Merge branch 'develop/calculator_inf_vs_exp_times' into 'master'

Disentangle infected and exposed presence times in model_generator

See merge request cara/cara!87

cara/apps/calculator/model_generator.py

@@ -172,7 +172,7 @@ class FormData:
             coffee_times.append((start, end))
         return tuple(coffee_times)
 
-    def present_interval(self) -> models.Interval:
+    def present_interval(self, start, finish) -> models.Interval:
         leave_times = []
         enter_times = []
         if self.lunch_option:
@@ -193,19 +193,19 @@ class FormData:
         # representing the infected person entering and leaving the room. Note that if one of the evenly spaced coffee-
         # breaks happens to coincide with the lunch-break, it is simply ignored.
         present_intervals = []
-        time = self.infected_start
+        time = start
         is_present = True
-        while time < self.infected_finish:
+        while time < finish:
             if is_present:
                 if not leave_times:
-                    present_intervals.append((time / 60, self.infected_finish / 60))
+                    present_intervals.append((time / 60, finish / 60))
                     break
 
                 if leave_times[-1] <= time:
                     leave_times.pop()
                 else:
                     new_time = leave_times.pop()
-                    present_intervals.append((time / 60, min(new_time, self.infected_finish) / 60))
+                    present_intervals.append((time / 60, min(new_time, finish) / 60))
                     is_present = False
                     time = new_time
 
@@ -221,6 +221,12 @@ class FormData:
 
         return models.SpecificInterval(tuple(present_intervals))
 
+    def infected_present_interval(self) -> models.Interval:
+        return self.present_interval(self.infected_start, self.infected_finish)
+
+    def exposed_present_interval(self) -> models.Interval:
+        return self.present_interval(self.activity_start, self.activity_finish)
+
 
 def model_from_form(form: FormData) -> models.ExposureModel:
     # Initializes room with volume either given directly or as product of area and height
@@ -262,7 +268,7 @@ def model_from_form(form: FormData) -> models.ExposureModel:
             infected=models.InfectedPopulation(
                 number=infected_occupants,
                 virus=virus,
-                presence=form.present_interval(),
+                presence=form.infected_present_interval(),
                 mask=mask,
                 activity=infected_activity,
                 expiration=infected_expiration
@@ -270,7 +276,7 @@ def model_from_form(form: FormData) -> models.ExposureModel:
         ),
         exposed=models.Population(
             number=exposed_occupants,
-            presence=form.present_interval(),
+            presence=form.exposed_present_interval(),
             activity=exposed_activity,
             mask=mask,
         )

cara/apps/calculator/report_generator.py

@@ -24,8 +24,10 @@ class RepeatEvents:
 def calculate_report_data(model: models.ExposureModel):
     resolution = 600
 
-    t_start = model.exposed.presence.boundaries()[0][0]
-    t_end = model.exposed.presence.boundaries()[-1][1]
+    t_start = min(model.exposed.presence.boundaries()[0][0],
+                  model.concentration_model.infected.presence.boundaries()[0][0])
+    t_end = max(model.exposed.presence.boundaries()[-1][1],
+                model.concentration_model.infected.presence.boundaries()[-1][1])
 
     times = list(np.linspace(t_start, t_end, resolution))
     concentrations = [model.concentration_model.concentration(time) for time in times]

cara/tests/apps/calculator/test_model_generator.py

@@ -98,7 +98,7 @@ def test_ventilation_window_hepa(baseline_form):
                                [baseline_form.ventilation().air_exchange(room, t) for t in ts])
 
 
-def test_present_intervals(baseline_form):
+def test_infected_present_intervals(baseline_form):
     baseline_form.coffee_duration = 15
     baseline_form.coffee_breaks = 2
     baseline_form.activity_start = 9 * 60
@@ -108,9 +108,21 @@ def test_present_intervals(baseline_form):
     baseline_form.infected_start = 10 * 60
     baseline_form.infected_finish = 15 * 60
     correct = ((10, 11), (11.25, 12.5), (13.5, 15.0))
-    assert baseline_form.present_interval().present_times == correct
+    assert baseline_form.infected_present_interval().present_times == correct
 
 
+def test_exposed_present_intervals(baseline_form):
+    baseline_form.coffee_duration = 15
+    baseline_form.coffee_breaks = 2
+    baseline_form.activity_start = 9 * 60
+    baseline_form.activity_finish = 17 * 60
+    baseline_form.lunch_start = 12 * 60 + 30
+    baseline_form.lunch_finish = 13 * 60 + 30
+    baseline_form.infected_start = 10 * 60
+    baseline_form.infected_finish = 15 * 60
+    correct = ((9, 11), (11.25, 12.5), (13.5, 15), (15.25, 17.0))
+    assert baseline_form.exposed_present_interval().present_times == correct
+
 def test_key_validation(baseline_form_data):
     baseline_form_data['activity_type'] = 'invalid key'
     with pytest.raises(ValueError):