def make_population():
geography = Geography.from_file({"area": ["E00062194"]})
demography = Demography.for_geography(geography)
population = Population()
for area in geography.areas:
population.people += demography.populate(area.name)
return population
def make_dummy_world():
teacher = Person.from_attributes(age=100, sex="f")
pupil_shift_1 = Person.from_attributes(age=12, sex="f")
pupil_shift_2 = Person.from_attributes(age=5, sex="m")
pupil_shift_3 = Person.from_attributes(age=11, sex="f")
learning_center = LearningCenter(coordinates=None, n_pupils_max=None)
household = Household()
household.add(person=teacher)
household.add(person=pupil_shift_1)
household.add(person=pupil_shift_2)
household.add(person=pupil_shift_3)
learning_center.add(person=teacher,
shift=0,
subgroup_type=learning_center.SubgroupType.teachers)
learning_center.add(person=teacher,
shift=1,
subgroup_type=learning_center.SubgroupType.teachers)
learning_center.add(person=teacher,
shift=2,
subgroup_type=learning_center.SubgroupType.teachers)
learning_center.add(person=pupil_shift_1, shift=0)
learning_center.add(person=pupil_shift_2, shift=1)
learning_center.add(person=pupil_shift_3, shift=2)
world = World()
world.learning_centers = LearningCenters([learning_center],
learning_centers_tree=False,
n_shifts=3)
world.households = Households([household])
world.people = Population(
[teacher, pupil_shift_1, pupil_shift_2, pupil_shift_3])
for person in world.people.members:
person.busy = False
learning_center.clear()
household.clear()
return (
teacher,
pupil_shift_1,
pupil_shift_2,
pupil_shift_3,
learning_center,
household,
world,
)
def infect_super_areas(
self, n_cases_per_super_area: pd.DataFrame, record: Optional["Record"] = None
):
"""
Infect super areas with numer of cases given by data frame
Parameters
----------
n_cases_per_super_area:
data frame containig the number of cases per super area
"""
for super_area in self.world.super_areas:
try:
n_cases = int(n_cases_per_super_area[super_area.name])
self.unleash_virus(
Population(super_area.people), n_cases=n_cases, record=record
)
except KeyError as e:
raise KeyError("There is no data on cases for super area: %s" % str(e))
def _populate_areas(areas: Areas, demography):
people = Population()
for area in areas:
area.populate(demography)
people.extend(area.people)
return people
def make_pop():
people = Population([])
for i in range(100):
people.add(Person.from_attributes(age=i))
return people
def load_population_from_hdf5(file_path: str, chunk_size=100000):
"""
Loads the population from an hdf5 file located at ``file_path``.
Note that this object will not be ready to use, as the links to
object instances of other classes need to be restored first.
This function should be rarely be called oustide world.py
"""
print("loading population from hdf5 ", end="")
with h5py.File(file_path, "r", libver="latest", swmr=True) as f:
people = []
population = f["population"]
# read in chunks of 100k people
n_people = population.attrs["n_people"]
n_chunks = int(np.ceil(n_people / chunk_size))
for chunk in range(n_chunks):
print(".", end="")
idx1 = chunk * chunk_size
idx2 = min((chunk + 1) * chunk_size, n_people)
ids = population["id"][idx1:idx2]
ages = population["age"][idx1:idx2]
sexes = population["sex"][idx1:idx2]
ethns = population["ethnicity"][idx1:idx2]
socioecon_indices = population["socioecon_index"][idx1:idx2]
home_city = population["home_city"][idx1:idx2]
group_ids = population["group_ids"][idx1:idx2]
group_specs = population["group_specs"][idx1:idx2]
subgroup_types = population["subgroup_types"][idx1:idx2]
sectors = population["sector"][idx1:idx2]
sub_sectors = population["sub_sector"][idx1:idx2]
lockdown_status = population["lockdown_status"][idx1:idx2]
mode_of_transport_is_public_list = population[
"mode_of_transport_is_public"][idx1:idx2]
mode_of_transport_description_list = population[
"mode_of_transport_description"][idx1:idx2]
areas = population["area"][idx1:idx2]
for k in range(idx2 - idx1):
if ethns[k].decode() == " ":
ethnicity = None
else:
ethnicity = ethns[k].decode()
if socioecon_indices[k] == nan_integer:
socioecon_index = None
else:
socioecon_index = socioecon_indices[k]
person = Person.from_attributes(
id=ids[k],
age=ages[k],
sex=sexes[k].decode(),
ethnicity=ethnicity,
socioecon_index=socioecon_index,
)
mode_of_transport_description = mode_of_transport_description_list[
k]
mode_of_transport_is_public = mode_of_transport_is_public_list[
k]
# mode of transport
if mode_of_transport_description.decode() == " ":
person.mode_of_transport = None
else:
person.mode_of_transport = ModeOfTransport(
description=mode_of_transport_description.decode(),
is_public=mode_of_transport_is_public,
)
hc = home_city[k]
if hc == nan_integer:
person.home_city = None
else:
person.home_city = hc
subgroups = []
for group_id, subgroup_type, group_spec in zip(
group_ids[k], subgroup_types[k], group_specs[k]):
if group_id == nan_integer:
group_id = None
subgroup_type = None
group_spec = None
else:
group_spec = group_spec.decode()
subgroups.append([group_spec, group_id, subgroup_type])
person.subgroups = subgroups
person.area = areas[k]
if sectors[k].decode() == " ":
person.sector = None
else:
person.sector = sectors[k].decode()
if sub_sectors[k].decode() == " ":
person.sub_sector = None
else:
person.sub_sector = sub_sectors[k].decode()
if lockdown_status[k].decode() == " ":
person.lockdown_status = None
else:
person.lockdown_status = lockdown_status[k].decode()
people.append(person)
print("\n", end="")
return Population(people)
def make_dummy_world():
g = Geography.from_file(filter_key={"super_area": ["E02002559"]})
super_area = g.super_areas.members[0]
company = Company(super_area=super_area, n_workers_max=100, sector="Q")
school = School(
coordinates=super_area.coordinates,
n_pupils_max=100,
age_min=4,
age_max=10,
sector="primary",
)
household = Household()
household.area = super_area.areas[0]
hospital = Hospital(
n_beds=40,
n_icu_beds=5,
super_area=super_area.name,
coordinates=super_area.coordinates,
)
worker = Person.from_attributes(age=40)
worker.area = super_area
household.add(worker, subgroup_type=household.SubgroupType.adults)
worker.sector = "Q"
company.add(worker)
pupil = Person.from_attributes(age=6)
pupil.area = super_area
household.add(pupil, subgroup_type=household.SubgroupType.kids)
household.area = super_area
school.add(pupil)
student = Person.from_attributes(age=21)
student.area = super_area
household.add(student, subgroup_type=household.SubgroupType.adults)
university = University(
coordinates=super_area.coordinates,
n_students_max=100,
)
university.add(student)
commuter = Person.from_attributes(sex="m", age=30)
commuter.mode_of_transport = ModeOfTransport(description="bus",
is_public=True)
commuter.mode_of_transport = "public"
household.add(commuter)
world = World()
world.schools = Schools([school])
world.hospitals = Hospitals([hospital])
world.households = Households([household])
world.universities = Universities([])
world.companies = Companies([company])
world.universities = Universities([university])
world.care_homes = CareHomes([CareHome()])
world.people = Population([worker, pupil, student, commuter])
world.areas = Areas([super_area.areas[0]])
world.areas[0].people = world.people
world.super_areas = SuperAreas([super_area])
cinema = Cinema()
cinema.coordinates = super_area.coordinates
world.cinemas = Cinemas([cinema])
pub = Pub()
pub.coordinates = super_area.coordinates
world.pubs = Pubs([pub])
grocery = Grocery()
grocery.coordinates = super_area.coordinates
world.groceries = Groceries([grocery])
# commute
city = CommuteCity()
hub = CommuteHub(None, None)
city.commutehubs = [hub]
world.commutehubs = CommuteHubs([city])
world.commutehubs.members = [hub]
world.commutecities = CommuteCities()
world.commutecities.members = [city]
world.commutehubs[0].add(commuter)
world.commuteunits = CommuteUnits(world.commutehubs.members)
world.commuteunits.init_units()
world.commutecityunits = CommuteCityUnits(world.commutecities)
world.cemeteries = Cemeteries()
return world
def load_population_from_hdf5(file_path: str,
chunk_size=100000,
domain_super_areas=None):
"""
Loads the population from an hdf5 file located at ``file_path``.
Note that this object will not be ready to use, as the links to
object instances of other classes need to be restored first.
This function should be rarely be called oustide world.py
"""
people = []
logger.info("loading population...")
with h5py.File(file_path, "r", libver="latest", swmr=True) as f:
# people = []
population = f["population"]
# read in chunks of 100k people
n_people = population.attrs["n_people"]
n_chunks = int(np.ceil(n_people / chunk_size))
for chunk in range(n_chunks):
logger.info(f"Loaded chunk {chunk} of {n_chunks}")
idx1 = chunk * chunk_size
idx2 = min((chunk + 1) * chunk_size, n_people)
length = idx2 - idx1
ids = read_dataset(population["id"], idx1, idx2)
ages = read_dataset(population["age"], idx1, idx2)
sexes = read_dataset(population["sex"], idx1, idx2)
ethns = read_dataset(population["ethnicity"], idx1, idx2)
socioecon_indices = read_dataset(population["socioecon_index"],
idx1, idx2)
super_areas = read_dataset(population["super_area"], idx1, idx2)
sectors = read_dataset(population["sector"], idx1, idx2)
sub_sectors = read_dataset(population["sub_sector"], idx1, idx2)
lockdown_status = read_dataset(population["lockdown_status"], idx1,
idx2)
mode_of_transport_is_public_list = read_dataset(
population["mode_of_transport_is_public"], idx1, idx2)
mode_of_transport_description_list = read_dataset(
population["mode_of_transport_description"], idx1, idx2)
for k in range(idx2 - idx1):
if domain_super_areas is not None:
super_area = super_areas[k]
if super_area == nan_integer:
raise ValueError(
"if ``domain_super_areas`` is True, I expect not Nones super areas."
)
if super_area not in domain_super_areas:
continue
if ethns[k].decode() == " ":
ethn = None
else:
ethn = ethns[k].decode()
if socioecon_indices[k] == nan_integer:
socioecon_index = None
else:
socioecon_index = socioecon_indices[k]
person = Person.from_attributes(
id=ids[k],
age=ages[k],
sex=sexes[k].decode(),
ethnicity=ethn,
socioecon_index=socioecon_index,
)
people.append(person)
mode_of_transport_description = mode_of_transport_description_list[
k]
mode_of_transport_is_public = mode_of_transport_is_public_list[
k]
# mode of transport
if mode_of_transport_description.decode() == " ":
person.mode_of_transport = None
else:
person.mode_of_transport = ModeOfTransport(
description=mode_of_transport_description.decode(),
is_public=mode_of_transport_is_public,
)
if sectors[k].decode() == " ":
person.sector = None
else:
person.sector = sectors[k].decode()
if sub_sectors[k].decode() == " ":
person.sub_sector = None
else:
person.sub_sector = sub_sectors[k].decode()
if lockdown_status[k].decode() == " ":
person.lockdown_status = None
else:
person.lockdown_status = lockdown_status[k].decode()
return Population(people)
def make_dummy_world(geog):
super_area = geog.super_areas.members[0]
company = Company(super_area=super_area, n_workers_max=100, sector="Q")
household1 = Household()
household1.area = super_area.areas[0]
hospital = Hospital(
n_beds=40,
n_icu_beds=5,
super_area=super_area.name,
coordinates=super_area.coordinates,
)
uni = University(
coordinates=super_area.coordinates,
n_students_max=2500,
)
worker1 = Person.from_attributes(age=44,
sex='f',
ethnicity='A1',
socioecon_index=5)
worker1.area = super_area.areas[0]
household1.add(worker1, subgroup_type=household1.SubgroupType.adults)
worker1.sector = "Q"
company.add(worker1)
worker2 = Person.from_attributes(age=42,
sex='m',
ethnicity='B1',
socioecon_index=5)
worker2.area = super_area.areas[0]
household1.add(worker2, subgroup_type=household1.SubgroupType.adults)
worker2.sector = "Q"
company.add(worker2)
student1 = Person.from_attributes(age=20,
sex='f',
ethnicity='A1',
socioecon_index=5)
student1.area = super_area.areas[0]
household1.add(student1, subgroup_type=household1.SubgroupType.adults)
uni.add(student1)
pupil1 = Person.from_attributes(age=8,
sex='m',
ethnicity='C1',
socioecon_index=5)
pupil1.area = super_area.areas[0]
household1.add(pupil1, subgroup_type=household1.SubgroupType.kids)
#school.add(pupil1)
pupil2 = Person.from_attributes(age=5,
sex='f',
ethnicity='A1',
socioecon_index=5)
pupil2.area = super_area.areas[0]
household1.add(pupil2, subgroup_type=household1.SubgroupType.kids)
#school.add(pupil2)
world = World()
world.schools = Schools([])
world.hospitals = Hospitals([hospital])
world.households = Households([household1])
world.universities = Universities([uni])
world.companies = Companies([company])
world.people = Population([worker1, worker2, student1, pupil1, pupil2])
world.super_areas = geog.super_areas
world.areas = geog.areas
world.cemeteries = Cemeteries()
cinema = Cinema()
cinema.coordinates = super_area.coordinates
world.cinemas = Cinemas([cinema])
pub = Pub()
pub.coordinates = super_area.coordinates
world.pubs = Pubs([pub])
world.areas[0].people = world.people
return world