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Merge branch 'feature/activity_vectorisation' into 'master'

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Activity vectorisation

See merge request cara/cara!179
This commit is contained in:
Philip James Elson 2021-05-25 09:26:36 +00:00
commit 97330e2316
3 changed files with 28 additions and 9 deletions
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4
cara/models.py
View file

@ -526,8 +526,8 @@ Expiration.types = {
@dataclass(frozen=True)
class Activity:
inhalation_rate: float
exhalation_rate: float
inhalation_rate: _VectorisedFloat
exhalation_rate: _VectorisedFloat
#: Pre-populated examples of activities.
types: typing.ClassVar[typing.Dict[str, "Activity"]]

27
cara/tests/models/test_exposure_model.py
View file

@ -46,20 +46,37 @@ populations = [
10, halftime, models.Mask(0.95, 0.15, np.array([0.3, 0.35])),
models.Activity.types['Standing'],
),
# A population with some array component for inhalation_rate.
models.Population(
10, halftime, models.Mask.types['Type I'],
models.Activity(np.array([0.51,0.57]), 0.57),
),
]
@pytest.mark.parametrize(
"population, cm, expected_exposure",[
[populations[1], KnownConcentrations(lambda t: 1.2), np.array([14.4, 14.4])],
[populations[0], KnownConcentrations(lambda t: np.array([1.2, 2.4])), np.array([14.4, 28.8])],
[populations[1], KnownConcentrations(lambda t: np.array([1.2, 2.4])), np.array([14.4, 28.8])],
"population, cm, expected_exposure, expected_probability",[
[populations[1], KnownConcentrations(lambda t: 1.2),
np.array([14.4, 14.4]), np.array([99.6803184113, 99.5181053773])],
[populations[2], KnownConcentrations(lambda t: 1.2),
np.array([14.4, 14.4]), np.array([99.4146994564, 99.6803184113])],
[populations[0], KnownConcentrations(lambda t: np.array([1.2, 2.4])),
np.array([14.4, 28.8]), np.array([99.6803184113, 99.9989780368])],
[populations[1], KnownConcentrations(lambda t: np.array([1.2, 2.4])),
np.array([14.4, 28.8]), np.array([99.6803184113, 99.9976777757])],
])
def test_exposure_model_ndarray(population, cm, expected_exposure):
def test_exposure_model_ndarray(population, cm,
expected_exposure, expected_probability):
model = ExposureModel(cm, population)
np.testing.assert_almost_equal(
model.quanta_exposure(), expected_exposure
)
np.testing.assert_almost_equal(
model.infection_probability(), expected_probability, decimal=10
)
assert isinstance(model.infection_probability(), np.ndarray)
assert isinstance(model.expected_new_cases(), np.ndarray)

6
cara/tests/test_infected_population.py
View file

@ -3,13 +3,14 @@ import pytest
import cara.models
@pytest.mark.parametrize(
"override_params", [
{'viral_load_in_sputum': np.array([5e8, 1e9])},
{'coefficient_of_infectivity': np.array([0.02, 0.05])},
{'η_exhale': np.array([0.92, 0.95])},
{'η_leaks': np.array([0.15, 0.20])},
{'exhalation_rate': np.array([0.75, 0.81])},
]
)
def test_infected_population_vectorisation(override_params):
@ -19,6 +20,7 @@ def test_infected_population_vectorisation(override_params):
'coefficient_of_infectivity': 0.02,
'η_exhale': 0.95,
'η_leaks': 0.15,
'exhalation_rate': 0.75,
}
defaults.update(override_params)
@ -33,7 +35,7 @@ def test_infected_population_vectorisation(override_params):
),
activity=cara.models.Activity(
0.51,
0.75,
defaults['exhalation_rate'],
),
virus=cara.models.Virus(
halflife=defaults['virus_halflife'],