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all times in front approach for the cumulative dose

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This commit is contained in:
Luis Aleixo 2021-09-15 11:26:45 +02:00
parent b6ecca5a62
commit 4388de9ed1
2 changed files with 24 additions and 37 deletions
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10
cara/apps/calculator/report_generator.py
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@ -110,15 +110,15 @@ def calculate_report_data(model: models.ExposureModel):
er = np.array(model.concentration_model.infected.emission_rate_when_present()).mean()
exposed_occupants = model.exposed.number
expected_new_cases = np.array(model.expected_new_cases()).mean()
cumulative_doses = [
np.array(model.inhaled_exposure_between_bounds(float(time))).mean()
for time in times
]
cumulative_doses = np.cumsum([
np.array(model.exposure_between_bounds(float(time1), float(time2))).mean()
for time1, time2 in zip(times[:-1], times[1:])
])
return {
"times": list(times),
"exposed_presence_intervals": [list(interval) for interval in model.exposed.presence.boundaries()],
"cumulative_doses": cumulative_doses,
"cumulative_doses": list(cumulative_doses),
"concentrations": concentrations,
"highest_const": highest_const,
"prob_inf": prob,

51
cara/models.py
View file

@ -877,50 +877,37 @@ class ExposureModel:
#: The fraction of viruses actually deposited in the respiratory tract
fraction_deposited: _VectorisedFloat = 0.6
def exposure_between_bounds(self, time: float) -> _VectorisedFloat:
"""The number of virions per meter^3 from model start to the given time."""
boundaries = []
def exposure_between_bounds(self, time1: float, time2: float) -> _VectorisedFloat:
"""The number of virions per meter^3 from model start to the given stop."""
for start, stop in self.exposed.presence.boundaries():
if start > time:
if start > time2:
result = 0.
break
elif time <= stop:
stop = time
boundaries.append([start, stop])
elif time2 <= stop:
result = self.concentration_model.integrated_concentration(time1, time2)
break
else:
boundaries.append([start, stop])
result = self.concentration_model.integrated_concentration(time1, time2)
return result
exposure = 0.0
for start, stop in boundaries:
exposure += self.concentration_model.integrated_concentration(start, stop)
return exposure
def exposure(self) -> _VectorisedFloat:
"""The number of virions per meter^3 for the full simulation time."""
if self.exposed.presence.transition_times():
return self.exposure_between_bounds(max(self.exposed.presence.transition_times()))
else:
return 0
"""The number of virus per meter^3."""
exposure = 0.0
def inhaled_exposure_between_bounds(self, time: float) -> _VectorisedFloat:
exposure = self.exposure_between_bounds(time)
return (
for start, stop in self.exposed.presence.boundaries():
exposure += self.concentration_model.integrated_concentration(start, stop)
return exposure * self.repeats
def infection_probability(self) -> _VectorisedFloat:
exposure = self.exposure()
inf_aero = (
self.exposed.activity.inhalation_rate *
(1 - self.exposed.mask.inhale_efficiency()) *
exposure * self.fraction_deposited
)
def inhaled_exposure(self) -> _VectorisedFloat:
if self.exposed.presence.transition_times():
return self.inhaled_exposure_between_bounds(max(self.exposed.presence.transition_times()))
else:
return 0
def infection_probability(self) -> _VectorisedFloat:
inf_aero = self.inhaled_exposure()
# Probability of infection.
return (1 - np.exp(-(inf_aero/self.concentration_model.virus.infectious_dose))) * 100