% 2n OBJECTIVES OPTIMIZATION
% This script optimize experimental data for n types of genetic circuits
% n FOD objectives + n OD objectives
clear all
% Experiment
directory = 'C:\Users\Usuario\Documents\Carlos AV\UPV\iGEM\Modelling\Experimentos\Experiment6_GFP_pITU6_20_21_2n\';
fname = 'Exp6_GFP_data.mat';

% Generate spMODEparam for optimization
run([directory 'spMODEparam_exp6GFP']);

% Optimization
OUT = spMODE(spMODEDat);

% Pareto solutions diagrams
levelDiagram(OUT.PFront,OUT.PSet)

%%
% Decision making of p, dp and mu values
Crl = input('Cr value for low promoter: ');
Crm = input('Cr value for medium promoter: ');
Crs = input('Cr value for strong promoter: ');
dp = input('dp value: ');
mul = input('mu value for low colony: ');
mum = input('mu value for medium colony: ');
mus = input('mu value for strong colony: ');

cn = 500;
Cr = cn*[Crl Crs Crm];%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
mu = [mul mus mum];%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Other parameters
p = 2.4; % min-1 
dm = 0.247; % min-1

Vculture = 200; % uL
Ccells_OD600_1 = 8e5; % cells/uL when OD = 1
% Kmax_exp = max(max(spMODEDat.DataOD,[],1)); % OD                                        
% Kmax = Vculture*Kmax_exp*Ccells_OD600_1; % cells
Kmax_exp = max(max(spMODEDat.DataOD,[],1)); % OD                                        
Kmax = Vculture*Kmax_exp*Ccells_OD600_1; % cells
OD_0 = min(min(spMODEDat.DataOD,[],1)); % OD 
Ncells_0 = Vculture*OD_0*Ccells_OD600_1; % cells

VAL_per_obj = length(indexes_VAL)/(spMODEDat.NOBJ/2);

% Colors
blue = [68 146 198]/255;
red = [246 80 88]/255;
yellow = [255 198 0]/255;
color = [blue; red; yellow]; 

k = 1;
fig = figure('Color','w');

for i=1:length(Cr)
    param = [Cr(i) p dm dp mu(i) Kmax];

    % Initial conditions
    PoI_0 = mean(spMODEDat.DataXFP_per_cell_VAL(1,k:(k+VAL_per_obj-1)));
    n0 = [Cr(i)/(dm+mu(i)) PoI_0 Ncells_0];

    % ODE options
    options = odeset('RelTol',1e-6,'Stats','off','Abstol',1e-6);
    
    % Model simulation
    [t,n]=ode45(@mc_simple,spMODEDat.DataTime,n0,options,param);

    % Graphs
    XFP = n(:,2);
    N = n(:,3);
    data_XFP_VAL = spMODEDat.DataXFP_per_cell_VAL(:,k:(k+VAL_per_obj-1))';
    data_Ncells_VAL = Vculture*Ccells_OD600_1*spMODEDat.DataOD_VAL(:,k:(k+VAL_per_obj-1))';
    
    hold on
    subplot(211)
    errorbar(t,mean(data_XFP_VAL,1),std(data_XFP_VAL),'Color',color(i,:),'MarkerSize',6,...
    'MarkerFaceColor',color(i,:), 'MarkerEdgeColor',[0 0 0],...
    'Marker','o', 'LineStyle','none');
    hold on
    plot(t,XFP,'Color',color(i,:),'LineWidth',1.8)
    title('Protein molecules per cell vs. MEFL (experimental data)','FontName','Lato','FontSize',14)
    xlabel('Time (min)','FontName','Lato')
    ylabel('Protein (MEFL)','FontName','Lato')
    xlim([t(1) t(end)])    
    
    subplot(212)
    errorbar(t,mean(data_Ncells_VAL,1),std(data_Ncells_VAL),'Color',color(i,:),'MarkerSize',6,...
    'MarkerFaceColor',color(i,:), 'MarkerEdgeColor',[0 0 0],...
    'Marker','o', 'LineStyle','none');    
    hold on
    plot(t,N,'Color',color(i,:),'LineWidth',1.8)
    title('Number of cells vs. Number of cells (experimental data)','FontName','Lato','FontSize',14)
    xlabel('Time (min)','FontName','Lato')
    ylabel('Number of cells','FontName','Lato')
    xlim([t(1) t(end)])
    hold on
    k = k + VAL_per_obj;

end
labels = {'BBa-id6 experimental','BBa-id simulation'...
        'BBa-id21 experimental','BBa-id simulation'...
        'BBa-id20 experimental','BBa-id simulation'};
legend(labels,'Location','southeastoutside')