def create_c_array(array, ctype):
"""
Create a C version of a numpy array or Python list
array : list or numpy array
Array for which a C representation is wanted
Returns
-------
array_c :
C array to which the Python array is to be copied
"""
N = len(array)
if ctype == "double":
array_c = covid19.doubleArray(N)
elif ctype == "long":
array_c = covid19.longArray(N)
elif ctype == "int":
array_c = covid19.intArray(N)
else:
print("Error: unknown data type")
return
for i in range(N):
array_c[i] = array[i]
return (array_c)
def __init__(
self,
frac_0_9 = 0,
frac_10_19 = 0,
frac_20_29 = 0,
frac_30_39 = 0,
frac_40_49 = 0,
frac_50_59 = 0,
frac_60_69 = 0,
frac_70_79 = 0,
frac_80 = 0,
vaccine_type = 0,
efficacy = 1.0,
time_to_protect = 15,
vaccine_protection_period = 365
):
fraction_to_vaccinate = [
frac_0_9, frac_10_19, frac_20_29, frac_30_39, frac_40_49,
frac_50_59, frac_60_69, frac_70_79, frac_80,
]
self.c_fraction_to_vaccinate = covid19.doubleArray( len(AgeGroupEnum) )
for age in AgeGroupEnum:
self.c_fraction_to_vaccinate[ age.value ] = fraction_to_vaccinate[ age.value ]
self.vaccine_type = vaccine_type
self.efficacy = efficacy
self.time_to_protect = time_to_protect
self.vaccine_protection_period = vaccine_protection_period
self.c_total_vaccinated = covid19.longArray( len(AgeGroupEnum) )
for age in AgeGroupEnum:
self.c_total_vaccinated[ age.value ] = 0
def add_new_strain(self, transmission_multiplier, hospitalised_fraction = None ):
"""
Add a new strain, note the total number of strains that can be added is set by the initial
parameters max_n_strains
transmission_multiplier - the relative transmissibility of the new strain
hospitalised_fraction - the fraction of symptomatic (not mild) who progress to hospital [default: None is no change)
"""
n_strains = self.c_model.n_initialised_strains;
max_n_strains = self._params_obj.get_param("max_n_strains")
if n_strains == max_n_strains :
raise ModelException( f"cannot add any more strains - increase the parameter max_n_strains at the initialisation of the model" )
hospitalised_fraction_c = covid19.doubleArray( len(AgeGroupEnum) )
if hospitalised_fraction == None :
covid19.get_param_array_hospitalised_fraction(self.c_params, hospitalised_fraction_c)
else :
for idx in range( len(AgeGroupEnum ) ) :
hospitalised_fraction_c[ idx ] = hospitalised_fraction[ idx ]
idx = covid19.add_new_strain( self.c_model, transmission_multiplier, hospitalised_fraction_c );
return Strain( self, idx )
def __init__(
self,
frac_0_9 = 0,
frac_10_19 = 0,
frac_20_29 = 0,
frac_30_39 = 0,
frac_40_49 = 0,
frac_50_59 = 0,
frac_60_69 = 0,
frac_70_79 = 0,
frac_80 = 0,
vaccine = -1,
):
fraction_to_vaccinate = [
frac_0_9, frac_10_19, frac_20_29, frac_30_39, frac_40_49,
frac_50_59, frac_60_69, frac_70_79, frac_80,
]
self.c_fraction_to_vaccinate = covid19.doubleArray( len(AgeGroupEnum) )
for age in AgeGroupEnum:
self.c_fraction_to_vaccinate[ age.value ] = fraction_to_vaccinate[ age.value ]
if not isinstance( vaccine, Vaccine ) :
ModelException( "argument vaccine must be an object of type Vaccine, add one using model.add_vaccine()")
self.vaccine = vaccine
self.c_total_vaccinated = covid19.longArray( len(AgeGroupEnum) )
for age in AgeGroupEnum:
self.c_total_vaccinated[ age.value ] = 0
def test_gamma_rate_curve(self, N, mu, sigma, factor):
a, b = get_gamma_params(mu, sigma)
array_scipy = factor * np.diff(
gamma.cdf((np.arange(N + 1)), a, loc=0, scale=b))
array_c = covid19.doubleArray(N)
covid19.gamma_rate_curve(array_c, N, mu, sigma, factor)
array_c = c_array_as_python_list(array_c, N)
np.testing.assert_array_almost_equal(array_c, array_scipy, decimal=4)
def test_copy_array(self):
N = 100
array = np.random.uniform(1, N, N)
array_from = create_c_array(array, ctype="double")
array_to = covid19.doubleArray(N)
covid19.copy_array(array_to, array_from, N)
# Convert back to Python objects
array_from = c_array_as_python_list(array_from, N)
array_to = c_array_as_python_list(array_to, N)
np.testing.assert_array_equal(array_from, array_to)
def test_set_get_array_parameters(self):
"""
Test that an array parameter inside the C parameters structure can be changed
"""
params = covid19.parameters()
# Define arrays
get_age_types = covid19.doubleArray(covid19.N_AGE_TYPES)
set_age_types = covid19.doubleArray(covid19.N_AGE_TYPES)
for i in range(covid19.N_AGE_TYPES):
set_age_types[i] = uniform(FLOAT_START, FLOAT_END)
get_work_networks = covid19.doubleArray(covid19.N_DEFAULT_OCCUPATION_NETWORKS)
set_work_networks = covid19.doubleArray(covid19.N_DEFAULT_OCCUPATION_NETWORKS)
for i in range(covid19.N_DEFAULT_OCCUPATION_NETWORKS):
set_work_networks[i] = uniform(FLOAT_START, FLOAT_END)
get_interaction_types = covid19.doubleArray(covid19.N_INTERACTION_TYPES)
set_interaction_types = covid19.doubleArray(covid19.N_INTERACTION_TYPES)
for i in range(covid19.N_INTERACTION_TYPES):
set_interaction_types[i] = uniform(FLOAT_START, FLOAT_END)
get_age_groups = covid19.doubleArray(covid19.N_AGE_GROUPS)
set_age_groups = covid19.doubleArray(covid19.N_AGE_GROUPS)
for i in range(covid19.N_AGE_GROUPS):
set_age_groups[i] = uniform(FLOAT_START, FLOAT_END)
get_household_max = covid19.doubleArray(covid19.N_HOUSEHOLD_MAX)
set_household_max = covid19.doubleArray(covid19.N_HOUSEHOLD_MAX)
for i in range(covid19.N_HOUSEHOLD_MAX):
set_household_max[i] = uniform(FLOAT_START, FLOAT_END)
# Test set/get functions
covid19.set_param_array_mean_random_interactions(params, set_age_types)
covid19.get_param_array_mean_random_interactions(params, get_age_types)
for i in range(covid19.N_AGE_TYPES):
np.testing.assert_equal(set_age_types[i], get_age_types[i])
covid19.set_param_array_sd_random_interactions(params, set_age_types)
covid19.get_param_array_sd_random_interactions(params, get_age_types)
for i in range(covid19.N_AGE_TYPES):
np.testing.assert_equal(set_age_types[i], get_age_types[i])
covid19.set_param_array_mean_work_interactions(params, set_work_networks)
covid19.get_param_array_mean_work_interactions(params, get_work_networks)
for i in range(covid19.N_DEFAULT_OCCUPATION_NETWORKS):
np.testing.assert_equal(set_work_networks[i], get_work_networks[i])
covid19.set_param_array_relative_susceptibility(params, set_age_groups)
covid19.get_param_array_relative_susceptibility(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_adjusted_susceptibility(params, set_age_groups)
covid19.get_param_array_adjusted_susceptibility(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_relative_transmission(params, set_interaction_types)
covid19.get_param_array_relative_transmission(params, get_interaction_types)
for i in range(covid19.N_INTERACTION_TYPES):
np.testing.assert_equal(set_interaction_types[i], get_interaction_types[i])
covid19.set_param_array_hospitalised_fraction(params, set_age_groups)
covid19.get_param_array_hospitalised_fraction(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_critical_fraction(params, set_age_groups)
covid19.get_param_array_critical_fraction(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_fatality_fraction(params, set_age_groups)
covid19.get_param_array_fatality_fraction(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_household_size(params, set_household_max)
covid19.get_param_array_household_size(params, get_household_max)
for i in range(covid19.N_HOUSEHOLD_MAX):
np.testing.assert_equal(set_household_max[i], get_household_max[i])
covid19.set_param_array_population(params, set_age_groups)
covid19.get_param_array_population(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_fraction_asymptomatic(params, set_age_groups)
covid19.get_param_array_fraction_asymptomatic(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_mild_fraction(params, set_age_groups)
covid19.get_param_array_mild_fraction(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_location_death_icu(params, set_age_groups)
covid19.get_param_array_location_death_icu(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])
covid19.set_param_array_app_users_fraction(params, set_age_groups)
covid19.get_param_array_app_users_fraction(params, get_age_groups)
for i in range(covid19.N_AGE_GROUPS):
np.testing.assert_equal(set_age_groups[i], get_age_groups[i])