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_seed_initial_infections_some_low_risk():
npeople = 200
snapshot = Snapshot.random(nplaces, npeople, nslots)
# set all people as high risk
snapshot.area_codes = np.full(npeople, "E02004187") # low risk area code
snapshot.area_codes[1:4] = "E02004143" # high risk area code
snapshot.not_home_probs = np.full(npeople, 0.0)
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)
expected_num_infections = 3 # taken from devon_initial_cases.csv file
num_people_infected = np.count_nonzero(people_statuses_after)
assert num_people_infected == expected_num_infections
def test_susceptible_become_infected():
snapshot = Snapshot.random(nplaces, npeople, nslots)
test_hazard = 0.4
people_hazards_test_data = np.full(npeople, test_hazard, dtype=np.float32)
people_statuses_test_data = np.full(npeople, DiseaseStatus.Susceptible.value, dtype=np.uint32)
people_transition_times_test_data = np.zeros(npeople, dtype=np.uint32)
snapshot.buffers.people_hazards[:] = people_hazards_test_data
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
assert np.array_equal(people_statuses_before, people_statuses_test_data)
simulator.step_kernel("people_update_statuses")
people_statuses_after = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after)
num_exposed = np.count_nonzero(people_statuses_after == DiseaseStatus.Exposed.value)
proportion_exposed = num_exposed / npeople
expected_proportion_infected = 1.0 - np.exp(-test_hazard)
assert np.isclose(expected_proportion_infected, proportion_exposed, atol=0.01)
def test_transmission_times_decremented():
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_transition_times_test_data = np.full(npeople, 3, dtype=np.uint32)
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
# check decremented after one step
simulator.step_kernel("people_update_statuses")
people_transmission_times_after = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_transition_times", people_transmission_times_after)
expected_people_transition_times = np.full(npeople, 2, dtype=np.uint32)
assert np.array_equal(expected_people_transition_times, people_transmission_times_after)
# check decremented after another step
simulator.step_kernel("people_update_statuses")
people_transmission_times_after = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_transition_times", people_transmission_times_after)
expected_people_transition_times = np.full(npeople, 1, dtype=np.uint32)
assert np.array_equal(expected_people_transition_times, people_transmission_times_after)
def test_diabetes_higher_mortality():
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_ages_test_data = np.full(npeople, 65, dtype=np.uint16)
people_statuses_test_data = np.full(npeople,
DiseaseStatus.Symptomatic.value,
dtype=np.uint32)
# set all people to diabetes=1
people_diabetes_test_data = np.ones(npeople, dtype=np.uint8)
people_transition_times_test_data = np.full(npeople, 1, dtype=np.uint32)
snapshot.buffers.people_ages[:] = people_ages_test_data
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.people_diabetes[:] = people_diabetes_test_data
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
params = Params()
diabetes_multiplier = 1.4
params.diabetes_multiplier = diabetes_multiplier
snapshot.update_params(params)
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
assert np.array_equal(people_statuses_before, people_statuses_test_data)
# run two timesteps so statuses should change
simulator.step_kernel("people_update_statuses")
simulator.step_kernel("people_update_statuses")
# assert that statuses change to either recovered or dead in the correct proportion
people_statuses_after_two_steps = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_two_steps)
num_recovered = np.count_nonzero(
people_statuses_after_two_steps == DiseaseStatus.Recovered.value)
proportion_recovered = num_recovered / npeople
num_dead = np.count_nonzero(
people_statuses_after_two_steps == DiseaseStatus.Dead.value)
proportion_dead = num_dead / npeople
# expected recovery probability for ages 60-70
expected_proportion_dead = 0.0193
expected_proportion_dead *= diabetes_multiplier
expected_proportion_recovered = 1 - expected_proportion_dead
assert np.isclose(expected_proportion_recovered,
proportion_recovered,
atol=0.01)
assert np.isclose(expected_proportion_dead, proportion_dead, atol=0.01)
def test_correct_send_hazard():
# Set up and upload the test data
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_place_ids = np.full((npeople, nslots),
sentinel_value,
dtype=np.uint32)
people_place_ids[0][0:4] = [0, 5, 7, 3]
people_place_ids[1][0:4] = [1, 5, 6, 4]
people_place_ids[2][0:4] = [2, 3, 7, 6]
people_flows = np.zeros((npeople, nslots), dtype=np.float32)
people_flows[0][0:4] = [0.8, 0.1, 0.06, 0.04]
people_flows[1][0:4] = [0.7, 0.18, 0.09, 0.03]
people_flows[2][0:4] = [0.6, 0.2, 0.16, 0.04]
people_statuses = np.full(npeople,
DiseaseStatus.Symptomatic.value,
dtype=np.uint32)
snapshot.buffers.people_flows[:] = people_flows.flatten()
snapshot.buffers.people_place_ids[:] = people_place_ids.flatten()
snapshot.buffers.people_statuses[:] = people_statuses
snapshot.buffers.place_activities[:] = np.random.randint(4,
size=nplaces,
dtype=np.uint32)
params = Params()
params.place_hazard_multipliers = np.ones(5, dtype=np.float32)
snapshot.update_params(params)
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
# Run the kernel
simulator.step_kernel("people_send_hazards")
# Download the result
place_hazards = np.zeros(nplaces, dtype=np.uint32)
simulator.download("place_hazards", place_hazards)
place_counts = np.zeros(nplaces, dtype=np.uint32)
simulator.download("place_counts", place_counts)
# Assert expected results
expected_place_hazards_floats = np.array(
[0.8, 0.7, 0.6, 0.24, 0.03, 0.28, 0.13, 0.22], dtype=np.float32)
expected_place_hazards = (fixed_factor *
expected_place_hazards_floats).astype(np.uint32)
expected_place_counts = np.array([1, 1, 1, 2, 1, 2, 2, 2], dtype=np.uint32)
assert np.allclose(expected_place_hazards, place_hazards)
assert np.array_equal(expected_place_counts, place_counts)
def test_places_are_reset_to_zero():
snapshot = Snapshot.random(nplaces, npeople, nslots)
hazards_test_data = np.array([4, 3, 5, 1, 6], dtype=np.uint32)
counts_test_data = np.array([1, 4, 8, 10, 2], dtype=np.uint32)
snapshot.buffers.place_hazards[:] = hazards_test_data
snapshot.buffers.place_counts[:] = counts_test_data
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
place_hazards_before = np.zeros(nplaces, dtype=np.uint32)
simulator.download("place_hazards", place_hazards_before)
place_counts_before = np.zeros(nplaces, dtype=np.uint32)
simulator.download("place_counts", place_counts_before)
assert np.array_equal(place_hazards_before, hazards_test_data)
assert np.array_equal(place_counts_before, counts_test_data)
simulator.step_kernel("places_reset")
# initialise host buffers randomly so we know they are filled to zeros
place_hazards_after = np.random.randint(0, 11, nplaces, dtype=np.uint32)
simulator.download("place_hazards", place_hazards_after)
place_counts_after = np.random.randint(0, 11, nplaces, dtype=np.uint32)
simulator.download("place_counts", place_counts_after)
assert np.array_equal(place_hazards_after,
np.zeros(nplaces, dtype=np.uint32))
assert np.array_equal(place_counts_after, np.zeros(nplaces,
dtype=np.uint32))
def test_symptomatic_become_recovered_or_dead_old_age():
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_ages_test_data = np.full(npeople, 92, dtype=np.uint16)
people_statuses_test_data = np.full(npeople,
DiseaseStatus.Symptomatic.value,
dtype=np.uint32)
people_transition_times_test_data = np.full(npeople, 1, dtype=np.uint32)
snapshot.buffers.people_ages[:] = people_ages_test_data
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
assert np.array_equal(people_statuses_before, people_statuses_test_data)
# run two timesteps so statuses should change
simulator.step_kernel("people_update_statuses")
simulator.step_kernel("people_update_statuses")
# assert that statuses change to either recovered or dead in the correct proportion
people_statuses_after_two_steps = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_two_steps)
num_recovered = np.count_nonzero(
people_statuses_after_two_steps == DiseaseStatus.Recovered.value)
proportion_recovered = num_recovered / npeople
num_dead = np.count_nonzero(
people_statuses_after_two_steps == DiseaseStatus.Dead.value)
proportion_dead = num_dead / npeople
# expected recovery probability for ages 80+
expected_proportion_dead = 0.1737
expected_proportion_recovered = 1 - expected_proportion_dead
assert np.isclose(expected_proportion_recovered,
proportion_recovered,
atol=0.01)
assert np.isclose(expected_proportion_dead, proportion_dead, atol=0.01)
def test_correct_send_hazard():
# Set up and upload the test data
snapshot = Snapshot.random(nplaces, npeople, nslots)
place_hazards_floats = np.array([0.2, 0.0, 0.5, 0.03, 0.0123, 0.22, 0.0001, 0.73], dtype=np.float32)
place_hazards = (fixed_factor * place_hazards_floats).astype(np.uint32)
people_place_ids = np.full((npeople, nslots), sentinel_value, dtype=np.uint32)
people_place_ids[0][0:4] = [1, 6, 0, 4]
people_place_ids[1][0:4] = [2, 6, 7, 5]
people_place_ids[2][0:4] = [3, 4, 0, 7]
people_flows = np.zeros((npeople, nslots), dtype=np.float32)
people_flows[0][0:4] = [0.6, 0.2, 0.16, 0.04]
people_flows[1][0:4] = [0.7, 0.18, 0.09, 0.03]
people_flows[2][0:4] = [0.8, 0.1, 0.06, 0.04]
people_statuses = np.full(npeople, DiseaseStatus.Susceptible.value, dtype=np.uint32)
people_statuses[0] = DiseaseStatus.Symptomatic.value
people_hazards = np.zeros(npeople, dtype=np.float32)
snapshot.buffers.people_flows[:] = people_flows.flatten()
snapshot.buffers.people_place_ids[:] = people_place_ids.flatten()
snapshot.buffers.people_statuses[:] = people_statuses
snapshot.buffers.place_hazards[:] = place_hazards
snapshot.buffers.people_hazards[:] = people_hazards
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
# Run the kernel
simulator.step_kernel("people_recv_hazards")
# Download the result
people_hazards = np.zeros(npeople, dtype=np.float32)
simulator.download("people_hazards", people_hazards)
# Assert expected results
expected_people_hazards = np.array([0.0, 0.422318, 0.06643], dtype=np.float32)
assert np.allclose(expected_people_hazards, people_hazards)
def test_all_asymptomatic_become_recovered():
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_statuses_test_data = np.full(npeople, DiseaseStatus.Asymptomatic.value, dtype=np.uint32)
people_transition_times_test_data = np.full(npeople, 1, dtype=np.uint32)
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
assert np.array_equal(people_statuses_before, people_statuses_test_data)
simulator.step_kernel("people_update_statuses")
# check that statuses don't change after one step
people_statuses_after_one_step = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_one_step)
assert np.array_equal(people_statuses_after_one_step, people_statuses_test_data)
# run another timestep, this time statuses should change
simulator.step_kernel("people_update_statuses")
# assert that all statuses change to presymptomatic after two timesteps
people_statuses_after_two_steps = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_two_steps)
assert np.all(people_statuses_after_two_steps == DiseaseStatus.Recovered.value)
def test_more_overweight_become_symptomatic():
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_statuses_test_data = np.full(npeople, DiseaseStatus.Exposed.value, dtype=np.uint32)
people_transition_times_test_data = np.full(npeople, 1, dtype=np.uint32)
# set all people to obesity=2, corresponding to overweight
people_obesity_test_data = np.full(npeople, 2, dtype=np.uint8)
people_transition_times_test_data = np.full(npeople, 1, dtype=np.uint32)
people_ages_test_data = np.full(npeople, 18, dtype=np.uint16)
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.people_obesity[:] = people_obesity_test_data
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
snapshot.buffers.people_ages[:] = people_ages_test_data
params = Params()
base_proportion_asymptomatic = 0.79
params.proportion_asymptomatic = base_proportion_asymptomatic
overweight_sympt_mplier = 1.46
params.overweight_sympt_mplier = overweight_sympt_mplier
snapshot.update_params(params)
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
assert np.array_equal(people_statuses_before, people_statuses_test_data)
simulator.step_kernel("people_update_statuses")
# check that statuses don't change after one step
people_statuses_after_one_step = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_one_step)
assert np.array_equal(people_statuses_after_one_step, people_statuses_test_data)
# run another timestep, this time statuses should change
simulator.step_kernel("people_update_statuses")
# assert that statuses change to either symptomatic or asymptomatic in the correct proportion
people_statuses_after_two_steps = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_two_steps)
num_asymptomatic = np.count_nonzero(people_statuses_after_two_steps == DiseaseStatus.Asymptomatic.value)
result_proportion_asymptomatic = num_asymptomatic / npeople
num_presymptomatic = np.count_nonzero(people_statuses_after_two_steps == DiseaseStatus.Presymptomatic.value)
result_proportion_presymptomatic = num_presymptomatic / npeople
base_proportion_symptomatic = 1 - base_proportion_asymptomatic
expected_proportion_presymptomatic = overweight_sympt_mplier * base_proportion_symptomatic
expected_proportion_asymptomatic = 1 - expected_proportion_presymptomatic
assert np.isclose(expected_proportion_asymptomatic, result_proportion_asymptomatic, atol=0.01)
assert np.isclose(expected_proportion_presymptomatic, result_proportion_presymptomatic, atol=0.01)
def test_symptomatic_become_recovered_or_dead_young_age():
# NB: run with more people since chance of young people dying is low
npeople = 500000
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_ages_test_data = np.full(npeople, 25, dtype=np.uint16)
people_statuses_test_data = np.full(npeople,
DiseaseStatus.Symptomatic.value,
dtype=np.uint32)
people_transition_times_test_data = np.full(npeople, 1, dtype=np.uint32)
snapshot.buffers.people_ages[:] = people_ages_test_data
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_statuses_before = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_before)
assert np.array_equal(people_statuses_before, people_statuses_test_data)
simulator.step_kernel("people_update_statuses")
# check that statuses don't change after one step
people_statuses_after_one_step = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_one_step)
assert np.array_equal(people_statuses_after_one_step,
people_statuses_test_data)
# run another timestep, this time statuses should change
simulator.step_kernel("people_update_statuses")
# assert that statuses change to either recovered or dead in the correct proportion
people_statuses_after_two_steps = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after_two_steps)
num_recovered = np.count_nonzero(
people_statuses_after_two_steps == DiseaseStatus.Recovered.value)
proportion_recovered = num_recovered / npeople
num_dead = np.count_nonzero(
people_statuses_after_two_steps == DiseaseStatus.Dead.value)
proportion_dead = num_dead / npeople
# expected recovery probability for ages 20 to 29
expected_proportion_dead = 0.0004
expected_proportion_recovered = 1 - expected_proportion_dead
assert np.isclose(expected_proportion_recovered,
proportion_recovered,
atol=0.0001)
assert np.isclose(expected_proportion_dead, proportion_dead, atol=0.0001)
def test_correct_flow_calculation_with_lockdown():
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_place_ids_test_data = np.full((npeople, nslots),
sentinel_value,
dtype=np.uint32)
people_place_ids_test_data[0][0:4] = [0, 5, 7, 3]
people_place_ids_test_data[1][0:4] = [1, 5, 6, 4]
people_place_ids_test_data[2][0:4] = [2, 3, 7, 6]
people_flows_test_data = np.zeros((npeople, nslots), dtype=np.float32)
people_flows_test_data[0][0:4] = [0.8, 0.1, 0.06, 0.04]
people_flows_test_data[1][0:4] = [0.7, 0.18, 0.09, 0.03]
people_flows_test_data[2][0:4] = [0.6, 0.2, 0.16, 0.04]
people_statuses_test_data = np.full(npeople,
DiseaseStatus.Susceptible.value,
dtype=np.uint32)
symptomatic_person_id = 1
people_statuses_test_data[symptomatic_person_id] = np.uint32(
DiseaseStatus.Symptomatic.value)
place_activities_test_data = np.full(nplaces,
Activity.Retail.value,
dtype=np.uint32)
place_activities_test_data[:3] = Activity.Home.value
snapshot.buffers.people_baseline_flows[:] = people_flows_test_data.flatten(
)
snapshot.buffers.people_flows[:] = people_flows_test_data.flatten()
snapshot.buffers.people_place_ids[:] = people_place_ids_test_data.flatten()
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.place_activities[:] = place_activities_test_data
params = Params()
params.set_lockdown_multiplier(lockdown_multipliers, 0)
params.symptomatic_multiplier = 0.5
snapshot.buffers.params[:] = params.asarray()
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_flows_before = np.zeros(npeople * nslots, dtype=np.float32)
simulator.download("people_flows", people_flows_before)
expected_people_flows_before = people_flows_test_data.flatten()
assert np.array_equal(people_flows_before, expected_people_flows_before)
simulator.step_kernel("people_update_flows")
people_flows_after = np.zeros(npeople * nslots, dtype=np.float32)
simulator.download("people_flows", people_flows_after)
assert not np.array_equal(people_flows_before, people_flows_after)
# assert correct flows for symptomatic person
expected_symptomatic_flows_after = np.array([0.85, 0.09, 0.045, 0.015])
symptomatic_person_start_idx = symptomatic_person_id * nslots
symptomatic_flows_after = people_flows_after[
symptomatic_person_start_idx:symptomatic_person_start_idx + 4]
assert np.allclose(expected_symptomatic_flows_after,
symptomatic_flows_after)
# assert correct flows for person who is not symptomatic
# adjustments calculated using first lockdown multiplier (approx. 0.9084687)
expected_non_symptomatic_flows_after = np.array(
[0.63661252, 0.18169374, 0.145354992, 0.036338748])
non_symptomatic_person_id = 2
person_start_idx = non_symptomatic_person_id * nslots
non_symptomatic_flows_after = people_flows_after[
person_start_idx:person_start_idx + 4]
assert np.allclose(expected_non_symptomatic_flows_after,
non_symptomatic_flows_after)
def test_correct_flow_calculation_no_lockdown():
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_place_ids_test_data = np.full((npeople, nslots),
sentinel_value,
dtype=np.uint32)
people_place_ids_test_data[0][0:4] = [0, 5, 7, 3]
people_place_ids_test_data[1][0:4] = [1, 5, 6, 4]
people_place_ids_test_data[2][0:4] = [2, 3, 7, 6]
people_flows_test_data = np.zeros((npeople, nslots), dtype=np.float32)
people_flows_test_data[0][0:4] = [0.8, 0.1, 0.06, 0.04]
people_flows_test_data[1][0:4] = [0.7, 0.18, 0.09, 0.03]
people_flows_test_data[2][0:4] = [0.6, 0.2, 0.16, 0.04]
people_statuses_test_data = np.full(npeople,
DiseaseStatus.Susceptible.value,
dtype=np.uint32)
symptomatic_person_id = 1
people_statuses_test_data[symptomatic_person_id] = np.uint32(
DiseaseStatus.Symptomatic.value)
place_activities_test_data = np.full(nplaces,
Activity.Retail.value,
dtype=np.uint32)
place_activities_test_data[:3] = Activity.Home.value
snapshot.buffers.people_baseline_flows[:] = people_flows_test_data.flatten(
)
snapshot.buffers.people_flows[:] = people_flows_test_data.flatten()
snapshot.buffers.people_place_ids[:] = people_place_ids_test_data.flatten()
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.place_activities[:] = place_activities_test_data
params = Params()
symptomatic_multiplier = 0.5
params.symptomatic_multiplier = symptomatic_multiplier
snapshot.update_params(params)
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
people_flows_before = np.zeros(npeople * nslots, dtype=np.float32)
simulator.download("people_flows", people_flows_before)
expected_people_flows_before = people_flows_test_data.flatten()
assert np.array_equal(people_flows_before, expected_people_flows_before)
simulator.step_kernel("people_update_flows")
people_flows_after = np.zeros(npeople * nslots, dtype=np.float32)
simulator.download("people_flows", people_flows_after)
# adjust symptomatic persons flows according to symptomatic multiplier
expected_people_flows_after = people_flows_test_data
expected_people_flows_after[symptomatic_person_id][0:4] = [
0.85, 0.09, 0.045, 0.015
]
expected_people_flows_after = expected_people_flows_after.flatten()
assert not np.array_equal(people_flows_before, people_flows_after)
assert np.array_equal(expected_people_flows_after, people_flows_after)
def test_asymptomatics_add_less_hazard():
# Set up and upload the test data
snapshot = Snapshot.random(nplaces, npeople, nslots)
people_place_ids = np.full((npeople, nslots),
sentinel_value,
dtype=np.uint32)
people_place_ids[0][0:4] = [0, 5, 7, 3]
people_place_ids[1][0:4] = [1, 5, 6, 4]
people_place_ids[2][0:4] = [2, 3, 7, 6]
people_flows = np.zeros((npeople, nslots), dtype=np.float32)
people_flows[0][0:4] = [0.8, 0.1, 0.06, 0.04]
people_flows[1][0:4] = [0.7, 0.18, 0.09, 0.03]
people_flows[2][0:4] = [0.6, 0.2, 0.16, 0.04]
people_statuses = np.full(npeople,
DiseaseStatus.Symptomatic.value,
dtype=np.uint32)
snapshot.buffers.people_flows[:] = people_flows.flatten()
snapshot.buffers.people_place_ids[:] = people_place_ids.flatten()
snapshot.buffers.people_statuses[:] = people_statuses
snapshot.buffers.place_activities[:] = np.random.randint(4,
size=nplaces,
dtype=np.uint32)
params = Params()
params.place_hazard_multipliers = np.ones(5, dtype=np.float32)
asymptomatic_multiplier = 0.5
params.individual_hazard_multipliers = np.array(
[1.0, asymptomatic_multiplier, 1.0])
snapshot.update_params(params)
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
# Run the kernel
simulator.step_kernel("people_send_hazards")
# Download the result
place_hazards = np.zeros(nplaces, dtype=np.uint32)
simulator.download("place_hazards", place_hazards)
place_counts = np.zeros(nplaces, dtype=np.uint32)
simulator.download("place_counts", place_counts)
# Assert expected results
expected_place_hazards_floats = np.array(
[0.8, 0.7, 0.6, 0.24, 0.03, 0.28, 0.13, 0.22], dtype=np.float32)
expected_place_hazards = (fixed_factor *
expected_place_hazards_floats).astype(np.uint32)
assert np.allclose(expected_place_hazards, place_hazards)
# Change statuses so all people are asymptomatic
people_statuses_asymptomatic = np.full(npeople,
DiseaseStatus.Asymptomatic.value,
dtype=np.uint32)
simulator.upload("people_statuses", people_statuses_asymptomatic)
# reset place hazards to zero
simulator.step_kernel("places_reset")
# run kernel with asymptomatic population
simulator.step_kernel("people_send_hazards")
# Download the result
place_hazards_asymptomatic = np.zeros(nplaces, dtype=np.uint32)
simulator.download("place_hazards", place_hazards_asymptomatic)
# Assert expected results
expected_place_hazards_floats_asymptomatic = expected_place_hazards_floats * asymptomatic_multiplier
expected_place_hazards_asymptomatic = (
fixed_factor * expected_place_hazards_floats_asymptomatic).astype(
np.uint32)
assert np.allclose(expected_place_hazards_asymptomatic,
place_hazards_asymptomatic)
assert place_hazards_asymptomatic.sum() < place_hazards.sum()
def run(self):
# If this is the first data assimilation window, we can just run the model as normal
if self.start_day == 0:
assert self.current_particle_pop_df is None # Shouldn't have any preivously-created particles
# load snapshot
snapshot = Snapshot.load_full_snapshot(path=self.snapshot_file)
# set params
snapshot.update_params(self.params)
# Can set the random seed to make it deterministic (None means np will choose one randomly)
snapshot.seed_prngs(seed=None)
# Create a simulator and upload the snapshot data to the OpenCL device
simulator = Simulator(snapshot,
opencl_dir=self.opencl_dir,
gpu=self.use_gpu)
simulator.upload_all(snapshot.buffers)
if not self.quiet:
# print(f"Running simulation {sim_number + 1}.")
print(f"Running simulation")
params = Params.fromarray(
snapshot.buffers.params
) # XX Why extract Params? Can't just use PARAMS?
summary = Summary(
snapshot,
store_detailed_counts=self.store_detailed_counts,
max_time=self.run_length # Total length of the simulation
)
# only show progress bar in quiet mode
timestep_iterator = range(self.run_length) if self.quiet \
else tqdm(range(self.quiet), desc="Running simulation")
iter_count = 0 # Count the total number of iterations
# Run for iterations days
for _ in timestep_iterator:
# Update parameters based on lockdown
params.set_lockdown_multiplier(snapshot.lockdown_multipliers,
iter_count)
simulator.upload("params", params.asarray())
# Step the simulator
simulator.step()
iter_count += 1
# Update the statuses
simulator.download("people_statuses",
snapshot.buffers.people_statuses)
summary.update(iter_count, snapshot.buffers.people_statuses)
if not self.quiet:
for i in range(self.run_length):
print(f"\nDay {i}")
summary.print_counts(i)
if not self.quiet:
print("\nFinished")
# Download the snapshot from OpenCL to host memory
# XX This is 'None'.
final_state = simulator.download_all(snapshot.buffers)
pass
else: # Otherwise we need to restart previous models stored in the current_particle_pop_df
# XXXX CAN GET OLD MODEL STATES, WITH ALL DISEASE STATUSES, FROM THE DF. TWO ISSUES
# 1. But need to work out how to draw these appropriately; can't assume they are each as good as
# each other. THIS SHOULD BE OK, surely there's a way to go from the final particles and weights
# to the DF of state vectors. Particle ID? Just try it out.
# 2. Also: what to do about stochasticity. For a given (global) parameter combination, we will
# get quite different results depending on the mode state. - I DON'T THINK THIS IS A PROBLEM.
# ABC Commonly used with stochastic models. E.g. https://eprints.lancs.ac.uk/id/eprint/80439/1/mainR1.pdf
#
raise Exception("Not implemented yet")
# Return the current state of the model in a dictionary describing what it is
#return {"simulator": simulator}
return {"simulator": snapshot}
def test_infection_transition_times_distribution(visualize=False):
npeople = 1000000
snapshot = Snapshot.random(nplaces, npeople, nslots)
test_hazard = 0.9
people_hazards_test_data = np.full(npeople, test_hazard, dtype=np.float32)
people_statuses_test_data = np.full(npeople, DiseaseStatus.Presymptomatic.value, dtype=np.uint32)
people_transition_times_test_data = np.zeros(npeople, dtype=np.uint32)
snapshot.buffers.people_hazards[:] = people_hazards_test_data
snapshot.buffers.people_statuses[:] = people_statuses_test_data
snapshot.buffers.people_transition_times[:] = people_transition_times_test_data
params = Params()
infection_log_scale = 0.75
infection_mode = 7.0
params.infection_log_scale = infection_log_scale
params.infection_mode = infection_mode
snapshot.update_params(params)
simulator = Simulator(snapshot, gpu=False)
simulator.upload_all(snapshot.buffers)
simulator.step_kernel("people_update_statuses")
people_statuses_after = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_statuses", people_statuses_after)
people_transition_times_after = np.zeros(npeople, dtype=np.uint32)
simulator.download("people_transition_times", people_transition_times_after)
# Check that transition times are distributed with a log-normal distribution
adjusted_transition_times = people_transition_times_after + 1
mean = adjusted_transition_times.mean()
std_dev = adjusted_transition_times.std()
mode = scipy.stats.mode(adjusted_transition_times)[0][0]
meanlog = infection_log_scale**2 + np.log(infection_mode)
expected_samples = np.random.lognormal(mean=meanlog, sigma=infection_log_scale, size=npeople)
# round samples to nearest integer
expected_samples = np.rint(expected_samples)
expected_mean = expected_samples.mean()
expected_std_dev = expected_samples.std()
expected_mode = scipy.stats.mode(expected_samples)[0][0]
# Float to integer rounding and clamping at zero makes the original random numbers hard
# to recover so we have slightly larger tolerances here to avoid false negatives.
assert np.isclose(expected_mean, mean, atol=0.7)
assert np.isclose(expected_std_dev, std_dev, atol=0.4)
assert np.isclose(expected_mode, mode, atol=1.0)
# check that mode is similar to original mode parameter
assert np.isclose(infection_mode, mode, atol=1.0)
if visualize: # show histogram of distribution
fig, ax = plt.subplots(1, 1)
ax.hist(adjusted_transition_times, bins=50, range=[0, 60])
plt.title("Result Samples")
plt.show()
fig, ax = plt.subplots(1, 1)
ax.hist(expected_samples, bins=50, range=[0, 60])
plt.title("Expected Samples")
plt.show()