%CREATED: JUNE 2009 by ARC
%This code is designed to calculate perfusion in the whole lung, with a symmetric large vessel structure.
%%-----------------------INPUT-------------------------
%The input to this function is inlet and outlet pressure (or one of these pressures and flow) for the system,

%%----------------------OUTPUT----------------------------
% This code outputs pressures and flow solutions in the each blood vessel, along with capillary transit time calculations.

function [P_A,P_V,FLOW_ACIN,GUESS_NEW,R_CAP_NEW,TT_CAP_NEW]=RUN_SYMM_PLUS_LADDER(Pin,Pout,Qin,Parameters,Flow)
Pin_all=Pin;
Pout_all=Pout;
Qinguess=Qin;

%Solution guesses
P_A=[Pin_all 100*(ones(1,Parameters.num_large_gen-1))];
P_V=[Pout_all 100*(ones(1,Parameters.num_large_gen-1))];
x=[Pin_all;Pout_all;Qinguess;Qinguess/2^Parameters.num_large_gen;Qinguess];

%artery  and vein lengths and radii
for i=1:Parameters.num_large_gen
    N=2^(i-1); %there is one branch in gen 1, 2 in gen 2 etc...
    D_A(i)=(N/exp(Parameters.A_A1))^(-1/Parameters.B_A1);
    D_V(i)=(N/exp(Parameters.A_V1))^(-1/Parameters.B_V1);
end
rad_A=D_A/2;rad_V=D_V/2;
for i=1:Parameters.num_large_gen
    L_A(i)=exp(Parameters.A_A2)*D_A(i)^Parameters.B_A2;
    L_V(i)=exp(Parameters.A_V2)*D_V(i)^Parameters.B_V2;
end 

%% Start of iterative loop
error=100;
iterations=0;
while (abs(error)>1e-6)&iterations<=100
RTOT_A=0;
RTOT_V=0;
iterations=iterations+1;
    if iterations==1
    else
        if Flow==1
         %% Flow Boundary conditions
         Pout_all=x(3);
         P_V(1)=Pout_all;
        elseif Flow==0
         %% Pressure Boundary conditions
         Qinguess=x(3);
        end
    end
    %artery resistances
    for i=1:Parameters.num_large_gen
        if (P_A(i)-Parameters.Ppl)<=Parameters.Pub_a_v
            radupdate(i)=rad_A(i)*(1+(P_A(i)-Parameters.Ppl)*Parameters.alpha_a);
        else
            radupdate(i)=rad_A(i)*(1+Parameters.Pub_a_v*Parameters.alpha_a);
        end
        R_Agen(i)=(8*Parameters.mu*L_A(i))/(pi*radupdate(i)^4);
        R_A=R_Agen(i)/2^(i-1);
        RTOT_A=RTOT_A+R_A;
        P_A(i+1)=Pin_all-Qinguess*RTOT_A;
    end
    Pin_acin=P_A(Parameters.num_large_gen+1);
    %vein resistances
    for i=1:Parameters.num_large_gen    
        if (P_V(i)-Parameters.Ppl)<=Parameters.Pub_a_v
            radupdate(i)=rad_V(i)*(1+(P_V(i)-Parameters.Ppl)*Parameters.alpha_v);
        else
            radupdate(i)=rad_V(i)*(1+Parameters.Pub_a_v*Parameters.alpha_v);
        end  
        R_Vgen(i)=(8*Parameters.mu*L_V(i))/(pi*radupdate(i)^4);
        R_V=R_Vgen(i)/2^(i-1);
        RTOT_V=RTOT_V+R_V;
        P_V(i+1)=Pout_all+Qinguess*RTOT_V;
    end
    Pout_acin=P_V(Parameters.num_large_gen+1);
    
    %CALCULATE ACINAR FLOW PROPERTIES
    [FLOW_ACIN,GUESS_NEW,R_CAP_NEW,TT_CAP_NEW]=RUN_LADDER(Pin_acin,Pout_acin,0,Parameters);
    R_ACIN=(Pin_acin-Pout_acin)/(FLOW_ACIN);

    if Flow==0
        matrix=[-1 0  -RTOT_A 0 0;
            1 -1 0 -R_ACIN 0;
            0 1 0 0 -RTOT_V;
            0 0 1 -1*2^(Parameters.num_large_gen-1) 0;
            0 0 1 0 -1];
            vector=[-Pin_all; 0; Pout_all; 0; 0];
    elseif Flow==1
        matrix=[-1 0 0 0 0;
            1 -1 0 -R_ACIN 0;
            0 1 -1 0 -RTOT_V;
            0 0 0 2^(Parameters.num_large_gen-1) 0;
            0 0 0 0 1];
        vector=[Qinguess*RTOT_A-Pin_all; 0;0; Qinguess;Qinguess]; 
    end
    %Solve system
    x2=matrix\vector;
    error=max(abs((x-x2)./(x2)));
    x=x2;
end
%% End iterative loop

%% OUTPUTTING SOME NICELY FORMATTED INFO ABOUT THE SYSTEM

[FLOW_ACIN,GUESS_NEW,R_CAP_NEW,TT_CAP_NEW]=RUN_LADDER(Pin_acin,Pout_acin,1,Parameters);

disp(sprintf('!!!FULL CIRCUIT SUMMARY!!!\n'))

if Flow==1
 disp(sprintf('Input: Flow = %g \n',Qin))
 disp(sprintf('Output: Pin = %g , Pout= %g\n', Pin_all, Pout_all))
else
 disp(sprintf('Input: Pin = %g , Pout= %g\n', Pin, Pout))
  disp(sprintf('Output: Flow = %g \n',Qinguess))
end
total_resistance1=(Pin_all-Pout_all)/x(5);%Pa.s /mm^3
total_resistance2=(Pin_all-Pout_all)*10^4/x(5);%dyne s /cm^5
disp(sprintf('Total resistance through the tree is  %g (Pa.s/mm^3).\n This is %g (dyne.s/cm^5).\n',total_resistance1,total_resistance2))


total_flow=60*x(5)/10^6; %l/min
disp(sprintf('Total flow through the system is %g (mm^3/s). \n This is %g (l/min).\n',x(5),total_flow))

percent_art_pressure_drop=(Pin_all-GUESS_NEW(4*Parameters.num_symm_gen-7))/(Pin_all-Pout_all)*100;
disp(sprintf('Percentage pressure drop across the arteries= %g \n',percent_art_pressure_drop))

percent_ac_pressure_drop=(P_A(Parameters.num_large_gen+1)-P_V(Parameters.num_large_gen+1))*100/(Pin_all-Pout_all);
disp(sprintf('Percentage pressure drop across the acinus= %g \n',percent_ac_pressure_drop))

disp(sprintf('!!!END FULL CIRCUIT SUMMARY!!!\n'))