# Generated Code

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

The raw code is available.

# Size of variable arrays: sizeAlgebraic = 13 sizeStates = 2 sizeConstants = 8 from math import * from numpy import * def createLegends(): legend_states = [""] * sizeStates legend_rates = [""] * sizeStates legend_algebraic = [""] * sizeAlgebraic legend_voi = "" legend_constants = [""] * sizeConstants legend_voi = "time in component environment (minute)" legend_constants[0] = "PPC in component pulmonary_fluid_dynamics (mmHg)" legend_constants[1] = "PPA in component pulmonary_fluid_dynamics (mmHg)" legend_constants[2] = "PLA in component pulmonary_fluid_dynamics (mmHg)" legend_constants[3] = "CPP in component pulmonary_fluid_dynamics (gram_per_L)" legend_constants[4] = "RPV in component pulmonary_fluid_dynamics (mmHg_minute_per_L)" legend_constants[5] = "RPA in component pulmonary_fluid_dynamics (mmHg_minute_per_L)" legend_constants[7] = "PCP in component pulmonary_capillary_pressure (mmHg)" legend_algebraic[4] = "POS in component colloid_osmotic_pressure_of_pulmonary_interstitium (mmHg)" legend_algebraic[1] = "PPI in component pulmonary_interstitial_fluid_pressure (mmHg)" legend_algebraic[5] = "PFI in component fluid_filtration_into_pulmonary_interstitium (L_per_minute)" legend_constants[6] = "CPF in component parameter_values (L_per_minute_per_mmHg)" legend_algebraic[7] = "PLF in component lung_lymphatic_protein_flow (L_per_minute)" legend_algebraic[10] = "DFP in component pulmonary_interstitial_free_fluid_volume (L_per_minute)" legend_algebraic[0] = "VPF in component pulmonary_interstitial_free_fluid_volume (litre)" legend_algebraic[8] = "DFZ in component pulmonary_interstitial_free_fluid_volume (L_per_minute)" legend_states[0] = "VPF1 in component pulmonary_interstitial_free_fluid_volume (litre)" legend_algebraic[9] = "PPO in component lung_lymphatic_protein_flow (gram_per_minute)" legend_algebraic[6] = "PPN in component protein_leakage_into_pulmonary_interstitium (gram_per_minute)" legend_algebraic[12] = "PPD in component concentration_of_protein_in_pulmonary_interstitium (gram_per_minute)" legend_algebraic[3] = "CPN in component concentration_of_protein_in_pulmonary_interstitium (gram_per_L)" legend_algebraic[11] = "PPZ in component concentration_of_protein_in_pulmonary_interstitium (gram_per_minute)" legend_states[1] = "PPR1 in component concentration_of_protein_in_pulmonary_interstitium (gram)" legend_algebraic[2] = "PPR in component concentration_of_protein_in_pulmonary_interstitium (gram)" legend_rates[0] = "d/dt VPF1 in component pulmonary_interstitial_free_fluid_volume (litre)" legend_rates[1] = "d/dt PPR1 in component concentration_of_protein_in_pulmonary_interstitium (gram)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; constants[0] = 29.9941 constants[1] = 15.6376 constants[2] = 2 constants[3] = 71.9719 constants[4] = 1.55719 constants[5] = 1.5683 constants[6] = 0.0003 states[0] = 0.0123238 states[1] = 0.419998 constants[7] = ((constants[1]-constants[2])*constants[4])/(constants[4]+constants[5])+constants[2] return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic algebraic[0] = custom_piecewise([less(states[0] , 0.00100000), 0.00100000 , True, states[0]]) algebraic[2] = custom_piecewise([less(states[1] , 0.0250000), 0.0250000 , True, states[1]]) algebraic[3] = algebraic[2]/algebraic[0] algebraic[4] = algebraic[3]*0.400000 algebraic[1] = 2.00000-0.150000/algebraic[0] algebraic[5] = (((constants[7]-algebraic[1])+algebraic[4])-constants[0])*constants[6] algebraic[7] = (algebraic[1]+11.0000)*0.000300000 algebraic[8] = algebraic[5]-algebraic[7] algebraic[10] = algebraic[8] rates[0] = algebraic[10] algebraic[9] = algebraic[7]*algebraic[3] algebraic[6] = (constants[3]-algebraic[3])*0.000225000 algebraic[11] = algebraic[6]-algebraic[9] algebraic[12] = algebraic[11] rates[1] = algebraic[12] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([less(states[0] , 0.00100000), 0.00100000 , True, states[0]]) algebraic[2] = custom_piecewise([less(states[1] , 0.0250000), 0.0250000 , True, states[1]]) algebraic[3] = algebraic[2]/algebraic[0] algebraic[4] = algebraic[3]*0.400000 algebraic[1] = 2.00000-0.150000/algebraic[0] algebraic[5] = (((constants[7]-algebraic[1])+algebraic[4])-constants[0])*constants[6] algebraic[7] = (algebraic[1]+11.0000)*0.000300000 algebraic[8] = algebraic[5]-algebraic[7] algebraic[10] = algebraic[8] algebraic[9] = algebraic[7]*algebraic[3] algebraic[6] = (constants[3]-algebraic[3])*0.000225000 algebraic[11] = algebraic[6]-algebraic[9] algebraic[12] = algebraic[11] return algebraic def custom_piecewise(cases): """Compute result of a piecewise function""" return select(cases[0::2],cases[1::2]) def solve_model(): """Solve model with ODE solver""" from scipy.integrate import ode # Initialise constants and state variables (init_states, constants) = initConsts() # Set timespan to solve over voi = linspace(0, 10, 500) # Construct ODE object to solve r = ode(computeRates) r.set_integrator('vode', method='bdf', atol=1e-06, rtol=1e-06, max_step=1) r.set_initial_value(init_states, voi[0]) r.set_f_params(constants) # Solve model states = array([[0.0] * len(voi)] * sizeStates) states[:,0] = init_states for (i,t) in enumerate(voi[1:]): if r.successful(): r.integrate(t) states[:,i+1] = r.y else: break # Compute algebraic variables algebraic = computeAlgebraic(constants, states, voi) return (voi, states, algebraic) def plot_model(voi, states, algebraic): """Plot variables against variable of integration""" import pylab (legend_states, legend_algebraic, legend_voi, legend_constants) = createLegends() pylab.figure(1) pylab.plot(voi,vstack((states,algebraic)).T) pylab.xlabel(legend_voi) pylab.legend(legend_states + legend_algebraic, loc='best') pylab.show() if __name__ == "__main__": (voi, states, algebraic) = solve_model() plot_model(voi, states, algebraic)