Generated Code

The following is matlab code generated by the CellML API from this CellML file. (Back to language selection)

The raw code is available.

function [VOI, STATES, ALGEBRAIC, CONSTANTS] = mainFunction()
    % This is the "main function".  In Matlab, things work best if you rename this function to match the filename.
   [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel();
end

function [algebraicVariableCount] = getAlgebraicVariableCount() 
    % Used later when setting a global variable with the number of algebraic variables.
    % Note: This is not the "main method".  
    algebraicVariableCount =12;
end
% There are a total of 1 entries in each of the rate and state variable arrays.
% There are a total of 11 entries in the constant variable array.
%

function [VOI, STATES, ALGEBRAIC, CONSTANTS] = solveModel()
    % Create ALGEBRAIC of correct size
    global algebraicVariableCount;  algebraicVariableCount = getAlgebraicVariableCount();
    % Initialise constants and state variables
    [INIT_STATES, CONSTANTS] = initConsts;

    % Set timespan to solve over 
    tspan = [0, 10];

    % Set numerical accuracy options for ODE solver
    options = odeset('RelTol', 1e-06, 'AbsTol', 1e-06, 'MaxStep', 1);

    % Solve model with ODE solver
    [VOI, STATES] = ode15s(@(VOI, STATES)computeRates(VOI, STATES, CONSTANTS), tspan, INIT_STATES, options);

    % Compute algebraic variables
    [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS);
    ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI);

    % Plot state variables against variable of integration
    [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends();
    figure();
    plot(VOI, STATES);
    xlabel(LEGEND_VOI);
    l = legend(LEGEND_STATES);
    set(l,'Interpreter','none');
end

function [LEGEND_STATES, LEGEND_ALGEBRAIC, LEGEND_VOI, LEGEND_CONSTANTS] = createLegends()
    LEGEND_STATES = ''; LEGEND_ALGEBRAIC = ''; LEGEND_VOI = ''; LEGEND_CONSTANTS = '';
    LEGEND_VOI = strpad('time in component environment (minute)');
    LEGEND_CONSTANTS(:,1) = strpad('VP in component red_cells_and_viscosity (litre)');
    LEGEND_STATES(:,1) = strpad('VRC in component RBC_volume (litre)');
    LEGEND_ALGEBRAIC(:,3) = strpad('HM in component hematocrit_fraction (dimensionless)');
    LEGEND_ALGEBRAIC(:,2) = strpad('HM1 in component hematocrit_fraction (dimensionless)');
    LEGEND_ALGEBRAIC(:,1) = strpad('VB in component hematocrit_fraction (litre)');
    LEGEND_ALGEBRAIC(:,4) = strpad('VIE in component viscosity_due_to_RBCs (dimensionless)');
    LEGEND_CONSTANTS(:,2) = strpad('HMK in component parameter_values (dimensionless)');
    LEGEND_CONSTANTS(:,3) = strpad('HKM in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,6) = strpad('VIM in component blood_viscosity (dimensionless)');
    LEGEND_ALGEBRAIC(:,5) = strpad('VIB in component blood_viscosity (dimensionless)');
    LEGEND_ALGEBRAIC(:,9) = strpad('HM7 in component oxygen_stimulation (mmHg)');
    LEGEND_CONSTANTS(:,4) = strpad('PO2AMB in component parameter_values (mmHg)');
    LEGEND_CONSTANTS(:,5) = strpad('HM6 in component parameter_values (mmHg)');
    LEGEND_CONSTANTS(:,10) = strpad('PO2AM1 in component oxygen_stimulation (mmHg)');
    LEGEND_ALGEBRAIC(:,7) = strpad('HM3 in component oxygen_stimulation (mmHg)');
    LEGEND_CONSTANTS(:,11) = strpad('HM4 in component oxygen_stimulation (mmHg)');
    LEGEND_ALGEBRAIC(:,8) = strpad('HM5 in component oxygen_stimulation (mmHg)');
    LEGEND_ALGEBRAIC(:,10) = strpad('RC1 in component RBC_production (L_per_minute)');
    LEGEND_CONSTANTS(:,6) = strpad('HM8 in component parameter_values (L_per_minute_per_mmHg)');
    LEGEND_CONSTANTS(:,7) = strpad('REK in component parameter_values (dimensionless)');
    LEGEND_ALGEBRAIC(:,11) = strpad('RC2 in component RBC_destruction (L_per_minute)');
    LEGEND_CONSTANTS(:,8) = strpad('RKC in component parameter_values (per_minute)');
    LEGEND_CONSTANTS(:,9) = strpad('TRRBC in component parameter_values (L_per_minute)');
    LEGEND_ALGEBRAIC(:,12) = strpad('RCD in component RBC_volume (L_per_minute)');
    LEGEND_RATES(:,1) = strpad('d/dt VRC in component RBC_volume (litre)');
    LEGEND_STATES  = LEGEND_STATES';
    LEGEND_ALGEBRAIC = LEGEND_ALGEBRAIC';
    LEGEND_RATES = LEGEND_RATES';
    LEGEND_CONSTANTS = LEGEND_CONSTANTS';
end

function [STATES, CONSTANTS] = initConsts()
    VOI = 0; CONSTANTS = []; STATES = []; ALGEBRAIC = [];
    CONSTANTS(:,1) = 3.00449;
    STATES(:,1) = 2.00439;
    CONSTANTS(:,2) = 90;
    CONSTANTS(:,3) = 0.53333;
    CONSTANTS(:,4) = 150;
    CONSTANTS(:,5) = 1850;
    CONSTANTS(:,6) = 4.714e-08;
    CONSTANTS(:,7) = 1;
    CONSTANTS(:,8) = 5.8e-06;
    CONSTANTS(:,9) = 0;
    CONSTANTS(:,10) = piecewise({CONSTANTS(:,4)>80.0000, 80.0000 }, CONSTANTS(:,4));
    CONSTANTS(:,11) = CONSTANTS(:,4) - 40.0000;
    if (isempty(STATES)), warning('Initial values for states not set');, end
end

function [RATES, ALGEBRAIC] = computeRates(VOI, STATES, CONSTANTS)
    global algebraicVariableCount;
    statesSize = size(STATES);
    statesColumnCount = statesSize(2);
    if ( statesColumnCount == 1)
        STATES = STATES';
        ALGEBRAIC = zeros(1, algebraicVariableCount);
        utilOnes = 1;
    else
        statesRowCount = statesSize(1);
        ALGEBRAIC = zeros(statesRowCount, algebraicVariableCount);
        RATES = zeros(statesRowCount, statesColumnCount);
        utilOnes = ones(statesRowCount, 1);
    end
    ALGEBRAIC(:,1) = CONSTANTS(:,1)+STATES(:,1);
    ALGEBRAIC(:,2) = STATES(:,1)./ALGEBRAIC(:,1);
    ALGEBRAIC(:,3) =  100.000.*ALGEBRAIC(:,2);
    ALGEBRAIC(:,7) =  (CONSTANTS(:,10) - 40.0000).*ALGEBRAIC(:,3);
    ALGEBRAIC(:,8) = piecewise({ALGEBRAIC(:,7)+CONSTANTS(:,11)<0.00000, 0.00000 }, ALGEBRAIC(:,7)+CONSTANTS(:,11));
    ALGEBRAIC(:,9) = CONSTANTS(:,5) - ALGEBRAIC(:,8);
    ALGEBRAIC(:,10) = piecewise({ ALGEBRAIC(:,9).*CONSTANTS(:,6).*CONSTANTS(:,7)+5.00000e-06<0.00000, 0.00000 },  ALGEBRAIC(:,9).*CONSTANTS(:,6).*CONSTANTS(:,7)+5.00000e-06);
    ALGEBRAIC(:,4) = ALGEBRAIC(:,3)./( (CONSTANTS(:,2) - ALGEBRAIC(:,3)).*CONSTANTS(:,3));
    ALGEBRAIC(:,5) = ALGEBRAIC(:,4)+1.50000;
    ALGEBRAIC(:,6) =  0.333300.*ALGEBRAIC(:,5);
    ALGEBRAIC(:,11) =  STATES(:,1).*CONSTANTS(:,8).*ALGEBRAIC(:,6);
    ALGEBRAIC(:,12) = (ALGEBRAIC(:,10) - ALGEBRAIC(:,11))+CONSTANTS(:,9);
    RATES(:,1) = ALGEBRAIC(:,12);
   RATES = RATES';
end

% Calculate algebraic variables
function ALGEBRAIC = computeAlgebraic(ALGEBRAIC, CONSTANTS, STATES, VOI)
    statesSize = size(STATES);
    statesColumnCount = statesSize(2);
    if ( statesColumnCount == 1)
        STATES = STATES';
        utilOnes = 1;
    else
        statesRowCount = statesSize(1);
        utilOnes = ones(statesRowCount, 1);
    end
    ALGEBRAIC(:,1) = CONSTANTS(:,1)+STATES(:,1);
    ALGEBRAIC(:,2) = STATES(:,1)./ALGEBRAIC(:,1);
    ALGEBRAIC(:,3) =  100.000.*ALGEBRAIC(:,2);
    ALGEBRAIC(:,7) =  (CONSTANTS(:,10) - 40.0000).*ALGEBRAIC(:,3);
    ALGEBRAIC(:,8) = piecewise({ALGEBRAIC(:,7)+CONSTANTS(:,11)<0.00000, 0.00000 }, ALGEBRAIC(:,7)+CONSTANTS(:,11));
    ALGEBRAIC(:,9) = CONSTANTS(:,5) - ALGEBRAIC(:,8);
    ALGEBRAIC(:,10) = piecewise({ ALGEBRAIC(:,9).*CONSTANTS(:,6).*CONSTANTS(:,7)+5.00000e-06<0.00000, 0.00000 },  ALGEBRAIC(:,9).*CONSTANTS(:,6).*CONSTANTS(:,7)+5.00000e-06);
    ALGEBRAIC(:,4) = ALGEBRAIC(:,3)./( (CONSTANTS(:,2) - ALGEBRAIC(:,3)).*CONSTANTS(:,3));
    ALGEBRAIC(:,5) = ALGEBRAIC(:,4)+1.50000;
    ALGEBRAIC(:,6) =  0.333300.*ALGEBRAIC(:,5);
    ALGEBRAIC(:,11) =  STATES(:,1).*CONSTANTS(:,8).*ALGEBRAIC(:,6);
    ALGEBRAIC(:,12) = (ALGEBRAIC(:,10) - ALGEBRAIC(:,11))+CONSTANTS(:,9);
end

% Compute result of a piecewise function
function x = piecewise(cases, default)
    set = [0];
    for i = 1:2:length(cases)
        if (length(cases{i+1}) == 1)
            x(cases{i} & ~set,:) = cases{i+1};
        else
            x(cases{i} & ~set,:) = cases{i+1}(cases{i} & ~set);
        end
        set = set | cases{i};
        if(set), break, end
    end
    if (length(default) == 1)
        x(~set,:) = default;
    else
        x(~set,:) = default(~set);
    end
end

% Pad out or shorten strings to a set length
function strout = strpad(strin)
    req_length = 160;
    insize = size(strin,2);
    if insize > req_length
        strout = strin(1:req_length);
    else
        strout = [strin, blanks(req_length - insize)];
    end
end