From d1ec9902556e88d91df7e13ac0914abc01e03d77 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Sun, 12 Sep 2021 13:05:17 +0200
Subject: [PATCH] Remove suprespreading event from the expiration types;
 replace by an optional parameter to fix directly the emission rate; updates
 the corresponding tests

---
 cara/models.py                                | 21 ++++++++++++++-----
 .../apps/calculator/test_model_generator.py   |  4 ++--
 cara/tests/test_monte_carlo_full_models.py    |  5 ++++-
 3 files changed, 22 insertions(+), 8 deletions(-)

diff --git a/cara/models.py b/cara/models.py
index 498308d3..d7f67d49 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -630,12 +630,14 @@ class MultipleExpiration(_ExpirationBase):
         ]).sum(axis=0)
 
 
+# Typical expirations. The aerosol diameter given is an equivalent
+# diameter, chosen in such a way that the aerosol volume is
+# the same as the total aerosol volume given by the full BLO model.
 _ExpirationBase.types = {
-    'Breathing': Expiration((1., 0., 0.), 1.3844),
-    'Talking': Expiration((1., 1., 1.), 5.8925),
-    'Shouting': Expiration((1., 5., 5.), 10.0411),
-    'Singing': Expiration((1., 5., 5.), 10.0411),
-    'Superspreading event': Expiration((np.inf, 0., 0.), 10.0411),
+    'Breathing': Expiration((1., 0., 0.)),
+    'Talking': Expiration((1., 1., 1.)),
+    'Shouting': Expiration((1., 5., 5.)),
+    'Singing': Expiration((1., 5., 5.)),
 }
 
 
@@ -688,6 +690,15 @@ class _PopulationWithVirus(Population):
     #: The virus with which the population is infected.
     virus: Virus
 
+    #: The type of expiration that is being emitted whilst doing the activity.
+    expiration: _ExpirationBase
+
+    #: Optionally, this provides directly the emission rate of a single individual,
+    # in units of virions * virus.infectious_dose / h (i.e. it is
+    # multiplied by the virus infectious dose, to get virions / h))
+    # This effectively overrides the "expiration" parameter.
+    known_individual_emission_rate: float = np.nan
+
     @method_cache
     def emission_rate_when_present(self) -> _VectorisedFloat:
         """
diff --git a/cara/tests/apps/calculator/test_model_generator.py b/cara/tests/apps/calculator/test_model_generator.py
index 6ee821c0..432790fb 100644
--- a/cara/tests/apps/calculator/test_model_generator.py
+++ b/cara/tests/apps/calculator/test_model_generator.py
@@ -27,8 +27,8 @@ def test_blend_expiration():
     r = model_generator.build_expiration(blend)
     mask = models.Mask.types['Type I']
     expected = models.Expiration(
-        (0.13466666666666668, 0.02866666666666667, 0.004333333333333334, 0.005)
-    )
+        (0.13466666666666668, 0.02866666666666667, 0.004333333333333334),
+        2.5)
     npt.assert_almost_equal(r.aerosols(mask), expected.aerosols(mask))
 
 
diff --git a/cara/tests/test_monte_carlo_full_models.py b/cara/tests/test_monte_carlo_full_models.py
index 08bd2dad..f153d389 100644
--- a/cara/tests/test_monte_carlo_full_models.py
+++ b/cara/tests/test_monte_carlo_full_models.py
@@ -218,7 +218,10 @@ def skagit_chorale_mc():
             presence=mc.SpecificInterval(((0., 2.5),)),
             mask=models.Mask.types["No mask"],
             activity=activity_distributions['Light activity'],
-            expiration=models.Expiration((5., 5., 5.)),
+            expiration=models.Expiration((5., 5., 5.), 10.0761),
+            # The aerosol diameter given (10.0761 microns) is an equivalent
+            # diameter, chosen in such a way that the aerosol volume is
+            # the same as the total aerosol volume given by the full BLO model.
         ),
     )
     return mc.ExposureModel(