# 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 = 2 sizeStates = 7 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 (second)" legend_states[0] = "Ca_t in component equations (uM_per_kg)" legend_states[1] = "TnCa_t in component equations (uM_per_kg)" legend_states[2] = "CB_on_t in component equations (uM_per_kg)" legend_states[3] = "Ca_released in component equations (uM_per_kg)" legend_states[4] = "Ca_sequestered in component equations (uM_per_kg)" legend_states[5] = "cumCB_on_t in component equations (uM_per_kg)" legend_states[6] = "cumCB_off_t in component equations (uM_per_kg)" legend_algebraic[0] = "Ca_release_rate in component equations (uM_per_kg_per_second)" legend_algebraic[1] = "dTnCa_t_dt in component equations (uM_per_kg_per_second)" legend_constants[0] = "Ca_tot_released in component equations (uM_per_kg)" legend_constants[1] = "total_Tn in component equations (uM_per_kg)" legend_constants[2] = "total_CB in component equations (uM_per_kg)" legend_constants[3] = "k_1 in component equations (kg_per_uM_per_second)" legend_constants[4] = "k_2 in component equations (per_second)" legend_constants[5] = "k_3 in component equations (per_second)" legend_constants[6] = "f in component equations (kg_per_uM_per_second)" legend_constants[7] = "g in component equations (per_second)" legend_rates[0] = "d/dt Ca_t in component equations (uM_per_kg)" legend_rates[1] = "d/dt TnCa_t in component equations (uM_per_kg)" legend_rates[2] = "d/dt CB_on_t in component equations (uM_per_kg)" legend_rates[3] = "d/dt Ca_released in component equations (uM_per_kg)" legend_rates[4] = "d/dt Ca_sequestered in component equations (uM_per_kg)" legend_rates[5] = "d/dt cumCB_on_t in component equations (uM_per_kg)" legend_rates[6] = "d/dt cumCB_off_t in component equations (uM_per_kg)" return (legend_states, legend_algebraic, legend_voi, legend_constants) def initConsts(): constants = [0.0] * sizeConstants; states = [0.0] * sizeStates; states[0] = 0 states[1] = 0 states[2] = 0 states[3] = 0 states[4] = 0 states[5] = 0 states[6] = 0 constants[0] = 35 constants[1] = 70 constants[2] = 150 constants[3] = 5e6 constants[4] = 10 constants[5] = 1000 constants[6] = 0.4e6 constants[7] = 10 return (states, constants) def computeRates(voi, states, constants): rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic rates[1] = constants[3]*states[0]*(constants[1]-states[1])-constants[4]*states[1] rates[2] = constants[6]*states[1]*(constants[2]-states[2])-constants[7]*states[2] rates[4] = constants[5]*states[0] rates[5] = constants[6]*states[1]*(constants[2]-states[2]) rates[6] = constants[7]*states[2] algebraic[0] = custom_piecewise([greater(voi , 0.100000), 0.00000 , True, 20.0000*constants[0]*(1.00000-10.0000*voi)]) rates[3] = algebraic[0] algebraic[1] = constants[3]*states[0]*(constants[1]-states[1])-constants[4]*states[1] rates[0] = (algebraic[0]-constants[5]*states[0])-algebraic[1] return(rates) def computeAlgebraic(constants, states, voi): algebraic = array([[0.0] * len(voi)] * sizeAlgebraic) states = array(states) voi = array(voi) algebraic[0] = custom_piecewise([greater(voi , 0.100000), 0.00000 , True, 20.0000*constants[0]*(1.00000-10.0000*voi)]) algebraic[1] = constants[3]*states[0]*(constants[1]-states[1])-constants[4]*states[1] 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)