added activity distributions from global store

CERN · Oct 13, 2023 · a96cc18 · a96cc18
1 parent 88f7f54
commit a96cc18
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Showing 2 changed files with 76 additions and 12 deletions.
diff --git a/caimira/apps/calculator/global_store/constants.py b/caimira/apps/calculator/global_store/constants.py
@@ -4,6 +4,59 @@
 # Global variable to keep track of whether data has been fetched
 data_fetched = False
 
+activity_distributions = {
+    'Seated': {
+        'inhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': -0.6872121723362303, 'standard_deviation_gaussian': 0.10498338229297108 },
+        },
+        'exhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': -0.6872121723362303, 'standard_deviation_gaussian': 0.10498338229297108 },
+        },
+    },
+    'Standing': {
+        'inhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': -0.5742377578494785, 'standard_deviation_gaussian': 0.09373162411398223 },
+        },
+        'exhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': -0.5742377578494785, 'standard_deviation_gaussian': 0.09373162411398223 },
+        },
+    },
+    'Light activity': {
+        'inhalation_rate': { 
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': 0.21380242785625422, 'standard_deviation_gaussian': 0.09435378091059601 },
+        },
+        'exhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': 0.21380242785625422, 'standard_deviation_gaussian': 0.09435378091059601 },
+        },
+    },
+    'Moderate activity': {
+        'inhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': 0.551771330362601, 'standard_deviation_gaussian': 0.1894616357138137 },
+        },
+        'exhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': 0.551771330362601, 'standard_deviation_gaussian': 0.1894616357138137 },
+        },
+    },
+    'Heavy exercise': {
+        'inhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': 1.1644665696723049, 'standard_deviation_gaussian': 0.21744554768657565 },
+        },
+        'exhalation_rate': {
+            'associated_distribution': 'Numpy Log-normal Distribution (random.lognormal)',
+            'parameters': { 'mean_gaussian': 1.1644665696723049, 'standard_deviation_gaussian': 0.21744554768657565 },
+        },
+    },
+}
+
 viable_to_RNA_ratio = {
     'low': 0.01,
     'high': 0.6,
@@ -72,6 +125,7 @@
     },
 }
 
+
 def update_local_reference(local_data, api_data):
     '''
     Recursive function that iterates through the keys and values of local and remote dictionaries.
@@ -87,7 +141,7 @@ def update_local_reference(local_data, api_data):
 
 
 async def populate_data():
-    global data_fetched, covid_overal_vl_data, infectious_dose, viable_to_RNA_ratio, virus_distributions
+    global data_fetched, covid_overal_vl_data, infectious_dose, viable_to_RNA_ratio, virus_distributions, activity_distributions
 
     if not data_fetched and os.environ.get('DATA_SERVICE_ENABLED', 'False').lower() == 'true':
         # Fetch data if it hasn't been fetched yet
@@ -100,8 +154,8 @@ async def populate_data():
         covid_overal_vl_data = update_local_reference(covid_overal_vl_data, data['covid_overal_vl_data'])
         viable_to_RNA_ratio = update_local_reference(viable_to_RNA_ratio, data['viable_to_RNA_ratio_distribution'])
         # TODO: reverse (error in schema)
-        # virus_distributions = update_local_reference(virus_distributions, data['virus_distributions'])
         virus_distributions = update_local_reference(data['virus_distributions'], virus_distributions)
+        activity_distributions = update_local_reference(data['activity_distributions'], activity_distributions)
 
         data_fetched = True
 

diff --git a/caimira/monte_carlo/data.py b/caimira/monte_carlo/data.py
@@ -172,20 +172,30 @@ def integrate(self, dmin, dmax):
 
 # From https://doi.org/10.1101/2021.10.14.21264988 and references therein
 activity_distributions = {
-    'Seated': mc.Activity(LogNormal(-0.6872121723362303, 0.10498338229297108),
-                          LogNormal(-0.6872121723362303, 0.10498338229297108)),
+    'Seated': mc.Activity(
+        inhalation_rate = param_evaluation(constants.activity_distributions['Seated'], 'inhalation_rate'),
+        exhalation_rate = param_evaluation(constants.activity_distributions['Seated'], 'exhalation_rate'),
+    ),
 
-    'Standing': mc.Activity(LogNormal(-0.5742377578494785, 0.09373162411398223),
-                            LogNormal(-0.5742377578494785, 0.09373162411398223)),
+    'Standing': mc.Activity(
+        inhalation_rate = param_evaluation(constants.activity_distributions['Standing'], 'inhalation_rate'),
+        exhalation_rate = param_evaluation(constants.activity_distributions['Standing'], 'exhalation_rate'),
+    ),
 
-    'Light activity': mc.Activity(LogNormal(0.21380242785625422,0.09435378091059601),
-                                  LogNormal(0.21380242785625422,0.09435378091059601)),
+    'Light activity': mc.Activity(
+        inhalation_rate = param_evaluation(constants.activity_distributions['Light activity'], 'inhalation_rate'),
+        exhalation_rate = param_evaluation(constants.activity_distributions['Light activity'], 'exhalation_rate'),
+    ),
 
-    'Moderate activity': mc.Activity(LogNormal(0.551771330362601, 0.1894616357138137),
-                                     LogNormal(0.551771330362601, 0.1894616357138137)),
+    'Moderate activity': mc.Activity(
+        inhalation_rate = param_evaluation(constants.activity_distributions['Moderate activity'], 'inhalation_rate'),
+        exhalation_rate = param_evaluation(constants.activity_distributions['Moderate activity'], 'exhalation_rate'),
+    ),
 
-    'Heavy exercise': mc.Activity(LogNormal(1.1644665696723049, 0.21744554768657565),
-                                  LogNormal(1.1644665696723049, 0.21744554768657565)),
+    'Heavy exercise': mc.Activity(
+        inhalation_rate = param_evaluation(constants.activity_distributions['Heavy exercise'], 'inhalation_rate'),
+        exhalation_rate = param_evaluation(constants.activity_distributions['Heavy exercise'], 'exhalation_rate'),
+    ),
 }