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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,
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.
"""
# Note on units: exhalation rate is in m^3/h -> 1e6 conversion factor
# Returns the emission rate times the number of infected hosts in the room
# Conversion factor explanation:
# 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 *
self.activity.exhalation_rate *
self.fraction_of_infectious_virus() *
10 ** 6)
10**6)
return ER
@property
@ -1376,6 +1378,10 @@ class ShortRangeModel:
return factors
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.
return self.expiration.aerosols(mask=Mask.types['No mask'])
@ -1416,10 +1422,18 @@ class ShortRangeModel:
return 0.
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
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)
def short_range_concentration(self, concentration_model: ConcentrationModel, time: float) -> _VectorisedFloat:
@ -1490,6 +1504,9 @@ class ShortRangeModel:
if stop<=start:
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 = (
concentration_model.integrated_concentration(start, stop)
/concentration_model.virus.viral_load_in_sputum