vidname, it);
        sumimg = unmFOV+okadaFOV+bpFOV+uFOV;

        % Find the bounding box that contains the pixels associated with at
        % least 1 registered video.
        [r c] = ind2sub(size(sumimg), find(sumimg >= 1));
        r = [min(r) max(r)];
        c = [min(c) max(c)];
        compvid = ov(r(1):r(2), c(1):c(2), :);

        % Generate the videos so that each registration uses the same field
        % of view in the unregistered video. Then replace any pixels for
        % which there is a registered video with the registered data.
        unmvid = compvid;
        [do1 do2 do3] = size(unmvid1);
        unmvid((1:(do1))+unmmax(3)-r(1)+1, (1:(do2))+unmmax(1)-c(1)+1, :) = unmvid1;
        clear unmvid1
        bpnmvid = compvid;
        [do1 do2 do3] = size(bpnmvid1);
        bpnmvid((1:(do1))+bpnmmax(3)-r(1)+1, (1:(do2))+bpnmmax(1)-c(1)+1, :) = bpnmvid1;
        clear bpnmvid1
        oknmvid = compvid;
        [do1 do2 do3] = size(oknmvid1);
        oknmvid((1:(do1))+oknmmax(3)-r(1)+1, (1:(do2))+oknmmax(1)-c(1)+1, :) = oknmvid1;
        clear oknmvid1
        okadavid = compvid;
        [do1 do2 do3] = size(okvid1);
        okadavid((1:(do1))+okadamax(3)-r(1)+1, (1:(do2))+okadamax(1)-c(1)+1, :) = okvid1;
        clear okvid1
         bpvid = compvid;
        [do1 do2 do3] = size(bpvid1);
        bpvid((1:(do1))+bpmax(3)-r(1)+1, (1:(do2))+bpmax(1)-c(1)+1, :) = bpvid1;
        clear bpvid1
        uvid = compvid;
        [do1 do2 do3] = size(uvid1);
        uvid((1:(do1))+umax(3)-r(1)+1, (1:(do2))+umax(1)-c(1)+1, :) = uvid1;
        clear uvid1

        % Calculate the correlation
        [unmC{fn}(it, :),mM2f,vM2f] = motion_metrics(unmvid, 0);
        [bpnmC{fn}(it, :),mM2f,vM2f] = motion_metrics(bpnmvid, 0);
        [oknmC{fn}(it, :),mM2f,vM2f] = motion_metrics(oknmvid, 0);
        [okC{fn}(it, :),mM2f,vM2f] = motion_metrics(okadavid, 0);
        [bpC{fn}(it, :),mM2f,vM2f] = motion_metrics(bpvid, 0);
        [uC{fn}(it, :),mM2f,vM2f] = motion_metrics(uvid, 0);
        [compC{fn}(it, :), m, vv] = motion_metrics(compvid, 0);
        it
    end
    clear ov compvid bpvid uvid okvid
    fn
end 

%% Save the data
cd(okadafolder)
savename = strcat(datestr(now,"yyyy.mm.dd_HH.MM.SS"), '_comparisonofcorrelation_1vidmatch_allsix.mat');
save(savename, 'bpnmC', 'oknmC', 'uC', 'bpC', 'unmC', 'okC', 'compC');

end