def test_seed_initial_infections_most_people_low_risk():
npeople = 200
snapshot = Snapshot.zeros(nplaces, npeople, nslots)
# set all people as low risk
snapshot.area_codes = np.full(npeople, "E02004187") # low risk area code
snapshot.not_home_probs = np.full(npeople, 0.0)
# set 3 people to be high risk
snapshot.area_codes[1:4] = "E02004143" # high risk area code
snapshot.not_home_probs[1:4] = 0.8
num_seed_days = 5
simulator = Simulator(snapshot, gpu=False, num_seed_days=num_seed_days)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
# assert that no people are infected before seeding
assert not people_statuses_before.any()
# run one step with seeding and check number of infections
simulator.step_with_seeding()
people_statuses_after = np.zeros(snapshot.npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after)
# only high risk people will get infected (eg. in a high risk area code and with a high not_home_prob)
# so only the 3 high risk people should be infected by the seeding
expected_num_infections = 3
num_people_infected = np.count_nonzero(people_statuses_after)
assert num_people_infected == expected_num_infections
def test_generate_zeros_snapshot():
nplaces = 10
npeople = 100
nslots = 16
snapshot = Snapshot.zeros(nplaces=nplaces, npeople=npeople, nslots=nslots)
assert snapshot.buffers.place_activities.shape[0] == nplaces
assert snapshot.buffers.people_ages.shape[0] == npeople
assert snapshot.buffers.people_place_ids.shape[0] == npeople * nslots
assert snapshot.buffers.place_coords.shape[0] == nplaces * 2
# check all zeros
assert not snapshot.buffers.place_activities.any()
assert not snapshot.buffers.people_ages.any()
assert not snapshot.buffers.people_place_ids.any()
assert not snapshot.buffers.place_coords.any()
def test_seed_initial_infections_all_high_risk():
npeople = 200
snapshot = Snapshot.zeros(nplaces, npeople, nslots)
# set all people as high risk
snapshot.area_codes = np.full(npeople, "E02004143") # high risk area code
snapshot.not_home_probs = np.full(npeople, 0.8)
num_seed_days = 5
simulator = Simulator(snapshot, gpu=False, num_seed_days=num_seed_days)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
# assert that no people are infected before seeding
assert not people_statuses_before.any()
# run one step with seeding and check number of infections
simulator.step_with_seeding()
people_statuses_after = np.zeros(snapshot.npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after)
expected_num_infections = _get_cases(
1) # taken from devon_initial_cases.csv file
num_people_infected = np.count_nonzero(people_statuses_after)
assert num_people_infected == expected_num_infections
# run another step with seeding and check number of infections
simulator.step_with_seeding()
people_statuses_after = np.zeros(snapshot.npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after)
expected_num_infections += _get_cases(
2) # taken from devon_initial_cases.csv file
num_people_infected = np.count_nonzero(people_statuses_after)
assert num_people_infected == expected_num_infections