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 _create_stations(
self,
world: World,
city_stations_filename: str,
commuters_dict: dict,
maximum_number_commuters_per_city_station: int,
):
"""
Generates cities, super stations, and stations on the given world.
"""
with open(city_stations_filename) as f:
inter_city_stations_per_city = yaml.load(
f, Loader=yaml.FullLoader)["number_of_inter_city_stations"]
logger.info("Creating stations...")
world.stations = Stations([])
for city in world.cities:
if city.name not in inter_city_stations_per_city:
continue
else:
n_inter_city_stations = inter_city_stations_per_city[city.name]
city.inter_city_stations = Stations.from_city_center(
city=city,
super_areas=world.super_areas,
number_of_stations=n_inter_city_stations,
type="inter_city_station",
distance_to_city_center=10,
)
city.inter_city_stations._construct_ball_tree()
world.stations += city.inter_city_stations
n_internal_commuters = len(
commuters_dict[city.name]["internal"])
n_city_stations = int(
np.ceil(n_internal_commuters /
maximum_number_commuters_per_city_station))
city.city_stations = Stations.from_city_center(
city=city,
super_areas=world.super_areas,
number_of_stations=n_city_stations,
type="city_station",
distance_to_city_center=5,
)
city.city_stations._construct_ball_tree()
world.stations += city.city_stations
# initialise ball tree for stations in the city.
logger.info(
f"City {city.name} has {n_city_stations} city "
f"and {n_inter_city_stations} inter city stations.")
for super_area in world.super_areas:
for city in world.cities:
if city.has_stations:
super_area.closest_inter_city_station_for_city[
city.name] = city.get_closest_inter_city_station(
super_area.coordinates)
if (world.areas.members[i].people[j].age >= KIDS_LOW) and (world.areas.members[i].people[j].age <= KIDS_UP):
try:
school_coordinates = world.areas.members[i].people[j].school.coordinates
distance_school.append(
distance(world.areas.members[i].coordinates,
school_coordinates)
)
except:
lost_kids += 1
print(f'CAREFUL! There are {lost_kids} lost kids')
return distance_school
if __name__=='__main__':
world = World.from_pickle()
distance_school = kids_school_distance(world)
distance_young = kids_school_distance(world, 5, 11)
distance_old = kids_school_distance(world, 12, 19)
fig = plt.figure()
plt.hist(
distance_school,
log=True,
alpha=0.3,
label = '5 - 19 years old'
)
plt.hist(
distance_young,
log=True,
parser.add_argument(
"--config",
default="box_simulator.yaml",
help="path to config file to run",
type=str,
)
args = parser.parse_args()
# *********** INITIALIZE WORLD ***************** #
t1 = time.time()
geography = Geography.from_file(
{"msoa": ["E02003999"]}
)
world = World.from_geography(geography, box_mode=True)
t2 = time.time()
print(f"Creating the world took {t2 -t1} seconds to run.")
# *********** INITIALIZE SEED ***************** #
symptoms = SymptomsConstant(recovery_rate=0.05)
transmission = TransmissionConstant(probability=0.3)
infection = Infection(transmission, symptoms)
interaction = DefaultInteraction.from_file()
seed = Seed(world.boxes, infection, )
# Use if you want to seed the disease per region
# with real data
#seed.unleash_virus_per_region()
seed.unleash_virus(100, box_mode=True)
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 generate_world_from_hdf5(file_path: str, chunk_size=500000) -> World:
"""
Loads the world from an hdf5 file. All id references are substituted
by actual references to the relevant instances.
Parameters
----------
file_path
path of the hdf5 file
chunk_size
how many units of supergroups to process at a time.
It is advise to keep it around 1e6
"""
logger.info("loading world from HDF5")
world = World()
with h5py.File(file_path, "r", libver="latest", swmr=True) as f:
f_keys = list(f.keys()).copy()
geography = load_geography_from_hdf5(file_path=file_path,
chunk_size=chunk_size)
world.areas = geography.areas
world.super_areas = geography.super_areas
world.regions = geography.regions
if "hospitals" in f_keys:
logger.info("loading hospitals...")
world.hospitals = load_hospitals_from_hdf5(file_path=file_path,
chunk_size=chunk_size)
if "schools" in f_keys:
logger.info("loading schools...")
world.schools = load_schools_from_hdf5(file_path=file_path,
chunk_size=chunk_size)
if "companies" in f_keys:
world.companies = load_companies_from_hdf5(file_path=file_path,
chunk_size=chunk_size)
if "care_homes" in f_keys:
logger.info("loading care homes...")
world.care_homes = load_care_homes_from_hdf5(file_path=file_path,
chunk_size=chunk_size)
if "universities" in f_keys:
logger.info("loading universities...")
world.universities = load_universities_from_hdf5(file_path=file_path,
chunk_size=chunk_size)
if "cities" in f_keys:
logger.info("loading cities...")
world.cities = load_cities_from_hdf5(file_path)
if "stations" in f_keys:
logger.info("loading stations...")
(
world.stations,
world.inter_city_transports,
world.city_transports,
) = load_stations_from_hdf5(file_path)
if "households" in f_keys:
world.households = load_households_from_hdf5(file_path,
chunk_size=chunk_size)
if "population" in f_keys:
world.people = load_population_from_hdf5(file_path,
chunk_size=chunk_size)
if "social_venues" in f_keys:
logger.info("loading social venues...")
social_venues_dict = load_social_venues_from_hdf5(file_path)
for social_venues_spec, social_venues in social_venues_dict.items():
setattr(world, social_venues_spec, social_venues)
# restore world
logger.info("restoring world...")
restore_geography_properties_from_hdf5(world=world,
file_path=file_path,
chunk_size=chunk_size)
if "population" in f_keys:
restore_population_properties_from_hdf5(world=world,
file_path=file_path,
chunk_size=chunk_size)
if "households" in f_keys:
restore_households_properties_from_hdf5(world=world,
file_path=file_path,
chunk_size=chunk_size)
if "care_homes" in f_keys:
logger.info("restoring care homes...")
restore_care_homes_properties_from_hdf5(world=world,
file_path=file_path,
chunk_size=chunk_size)
if "hospitals" in f_keys:
logger.info("restoring hospitals...")
restore_hospital_properties_from_hdf5(world=world,
file_path=file_path,
chunk_size=chunk_size)
if "cities" and "stations" in f_keys:
logger.info("restoring commute...")
restore_cities_and_stations_properties_from_hdf5(world=world,
file_path=file_path,
chunk_size=chunk_size)
if "companies" in f_keys:
logger.info("restoring companies...")
restore_companies_properties_from_hdf5(
world=world,
file_path=file_path,
chunk_size=chunk_size,
)
if "schools" in f_keys:
logger.info("restoring schools...")
restore_school_properties_from_hdf5(
world=world,
file_path=file_path,
chunk_size=chunk_size,
)
if "universities" in f_keys:
logger.info("restoring unis...")
restore_universities_properties_from_hdf5(world=world,
file_path=file_path)
if "social_venues" in f_keys:
logger.info("restoring social venues...")
restore_social_venues_properties_from_hdf5(world=world,
file_path=file_path)
world.cemeteries = Cemeteries()
return world
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