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adapted comments and docstrings of some methods

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lrdossan 2024-06-20 15:51:03 +02:00
parent fa38282186
commit 7924af041f
1 changed files with 22 additions and 5 deletions
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27
caimira/models.py
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@ -964,15 +964,17 @@ class InfectedPopulation(_PopulationWithVirus):
""" """
The emission rate of virions in the expired air per mL of respiratory fluid, The emission rate of virions in the expired air per mL of respiratory fluid,
if the infected population is present, in (virion.cm^3)/(mL.h). if the infected population is present, in (virion.cm^3)/(mL.h).
This method includes only the diameter-independent variables within the emission rate. This method returns only the diameter-independent variables within the emission rate.
It should not be a function of time. It should not be a function of time.
""" """
# Note on units: exhalation rate is in m^3/h -> 1e6 conversion factor # Conversion factor explanation:
# Returns the emission rate times the number of infected hosts in the room # The exhalation rate is in m^3/h, therefore the 1e6 conversion factor
# is to convert m^3/h into cm^3/h to return (virions.cm^3)/(mL.h),
# so that we can then multiply by aerosols (mL/cm^3).
ER = (self.virus.viral_load_in_sputum * ER = (self.virus.viral_load_in_sputum *
self.activity.exhalation_rate * self.activity.exhalation_rate *
self.fraction_of_infectious_virus() * self.fraction_of_infectious_virus() *
10 ** 6) 10**6)
return ER return ER
@property @property
@ -1376,6 +1378,10 @@ class ShortRangeModel:
return factors return factors
def _normed_jet_origin_concentration(self) -> _VectorisedFloat: def _normed_jet_origin_concentration(self) -> _VectorisedFloat:
'''
The initial emission concentration at the source origin (mouth/nose)
normalized by the viral load and f_inf factors. Results in mL.cm^3.
'''
# The short range origin concentration does not consider the mask contribution. # The short range origin concentration does not consider the mask contribution.
return self.expiration.aerosols(mask=Mask.types['No mask']) return self.expiration.aerosols(mask=Mask.types['No mask'])
@ -1416,10 +1422,18 @@ class ShortRangeModel:
return 0. return 0.
def normalization_factor(self, infected: InfectedPopulation) -> _VectorisedFloat: def normalization_factor(self, infected: InfectedPopulation) -> _VectorisedFloat:
# The normalization factor does not consider the BR contribution """
The normalization factor applied to the short-range results. It refers
to the emission rate per aerosol without accounting for the exhalation rate.
Result in virions/mL.
"""
# Re-use the emission rate method divided by the BR contribution.
return infected.emission_rate_per_aerosol_per_person_when_present() / infected.activity.exhalation_rate return infected.emission_rate_per_aerosol_per_person_when_present() / infected.activity.exhalation_rate
def jet_origin_concentration(self, infected: InfectedPopulation) -> _VectorisedFloat: def jet_origin_concentration(self, infected: InfectedPopulation) -> _VectorisedFloat:
"""
The initial emission concentration at the source origin (mouth/nose).
"""
return self._normed_jet_origin_concentration() * self.normalization_factor(infected) return self._normed_jet_origin_concentration() * self.normalization_factor(infected)
def short_range_concentration(self, concentration_model: ConcentrationModel, time: float) -> _VectorisedFloat: def short_range_concentration(self, concentration_model: ConcentrationModel, time: float) -> _VectorisedFloat:
@ -1490,6 +1504,9 @@ class ShortRangeModel:
if stop<=start: if stop<=start:
return 0. return 0.
# Note that the emission_rate_per_aerosol_per_person_when_present method
# is not used here due to the influence that the conversion factor (10**6)
# could have in the interpolation.
normed_int_concentration = ( normed_int_concentration = (
concentration_model.integrated_concentration(start, stop) concentration_model.integrated_concentration(start, stop)
/concentration_model.virus.viral_load_in_sputum /concentration_model.virus.viral_load_in_sputum