updated expiration definition

caimira/src/caimira/calculator/models/models.py

@@ -711,6 +711,9 @@ class Expiration(_ExpirationBase):
     # to c_n,i in Eq. (4) of https://doi.org/10.1101/2021.10.14.21264988)
     cn: float = 1.
 
+    #: Expiration name
+    name: typing.Optional[str] = None
+
     @property
     def particle(self) -> Particle:
         """
@@ -1313,7 +1316,7 @@ class ShortRangeModel:
     data_registry: DataRegistry
 
     #: Expiration type
-    expiration: _ExpirationBase
+    expiration: Expiration
 
     #: Activity type
     activity: Activity
@@ -1324,9 +1327,6 @@ class ShortRangeModel:
     #: Interpersonal distances
     distance: _VectorisedFloat
 
-    #: Expiration definition
-    expiration_def: typing.Optional[str] = None
-
     def dilution_factor(self) -> _VectorisedFloat:
         '''
         The dilution factor for the respective expiratory activity type.

caimira/src/caimira/calculator/models/monte_carlo/data.py

@@ -365,6 +365,7 @@ def expiration_distribution(
         BLO_factors,
         d_min=0.1,
         d_max=30.,
+        exp_type=None,
 ):
     """
     Returns an Expiration with an aerosol diameter distribution, defined
@@ -382,6 +383,7 @@ def expiration_distribution(
             kernel_bandwidth=0.1,
         ),
         cn=BLOmodel(data_registry, BLO_factors).integrate(d_min, d_max),
+        name=exp_type,
     )
 
 
@@ -432,7 +434,8 @@ def short_range_expiration_distributions(data_registry):
             data_registry=data_registry,
             BLO_factors=BLO_factors,
             d_min=param_evaluation(data_registry.expiration_particle['particle_size_range']['short_range'], 'minimum_diameter'),
-            d_max=param_evaluation(data_registry.expiration_particle['particle_size_range']['short_range'], 'maximum_diameter')
+            d_max=param_evaluation(data_registry.expiration_particle['particle_size_range']['short_range'], 'maximum_diameter'),
+            exp_type=exp_type,
         )
         for exp_type, BLO_factors in expiration_BLO_factors(data_registry).items()
     }

caimira/src/caimira/calculator/report/virus_report_data.py

@@ -5,8 +5,6 @@ import io
 import typing
 import numpy as np
 import matplotlib.pyplot as plt
-import matplotlib
-matplotlib.use('Agg')
 from collections import defaultdict
 
 from caimira.calculator.models import models, dataclass_utils, profiler, monte_carlo as mc
@@ -226,7 +224,7 @@ def group_results(form: VirusFormData, model_group: models.ExposureModelGroup) -
             # Short range outputs
             short_range_interactions: dict = defaultdict(list)
             for short_range_model in single_group.short_range:
-                short_range_interactions[short_range_model.expiration_def].extend(
+                short_range_interactions[short_range_model.expiration.name].extend(
                     short_range_model.presence.boundaries()
                 )
 

caimira/src/caimira/calculator/validators/virus/virus_validator.py

@@ -258,9 +258,10 @@ class VirusFormData(FormData):
 
         short_range = defaultdict(list)
         if self.short_range_option == "short_range_yes":
+            sr_expiration_distributions = short_range_expiration_distributions(self.data_registry)
             for key, group in self.short_range_interactions.items():
                 for interaction in group:
-                    expiration = short_range_expiration_distributions(self.data_registry)[interaction['expiration']]
+                    expiration = sr_expiration_distributions[interaction['expiration']]
                     presence = self.short_range_interval(interaction)
                     distances = short_range_distances(self.data_registry)
                     short_range[key].append(mc.ShortRangeModel(
@@ -269,7 +270,6 @@ class VirusFormData(FormData):
                         activity=infected_population.activity,
                         presence=presence,
                         distance=distances,
-                        expiration_def=interaction['expiration']
                     ))
 
         concentration_model: models.ConcentrationModel = mc.ConcentrationModel(

cern_caimira/src/cern_caimira/apps/calculator/static/js/report.js

@@ -290,7 +290,7 @@ function draw_plot(svg_id, group_id, times, concentrations_zoomed,
         });
 
         // Short-Range Area.
-        short_range_intervals.forEach((b, index) => {
+        short_range_intervals.flat().forEach((b, index) => {
             shortRangeArea[index].x(d => xTimeRange(d.time))
                 .y0(graph_height - 50)
                 .y1(d => yRange(d.concentration));