From 9d4ffdb89053db2715e0ebdde5c9af5e573102bd Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Wed, 26 May 2021 18:57:56 +0200
Subject: [PATCH 01/14] Introducing _MaskBase class, of which Mask is a
 subclass

---
 cara/models.py | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/cara/models.py b/cara/models.py
index 0943bd87..55989ec5 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -472,8 +472,21 @@ Virus.types = {
 
 
 @dataclass(frozen=True)
-class Mask:
-    #: Filtration efficiency. (In %/100)
+class _MaskBase:
+    """
+    Represents the filtration of aerosols by a mask, both inward and 
+    outward.
+    The nature of the various air exchange schemes means that it is expected
+    for subclasses of _MaskBase to exist.
+    """
+    def exhale_efficiency(self, diameter: float) -> _VectorisedFloat:
+        # Overall efficiency, including the effect of the leaks.
+        raise NotImplementedError("Subclass must implement")
+
+
+@dataclass(frozen=True)
+class Mask(_MaskBase):
+    #: Filtration efficiency.
     η_exhale: _VectorisedFloat
 
     #: Leakage through side of masks.

From 676fd64844cc7c83069f44ed265ef111c1e6ed4a Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Wed, 26 May 2021 23:37:10 +0200
Subject: [PATCH 02/14] Adding tests on Mask (new classes and new methods)

---
 cara/tests/models/test_mask.py | 58 ++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 cara/tests/models/test_mask.py

diff --git a/cara/tests/models/test_mask.py b/cara/tests/models/test_mask.py
new file mode 100644
index 00000000..f2069cbd
--- /dev/null
+++ b/cara/tests/models/test_mask.py
@@ -0,0 +1,58 @@
+
+import dataclasses
+
+import numpy as np
+import numpy.testing as npt
+import pytest
+
+from cara import models
+
+@pytest.mark.parametrize(
+    "η_inhale, expected_inhale_efficiency",
+    [
+        [0.5, 0.5],
+        [np.array([0.3, 0.5]), np.array([0.3, 0.5])],
+    ],
+)
+def test_masks_inhale(η_inhale, expected_inhale_efficiency):
+    mask = models.Mask(η_inhale=η_inhale,η_exhale=0.95,η_leaks=0.15)
+    measuredmask = models.MeasuredMask(η_inhale=η_inhale)
+    npt.assert_equal(mask.inhale_efficiency(), 
+                     expected_inhale_efficiency)
+    npt.assert_equal(measuredmask.inhale_efficiency(),
+                     expected_inhale_efficiency)
+
+
+@pytest.mark.parametrize(
+    "η_exhale, η_leaks, expected_exhale_efficiency_small, expected_exhale_efficiency_large",
+    [
+        [0.95, 0.15, 0., 0.8075],
+        [np.array([0.95, 1.]), 0.15, np.zeros(2), np.array([0.8075, 0.85])],
+        [0.95, np.array([0.15, 0.]), np.zeros(2), np.array([0.8075, 0.95])],
+        [np.array([0.95, 1.]), np.array([0.15, 0.]), np.zeros(2), np.array([0.8075, 1.])],
+    ],
+)
+def test_mask_exhale(η_exhale, η_leaks, expected_exhale_efficiency_small,
+                     expected_exhale_efficiency_large):
+    mask = models.Mask(η_inhale=0.3,η_exhale=η_exhale,η_leaks=η_leaks)
+    # we test one small and one large diameter (resp. 1 and 4 microns)
+    npt.assert_equal(mask.exhale_efficiency(1.e-4), 
+                     expected_exhale_efficiency_small)
+    npt.assert_equal(mask.exhale_efficiency(4.e-4), 
+                     expected_exhale_efficiency_large)
+
+
+@pytest.mark.parametrize(
+    "diameter, expected_exhale_efficiency",
+    [
+        [0.3e-4, 0.],
+        [0.7e-4, 0.56711],
+        [1.e-4, 0.7149],
+        [4.e-4, 0.8167],
+    ],
+)
+def test_measuredmask_exhale(diameter, expected_exhale_efficiency):
+    mask = models.MeasuredMask(η_inhale=0.3)
+    npt.assert_almost_equal(mask.exhale_efficiency(diameter),
+                            expected_exhale_efficiency)
+

From 48f0c395819f9738b4ad146b89c2d47a6a3d6aa8 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Wed, 26 May 2021 23:39:33 +0200
Subject: [PATCH 03/14] New method inhale_efficiency in _MaskBase; using
 _MaskBase everywhere needed (also for types); new MeasuredMask with different
 exhale_efficiency functions; new mask types

---
 cara/apps/calculator/model_generator.py |  4 +-
 cara/apps/expert.py                     | 14 +++---
 cara/models.py                          | 58 +++++++++++++++++++++----
 3 files changed, 58 insertions(+), 18 deletions(-)

diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py
index fb34392d..1ec76a77 100644
--- a/cara/apps/calculator/model_generator.py
+++ b/cara/apps/calculator/model_generator.py
@@ -269,10 +269,10 @@ class FormData:
         else:
             return ventilation
 
-    def mask(self) -> models.Mask:
+    def mask(self) -> models._MaskBase:
         # Initializes the mask type if mask wearing is "continuous", otherwise instantiates the mask attribute as
         # the "No mask"-mask
-        mask = models.Mask.types[self.mask_type if self.mask_wearing_option == "mask_on" else 'No mask']
+        mask = models._MaskBase.types[self.mask_type if self.mask_wearing_option == "mask_on" else 'No mask']
         return mask
 
     def infected_population(self) -> models.InfectedPopulation:
diff --git a/cara/apps/expert.py b/cara/apps/expert.py
index 31903b79..a0f273e1 100644
--- a/cara/apps/expert.py
+++ b/cara/apps/expert.py
@@ -390,10 +390,10 @@ class ModelWidgets(View):
 
     def _build_mask(self, node):
         mask = node.dcs_instance()
-        for name, mask_ in models.Mask.types.items():
+        for name, mask_ in models._MaskBase.types.items():
             if mask == mask_:
                 break
-        mask_choice = widgets.Select(options=list(models.Mask.types.keys()), value=name)
+        mask_choice = widgets.Select(options=list(models._MaskBase.types.keys()), value=name)
 
         def on_mask_change(change):
             node.dcs_select(change['new'])
@@ -496,7 +496,7 @@ baseline_model = models.ExposureModel(
             number=1,
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(((8, 12), (13, 17))),
-            mask=models.Mask.types['No mask'],
+            mask=models._MaskBase.types['No mask'],
             activity=models.Activity.types['Seated'],
             expiration=models.Expiration.types['Talking'],
         ),
@@ -505,7 +505,7 @@ baseline_model = models.ExposureModel(
         number=10,
         presence=models.SpecificInterval(((8, 12), (13, 17))),
         activity=models.Activity.types['Seated'],
-        mask=models.Mask.types['No mask'],
+        mask=models._MaskBase.types['No mask'],
     ),
 )
 
@@ -515,10 +515,10 @@ class CARAStateBuilder(state.StateBuilder):
     # For example, build_type__VentilationBase is called when dealing with ConcentrationModel
     # types as it has a ventilation: _VentilationBase field.
 
-    def build_type_Mask(self, _: dataclasses.Field):
+    def build_type__MaskBase(self, _: dataclasses.Field):
         return state.DataclassStatePredefined(
-            models.Mask,
-            choices=models.Mask.types,
+            models._MaskBase,
+            choices=models._MaskBase.types,
         )
 
     def build_type_Virus(self, _: dataclasses.Field):
diff --git a/cara/models.py b/cara/models.py
index 55989ec5..2987d613 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -474,13 +474,20 @@ Virus.types = {
 @dataclass(frozen=True)
 class _MaskBase:
     """
-    Represents the filtration of aerosols by a mask, both inward and 
+    Represents the filtration of aerosols by a mask, both inward and
     outward.
     The nature of the various air exchange schemes means that it is expected
     for subclasses of _MaskBase to exist.
     """
+    #: Pre-populated examples of Masks.
+    types: typing.ClassVar[typing.Dict[str, "_MaskBase"]]
+
     def exhale_efficiency(self, diameter: float) -> _VectorisedFloat:
-        # Overall efficiency, including the effect of the leaks.
+        # Overall exhale efficiency, including the effect of the leaks.
+        raise NotImplementedError("Subclass must implement")
+
+    def inhale_efficiency(self) -> _VectorisedFloat:
+        # Overall inhale efficiency, including the effect of the leaks.
         raise NotImplementedError("Subclass must implement")
 
 
@@ -495,9 +502,6 @@ class Mask(_MaskBase):
     #: Filtration efficiency of masks when inhaling.
     η_inhale: _VectorisedFloat
 
-    #: Pre-populated examples of Masks.
-    types: typing.ClassVar[typing.Dict[str, "Mask"]]
-
     def exhale_efficiency(self, diameter: float) -> _VectorisedFloat:
         # Overall efficiency with the effect of the leaks for aerosol emission
         #  Gammaitoni et al (1997). Diameter is in cm.
@@ -507,8 +511,38 @@ class Mask(_MaskBase):
             eta_out = self.η_exhale * (1 - self.η_leaks)
         return eta_out
 
+    def inhale_efficiency(self) -> _VectorisedFloat:
+        # Overall inhale efficiency, including the effect of the leaks.
+        return self.η_inhale
 
-Mask.types = {
+
+@dataclass(frozen=True)
+class MeasuredMask(_MaskBase):
+    #: Filtration efficiency of masks when inhaling.
+    η_inhale: _VectorisedFloat
+
+    def exhale_efficiency(self, diameter: float) -> _VectorisedFloat:
+        # See CERN-OPEN-2021-004 (doi: 10.17181/CERN.1GDQ.5Y75), and Ref.
+        # therein (Asadi 2020).
+        # Obtained from measurements of filtration efficiency and of 
+        # the leakage through the sides.
+        # Diameter is in cm.
+        if diameter < 0.5e-4:
+            eta_out = 0.
+        elif diameter < 0.94614e-4:
+            eta_out = 0.5893 * diameter * 1e4 + 0.1546
+        elif diameter < 3e-4:
+            eta_out = 0.0509 * diameter * 1e4 + 0.664
+        else:
+            eta_out = 0.8167
+        return eta_out
+
+    def inhale_efficiency(self) -> _VectorisedFloat:
+        # Overall inhale efficiency, including the effect of the leaks.
+        return self.η_inhale
+
+
+_MaskBase.types = {
     'No mask': Mask(0, 0, 0),
     'Type I': Mask(
         η_exhale=0.95,
@@ -520,6 +554,12 @@ Mask.types = {
         η_leaks=0.15,  # (same outward effect as type 1 - Asadi 2020)
         η_inhale=0.865,  # (94% penetration efficiency + 8% max inward leakage -> EN 149)
     ),
+    'Type I measured': MeasuredMask(
+        η_inhale=0.3,  # (Browen 2010)
+    ),
+    'FFP2 measured': MeasuredMask(
+        η_inhale=0.865,  # (94% penetration efficiency + 8% max inward leakage -> EN 149)
+    ),
 }
 
 
@@ -531,7 +571,7 @@ class Expiration:
     #: Pre-populated examples of Expiration.
     types: typing.ClassVar[typing.Dict[str, "Expiration"]]
 
-    def aerosols(self, mask: Mask):
+    def aerosols(self, mask: _MaskBase):
         def volume(diameter):
             return (4 * np.pi * (diameter/2)**3) / 3
         total = 0
@@ -583,7 +623,7 @@ class Population:
     presence: Interval
 
     #: The kind of mask being worn by the people.
-    mask: Mask
+    mask: _MaskBase
 
     #: The physical activity being carried out by the people.
     activity: Activity
@@ -806,7 +846,7 @@ class ExposureModel:
 
         inf_aero = (
             self.exposed.activity.inhalation_rate *
-            (1 - self.exposed.mask.η_inhale) *
+            (1 - self.exposed.mask.inhale_efficiency()) *
             exposure
         )
 

From fec6a71c62d6cc0ba53627fa0e415835c707c7ef Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Thu, 27 May 2021 09:20:28 +0200
Subject: [PATCH 04/14] Correction in docstring of _MaskBase

---
 cara/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cara/models.py b/cara/models.py
index 2987d613..620e6ca4 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -476,7 +476,7 @@ class _MaskBase:
     """
     Represents the filtration of aerosols by a mask, both inward and
     outward.
-    The nature of the various air exchange schemes means that it is expected
+    The nature of the various mask models means that it is expected
     for subclasses of _MaskBase to exist.
     """
     #: Pre-populated examples of Masks.

From 213dd2fb929d848f0c76d8d88cb4c27df996ff78 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Thu, 27 May 2021 13:44:03 +0200
Subject: [PATCH 05/14] Modifying eta_inhale of Type I measured mask according
 to CERN report

---
 cara/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cara/models.py b/cara/models.py
index 620e6ca4..f95e28ed 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -555,7 +555,7 @@ _MaskBase.types = {
         η_inhale=0.865,  # (94% penetration efficiency + 8% max inward leakage -> EN 149)
     ),
     'Type I measured': MeasuredMask(
-        η_inhale=0.3,  # (Browen 2010)
+        η_inhale=0.5,  # (CERN-OPEN-2021-004)
     ),
     'FFP2 measured': MeasuredMask(
         η_inhale=0.865,  # (94% penetration efficiency + 8% max inward leakage -> EN 149)

From b04dfbad01806cf18dc742510bf68e6d965afb2b Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Sun, 30 May 2021 07:56:06 +0200
Subject: [PATCH 06/14] Fixing previous merge

---
 cara/models.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cara/models.py b/cara/models.py
index 6efa29db..a72f1b48 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -572,7 +572,7 @@ class _ExpirationBase:
     #: Pre-populated examples of Masks.
     types: typing.ClassVar[typing.Dict[str, "_ExpirationBase"]]
 
-    def aerosols(self, mask: Mask):
+    def aerosols(self, mask: _MaskBase):
         # total volume of aerosols expired per volume of air (mL/cm^3).
         raise NotImplementedError("Subclass must implement")
 
@@ -617,7 +617,7 @@ class MultipleExpiration(_ExpirationBase):
             raise ValueError("expirations and weigths should contain the"
                              "same number of elements")
 
-    def aerosols(self, mask: Mask):
+    def aerosols(self, mask: _MaskBase):
         return np.array([
             weight * expiration.aerosols(mask) / sum(self.weights)
             for weight,expiration in zip(self.weights,self.expirations)

From 947bd013e0c07131eb8ddc33c4c876f2bbead2e8 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Sun, 30 May 2021 19:25:39 +0200
Subject: [PATCH 07/14] Modifying tests on mask to comply with a single Mask
 class

---
 cara/tests/models/test_mask.py | 43 +++++++---------------------------
 1 file changed, 9 insertions(+), 34 deletions(-)

diff --git a/cara/tests/models/test_mask.py b/cara/tests/models/test_mask.py
index f2069cbd..7f7cb242 100644
--- a/cara/tests/models/test_mask.py
+++ b/cara/tests/models/test_mask.py
@@ -1,6 +1,3 @@
-
-import dataclasses
-
 import numpy as np
 import numpy.testing as npt
 import pytest
@@ -15,44 +12,22 @@ from cara import models
     ],
 )
 def test_masks_inhale(η_inhale, expected_inhale_efficiency):
-    mask = models.Mask(η_inhale=η_inhale,η_exhale=0.95,η_leaks=0.15)
-    measuredmask = models.MeasuredMask(η_inhale=η_inhale)
+    mask = models.Mask(η_inhale=η_inhale)
     npt.assert_equal(mask.inhale_efficiency(), 
                      expected_inhale_efficiency)
-    npt.assert_equal(measuredmask.inhale_efficiency(),
-                     expected_inhale_efficiency)
 
 
 @pytest.mark.parametrize(
-    "η_exhale, η_leaks, expected_exhale_efficiency_small, expected_exhale_efficiency_large",
+    "diameter, factor_exhale, expected_exhale_efficiency",
     [
-        [0.95, 0.15, 0., 0.8075],
-        [np.array([0.95, 1.]), 0.15, np.zeros(2), np.array([0.8075, 0.85])],
-        [0.95, np.array([0.15, 0.]), np.zeros(2), np.array([0.8075, 0.95])],
-        [np.array([0.95, 1.]), np.array([0.15, 0.]), np.zeros(2), np.array([0.8075, 1.])],
+        [0.3e-4, 1., 0.],
+        [0.7e-4, 0.3, 0.56711*0.3],
+        [1.e-4, 1., 0.7149],
+        [4.e-4, 0.5, 0.8167*0.5],
+        [5.e-4, 0., 0.],
     ],
 )
-def test_mask_exhale(η_exhale, η_leaks, expected_exhale_efficiency_small,
-                     expected_exhale_efficiency_large):
-    mask = models.Mask(η_inhale=0.3,η_exhale=η_exhale,η_leaks=η_leaks)
-    # we test one small and one large diameter (resp. 1 and 4 microns)
-    npt.assert_equal(mask.exhale_efficiency(1.e-4), 
-                     expected_exhale_efficiency_small)
-    npt.assert_equal(mask.exhale_efficiency(4.e-4), 
-                     expected_exhale_efficiency_large)
-
-
-@pytest.mark.parametrize(
-    "diameter, expected_exhale_efficiency",
-    [
-        [0.3e-4, 0.],
-        [0.7e-4, 0.56711],
-        [1.e-4, 0.7149],
-        [4.e-4, 0.8167],
-    ],
-)
-def test_measuredmask_exhale(diameter, expected_exhale_efficiency):
-    mask = models.MeasuredMask(η_inhale=0.3)
+def test_mask_exhale(diameter, factor_exhale, expected_exhale_efficiency):
+    mask = models.Mask(η_inhale=0.3, factor_exhale=factor_exhale)
     npt.assert_almost_equal(mask.exhale_efficiency(diameter),
                             expected_exhale_efficiency)
-

From fa0550233c8369f81158ad6abf1cb4bc8bf12817 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Sun, 30 May 2021 19:28:51 +0200
Subject: [PATCH 08/14] Removing _MaskBase and old Mask class, which is
 replaced by MeasuredMask

---
 cara/models.py | 100 ++++++++++++++-----------------------------------
 1 file changed, 28 insertions(+), 72 deletions(-)

diff --git a/cara/models.py b/cara/models.py
index a72f1b48..736e0992 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -472,61 +472,25 @@ Virus.types = {
 
 
 @dataclass(frozen=True)
-class _MaskBase:
-    """
-    Represents the filtration of aerosols by a mask, both inward and
-    outward.
-    The nature of the various mask models means that it is expected
-    for subclasses of _MaskBase to exist.
-    """
+class Mask:
+    #: Filtration efficiency of masks when inhaling.
+    η_inhale: _VectorisedFloat
+
+    #: Global factor applied to filtration efficiency of masks when exhaling.
+    factor_exhale: _VectorisedFloat = 1.
+
     #: Pre-populated examples of Masks.
-    types: typing.ClassVar[typing.Dict[str, "_MaskBase"]]
+    types: typing.ClassVar[typing.Dict[str, "Mask"]]
 
     def exhale_efficiency(self, diameter: float) -> _VectorisedFloat:
-        # Overall exhale efficiency, including the effect of the leaks.
-        raise NotImplementedError("Subclass must implement")
-
-    def inhale_efficiency(self) -> _VectorisedFloat:
-        # Overall inhale efficiency, including the effect of the leaks.
-        raise NotImplementedError("Subclass must implement")
-
-
-@dataclass(frozen=True)
-class Mask(_MaskBase):
-    #: Filtration efficiency.
-    η_exhale: _VectorisedFloat
-
-    #: Leakage through side of masks.
-    η_leaks: _VectorisedFloat
-
-    #: Filtration efficiency of masks when inhaling.
-    η_inhale: _VectorisedFloat
-
-    def exhale_efficiency(self, diameter: float) -> _VectorisedFloat:
-        # Overall efficiency with the effect of the leaks for aerosol emission
-        #  Gammaitoni et al (1997). Diameter is in cm.
-        if diameter < 3e-4:
-            eta_out = 0.
-        else:
-            eta_out = self.η_exhale * (1 - self.η_leaks)
-        return eta_out
-
-    def inhale_efficiency(self) -> _VectorisedFloat:
-        # Overall inhale efficiency, including the effect of the leaks.
-        return self.η_inhale
-
-
-@dataclass(frozen=True)
-class MeasuredMask(_MaskBase):
-    #: Filtration efficiency of masks when inhaling.
-    η_inhale: _VectorisedFloat
-
-    def exhale_efficiency(self, diameter: float) -> _VectorisedFloat:
-        # See CERN-OPEN-2021-004 (doi: 10.17181/CERN.1GDQ.5Y75), and Ref.
-        # therein (Asadi 2020).
-        # Obtained from measurements of filtration efficiency and of 
-        # the leakage through the sides.
-        # Diameter is in cm.
+        """
+        Overall exhale efficiency, including the effect of the leaks.
+        See CERN-OPEN-2021-004 (doi: 10.17181/CERN.1GDQ.5Y75), and Ref.
+        therein (Asadi 2020).
+        Obtained from measurements of filtration efficiency and of
+        the leakage through the sides.
+        Diameter is in cm.
+        """
         if diameter < 0.5e-4:
             eta_out = 0.
         elif diameter < 0.94614e-4:
@@ -535,29 +499,21 @@ class MeasuredMask(_MaskBase):
             eta_out = 0.0509 * diameter * 1e4 + 0.664
         else:
             eta_out = 0.8167
-        return eta_out
+        return eta_out*self.factor_exhale
 
     def inhale_efficiency(self) -> _VectorisedFloat:
-        # Overall inhale efficiency, including the effect of the leaks.
+        """
+        Overall inhale efficiency, including the effect of the leaks.
+        """
         return self.η_inhale
 
 
-_MaskBase.types = {
-    'No mask': Mask(0, 0, 0),
+Mask.types = {
+    'No mask': Mask(0, 0),
     'Type I': Mask(
-        η_exhale=0.95,
-        η_leaks=0.15,  # (Huang 2007)
-        η_inhale=0.3,  # (Browen 2010)
-    ),
-    'FFP2': Mask(
-        η_exhale=0.95,  # (same outward effect as type 1 - Asadi 2020)
-        η_leaks=0.15,  # (same outward effect as type 1 - Asadi 2020)
-        η_inhale=0.865,  # (94% penetration efficiency + 8% max inward leakage -> EN 149)
-    ),
-    'Type I measured': MeasuredMask(
         η_inhale=0.5,  # (CERN-OPEN-2021-004)
     ),
-    'FFP2 measured': MeasuredMask(
+    'FFP2': Mask(
         η_inhale=0.865,  # (94% penetration efficiency + 8% max inward leakage -> EN 149)
     ),
 }
@@ -569,10 +525,10 @@ class _ExpirationBase:
     Represents the expiration of aerosols by a person.
     Subclasses of _ExpirationBase represent different models.
     """
-    #: Pre-populated examples of Masks.
+    #: Pre-populated examples of Expirations.
     types: typing.ClassVar[typing.Dict[str, "_ExpirationBase"]]
 
-    def aerosols(self, mask: _MaskBase):
+    def aerosols(self, mask: Mask):
         # total volume of aerosols expired per volume of air (mL/cm^3).
         raise NotImplementedError("Subclass must implement")
 
@@ -589,7 +545,7 @@ class Expiration(_ExpirationBase):
     ejection_factor: typing.Tuple[float, ...]
     particle_sizes: typing.Tuple[float, ...] = (0.8e-4, 1.8e-4, 3.5e-4, 5.5e-4)  # In cm.
 
-    def aerosols(self, mask: _MaskBase):
+    def aerosols(self, mask: Mask):
         def volume(diameter):
             return (4 * np.pi * (diameter/2)**3) / 3
         total = 0
@@ -617,7 +573,7 @@ class MultipleExpiration(_ExpirationBase):
             raise ValueError("expirations and weigths should contain the"
                              "same number of elements")
 
-    def aerosols(self, mask: _MaskBase):
+    def aerosols(self, mask: Mask):
         return np.array([
             weight * expiration.aerosols(mask) / sum(self.weights)
             for weight,expiration in zip(self.weights,self.expirations)
@@ -665,7 +621,7 @@ class Population:
     presence: Interval
 
     #: The kind of mask being worn by the people.
-    mask: _MaskBase
+    mask: Mask
 
     #: The physical activity being carried out by the people.
     activity: Activity

From 26075cd53cc22a0aba35185d28c8b49e496e4108 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Sun, 30 May 2021 19:30:25 +0200
Subject: [PATCH 09/14] Modifying infected populations tests and concentration
 tests, according to the new Mask class

---
 cara/tests/models/test_concentration_model.py | 12 +++++-------
 cara/tests/test_infected_population.py        |  9 +++------
 2 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/cara/tests/models/test_concentration_model.py b/cara/tests/models/test_concentration_model.py
index 48ef0b66..f7230430 100644
--- a/cara/tests/models/test_concentration_model.py
+++ b/cara/tests/models/test_concentration_model.py
@@ -1,6 +1,7 @@
 import re
 
 import numpy as np
+import numpy.testing as npt
 import pytest
 
 from cara import models
@@ -13,8 +14,7 @@ from cara import models
         {'air_change': np.array([100, 120])},
         {'viral_load_in_sputum': np.array([5e8, 1e9])},
         {'quantum_infectious_dose': np.array([50, 20])},
-        {'η_exhale': np.array([0.92, 0.95])},
-        {'η_leaks': np.array([0.15, 0.20])},
+        {'factor_exhale': np.array([0.92, 0.95])},
     ]
 )
 def test_concentration_model_vectorisation(override_params):
@@ -24,8 +24,7 @@ def test_concentration_model_vectorisation(override_params):
         'air_change': 100,
         'viral_load_in_sputum': 1e9,
         'quantum_infectious_dose': 50,
-        'η_exhale': 0.95,
-        'η_leaks': 0.15,
+        'factor_exhale': 0.95,
     }
     defaults.update(override_params)
 
@@ -37,8 +36,7 @@ def test_concentration_model_vectorisation(override_params):
             number=1,
             presence=always,
             mask=models.Mask(
-                η_exhale=defaults['η_exhale'],
-                η_leaks=defaults['η_leaks'],
+                factor_exhale=defaults['factor_exhale'],
                 η_inhale=0.3,
             ),
             activity=models.Activity(
@@ -128,4 +126,4 @@ def test_integrated_concentration(simple_conc_model):
     c2 = simple_conc_model.integrated_concentration(0, 1)
     c3 = simple_conc_model.integrated_concentration(1, 2)
     assert c1 != 0
-    assert c1 == c2 + c3
+    npt.assert_almost_equal(c1, c2 + c3, decimal=15)
diff --git a/cara/tests/test_infected_population.py b/cara/tests/test_infected_population.py
index e87ddb20..8ef94729 100644
--- a/cara/tests/test_infected_population.py
+++ b/cara/tests/test_infected_population.py
@@ -8,8 +8,7 @@ import cara.models
     "override_params", [
         {'viral_load_in_sputum': np.array([5e8, 1e9])},
         {'quantum_infectious_dose': np.array([50, 20])},
-        {'η_exhale': np.array([0.92, 0.95])},
-        {'η_leaks': np.array([0.15, 0.20])},
+        {'factor_exhale': np.array([0.92, 0.95])},
         {'exhalation_rate': np.array([0.75, 0.81])},
     ]
 )
@@ -17,8 +16,7 @@ def test_infected_population_vectorisation(override_params):
     defaults = {
         'viral_load_in_sputum': 1e9,
         'quantum_infectious_dose': 50,
-        'η_exhale': 0.95,
-        'η_leaks': 0.15,
+        'factor_exhale': 0.95,
         'exhalation_rate': 0.75,
     }
     defaults.update(override_params)
@@ -28,8 +26,7 @@ def test_infected_population_vectorisation(override_params):
             number=1,
             presence=office_hours,
             mask=cara.models.Mask(
-                η_exhale=defaults['η_exhale'],
-                η_leaks=defaults['η_leaks'],
+                factor_exhale=defaults['factor_exhale'],
                 η_inhale=0.3,
             ),
             activity=cara.models.Activity(

From 0087bff41ed69b9dcb561189978b6e1d623a6e1e Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Sun, 30 May 2021 19:31:13 +0200
Subject: [PATCH 10/14] Propagating the change in Mask class to the calculator
 and expoert apps

---
 cara/apps/calculator/model_generator.py |  4 ++--
 cara/apps/expert.py                     | 14 +++++++-------
 2 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py
index 0d7506ae..ad65795e 100644
--- a/cara/apps/calculator/model_generator.py
+++ b/cara/apps/calculator/model_generator.py
@@ -269,10 +269,10 @@ class FormData:
         else:
             return ventilation
 
-    def mask(self) -> models._MaskBase:
+    def mask(self) -> models.Mask:
         # Initializes the mask type if mask wearing is "continuous", otherwise instantiates the mask attribute as
         # the "No mask"-mask
-        mask = models._MaskBase.types[self.mask_type if self.mask_wearing_option == "mask_on" else 'No mask']
+        mask = models.Mask.types[self.mask_type if self.mask_wearing_option == "mask_on" else 'No mask']
         return mask
 
     def infected_population(self) -> models.InfectedPopulation:
diff --git a/cara/apps/expert.py b/cara/apps/expert.py
index a0f273e1..31903b79 100644
--- a/cara/apps/expert.py
+++ b/cara/apps/expert.py
@@ -390,10 +390,10 @@ class ModelWidgets(View):
 
     def _build_mask(self, node):
         mask = node.dcs_instance()
-        for name, mask_ in models._MaskBase.types.items():
+        for name, mask_ in models.Mask.types.items():
             if mask == mask_:
                 break
-        mask_choice = widgets.Select(options=list(models._MaskBase.types.keys()), value=name)
+        mask_choice = widgets.Select(options=list(models.Mask.types.keys()), value=name)
 
         def on_mask_change(change):
             node.dcs_select(change['new'])
@@ -496,7 +496,7 @@ baseline_model = models.ExposureModel(
             number=1,
             virus=models.Virus.types['SARS_CoV_2'],
             presence=models.SpecificInterval(((8, 12), (13, 17))),
-            mask=models._MaskBase.types['No mask'],
+            mask=models.Mask.types['No mask'],
             activity=models.Activity.types['Seated'],
             expiration=models.Expiration.types['Talking'],
         ),
@@ -505,7 +505,7 @@ baseline_model = models.ExposureModel(
         number=10,
         presence=models.SpecificInterval(((8, 12), (13, 17))),
         activity=models.Activity.types['Seated'],
-        mask=models._MaskBase.types['No mask'],
+        mask=models.Mask.types['No mask'],
     ),
 )
 
@@ -515,10 +515,10 @@ class CARAStateBuilder(state.StateBuilder):
     # For example, build_type__VentilationBase is called when dealing with ConcentrationModel
     # types as it has a ventilation: _VentilationBase field.
 
-    def build_type__MaskBase(self, _: dataclasses.Field):
+    def build_type_Mask(self, _: dataclasses.Field):
         return state.DataclassStatePredefined(
-            models._MaskBase,
-            choices=models._MaskBase.types,
+            models.Mask,
+            choices=models.Mask.types,
         )
 
     def build_type_Virus(self, _: dataclasses.Field):

From d7bd53c288416a41c229ed8ddefd87523733a7d0 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Sun, 30 May 2021 19:31:56 +0200
Subject: [PATCH 11/14] Starting to modify exposure tests according to new Mask
 class

---
 cara/tests/models/test_exposure_model.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cara/tests/models/test_exposure_model.py b/cara/tests/models/test_exposure_model.py
index 464f25a9..c1e9090d 100644
--- a/cara/tests/models/test_exposure_model.py
+++ b/cara/tests/models/test_exposure_model.py
@@ -43,7 +43,7 @@ populations = [
     ),
     # A population with some array component for η_inhale.
     models.Population(
-        10, halftime, models.Mask(0.95, 0.15, np.array([0.3, 0.35])),
+        10, halftime, models.Mask(np.array([0.3, 0.35])),
         models.Activity.types['Standing'],
     ),
     # A population with some array component for inhalation_rate.

From ffb85c6b72b39b7fe62e1cdfa420282452960650 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Mon, 31 May 2021 06:32:17 +0200
Subject: [PATCH 12/14] Fixing the remaining tests, with the new masks

---
 cara/tests/models/test_exposure_model.py | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/cara/tests/models/test_exposure_model.py b/cara/tests/models/test_exposure_model.py
index c1e9090d..009cf092 100644
--- a/cara/tests/models/test_exposure_model.py
+++ b/cara/tests/models/test_exposure_model.py
@@ -60,10 +60,10 @@ populations = [
      np.array([14.4, 14.4]), np.array([99.6803184113, 99.5181053773])],
 
     [populations[2], KnownConcentrations(lambda t: 1.2),
-     np.array([14.4, 14.4]), np.array([99.4146994564, 99.6803184113])],
+     np.array([14.4, 14.4]), np.array([97.4574432074, 98.3493482895])],
 
     [populations[0], KnownConcentrations(lambda t: np.array([1.2, 2.4])),
-     np.array([14.4, 28.8]), np.array([99.6803184113, 99.9989780368])],
+     np.array([14.4, 28.8]), np.array([98.3493482895, 99.9727534893])],
 
     [populations[1], KnownConcentrations(lambda t: np.array([1.2, 2.4])),
      np.array([14.4, 28.8]), np.array([99.6803184113, 99.9976777757])],
@@ -123,22 +123,22 @@ def conc_model():
         models.InfectedPopulation(
             number=1,
             presence=interesting_times,
-            mask=models.Mask.types['Type I'],
+            mask=models.Mask.types['No mask'],
             activity=models.Activity.types['Seated'],
             virus=models.Virus.types['SARS_CoV_2'],
-            expiration=models.Expiration.types['Breathing'],
+            expiration=models.Expiration.types['Superspreading event'],
         )
     )
 
 # expected quanta were computed with a trapezoidal integration, using
 # a mesh of 10'000 pts per exposed presence interval.
 @pytest.mark.parametrize("exposed_time_interval, expected_quanta", [
-        [(0, 1), 0.0055680845],
-        [(1, 1.01), 6.4960491e-05],
-        [(1.01, 1.02), 6.3187723e-05],
-        [(12, 12.01), 1.9307359e-06],
-        [(12, 24), 0.079347465],
-        [(0, 24), 0.086122050],
+        [(0, 1), 5.4869151],
+        [(1, 1.01), 0.064013521],
+        [(1.01, 1.02), 0.062266596],
+        [(12, 12.01), 0.0019025904],
+        [(12, 24), 78.190763],
+        [(0, 24), 84.866592],
     ]
 )
 def test_exposure_model_integral_accuracy(exposed_time_interval,

From bfdb3e322e1b6f1de291fb64adeb4f1591974a10 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Mon, 31 May 2021 06:55:07 +0200
Subject: [PATCH 13/14] Mask exhale_efficiency use now a diameter in microns

---
 cara/models.py                 | 14 +++++++-------
 cara/tests/models/test_mask.py | 12 ++++++------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/cara/models.py b/cara/models.py
index 736e0992..56f663f4 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -489,14 +489,14 @@ class Mask:
         therein (Asadi 2020).
         Obtained from measurements of filtration efficiency and of
         the leakage through the sides.
-        Diameter is in cm.
+        Diameter is in microns.
         """
-        if diameter < 0.5e-4:
+        if diameter < 0.5:
             eta_out = 0.
-        elif diameter < 0.94614e-4:
-            eta_out = 0.5893 * diameter * 1e4 + 0.1546
-        elif diameter < 3e-4:
-            eta_out = 0.0509 * diameter * 1e4 + 0.664
+        elif diameter < 0.94614:
+            eta_out = 0.5893 * diameter + 0.1546
+        elif diameter < 3.:
+            eta_out = 0.0509 * diameter + 0.664
         else:
             eta_out = 0.8167
         return eta_out*self.factor_exhale
@@ -551,7 +551,7 @@ class Expiration(_ExpirationBase):
         total = 0
         for diameter, factor in zip(self.particle_sizes, self.ejection_factor):
             contribution = (volume(diameter) * factor *
-                            (1 - mask.exhale_efficiency(diameter)))
+                            (1 - mask.exhale_efficiency(diameter*1e4)))
             total += contribution
         return total
 
diff --git a/cara/tests/models/test_mask.py b/cara/tests/models/test_mask.py
index 7f7cb242..4a71d13c 100644
--- a/cara/tests/models/test_mask.py
+++ b/cara/tests/models/test_mask.py
@@ -11,7 +11,7 @@ from cara import models
         [np.array([0.3, 0.5]), np.array([0.3, 0.5])],
     ],
 )
-def test_masks_inhale(η_inhale, expected_inhale_efficiency):
+def test_mask_inhale(η_inhale, expected_inhale_efficiency):
     mask = models.Mask(η_inhale=η_inhale)
     npt.assert_equal(mask.inhale_efficiency(), 
                      expected_inhale_efficiency)
@@ -20,11 +20,11 @@ def test_masks_inhale(η_inhale, expected_inhale_efficiency):
 @pytest.mark.parametrize(
     "diameter, factor_exhale, expected_exhale_efficiency",
     [
-        [0.3e-4, 1., 0.],
-        [0.7e-4, 0.3, 0.56711*0.3],
-        [1.e-4, 1., 0.7149],
-        [4.e-4, 0.5, 0.8167*0.5],
-        [5.e-4, 0., 0.],
+        [0.3, 1., 0.],
+        [0.7, 0.3, 0.56711*0.3],
+        [1., 1., 0.7149],
+        [4., 0.5, 0.8167*0.5],
+        [5., 0., 0.],
     ],
 )
 def test_mask_exhale(diameter, factor_exhale, expected_exhale_efficiency):

From 9325eea09e5d339c103df48dfda2ba773cecda14 Mon Sep 17 00:00:00 2001
From: Nicolas Mounet <nicolas.mounet@cern.ch>
Date: Mon, 31 May 2021 08:55:55 +0200
Subject: [PATCH 14/14] Fixing docstring

---
 cara/models.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cara/models.py b/cara/models.py
index 56f663f4..88e5493a 100644
--- a/cara/models.py
+++ b/cara/models.py
@@ -529,7 +529,7 @@ class _ExpirationBase:
     types: typing.ClassVar[typing.Dict[str, "_ExpirationBase"]]
 
     def aerosols(self, mask: Mask):
-        # total volume of aerosols expired per volume of air (mL/cm^3).
+        # total volume of aerosols expired (cm^3).
         raise NotImplementedError("Subclass must implement")