% PARSE_TRANSFUSION produces the plots necessary to our micro-transfusion protocol.
%
% Blanchoud Group, UNIFR
% Simon Blanchoud
% 11/01/2021
function parse_transfusion

  purity = '/home/blanchou/Documents/Manuscripts/transfusion_MiMB/data/purity_scale.csv';
  data = csvread(purity);
  x = data(:,1);
  data = data(:,2:end);
  samples = (data(1,:)~=0);
  meas = data(:, samples);
  data = data(:,~samples);

  meas = sort(meas(:));

  t = sum((data(:) - mean(data(:))).^2);

  [p, e_var, r, p_var, fit_var] = LinearRegression(repmat(x, size(data,2), 1), data(:));

  val = 1 - (meas / p);
  upper = (val > 0.88);
  lower = (val <= 0.88);

  [mu, su] = mymean(val(upper));
  [ml, sl] = mymean(val(lower));

  figure;hold on;
  plot(1-x, data, '-ok')
  plot(1-x, [x*(p+1.96*sqrt(p_var)) x*p x*(p-1.96*sqrt(p_var))], 'r')
  scatter(val(lower), meas(lower), 'ob')
  scatter(val(upper), meas(upper), 'oc')
  scatter([mu mu+su ml ml+sl], [0 1 0 1], 'k')
  title(num2str(1-r^2/t))
  xlim([0 1]);
  ylim([0 4]);
  ylabel('Absorbance')
  xlabel('Purity (%)')

  injection = '/home/blanchou/Documents/Manuscripts/transfusion_MiMB/data/injection_speed.csv';
  data = csvread(injection);
  x = data(:,1);
  data = data(:,2:end);
  zooid = data(:,1:5);
  vessel = data(:,6:end);

  [m,s] = mymean(data,2);
  [mz,sz] = mymean(zooid,2);
  [mv,sv] = mymean(vessel,2);

  figure; hold on;
  plot(x, zooid, 'r')
  plot(x, vessel, 'b')
  plot(x, mz + [sz zeros(9,1) -sz], 'm')
  plot(x, mv + [sv zeros(9,1) -sv], 'c')
  plot(x, m + [s zeros(9,1) -s], 'k')
  ylim([0 40])
  ylabel('Time (min)')
  xlim([0 40])
  xlabel('Injected volume (µL)')


  collection = '/home/blanchou/Documents/Manuscripts/transfusion_MiMB/data/collection_speed.csv';
  pipette_changes = [1 20; 2 1; 2 6; 2 7; 3 10; 3 15; 3 17.45; 3 20; 4 3; 4 13.45];
  puncture_change = [1 1.283; 1 6; 2 13.5; 2 28.616; 3 16; 4 14.25; 5 1.333; 5 12];

  data = csvread(collection);
  x = data(:,1);
  data = data(:,2:end);

  [m,s] = mymean(data,2);

  pc = NaN(0,2);
  for i=1:size(data,2)
    xp = pipette_changes(pipette_changes(:,1)==i, 2);
    y = interp1(x, data(:,i), xp);
    pc = [pc; [xp y]];
  end

  cp = NaN(0,2);
  for i=1:size(data,2)
    xp = puncture_change(puncture_change(:,1)==i, 2);
    y = interp1(x, data(:,i), xp);
    cp = [cp; [xp y]];
  end

  figure; hold on;
  plot(x, data, 'k')
  plot(x,m, 'r')
  plot(x, m + [s -s], 'b')
  scatter(pc(:,1), pc(:,2), 'v')
  scatter(cp(:,1), cp(:,2), 'o')
  ylim([0 40])
  ylabel('Time (min)')
  xlim([0 40])
  xlabel('Collected volume (µL)')

  keyboard

  return;
end