clear all
% Data extraction:
directory = 'C:\Users\Usuario\Documents\Carlos AV\UPV\iGEM\Modelling\Experimentos\Spectrum\amilCP Spectrum\';
sheet = 'Plate 1 - Sheet1';
fname = 'mRFP_amilCP_Spectrum';

wavelengths = xlsread([directory fname '.xlsx'],sheet,'B353:B748');
F_blue = xlsread([directory fname '.xlsx'],sheet,'L353:N748');
F_cells = xlsread([directory fname '.xlsx'],sheet,'F353:H748');
F_blank = xlsread([directory fname '.xlsx'],sheet,'C353:E748');
OD_blue = xlsread([directory fname '.xlsx'],sheet,'D79:F79');
OD_cells = xlsread([directory fname '.xlsx'],sheet,'D77:F77');
save([directory fname '.mat'],'wavelengths','F_blue','F_cells','F_blank','OD_cells','OD_blue');

%% amilCP GRAPH

clear all
directory = 'C:\Users\Usuario\Documents\Carlos AV\UPV\iGEM\Modelling\Experimentos\Spectrum\amilCP Spectrum\';
fname = 'mRFP_amilCP_Spectrum';
load([directory fname '.mat'])

% F Vectors 
F_corrected = F_blue - F_cells;
F_mean = mean(F_corrected,2);

% RGB Colours
color = [0 51 153]/255;

% Maximum peaks
idexmax = find(max(F_mean) == F_mean);
idexmin = find(min(F_mean) == F_mean);
wlmax = wavelengths(idexmax);
Fmax = F_mean(idexmax);
Fmin = F_mean(idexmin);

% Normalised data
F_norm = ((F_mean-Fmin)/(Fmax-Fmin))*100;
Fmax_norm = F_norm(idexmax);

title_spec = 'amilCP Spectrum';

% Spectrum
% Create figure
fig_spectrum = figure('Color','w');
% Create axis
axes = axes('Parent',fig_spectrum);
hold(axes,'on');

% Areas/plots
area_em = area(wavelengths,F_norm,'FaceColor',color,'EdgeColor',color,'FaceAlpha',0.6,'LineWidth',1);
hold on
line([wlmax wlmax],get(axes,'YLim'),'Color','k','LineStyle','--')
hold on

% Plot peaks
plot(wlmax,Fmax_norm,'k.','LineWidth',1,'MarkerSize',12,'MarkerFaceColor','k')

% Text
descr = {['Absorbance maximum: ' int2str(wlmax) ' nm']};
text(0.9,0.9,descr,'Units','normalized','HorizontalAlignment','right','FontName','Lato','FontSize',11)

% Other properties
title(title_spec,'FontName','Lato','FontSize',14)
xlabel('Wavelength (nm)','FontName','Lato')
ylabel('Relative absorbance (%)','FontName','Lato')
legend({'Absorbance Spectrum'},'FontName','Lato','Location','east');
wlMIN = min(wavelengths);
wlMAX = max(wavelengths);
xlim([wlMIN wlMAX])
box(axes,'on');
set(axes,'FontName','Lato','XGrid','on','YGrid','on');