function [] = assemblevideo(folder, gangmat, maxmove, nGang, nNeuron, seed)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Creates the simulation data used in figure 3
% Inputs:
%     - folder: The folder to save the data to; location of gangmat and
%     background png files
%     - gangmat: string of the name of the .mat that contains the
%       identified groups of neurons that form ganglia
%     - maxmove: The peak movement in pixels for the video
%     - nGang: The number of ganglia to have within the field of view
%     - nNeuron: The maxium number of neurons each ganglia can have
%     - seed: The seed for the run
% Output:
%Saves a .mat file that can be used to generate the simulation data along
%with an h5 file of simulated data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

cd(folder)
load(gangmat)

% Generate the random seed from the input values
if isa(maxmove, 'char')
    maxmove = str2num(maxmove);
    nGang = str2num(nGang);
    nNeuron = str2num(nNeuron);
    seed = str2num(seed);
end
rng(str2num(strcat(num2str(maxmove), num2str(seed), num2str(nGang), num2str(nNeuron))));
ID = datestr(datetime('now'));
sind = strfind(ID, ' ');
ID(sind) = '-';
cind = strfind(ID, ':');
ID(cind) = '-';
ID = strcat(ID, 'Amplitude', num2str(maxmove), 'nGanglia', num2str(nGang), 'nNeuron', num2str(nNeuron), 'seed', num2str(seed));

tic

% Randomly select which ganglia to use in the field of view and place them
% in a roughly grid like formation in the field of view
delay = 40; % set the time before a large motor complex occurs
totaltime = 119; % Set length fo the simulation


t = 0.05:0.05:totaltime; 
% Determine time point of the motor complex
enddelay = find(t > delay, 1, 'first');
d1 = 600;
d2 = 600;

% Calculate movement for the X and Y dimensions, the propagation angle of
% the movement, and the frame at which a large motor complex begins
class(maxmove)
[movement] = genMovement_fit(t, enddelay, maxmove);
MoveXt = movement.MoveXmajor+movement.MoveXminor;
MoveYt = movement.MoveYmajor+movement.MoveYminor;

movefac = 0.98;
c = [ceil(max([max(MoveXt) max(MoveXt*movefac)])) floor(d2+min([0 min([min(MoveXt) min(MoveXt*movefac)])]))];
r =  [ceil(max([max(MoveYt) max(MoveYt*movefac)])) floor(d1+min([0 min([min(MoveYt) min(MoveYt*movefac)])]))];

% Place the ganglia in a random lattice across the field of view
[newgang, gangCOM, neighGanglia, gangMask] = placeGanglia(gangmat, r, c, nNeuron, nGang);

% Smooth out the edges of the neurons so that they look more like realistic
% neurons
[filtgang] = smoothNeuron(newgang, 1);
masks = cat(3, filtgang{:});
[fluo] = genSimulatedF(t, enddelay-20, masks);
fluo = fluo';
toc

% Generate a video of the ganglia and internodal strands moving without
% background
[svid, MoveXt, MoveYt, offset, useorder, saveMove] = moveGanglia(filtgang, gangCOM, neighGanglia, gangMask, fluo, movement, t);
saveName = strcat('simulated data_', ID, '.mat');

A = dir('*_Green_background.png');
useback = randsample(length(A), 1);
offsetbg = 0; 

save(saveName, 'newgang', 'gangCOM', 'neighGanglia', 'gangMask', 'saveMove',...
     'offset', 'useorder', 'svid', 'MoveXt', 'MoveYt', 'movefac', 'maxmove', 'nGang', 'nNeuron', '-v7.3')

% Apply the data to the pre-filtered background images
for vid = 1:length(useback)
    
    img = imread(A(useback(vid)).name);
    img = single(img);
    avgval = mean(img(:));

    % Randomly select how much brighter than the background the entire
    % simulated set of ganglia and internodal strands is compared to the
    % background
    scalefac = 1.15; 
    
    scalevid = svid*(avgval*scalefac(vid)-avgval);

    % Make the background move at a lower amplitude than the overlying
    % ganglia and internodal strands
    simvid = [];
    for fn = 1:size(svid, 3)
        if fn - offsetbg >= 1
            ind = fn - offsetbg;
            moveX = MoveXt(ind);
            moveY = MoveYt(ind);
            tCOMn = [moveX*movefac moveY*movefac];
            newback = imtranslate(img, tCOMn);
        else
            newback = img;
        end
        framemed = median(newback(:));
        frame =  scalevid(:, :, fn);
        ind = find(frame(:));
        fback = imgaussfilt(newback, 2);
        gnoise = normrnd(0, mad(newback(:), 1)/2, size(fback));
        simvid(:, :, fn) = frame + fback + gnoise ;
    end
    [d1 d2 d3] = size(simvid);
    
    simvid = simvid(r(1):r(2), c(1):c(2), :);
    
    vidname = strcat(A(useback(vid)).name(1:end-4), ID, 'uint8.h5');
    simvid = uint8(simvid);
    h5create(vidname, '/video', size(simvid), 'Datatype', 'uint8');
    h5write(vidname, '/video', simvid);
    
end
end