Generated Code

# Size of variable arrays:
sizeAlgebraic = 3
sizeStates = 2
sizeConstants = 15
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 (week)"
    legend_algebraic[0] = "rem_time in component environment (week)"
    legend_algebraic[2] = "Exposure in component environment (mg)"
    legend_constants[0] = "Dose in component environment (mg)"
    legend_constants[1] = "Dose_Int1 in component environment (week)"
    legend_constants[2] = "Dose_Int2 in component environment (week)"
    legend_constants[3] = "Dose_Length in component environment (week)"
    legend_constants[4] = "Cycle_Int in component environment (week)"
    legend_constants[5] = "N_Cycle in component environment (dimensionless)"
    legend_constants[6] = "conversion_factor in component environment (sec_per_week)"
    legend_algebraic[1] = "Effect in component effect_compartment (dimensionless)"
    legend_states[0] = "Ce in component effect_compartment (mg)"
    legend_constants[7] = "E_max in component effect_compartment (dimensionless)"
    legend_constants[8] = "Amt_50 in component effect_compartment (mg)"
    legend_constants[12] = "k_1 in component effect_compartment (per_week)"
    legend_constants[9] = "t_half_eq in component effect_compartment (week)"
    legend_states[1] = "Size in component response_compartment (cm)"
    legend_constants[10] = "Size_0 in component response_compartment (cm)"
    legend_constants[14] = "RateIn in component response_compartment (per_week)"
    legend_constants[11] = "T_Turnover in component response_compartment (cm_week)"
    legend_constants[13] = "k_2 in component response_compartment (per_cm_per_week)"
    legend_rates[0] = "d/dt Ce in component effect_compartment (mg)"
    legend_rates[1] = "d/dt Size in component response_compartment (cm)"
    return (legend_states, legend_algebraic, legend_voi, legend_constants)

def initConsts():
    constants = [0.0] * sizeConstants; states = [0.0] * sizeStates;
    constants[0] = 5203.84
    constants[1] = 0
    constants[2] = 1
    constants[3] = 0.44359
    constants[4] = 3
    constants[5] = 6
    constants[6] = 604800
    states[0] = 0
    constants[7] = 1
    constants[8] = 10600
    constants[9] = 7.67
    states[1] = 6.66
    constants[10] = 6.66
    constants[11] = 21.8
    constants[12] = log(2.00000)/constants[9]
    constants[13] = log(2.00000)/constants[11]
    constants[14] = constants[10]*constants[13]
    return (states, constants)

def computeRates(voi, states, constants):
    rates = [0.0] * sizeStates; algebraic = [0.0] * sizeAlgebraic
    algebraic[1] = 1.00000-(constants[7]*states[0])/(constants[8]+states[0])
    rates[1] = (constants[14]*algebraic[1]-constants[13]*states[1])*states[1]
    algebraic[0] = ( voi*constants[6] % constants[4]*constants[6])/constants[6]
    algebraic[2] = custom_piecewise([less(voi , constants[4]*constants[5]) & less(constants[1] , algebraic[0]) & less(algebraic[0] , constants[3]), constants[0] , less(voi , constants[4]*constants[5]) & less(constants[2] , algebraic[0]) & less(algebraic[0] , constants[2]+constants[3]), constants[0] , True, 0.00000])
    rates[0] = algebraic[2]/1.00000-states[0]*constants[12]
    return(rates)

def computeAlgebraic(constants, states, voi):
    algebraic = array([[0.0] * len(voi)] * sizeAlgebraic)
    states = array(states)
    voi = array(voi)
    algebraic[1] = 1.00000-(constants[7]*states[0])/(constants[8]+states[0])
    algebraic[0] = ( voi*constants[6] % constants[4]*constants[6])/constants[6]
    algebraic[2] = custom_piecewise([less(voi , constants[4]*constants[5]) & less(constants[1] , algebraic[0]) & less(algebraic[0] , constants[3]), constants[0] , less(voi , constants[4]*constants[5]) & less(constants[2] , algebraic[0]) & less(algebraic[0] , constants[2]+constants[3]), constants[0] , True, 0.00000])
    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)