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