def __init__(
self,
input_param_file: str = None,
param_line_number: int = 1,
output_file_dir: str = "./",
input_households: Union[str, pd.DataFrame] = None,
read_param_file=True,
):
"""[summary]
Arguments:
object {[type]} -- [description]
Keyword Arguments:
input_param_file {str} -- [Parameters file path] (default: {None})
param_line_number {int} -- [Which column of the input param file to read] (default: 1)
output_file_dir {str} -- [Where to write output files to] (default: {"./"})
input_households {str} -- [Household demographics file (required)] (default: {None})
read_param_file {bool} -- [Read param file, all params can be set from python interface] (default: {True})
Raises:
ParameterException: [Warnings if parameters are not correctly set]
Sys.exit(0): [Underlaying C code will exist if params are not viable]
"""
self.c_params = covid19.parameters()
if input_param_file:
self.c_params.input_param_file = input_param_file
elif not input_param_file and read_param_file:
raise ParameterException(
"Input param path is None and read param file set to true")
else:
LOGGER.info(
"Have not passed input file for params, use set_param or set_param_dict"
)
if param_line_number:
self.c_params.param_line_number = int(param_line_number)
self.c_params.output_file_dir = output_file_dir
if isinstance(input_households, str):
self.c_params.input_household_file = input_households
self.household_df = None
elif isinstance(input_households, pd.DataFrame):
self.household_df = input_households
elif not input_households:
raise ParameterException(
"Household data must be supplied as a csv")
if read_param_file and input_param_file != None:
self._read_and_check_from_file()
if output_file_dir:
self.c_params.sys_write_individual = 1
self.update_lock = False
def __init__(
self,
input_param_file: str = None,
param_line_number: int = 1,
output_file_dir: str = "./",
input_households: Union[str, pd.DataFrame] = None,
hospital_input_param_file: str = None,
hospital_param_line_number: int = 1,
read_param_file=True,
read_hospital_param_file=False,
):
"""[summary]
Arguments:
object {[type]} -- [description]
Keyword Arguments:
input_param_file {str} -- [Parameters file path] (default: {None})
param_line_number {int} -- [Which column of the input param file to read] (default: 1)
output_file_dir {str} -- [Where to write output files to] (default: {"./"})
input_households {str} -- [Household demographics file (required)] (default: {None})
read_param_file {bool} -- [Read param file, all params can be set from python interface] (default: {True})
Raises:
ParameterException: [Warnings if parameters are not correctly set]
Sys.exit(0): [Underlaying C code will exist if params are not viable]
"""
self.c_params = covid19.parameters()
covid19.initialize_params( self.c_params );
# if no input_param_file is given use default
if not input_param_file :
input_param_file = pkg_resources.resource_filename('COVID19', 'default_params/baseline_parameters.csv')
if read_param_file :
self.c_params.input_param_file = input_param_file
else:
LOGGER.info( "Have not passed input file for params, use set_param or set_param_dict" )
if param_line_number:
self.c_params.param_line_number = int(param_line_number)
self.c_params.output_file_dir = output_file_dir
if isinstance(input_households, pd.DataFrame):
self.household_df = input_households
else :
if not input_households :
input_households = pkg_resources.resource_filename('COVID19', 'default_params/baseline_household_demographics.csv')
self.c_params.input_household_file = input_households
self.household_df = None
if hospital_param_line_number:
self.c_params.hospital_param_line_number = int(hospital_param_line_number)
# if no hospital_input_param_file is given use default
if not hospital_input_param_file :
hospital_input_param_file = pkg_resources.resource_filename('COVID19', 'default_params/hospital_baseline_parameters.csv')
if read_hospital_param_file:
self.c_params.hospital_input_param_file = hospital_input_param_file
else:
LOGGER.info("Have not passed hospital input file for params, use set_param or set_param_dict// crick todo look into this")
if read_hospital_param_file and hospital_input_param_file != None:
self._read_hospital_param_file()
if read_param_file and input_param_file != None:
self._read_and_check_from_file()
if output_file_dir:
self.c_params.sys_write_individual = 1
self.update_lock = False
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])
