Merge branch 'feature/short_range_bug_fix_and_tests' into 'master'

Adding breathing rate factor in short-range deposited exposure (bug fix), and exposure tests for short-range See merge request cara/cara!345
CERN · Apr 7, 2022 · c1589a0 · c1589a0
2 parents 0b58d59 + 4dd5b8a
commit c1589a0
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diff --git a/cara/apps/calculator/__init__.py b/cara/apps/calculator/__init__.py
@@ -33,7 +33,7 @@
 # calculator version. If the calculator needs to make breaking changes (e.g. change
 # form attributes) then it can also increase its MAJOR version without needing to
 # increase the overall CARA version (found at ``cara.__version__``).
-__version__ = "4.1.0"
+__version__ = "4.1.1"
 
 
 class BaseRequestHandler(RequestHandler):

diff --git a/cara/models.py b/cara/models.py
@@ -501,7 +501,7 @@ def halflife(self, humidity: _VectorisedFloat) -> _VectorisedFloat:
     ),
     'SARS_CoV_2_OMICRON': SARSCoV2(
         viral_load_in_sputum=1e9,
-        infectious_dose=20.,
+        infectious_dose=50.,
         viable_to_RNA_ratio=0.5,
         transmissibility_factor=0.2
     ),
@@ -1175,12 +1175,21 @@ def normed_exposure_between_bounds(self, concentration_model: ConcentrationModel
         """
         start_bound, stop_bound = self.presence.boundaries()[0]
 
-        jet_origin_integrated = self.expiration.jet_origin_concentration()
+        jet_origin = self.expiration.jet_origin_concentration()
         dilution = self.dilution_factor()
 
-        total_normed_concentration = -(concentration_model.integrated_concentration(start_bound, stop_bound)/concentration_model.virus.viral_load_in_sputum/dilution)
-        total_normed_concentration_interpolated = np.interp(self.expiration.particle.diameter, concentration_model.infected.particle.diameter, total_normed_concentration)
-        return (jet_origin_integrated/dilution * (stop_bound - start_bound)) + total_normed_concentration_interpolated
+        total_normed_concentration_diluted = (
+            concentration_model.integrated_concentration(start_bound,
+                stop_bound)/dilution/
+                concentration_model.virus.viral_load_in_sputum
+                )
+        total_normed_concentration_interpolated = np.interp(
+                self.expiration.particle.diameter,
+                concentration_model.infected.particle.diameter,
+                total_normed_concentration_diluted
+                )
+        return (jet_origin/dilution * (stop_bound - start_bound)
+                ) - total_normed_concentration_interpolated
 
 
 @dataclass(frozen=True)
@@ -1318,14 +1327,20 @@ def deposited_exposure_between_bounds(self, time1: float, time2: float) -> _Vect
                 # in the case of a single diameter or no diameter defined,
                 # one should not take any mean at this stage.
                 deposited_exposure += short_range_exposure*fdep  
-
-        # then we multiply by the diameter-independent quantity virus viral load
-        deposited_exposure *= self.concentration_model.virus.viral_load_in_sputum
-        # long-range concentration
+
+            # multiply by the (diameter-independent) inhalation rate
+            deposited_exposure *= interaction.activity.inhalation_rate
+
+        # then we multiply by diameter-independent quantities: viral load
+        # and fraction of infected virions
         f_inf = self.concentration_model.infected.fraction_of_infectious_virus()
-        deposited_exposure += self.long_range_deposited_exposure_between_bounds(time1, time2)/f_inf
+        deposited_exposure *= (f_inf
+                * self.concentration_model.virus.viral_load_in_sputum
+                )
+        # long-range concentration
+        deposited_exposure += self.long_range_deposited_exposure_between_bounds(time1, time2)
 
-        return deposited_exposure * f_inf
+        return deposited_exposure
 
     def deposited_exposure(self) -> _VectorisedFloat:
         """