From 2165c71bf5e7e5b745165a0f0cd9da6e65ca6698 Mon Sep 17 00:00:00 2001
From: Luis Aleixo <luis.aleixo@cern.ch>
Date: Tue, 22 Mar 2022 14:52:50 +0100
Subject: [PATCH] Changed short range distance distribution to lognormal

---
 cara/apps/calculator/model_generator.py     |  2 +-
 cara/monte_carlo/data.py                    |  8 ++++++--
 cara/tests/models/test_short_range_model.py | 19 ++++++++-----------
 3 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py
index 4b8c0be0..ee76f162 100644
--- a/cara/apps/calculator/model_generator.py
+++ b/cara/apps/calculator/model_generator.py
@@ -250,7 +250,7 @@ class FormData:
             sr_presence=self.short_range_intervals()
             sr_activities=self.short_range_activities()
             short_range_expirations = tuple(short_range_expiration_distributions[activity] for activity in sr_activities)
-            dilutions=dilution_factor(activities=sr_activities, distance=np.random.uniform(0.5, 1.5, 250000))
+            dilutions=dilution_factor(activities=sr_activities)
         else:
             sr_presence=()
             short_range_expirations=()
diff --git a/cara/monte_carlo/data.py b/cara/monte_carlo/data.py
index e4c99552..98095389 100644
--- a/cara/monte_carlo/data.py
+++ b/cara/monte_carlo/data.py
@@ -5,7 +5,7 @@ import numpy as np
 from scipy import special as sp
 
 import cara.monte_carlo as mc
-from cara.monte_carlo.sampleable import Normal,LogNormal,LogCustomKernel,CustomKernel,Uniform
+from cara.monte_carlo.sampleable import LogNormal,LogCustomKernel,CustomKernel,Uniform
 
 
 sqrt2pi = np.sqrt(2.*np.pi)
@@ -182,7 +182,11 @@ def expiration_distribution(
     )
 
 
-def dilution_factor(activities, distance, D=0.02):
+def dilution_factor(activities):
+    D = 0.02
+    # From https://www.mdpi.com/1660-4601/17/4/1445/htm
+    distance = LogNormal(0.8542127255693238, 0.42755967248106513).generate_samples(250_000)
+    
     factors = []
     for activity in activities:
         u0 = 0.98 if activity == "Breathing" else 3.9
diff --git a/cara/tests/models/test_short_range_model.py b/cara/tests/models/test_short_range_model.py
index 3e40cc56..bc1546da 100644
--- a/cara/tests/models/test_short_range_model.py
+++ b/cara/tests/models/test_short_range_model.py
@@ -47,10 +47,7 @@ def expirations(presences) -> typing.Tuple[mc_models.Expiration, ...]:
 
 @pytest.fixture
 def dilutions(presences):
-    return dilution_factor(
-        activities=[activity for (activity, presence) in presences],
-        distance=np.random.uniform(0.5, 1.5, 250_000),
-    )
+    return dilution_factor(activities=[activity for (activity, presence) in presences])
 
 
 def test_short_range_model_ndarray(concentration_model, presences, expirations, dilutions):
@@ -64,9 +61,9 @@ def test_short_range_model_ndarray(concentration_model, presences, expirations,
 
 @pytest.mark.parametrize(
     "start, stop, expected_exposure", [
-        [8.5, 12.5, 5.844666077067048e-09],
-        [10.5, 11.0, 5.830120846251791e-09],
-        [10.6, 11.9, 4.6397748633454945e-09],
+        [8.5, 12.5, 5.963061627547172e-10],
+        [10.5, 11.0,  5.934552264225482e-10],
+        [10.6, 11.9, 4.709684623109963e-10],
     ]
 )
 def test_normed_exposure_between_bounds(
@@ -76,15 +73,15 @@ def test_normed_exposure_between_bounds(
     model = mc_models.ShortRangeModel(presences, expirations, dilutions)
     model = model.build_model(250_000)
     np.testing.assert_almost_equal(
-        model.normed_exposure_between_bounds(concentration_model, start, stop).mean(), expected_exposure
+        model.normed_exposure_between_bounds(concentration_model, start, stop).mean(), expected_exposure, decimal=10
     )
 
 
 @pytest.mark.parametrize(
     "time, expected_sr_normed_concentration, expected_concentration", [
-        [10.75, 1.1670056689678455e-08, 11.67005668967846],
-        # [14.75, 3.6414877020308386e-06, 3641.4877020308395],
-        # [16.75, 1.973757599365769e-05, 19737.57599365769],
+        [10.75, 1.1670056689678455e-08, 1.1731466540816526],
+        # [14.75, 3.6414877020308386e-06, 474.36376505412574],
+        # [16.75, 1.973757599365769e-05, 2850.6219623225024],
     ]
 )
 def test_short_range_model(