%% Automated Regeneration and Detection on Chip v3.0 %%

%% Y. Shrike Zhang, T. Kilic 2015-07-22 %%

%% Bioreactor Integrated %%


clear; clc; clf;


%% Create object and initiate communication

clear('wago');
wObj = wagoNModbus('192.168.1.10', zeros(1, 56), false);

%% Define valves
A1 = 0; A2 = 1; A3 = 2; A4 = 3; A5 = 4; A6 = 5; A7 = 6; A8 = 7; A9 = 8; A10 = 9;  
A11 = 10; A12 = 11; A13 = 12; A14 = 13; A15 = 14; A16 = 15; A17 = 16; A18 = 17; A19 = 18; A20 = 19;  
A21 = 20; A22 = 21; A23 = 22; A24 = 23; A25 = 24; A26 = 25; A27 = 26; A28 = 27; A29 = 28; A30 = 29;
A31 = 30; A32 = 31;

B1 = 32; B2 = 33; B3 = 34; B4 = 35; B5 = 36; B6 = 37; B7 = 38; B8 = 39; B9 = 40; B10 = 41; 
B11 = 42; B12 = 43; B13 = 44; B14 = 45; B15 = 46; B16 = 47; B17 = 48; B18 = 49; B19 = 50; B20 = 51; 
B21 = 52; B22 = 53; B23 = 54; B24 = 55;

%% Define constants
Cycle = 5; Inj_on_Sample = 7*60; Inc_on_Sample = 10*60; Inj_on= 7*60;

Stop_Flow = 10; Inj_on_PBS = 7*60; Inj_off = 5; Inj_on_ETOH = 3*60; Inj_on_SAM = 5*60; Incubation = 60*60; Inc_on_NHSEDC = 3*60;

NormalizedRct = 0;
NormalizedRctArray_albumin = zeros(1, Cycle);


Rct_Media = 0; Rct_sample = 0;


%% All valves off (gas off)

for ii = A1:B16

    wObj.setValves(ii, 1);

    pause(0.1);

end

[err, desc] = wObj.error();

disp([num2str(err) ': ' desc]);

pause(0.1);



%% All valves for valve control on (gas on)

for jj = A1:A5

    wObj.setValves(jj, 0);

     disp([num2str(jj)]);

    pause(0.1);

end

[err, desc] = wObj.error();

disp([num2str(err) ': ' desc]);

wObj.setValves(A7, 0);

for jj = A9:A17

    wObj.setValves(jj, 0);

     disp([num2str(jj)]);

    pause(0.1);

end

[err, desc] = wObj.error();

disp([num2str(err) ': ' desc]);

pause(1);



%% Functionalization & Detection

for Reg = 1:Cycle

%%%%%% H2SO4 Cleaning
disp(sprintf('\n'));

disp('Step 1, H2SO4');

% Valves B10 on, A10/A16/A17 off

disp([' Valves B10 on, A10/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s1 = 1:Inj_on/30

wObj.setValves(A10, 1);

wObj.setValves(B10, 0);

pause(30);

end

toc



%%%%%%%%%%%%%%%%% Step 2, H2SO4 CV CLEANING


% Call 'libec660eNew2.dll'
if ~libisloaded('libec660eNew2')
    loadlibrary('libec660eNew2.dll', 'labview.h')
end

% calllib('libec660eNew2', 'CHI_set_mch', 1);

% H2SO4 Cleaning
calllib('libec660eNew2', 'CHI_setTechnique', 0);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ei', 0);
calllib('libec660eNew2', 'CHI_setParameter', 'm_eh', 1.8); 
calllib('libec660eNew2', 'CHI_setParameter', 'm_el', 0);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ef', 0);
calllib('libec660eNew2', 'CHI_setParameter', 'm_pn', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_vv', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_inpcl', 6);
calllib('libec660eNew2', 'CHI_setParameter', 'm_inpsi', 0.001);
calllib('libec660eNew2', 'CHI_setParameter', 'm_qt', 2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iSens', power(10, -2));

calllib('libec660eNew2', 'CHI_runExperiment');
disp 'Waiting for experiment to end'
while calllib('libec660eNew2', 'CHI_experimentIsRunning')
    disp '...' % <- call CHI_getExperimentData() in real time
    pause(10)
    wObj.setValves([A16 A17], ones(1, 2)); % Keep communication with valves
end


% % Clear All Previous Data First

clearvars n_H2SO4 x_H2SO4 y_H2SO4 px_H2SO4 py_H2SO4

clearvars YEAR MON DAY HOUR MIN SEC CV_H2SO4_data

% clearvars filename_mat filename_txt filename_xls

clearvars T

figure(2);
n_H2SO4 = 10800;
x_H2SO4 = zeros(n_H2SO4, 1);
y_H2SO4 = zeros(n_H2SO4, 1);
px_H2SO4= libpointer('singlePtr', x_H2SO4);
py_H2SO4= libpointer('singlePtr', y_H2SO4);
calllib('libec660eNew2', 'CHI_getExperimentData', px_H2SO4, py_H2SO4, n_H2SO4)
plot(px_H2SO4.value, py_H2SO4.value, 'LineWidth', 3);
hold on;

%% Save Data

CV_H2SO4_data = cat(2, px_H2SO4.value, py_H2SO4.value);

[YEAR, MON, DAY, HOUR, MIN, SEC] = datevec(datestr(now));

filename_CV_H2SO4_data_mat = ['CV_H2SO4_data_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.mat'];

filename_CV_H2SO4_data_txt = ['CV_H2SO4_data_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.txt'];

filename_CV_H2SO4_data_xls = ['CV_H2SO4_data_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.xls'];

save(filename_CV_H2SO4_data_mat, 'CV_H2SO4_data');



%% Step 3, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 3, stop flow, 5 s');
wObj.setValves(B10, 1);

wObj.setValves(A10, 0);

tic;
pause(5);
toc



%% Valves A16/A17 off (gas off)

%%%%%% Step 4, PBS washing

disp(sprintf('\n'));

disp('Step 4, Inj_on_PBS');

% Valves B1 on, A1/A16/A17 off

disp(['Valves B1 on, A1/A16/A17 off, ' num2str(Inj_on_PBS) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s4 = 1:Inj_on_PBS/30

wObj.setValves(A1, 1);

wObj.setValves(B1, 0);

pause(30);

end

toc

%% Step 5, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 5, stop flow, 5 s');
wObj.setValves(B1, 1);

wObj.setValves(A1, 0);

tic;
pause(5);
toc


%% Valves A16/A17 off (gas off)

%%%%%% Step 6, Ferricyanide flow, 420 s

disp(sprintf('\n'));

disp('Step 6, Inj_on_Fe');

% Valves B1 on, A1/A16/A17 off

disp(['Valves B11 on, A11/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s6 = 1:Inj_on/30

wObj.setValves(A11, 1);

wObj.setValves(B11, 0);

pause(30);

end

toc


%% Step 7, Ferricyanide cleaining by CV

if ~libisloaded('libec660eNew2')
    loadlibrary('libec660eNew2.dll', 'labview.h')
end

% Fe Cleaning
calllib('libec660eNew2', 'CHI_setTechnique', 0);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ei', 1.0);
calllib('libec660eNew2', 'CHI_setParameter', 'm_eh', 1.2); 
calllib('libec660eNew2', 'CHI_setParameter', 'm_el', -1.2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ef', 0);
calllib('libec660eNew2', 'CHI_setParameter', 'm_pn', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_vv', 0.2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_inpcl', 6);
calllib('libec660eNew2', 'CHI_setParameter', 'm_inpsi', 0.002);
calllib('libec660eNew2', 'CHI_setParameter', 'm_qt', 2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iSens', power(10, -4));

calllib('libec660eNew2', 'CHI_runExperiment');
disp 'Waiting for experiment to end'
while calllib('libec660eNew2', 'CHI_experimentIsRunning')
    disp '...' % <- call CHI_getExperimentData() in real time
    pause(10)
    wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves
end

% % Clear All Previous Data First

clearvars n_Fe x_Fe y_Fe px_Fe py_Fe

clearvars YEAR MON DAY HOUR MIN SEC CV_Fe_data

clearvars T

figure(3);
n_Fe = 14400;
x_Fe = zeros(n_Fe, 1);
y_Fe = zeros(n_Fe, 1);
px_Fe= libpointer('singlePtr', x_Fe);
py_Fe= libpointer('singlePtr', y_Fe);
calllib('libec660eNew2', 'CHI_getExperimentData', px_Fe, py_Fe, n_Fe)
plot(px_Fe.value, py_Fe.value, 'LineWidth', 3);

%% Save Data

CV_Fe_data = cat(2, px_Fe.value, py_Fe.value);

[YEAR, MON, DAY, HOUR, MIN, SEC] = datevec(datestr(now));

filename_CV_Fe_data_mat = ['CV_Fe_data_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.mat'];

filename_CV_Fe_data_txt = ['CV_Fe_data_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.txt'];

filename_CV_Fe_data_xls = ['CV_Fe_data_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.xls'];

save(filename_CV_Fe_data_mat, 'CV_Fe_data');


%% Step 8 stop flow, 5 s

disp(sprintf('\n'));
disp('Step 8, stop flow, 5 s');
wObj.setValves(B11, 1);

wObj.setValves(A11, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc



%% Valves A16/A17 off (gas off)

%% Step 9, EC detection

disp(sprintf('\n'));

disp('Step 9, EC detection');

if ~libisloaded('libec660eNew2')

    loadlibrary('libec660eNew2.dll', 'labview.h')

end

%%Electrochemical Impedance spectroscopy
calllib('libec660eNew2', 'CHI_setTechnique', 14);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ei', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_fh', 100000); 
calllib('libec660eNew2', 'CHI_setParameter', 'm_fl', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_amp', 0.005);
calllib('libec660eNew2', 'CHI_setParameter', 'm_qt', 2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iImpmode', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1M', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl2',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl3',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl4',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl5',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1M',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP2',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP3',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP4',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP5',12);
% % 


%% EIS Measurement

calllib('libec660eNew2', 'CHI_runExperiment');

disp 'Waiting for experiment to end'

while calllib('libec660eNew2', 'CHI_experimentIsRunning')

	disp '...' % <- call CHI_getExperimentData() in real time

	pause(10);

	wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

end



%% Get Data
% % Clear All Previous Data First
clearvars Phase_imp Real_imp Imag_imp pPhase_imp pReal_imp pImag_imp pPhase_imp_value
clearvars pReal_imp_value pImag_imp_value YEAR MON DAY HOUR MIN SEC Imp_data

% %
n = 12*6;
Phase_imp = zeros(n, 1);
Real_imp = zeros(n, 1);
Imag_imp = zeros(n, 1);
pPhase_imp= libpointer('singlePtr', Phase_imp);
pReal_imp= libpointer('singlePtr', Real_imp);
pImag_imp= libpointer('singlePtr', Imag_imp);
% %
wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves
% %
% %
calllib('libec660eNew2', 'CHI_getExperimentData_2channel', pPhase_imp, pReal_imp, pImag_imp, n)
% %
wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves
% %

pPhase_imp_value = pPhase_imp.value;
pReal_imp_value = pReal_imp.value;
pImag_imp_value = pImag_imp.value.*-1;

% %
figure(4);
plot(pReal_imp_value, pImag_imp_value,  'b-', 'LineWidth', 3)
xlabel('Z (Real)'); ylabel('Z (Imag)');
%title('albumin');
hold on;
% %
wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves
% % %
%% Save Data
Imp_data = cat(2, pPhase_imp_value, pReal_imp_value, pImag_imp_value);
[YEAR, MON, DAY, HOUR, MIN, SEC] = datevec(datestr(now));
filename_albumin_baseline_mat = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.mat'];
filename_albumin_baseline_txt = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.txt'];
filename_albumin_baseline_xls = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.xls'];
save(filename_albumin_baseline_mat, 'Imp_data');



%% Step 10, post detection

disp(sprintf('\n'));

disp([' Step 10, post detection, ' num2str(Stop_Flow) ' s']);


tic;

wObj.setValves([A16 A17], zeros(1, 2));

pause(Stop_Flow);

toc


%%%%%%% Step 11, PBS washing

disp(sprintf('\n'));

disp('Step 11, Inj_on_PBS');

% Valves B1 on, A1/A16/A17 off

disp([' Valves B1 on, A1/A16/A17 off, ' num2str(Inj_on_PBS) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s11 = 1:Inj_on/30

wObj.setValves(A1, 1);

wObj.setValves(B1, 0);

pause(30);

end

toc


%% Step 12, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 5, stop flow, 5 s');
wObj.setValves(B1, 1);

wObj.setValves(A1, 0);

tic;
pause(5);
toc


% Valves A16/A17 off (gas off)

disp('Valves A16/A17 off (gas off)');

wObj.setValves([A16 A17], ones(1, 2));


%% Step 13, EtOH, 600 s

disp(sprintf('\n'));

disp('Step 13, Inj_on_ETOH');

% Valves B1 on, A1/A16/A17 off

disp([' Valves B13 on, A13/A15/A16/A17 off, ' num2str(Inj_on_ETOH) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s13 = 1:Inj_on_ETOH/30

wObj.setValves(A13, 1);
wObj.setValves(A15, 1);
wObj.setValves(B13, 0);

pause(30);

end

toc


%% Step 14, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 5, stop flow, 5 s');
wObj.setValves(B13, 1);

wObj.setValves([A13 A15], [0 0]);

tic;
pause(5);
toc


%% Step 15, SAM

disp(sprintf('\n'));

disp('Step 15, Inj_on_SAM');

% Valves B1 on, A1/A16/A17 off

disp(['Valves B14 on, A14/A15/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s15 = 1:Inj_on_SAM/30

wObj.setValves(A14, 1);
wObj.setValves(A15, 1);

wObj.setValves(B14, 0);

pause(30);

end

toc


%% Step 16, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 5, stop flow, 5 s');
wObj.setValves(B14, 1);

wObj.setValves(A14, 0);
wObj.setValves(A15, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


%% Step 17, Incubation, 3600 s

disp(sprintf('\n'));

disp('Step 17, Incubation, 3600 s');

tic;

for s17 = Incubation/30


wObj.setValves([A16 A17], zeros(1, 2));

pause(30);

end

toc



%% Step 18, EtOH, 600 s

disp(sprintf('\n'));

disp('Step 18, Inj_on_ETOH');

% Valves B13 on, A13/A15/A16/A17 off

disp([' Valves B13 on, A13/A15/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s18 = 1:Inj_on/30

wObj.setValves(A13, 1);
wObj.setValves(A15, 1);
wObj.setValves(B13, 0);

pause(30);

end

toc


%% Step 19, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 19, stop flow, 5 s');
wObj.setValves(B13, 1);

wObj.setValves([A13 A15], [0 0]);

tic;
pause(5);
toc


%% Step 20, PBS, 420 s

disp(sprintf('\n'));

disp('Step 20, Inj_on_PBS');

% Valves B1 on, A1/A16/A17 off

disp([' Valves B1 on, A1/A16/A17 off, ' num2str(Inj_on_PBS) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s20 = 1:Inj_on/30

wObj.setValves(A1, 1);

wObj.setValves(B1, 0);

pause(30);

end

toc


%% Step 21, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 21, stop flow, 5 s');
wObj.setValves(B1, 1);

wObj.setValves(A1, 0);

tic;
pause(5);
toc


% Valves A16/A17 off (gas off)

disp('Valves A16/A17 off (gas off)');

wObj.setValves([A16 A17], ones(1, 2));


%% Step 22, NHS/EDC Flow

disp(sprintf('\n'));

disp('Step 22, Inj_on_NHSEDC');

% Valves B3 on, A3/A16/A17 off

disp([' Valves B3 on, A3/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s22 = 1:Inj_on/30

wObj.setValves(A3, 1);

wObj.setValves(B3, 0);

pause(30);

end

toc


%% Step 23, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 23, stop flow, 5 s');
wObj.setValves(B3, 1);

wObj.setValves(A3, 0);

%wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


%% Step 24, NHS/EDC Incubation

disp(sprintf('\n'));

disp(['Step 24, NHS/EDC Incubation, ' num2str(Inc_on_NHSEDC) ' s']);

% Valve B5 off, Valves A5/A16/A17 on

disp(['Valve B5 off, Valves A5/A16/A17 on, ' num2str(Inc_on_NHSEDC) ' s']);


tic;

for s24 = 1:Inc_on_NHSEDC/30

wObj.setValves([A16 A17], zeros(0, 2));

pause(30);

end

toc;


%% Step 25, Streptavidine flow

disp(sprintf('\n'));

disp('Step 25, Inj_on_SPV');

% Valves B3 on, A3/A16/A17 off

disp([' Valves B12 on, A12/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s25 = 1:Inj_on/30

wObj.setValves(A12, 1);

wObj.setValves(B12, 0);

pause(30);

end

toc


%% Step 26, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 26, stop flow, 5 s');
wObj.setValves(B12, 1);

wObj.setValves(A12, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


%% Step 27, STREPTAVIDINE Incubation

disp(sprintf('\n'));

disp(['Step 27, STREPTAVIDINE Incubation, ' num2str(Incubation) ' s']);

% Valve B3 off, Valves A3/A16/A17 on

disp(['Valve B12 off, Valves A12/A16/A17 on, ' num2str(Incubation) ' s']);

tic;

for s27 = 1:Incubation/30

wObj.setValves([A16 A17], zeros(0, 2));

pause(30);

end

toc;


%% Step 28, Washing Buffer (1x)

disp(sprintf('\n'));

disp('Step 28, Inj_on_WB');

% Valves B3 on, A3/A16/A17 off

disp(['Valves B9 on, A9/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s28 = 1:Inj_on/30

wObj.setValves(A9, 1);

wObj.setValves(B9, 0);

pause(30);

end

toc


%% Step 29 stop flow, 5 s
disp(sprintf('\n'));
disp('Step 29, stop flow, 5 s');
wObj.setValves(B9, 1);

wObj.setValves(A9, 0);


tic;
pause(5);
toc


%% Step 30, Biotinylated Antibody

disp(sprintf('\n'));

disp('Step 30, Inj_on_BiotAB');

% Valves B3 on, A3/A16/A17 off

disp([' Valves B4 on, A4/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s30 = 1:Inj_on/30

wObj.setValves(A4, 1);

wObj.setValves(B4, 0);

pause(30);

end

toc


%% Step 31, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 31, stop flow, 5 s');
wObj.setValves(B4, 1);

wObj.setValves(A4, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


%% Step 32, close Biotinylated antibody/start Incubation

disp(sprintf('\n'));

disp(['Step 32, close sampling/start Incubation, ' num2str(Incubation) ' s']);


tic;

for s32 = 1:Incubation/30

wObj.setValves([A16 A17], zeros(0, 2));

pause(30);

end

toc;


%% Step 33, Washing Buffer (1x)

disp(sprintf('\n'));

disp('Step 33, Inj_on_WB');

% Valves B9 on, A9/A16/A17 off

disp(['Valves B9 on, A9/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s1 = 1:Inj_on/30

wObj.setValves(A9, 1);

wObj.setValves(B9, 0);

pause(30);

end

toc


%% Step 34, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 30, stop flow, 5 s');
wObj.setValves(B9, 1);

wObj.setValves(A9, 0);


tic;
pause(5);
toc


%% Step 35, Ferricyanide flow, 420 s

disp(sprintf('\n'));

disp('Step 35, Inj_on_Fe');

% Valves B11 on, A11/A16/A17 off

disp([' Valves B11 on, A11/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s35 = 1:Inj_on/30

wObj.setValves(A11, 1);

wObj.setValves(B11, 0);

pause(30);

end

toc


%% Step 36, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 36, stop flow, 5 s');
wObj.setValves(B11, 1);

wObj.setValves(A11, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


%% Step 37, EC detection of BIOTINYLATED AB SIGNAL

disp(sprintf('\n'));

disp('Step 37, EC detection');


if ~libisloaded('libec660eNew2')

    loadlibrary('libec660eNew2.dll', 'labview.h')

end


%%Electrochemical Impedance spectroscopy
calllib('libec660eNew2', 'CHI_setTechnique', 14);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ei', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_fh', 100000); 
calllib('libec660eNew2', 'CHI_setParameter', 'm_fl', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_amp', 0.005);
calllib('libec660eNew2', 'CHI_setParameter', 'm_qt', 2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iImpmode', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1M', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl2',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl3',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl4',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl5',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1M',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP2',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP3',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP4',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP5',12);

% % 

%% EIS Measurement

calllib('libec660eNew2', 'CHI_runExperiment');

disp 'Waiting for experiment to end'

while calllib('libec660eNew2', 'CHI_experimentIsRunning')

	disp '...' % <- call CHI_getExperimentData() in real time

	pause(10);

	wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

end


%% Get Data

% % Clear All Previous Data First

clearvars Phase_imp Real_imp Imag_imp pPhase_imp pReal_imp pImag_imp pPhase_imp_value

clearvars pReal_imp_value pImag_imp_value YEAR MON DAY HOUR MIN SEC Imp_data


clearvars T Rct_Ab deltaRct

% %

n = 12*6;

Phase_imp = zeros(n, 1);

Real_imp = zeros(n, 1);

Imag_imp = zeros(n, 1);

pPhase_imp= libpointer('singlePtr', Phase_imp);

pReal_imp= libpointer('singlePtr', Real_imp);

pImag_imp= libpointer('singlePtr', Imag_imp);

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves



% %

calllib('libec660eNew2', 'CHI_getExperimentData_2channel', pPhase_imp, pReal_imp, pImag_imp, n)

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% %

pPhase_imp_value = pPhase_imp.value;

pReal_imp_value = pReal_imp.value;

pImag_imp_value = pImag_imp.value.*-1;


% %

figure(4);

plot(pReal_imp_value, pImag_imp_value,  'r-', 'LineWidth', 3)

xlabel('Z (Real)'); ylabel('Z (Imag)');

title('Albumin');

hold on;

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% % %

%% Save Data

Imp_data = cat(2, pPhase_imp_value, pReal_imp_value, pImag_imp_value);

[YEAR, MON, DAY, HOUR, MIN, SEC] = datevec(datestr(now));

filename_albumin_baseline_mat = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.mat'];

filename_albumin_baseline_txt = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.txt'];

filename_albumin_baseline_xls = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.xls'];

save(filename_albumin_baseline_mat, 'Imp_data');



%% Step 38, post detection

disp(sprintf('\n'));

disp(['Step 38, post detection, ' num2str(Stop_Flow) ' s']);


tic;

wObj.setValves([A16 A17], zeros(1, 2));

pause(Stop_Flow);

toc



%%%%%%% Step 39, PBS washing


disp(sprintf('\n'));

disp('Step 39, Inj_on_PBS');

% Valves B1 on, A1/A16/A17 off

disp(['Valves B1 on, A1/A16/A17 off, ' num2str(Inj_on_PBS) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s39 = 1:Inj_on/30

wObj.setValves(A1, 1);

wObj.setValves(B1, 0);

pause(30);

end

toc

%% Step 40, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 40, stop flow, 5 s');
wObj.setValves(B1, 1);

wObj.setValves(A1, 0);

tic;
pause(5);
toc


%% Step 41, Media Blocking

disp(sprintf('\n'));

disp('Step 41, Inj_on_media');

% Valves B5 on, A5/A16/A17 off

disp(['Valves B5 on, A5/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s41 = 1:Inj_on/30

wObj.setValves(A5, 1);

wObj.setValves(B5, 0);

pause(30);

end

toc


%% Step 42, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 42, stop flow, 5 s');
wObj.setValves(B5, 1);

wObj.setValves(A5, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


%% Step 43, media blocking /start Incubation

disp(sprintf('\n'));

disp([' Step 43, media blocking /start Incubation, ' num2str(Incubation) ' s']);


tic;

for s43 = 1:Incubation/30

wObj.setValves([A16 A17], zeros(1, 2));

pause(30);

end

toc;


%% Step 44, Washing Buffer (1x)

disp(sprintf('\n'));

disp('Step 44, Inj_on_WB');

% Valves B3 on, A3/A16/A17 off

disp(['Valves B9 on, A9/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s44 = 1:Inj_on/30

wObj.setValves(A9, 1);

wObj.setValves(B9, 0);

pause(30);

end

toc


%% Step 45, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 45, stop flow, 5 s');
wObj.setValves(B9, 1);

wObj.setValves(A9, 0);

tic;
pause(5);
toc


%% Step 46, Ferricyanide flow

disp(sprintf('\n'));

disp('Step 46, Inj_on_Fe');

% Valves B11 on, A11/A16/A17 off

disp(['Valves B11 on, A11/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s46 = 1:Inj_on/30

wObj.setValves(A11, 1);

wObj.setValves(B11, 0);

pause(30);

end

toc

%% Step 47, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 47, stop flow, 5 s');
wObj.setValves(B11, 1);

wObj.setValves(A11, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc




%% Step 48, EC detection

disp(sprintf('\n'));

disp('Step 9, EC detection');


% Call 'libec660eNew2.dll'

if ~libisloaded('libec660eNew2')

    loadlibrary('libec660eNew2.dll', 'labview.h')

end



%%Electrochemical Impedance spectroscopy
calllib('libec660eNew2', 'CHI_setTechnique', 14);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ei', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_fh', 100000); 
calllib('libec660eNew2', 'CHI_setParameter', 'm_fl', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_amp', 0.005);
calllib('libec660eNew2', 'CHI_setParameter', 'm_qt', 2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iImpmode', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1M', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl2',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl3',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl4',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl5',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1M',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP2',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP3',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP4',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP5',12);

% % 

%% EIS Measurement

calllib('libec660eNew2', 'CHI_runExperiment');

disp 'Waiting for experiment to end'

while calllib('libec660eNew2', 'CHI_experimentIsRunning')

	disp '...' % <- call CHI_getExperimentData() in real time

	pause(10);

	wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

end


%% Get Data

% % Clear All Previous Data First

clearvars Phase_imp Real_imp Imag_imp pPhase_imp pReal_imp pImag_imp pPhase_imp_value

clearvars pReal_imp_value pImag_imp_value YEAR MON DAY HOUR MIN SEC Imp_data

clearvars T Rct_Media

% %

n = 12*6;

Phase_imp = zeros(n, 1);

Real_imp = zeros(n, 1);

Imag_imp = zeros(n, 1);

pPhase_imp= libpointer('singlePtr', Phase_imp);

pReal_imp= libpointer('singlePtr', Real_imp);

pImag_imp= libpointer('singlePtr', Imag_imp);

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% %

% %

calllib('libec660eNew2', 'CHI_getExperimentData_2channel', pPhase_imp, pReal_imp, pImag_imp, n)

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% %

pPhase_imp_value = pPhase_imp.value;

pReal_imp_value = pReal_imp.value;

pImag_imp_value = pImag_imp.value.*-1;


% %

figure(4);

plot(pReal_imp_value, pImag_imp_value,  'g-', 'LineWidth', 3)

xlabel('Z (Real)'); ylabel('Z (Imag)');

title('Albumin');

hold on;

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% % %

%% Save Data

Imp_data = cat(2, pPhase_imp_value, pReal_imp_value, pImag_imp_value);

[YEAR, MON, DAY, HOUR, MIN, SEC] = datevec(datestr(now));

filename_albumin_baseline_mat = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.mat'];

filename_albumin_baseline_txt = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.txt'];

filename_albumin_baseline_xls = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.xls'];

save(filename_albumin_baseline_mat, 'Imp_data');


% %

%% Calculate deltaRct

Rct_Media = evaluation_Rct_sample(Imp_data);



%% Step 49, post detection

disp(sprintf('\n'));

disp(['Step 10, post detection, ' num2str(Stop_Flow) ' s']);


tic;

wObj.setValves([A16 A17], zeros(1, 2));

pause(Stop_Flow);

toc



%%%%%%% Step 50, PBS washing


disp(sprintf('\n'));

disp('Step 50, Inj_on_PBS');

% Valves B1 on, A1/A16/A17 off

disp(['Valves B1 on, A1/A16/A17 off, ' num2str(Inj_on_PBS) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s50 = 1:Inj_on/30

wObj.setValves(A1, 1);

wObj.setValves(B1, 0);

pause(30);

end

toc

%% Step 51, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 5, stop flow, 5 s');
wObj.setValves(B1, 1);

wObj.setValves(A1, 0);


tic;
pause(5);
toc


%% Step 52, Bioreactor sampling

disp(sprintf('\n'));

disp(['Step 52, Bioreactor sampling/Incubation, ' num2str(Inc_on_Sample) ' s']);


% Valve A7 off

disp(['Valve A7 off, ' num2str(Inj_on_Sample) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s50 = 1:Inj_on_Sample/30

wObj.setValves(A7, 1);

pause(30);

end

toc

%% Step 53, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 53, stop flow, 5 s');
% wObj.setValves(B6, 1);

wObj.setValves(A7, 0);

tic;
pause(5);
toc


%% Step 54, BIOREACTOR Incubation

disp(sprintf('\n'));

disp(['Step 54, Bioreactor Incubation, ' num2str(Incubation) ' s']);


% Valve B6 off, Valves A6/A7/A16/A17 on

disp(['Valves A16/A17 on, ' num2str(Incubation) ' s']);


tic;

for s54 = 1:Incubation/30

wObj.setValves([A16 A17], zeros(1, 2));

pause(30);

end

toc;



%% Step 55, Washing Buffer (1x)

disp(sprintf('\n'));

disp('Step 55, Inj_on_WB');

% Valves B3 on, A3/A16/A17 off

disp([' Valves B9 on, A9/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s55 = 1:Inj_on/30

wObj.setValves(A9, 1);

wObj.setValves(B9, 0);

pause(30);

end

toc


%% Step 56, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 56, stop flow, 5 s');
wObj.setValves(B9, 1);

wObj.setValves(A9, 0);

tic;
pause(5);
toc


%% Step 57, Ferricyanide flow

disp(sprintf('\n'));

disp('Step 57, Inj_on_Fe');

% Valves B1 on, A1/A16/A17 off

disp(['Valves B11 on, A11/A16/A17 off, ' num2str(Inj_on) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s57 = 1:Inj_on/30

wObj.setValves(A11, 1);

wObj.setValves(B11, 0);

pause(30);

end

toc


%% Step 58, stop flow, 5 s

disp(sprintf('\n'));
disp('Step 58, stop flow, 5 s');
wObj.setValves(B11, 1);

wObj.setValves(A11, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


%% Step 59, EC detection of antigen SIGNAL

disp(sprintf('\n'));

disp('Step 59, EC detection');


% Call 'libec660eNew2.dll'

if ~libisloaded('libec660eNew2')

    loadlibrary('libec660eNew2.dll', 'labview.h')

end



%%Electrochemical Impedance spectroscopy
calllib('libec660eNew2', 'CHI_setTechnique', 14);
calllib('libec660eNew2', 'CHI_setParameter', 'm_ei', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_fh', 100000); 
calllib('libec660eNew2', 'CHI_setParameter', 'm_fl', 0.1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_amp', 0.005);
calllib('libec660eNew2', 'CHI_setParameter', 'm_qt', 2);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iImpmode', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1M', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1K', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl100', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl10', 1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl1',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl2',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl3',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl4',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_impcl5',1);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1M',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1K',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP100',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP10',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP1',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP2',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP3',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP4',12);
calllib('libec660eNew2', 'CHI_setParameter', 'm_iP5',12);

% % 

% % 

% % 

%% EIS Measurement

calllib('libec660eNew2', 'CHI_runExperiment');

disp 'Waiting for experiment to end'

while calllib('libec660eNew2', 'CHI_experimentIsRunning')

	disp '...' % <- call CHI_getExperimentData() in real time

	pause(10);

	wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

end



%% Get Data

% % Clear All Previous Data First

clearvars Phase_imp Real_imp Imag_imp pPhase_imp pReal_imp pImag_imp pPhase_imp_value

clearvars pReal_imp_value pImag_imp_value YEAR MON DAY HOUR MIN SEC Imp_data


clearvars T Rct_sample

% %

n = 12*6;

Phase_imp = zeros(n, 1);

Real_imp = zeros(n, 1);

Imag_imp = zeros(n, 1);

pPhase_imp= libpointer('singlePtr', Phase_imp);

pReal_imp= libpointer('singlePtr', Real_imp);

pImag_imp= libpointer('singlePtr', Imag_imp);

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% %

% %

calllib('libec660eNew2', 'CHI_getExperimentData_2channel', pPhase_imp, pReal_imp, pImag_imp, n)

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% %

pPhase_imp_value = pPhase_imp.value;

pReal_imp_value = pReal_imp.value;

pImag_imp_value = pImag_imp.value.*-1;

% %

figure(4);

plot(pReal_imp_value, pImag_imp_value,  'b-', 'LineWidth', 3)

xlabel('Z (Real)'); ylabel('Z (Imag)');

title('Albumin');

hold off;

% %

wObj.setValves([A16 A17], zeros(1, 2)); % Keep communication with valves

% % %

%% Save Data

Imp_data = cat(2, pPhase_imp_value, pReal_imp_value, pImag_imp_value);

[YEAR, MON, DAY, HOUR, MIN, SEC] = datevec(datestr(now));

filename_albumin_baseline_mat = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.mat'];

filename_albumin_baseline_txt = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.txt'];

filename_albumin_baseline_xls = ['EC_Imp_Data_albumin_baseline_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.xls'];

save(filename_albumin_baseline_mat, 'Imp_data');

% %

%% Calculate deltaRct

Rct_sample = evaluation_Rct_sample(Imp_data);

NormalizedRct = Rct_sample/Rct_Media;


f5 = figure(5);

% set(f2, 'Name', 'Albumin');

set(f5, 'Position', [800 300 600 450]);

% deltaRct_time = Inj_on/3600*(i-1);

plot(ii, NormalizedRct, 'ko', 'LineWidth', 5);

% grid on;

xlabel('Regeneration');

ylabel('Normalized Rct');

hold on;

NormalizedRctArray_albumin(1, ii) = NormalizedRct;



%% Step 60, post detection

disp(sprintf('\n'));

disp(['Step 60, post detection, ' num2str(Stop_Flow) ' s']);


tic;

wObj.setValves([A16 A17], zeros(1, 2));

pause(Stop_Flow);

toc



%%%%%%% Step 61, PBS washing


disp(sprintf('\n'));

disp('Step 61, Inj_on_PBS');

% Valves B1 on, A1/A16/A17 off

disp(['Valves B1 on, A1/A16/A17 off, ' num2str(Inj_on_PBS) ' s']);

wObj.setValves([A16 A17], ones(1, 2));

tic;

for s63 = 1:Inj_on_PBS/30

wObj.setValves(A1, 1);

wObj.setValves(B1, 0);

pause(30);

end

toc


%% Step 62, stop flow, 5 s
disp(sprintf('\n'));
disp('Step 62, stop flow, 5 s');
wObj.setValves(B1, 1);

wObj.setValves(A1, 0);

wObj.setValves([A16 A17], zeros(1, 2));

tic;
pause(5);
toc


end

% save NormalizedRctArray_albumin;

filename_NormalizedRct_albumin_mat = ['EC_Imp_NormalizedRctArray_albumin_' num2str(YEAR) '_' num2str(MON) '_' num2str(DAY) '_' num2str(HOUR) '_' num2str(MIN) '_' num2str(SEC) '.mat'];
NormalizedRctArray_albumin = NormalizedRctArray_albumin';
save(filename_NormalizedRct_albumin_mat, 'NormalizedRctArray_albumin');


%% Close connection

wObj.close();

clear wObj;