import json
params = {
"Demographics_Filenames": [],
"Population_Scale_Type": "FIXED_SCALING",
"x_Base_Population": 1,
"Enable_Aging": 1,
"Age_Initialization_Distribution_Type": "DISTRIBUTION_SIMPLE",
"Enable_Demographics_Birth": 1,
"Enable_Demographics_Initial": 1,
"Enable_Demographics_Other": 0,
"Enable_Demographics_Reporting": 0,
"Enable_Demographics_Builtin": 0,
"Enable_Demographics_Risk": 0,
"Enable_Immunity_Initialization_Distribution": 0, # compatibility with EMOD v2.0 and earlier
"Susceptibility_Initialization_Distribution_Type": "DISTRIBUTION_OFF",
"Enable_Initial_Prevalence": 1,
"Enable_Vital_Dynamics": 1,
"Death_Rate_Dependence": "NONDISEASE_MORTALITY_BY_AGE_AND_GENDER",
"Enable_Birth": 1,
"Birth_Rate_Dependence": "POPULATION_DEP_RATE",
"Birth_Rate_Time_Dependence": "NONE",
"x_Birth": 1,
"Enable_Disease_Mortality": 0,
"Base_Mortality": 0,
"Mortality_Time_Course": "DAILY_MORTALITY",
"x_Other_Mortality": 1,
"Enable_Natural_Mortality": 1,
"Individual_Sampling_Type": "TRACK_ALL",
"Base_Individual_Sample_Rate": 1, # all parameters below are unused without sampling
"Max_Node_Population_Samples": 40,
"Sample_Rate_0_18mo": 1,
"Sample_Rate_10_14": 1,
"Sample_Rate_15_19": 1,
"Sample_Rate_18mo_4yr": 1,
"Sample_Rate_20_Plus": 1,
"Sample_Rate_5_9": 1,
"Sample_Rate_Birth": 2,
}
distribution_types = {
"CONSTANT_DISTRIBUTION": 0,
"UNIFORM_DISTRIBUTION": 1,
"GAUSSIAN_DISTRIBUTION": 2,
"EXPONENTIAL_DISTRIBUTION": 3,
"POISSON_DISTRIBUTION": 4,
"LOG_NORMAL": 5,
"BIMODAL_DISTRIBUTION": 6,
}
[docs]def set_risk_mod(filename, distribution, par1, par2):
"""
Set the ``RiskDistributionFlag``, ``RiskDistribution1`` and ``RiskDistribution2`` in a demographics file.
:param filename: The demographics file location
:param distribution: The selected distribution (need to come from ``distribution_types``)
:param par1: Parameter 1 of the distribution
:param par2: Parameter 2 of the distribution (may be unused depending on the selected distribution)
:return: Nothing
"""
set_demog_distributions(filename, [("Risk", distribution, par1, par2)])
[docs]def set_immune_mod(filename, distribution, par1, par2):
"""
Set the ``ImmunityDistributionFlag``, ``ImmunityDistribution1`` and ``ImmunityDistribution2`` in a demographics file.
:param filename: The demographics file location
:param distribution: The selected distribution (need to come from `distribution_types`)
:param par1: Parameter 1 of the distribution
:param par2: Parameter 2 of the distribution (may be unused depending on the selected distribution)
:return: Nothing
"""
set_demog_distributions(filename, [("Immunity", distribution, par1, par2)])
[docs]def apply_to_defaults_or_nodes(demog, fn, *args):
"""
Apply the ``fn`` function either to the ``Defaults`` dictionary or to each of the nodes depending
if the ``IndividualAttributes`` parameter is present in the ``Defaults`` or not.
.. todo::
This function should be refactored to look at both the ``Defaults`` and each individual nodes.
It will make sure that if a node override the default ``IndividualAttributes`` the change will still
be effective.
:param demog: The demographic file represented as a dictionary
:param fn: The function to apply the ``Defaults`` or individual nodes
:param args: Argument list needed by ``fn``
:return: Nothing
"""
if "Defaults" in demog and "IndividualAttributes" in demog["Defaults"]:
fn(demog["Defaults"], *args)
else:
for node in demog["Nodes"]:
fn(node, *args)
[docs]def set_demog_distributions(filename, distributions):
"""
Apply distributions to a given demographics file.
The distributions needs to be formatted as a list of (name, distribution, par1, par2) with:
* **name:** Immunity, Risk, Age, Prevalence or MigrationHeterogeneity
* **distribution:** One distribution contained in ``distribution_types``
* **par1, par2:** the values for the distribution parameters
.. code-block:: python
# Set the PrevalenceDistribution to a uniform distribution with 0.1 and 0.2
# and the ImmunityDistributionFlag to a constant distribution with 1
demog = json.load(open("demographics.json","r"))
distributions = list()
distributions.add(("Prevalence","UNIFORM_DISTRIBUTION",0.1,0.2))
distributions.add(("Immunity","CONSTANT_DISTRIBUTION",1,0))
set_demog_distribution(demog, distributions)
:param filename: the demographics file as json
:param distributions: the different distributions to set contained in a list
:return: Nothing
"""
with open(filename, "r") as demogjson_file:
demog = json.loads(demogjson_file.read())
def set_attributes(d, dist_type, par1, par2):
d["IndividualAttributes"].update(
{
dist_type + "DistributionFlag": distribution_types[distribution],
dist_type + "Distribution1": par1,
dist_type + "Distribution2": par2,
}
)
for (dist_type, distribution, par1, par2) in distributions:
if distribution not in distribution_types.keys():
raise Exception("Don't recognize distribution type %s" % distribution)
apply_to_defaults_or_nodes(demog, set_attributes, dist_type, par1, par2)
with open(filename, "w") as output_file:
output_file.write(json.dumps(demog, sort_keys=True, indent=4))
# the following two methods need a refactor
# we can have a single demographics file object and adjust attribute depending on usage
[docs]def set_static_demographics(cb, use_existing=False):
"""
Create a static demographics based on the demographics file specified in the config file
of the :py:class:`DTKConfigBuilder` object passed to the function.
This function takes the current demographics file and adjust the birth rate/death rate
to get a static population (the deaths are always compensated by new births).
.. todo::
Make sure that the population is 1000 individuals. For now rely on the fact that the base
demographics file will be 1000 Initial Population.
:param cb: The config builder object
:param use_existing: If ``True`` will only take the demographics file name and add the .static to it. If ``False`` will create a static demographics file based on the specified demographics file.
:return: Nothing
"""
demog_filenames = cb.get_param("Demographics_Filenames")
if len(demog_filenames) != 1:
raise Exception("Expecting only one demographics filename.")
demog_filename = demog_filenames[0]
static_demog_filename = demog_filename.replace("compiled.", "").replace(
".json", ".static.json", 1
)
cb.set_param("Demographics_Filenames", [static_demog_filename])
cb.set_param("Birth_Rate_Dependence", "FIXED_BIRTH_RATE")
if use_existing:
return
with open(demog_filename, "r") as demogjson_file:
demog = json.loads(demogjson_file.read())
birthrate = 0.12329
exponential_age_param = 0.000118
population_removal_rate = 45
mod_mortality = {
"NumDistributionAxes": 2,
"AxisNames": ["gender", "age"],
"AxisUnits": ["male=0,female=1", "years"],
"AxisScaleFactors": [1, 365],
"NumPopulationGroups": [2, 1],
"PopulationGroups": [[0, 1], [0]],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.74e-06,
"ResultValues": [[population_removal_rate], [population_removal_rate]],
}
def set_attributes(d):
if not "IndividualAttributes" in d:
d["IndividualAttributes"] = {}
d["IndividualAttributes"].update(
{
"MortalityDistribution": mod_mortality,
"AgeDistributionFlag": distribution_types["EXPONENTIAL_DISTRIBUTION"],
"AgeDistribution1": exponential_age_param,
}
)
d["NodeAttributes"].update({"BirthRate": birthrate})
apply_to_defaults_or_nodes(demog, set_attributes)
output_file_path = demog_filename.replace(".json", ".static.json", 1)
with open(output_file_path, "w") as output_file:
output_file.write(json.dumps(demog, sort_keys=True, indent=4))
[docs]def set_growing_demographics(cb, use_existing=False):
"""
This function creates a growing population. It works the same way as the :any:`set_static_demographics` but with
a birth rate more important than the death rate which leads to a growing population.
.. todo::
Make sure that the population is 1000 individuals. For now rely on the fact that the base
demographics file will be 1000 Initial Population.
:param cb: The :py:class:`DTKConfigBuilder <dtk.utils.core.DTKConfigBuilder>` object
:param use_existing: If ``True`` will only take the demographics file name and add the .growing to it. If ``False`` will create a growing demographics file based on the specified demographics file.
:return: Nothing
"""
demog_filenames = cb.get_param("Demographics_Filenames")
if len(demog_filenames) != 1:
raise Exception("Expecting only one demographics filename.")
demog_filename = demog_filenames[0]
growing_demog_filename = demog_filename.replace("compiled.", "").replace(
".json", ".growing.json", 1
)
cb.set_param("Demographics_Filenames", [growing_demog_filename])
cb.set_param("Birth_Rate_Dependence", "POPULATION_DEP_RATE")
if use_existing:
return
with open(demog_filename, "r") as demogjson_file:
demog = json.loads(demogjson_file.read())
birthrate = 0.0001
mod_mortality = {
"NumDistributionAxes": 2,
"AxisNames": ["gender", "age"],
"AxisUnits": ["male=0,female=1", "years"],
"AxisScaleFactors": [1, 365],
"NumPopulationGroups": [2, 5],
"PopulationGroups": [[0, 1], [0, 2, 10, 100, 2000]],
"ResultUnits": "annual deaths per 1000 individuals",
"ResultScaleFactor": 2.74e-06,
"ResultValues": [[60, 8, 2, 20, 400], [60, 8, 2, 20, 400]],
}
def set_attributes(d):
d["IndividualAttributes"].update({"MortalityDistribution": mod_mortality})
d["NodeAttributes"].update({"BirthRate": birthrate})
apply_to_defaults_or_nodes(demog, set_attributes)
output_file_path = demog_filename.replace(".json", ".growing.json", 1)
with open(output_file_path, "w") as output_file:
output_file.write(json.dumps(demog, sort_keys=True, indent=4))
