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models.py: some re-structuring to removing some code-smells (introduction of a Particle class where settling velocity and deposited fraction are computed)

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Nicolas Mounet 2022-01-26 13:03:37 +01:00
parent 9da5b5b929
commit c9329da4d1
1 changed files with 78 additions and 30 deletions
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108
cara/models.py
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@ -563,6 +563,56 @@ Mask.types = {
}
@dataclass(frozen=True)
class Particle:
"""
Represents an aerosol particle.
"""
#: diameter of the aerosol in microns
diameter: typing.Union[None,_VectorisedFloat] = None
def settling_velocity(self, evaporation_factor: float=0.3) -> _VectorisedFloat:
"""
Settling velocity (i.e. speed of deposition on the floor due
to gravity), for aerosols, in m/s. Diameter-dependent expression
from https://doi.org/10.1101/2021.10.14.21264988
When an aerosol-diameter is not given, returns
the default value of 1.88e-4 m/s (corresponds to diameter of
2.5 microns, i.e. geometric average of the breathing
expiration distribution, taking evaporation into account, see
https://doi.org/10.1101/2021.10.14.21264988)
evaporation_factor represents the factor applied to the diameter,
due to instantaneous evaporation of the particle in the air.
"""
if self.diameter is None:
vg = 1.88e-4
else:
vg = 1.88e-4 * (self.diameter*evaporation_factor / 2.5)**2
return vg
def fraction_deposited(self, evaporation_factor: float=0.3):
"""
The fraction of particles actually deposited in the respiratory tract.
From W. C. Hinds, New York, Wiley, 1999 (pp. 233 – 259).
evaporation_factor represents the factor applied to the diameter,
due to instantaneous evaporation of the particle in the air.
"""
if self.diameter is None:
# model is not evaluated for specific values of aerosol
# diameters - we choose a single "average" deposition factor,
# as in https://doi.org/10.1101/2021.10.14.21264988.
fdep = 0.6
else:
# deposition fraction depends on aerosol particle diameter.
d = (self.diameter * evaporation_factor)
IFrac = 1 - 0.5 * (1 - (1 / (1 + (0.00076*(d**2.8)))))
fdep = IFrac * (0.0587
+ (0.911/(1 + np.exp(4.77 + 1.485 * np.log(d))))
+ (0.943/(1 + np.exp(0.508 - 2.58 * np.log(d)))))
return fdep
@dataclass(frozen=True)
class _ExpirationBase:
"""
@ -572,6 +622,12 @@ class _ExpirationBase:
#: Pre-populated examples of Expirations.
types: typing.ClassVar[typing.Dict[str, "_ExpirationBase"]]
def particle(self) -> Particle:
"""
the Particle object representing the aerosol - here the default one
"""
return Particle()
def aerosols(self, mask: Mask):
"""
total volume of aerosols expired per volume of air (mL/cm^3).
@ -594,6 +650,12 @@ class Expiration(_ExpirationBase):
# to c_n,i in Eq. (4) of https://doi.org/10.1101/2021.10.14.21264988)
cn: float = 1.
def particle(self) -> Particle:
"""
the Particle object representing the aerosol
"""
return Particle(diameter=self.diameter)
@cached()
def aerosols(self, mask: Mask):
""" Result is in mL.cm^-3 """
@ -732,6 +794,13 @@ class _PopulationWithVirus(Population):
return self.emission_rate_when_present()
def particle(self) -> Particle:
"""
the Particle object representing the aerosol expired by the
population - here we take the default Particle object
"""
return Particle()
@dataclass(frozen=True)
class EmittingPopulation(_PopulationWithVirus):
@ -778,6 +847,12 @@ class InfectedPopulation(_PopulationWithVirus):
return ER * self.number
def particle(self) -> Particle:
"""
the Particle object representing the aerosol - here the default one
"""
return self.expiration.particle()
@dataclass(frozen=True)
class ConcentrationModel:
@ -796,20 +871,7 @@ class ConcentrationModel:
def infectious_virus_removal_rate(self, time: float) -> _VectorisedFloat:
# Equilibrium velocity of particle motion toward the floor
if (isinstance(self.infected, InfectedPopulation)
and isinstance(self.infected.expiration, Expiration)):
d = self.infected.expiration.diameter * self.evaporation_factor
vg = 1.88e-4 * (d / 2.5)**2
# see https://doi.org/10.1101/2021.10.14.21264988
# (velocity of 1.88e-4 corresponds to diameter of 2.5 microns)
else:
# model is not evaluated for specific values of aerosol
# diameters - we choose a single velocity value
# corresponding to that obtained with a diameter of 2.5 microns
# (geometric average of the breathing expiration distribution,
# taking evaporation into account, see
# https://doi.org/10.1101/2021.10.14.21264988)
vg = 1.88e-4
vg = self.infected.particle().settling_velocity(self.evaporation_factor)
# Height of the emission source to the floor - i.e. mouth/nose (m)
h = 1.5
# Deposition rate (h^-1)
@ -990,23 +1052,9 @@ class ExposureModel:
def fraction_deposited(self):
"""
The fraction of viruses actually deposited in the respiratory tract.
From W. C. Hinds, New York, Wiley, 1999 (pp. 233 – 259).
"""
if not (isinstance(self.concentration_model.infected,InfectedPopulation)
and isinstance(self.concentration_model.infected.expiration,Expiration)):
# model is not evaluated for specific values of aerosol
# diameters - we choose a single "average" deposition factor,
# as in https://doi.org/10.1101/2021.10.14.21264988.
fdep = 0.6
else:
# deposition factor depends on aerosol particle diameter.
d = (self.concentration_model.infected.expiration.diameter
* self.concentration_model.evaporation_factor)
IFrac = 1 - 0.5 * (1 - (1 / (1 + (0.00076*(d**2.8)))))
fdep = IFrac * (0.0587
+ (0.911/(1 + np.exp(4.77 + 1.485 * np.log(d))))
+ (0.943/(1 + np.exp(0.508 - 2.58 * np.log(d)))))
return fdep
return self.concentration_model.infected.particle().fraction_deposited(
self.concentration_model.evaporation_factor)
def _normed_exposure_between_bounds(self, time1: float, time2: float) -> _VectorisedFloat:
"""The number of virions per meter^3 between any two times, normalized