close all;
clear all;
warn = warning ('off','all');
poolobj = gcp('nocreate');
if isempty(poolobj)
    parpool;
end
pctRunOnAll warning('off','all')

%% set path
fnIJ='/home/aymanns/registration/ij.jar';     % Path to "ij.jar"
fnMIJ='/home/aymanns/registration/mij.jar';   % Path to "mij.jar"
javaaddpath(fnIJ);
javaaddpath(fnMIJ);
addpath('code');
addpath('code/external/utils');
addpath(genpath('code/external/InvPbLib'));

%% load file names
fname = 'files.json'; 
fid = fopen(fname); 
raw = fread(fid,inf); 
str = char(raw'); 
fclose(fid); 
files = parse_json(str);

%% Parameters
param = default_parameters();
param.lambda = 1000;    % Regularization parameter
param.gamma = 100;      % Sets the strength of the feature matching constraint

%% Input - Output
type=1;                                     % 0 for Mac users, 1 for Linux users
fnMatch=files.tdTom_input;%'/home/aymanns/data/1_Horizontal_VNC/tdTom.tif';  % Sequence used for the feature matching similarity term
fnIn1=files.GC6s_input;     % Sequence used for the brightness constancy term 
fnIn2=files.tdTom_input;    % Sequence warped with the motion field estimated from fnIn1 and fnMatch
N=3;                                        % Motion is estimated on frames 1 to N. If N=-1, motion is estimated on
                                            % the whole sequence

fnOut1=files.GC6s_registered;              % Sequence fnIn1 warped
fnOut2=files.tdTom_registered;              % Sequence fnIn2 warped
fnColor=files.color_flow_out;           % Color visualization of the motion field
fnVector=files.vectors_out;

if type==0
    fnDeepMatching='code/external/deepmatching_1.2.2_c++_mac';      
elseif type==1
    fnDeepMatching='code/external/deepmatching_1.2.2_c++_linux';      
end
addpath(fnDeepMatching);

%% Perform motion compensation
motion_compensate(fnIn1,fnIn2,fnMatch,fnDeepMatching,fnOut1,fnOut2,fnColor,fnVector,N,param);