Merge branch 'feature/expected_reproduction_sr' into 'master'

Expected number of new cases fix See merge request caimira/caimira!493
CERN · May 24, 2024 · 3f1e373 · 3f1e373
2 parents 4ca9816 + 7b17243
commit 3f1e373
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Showing 11 changed files with 110 additions and 22 deletions.
diff --git a/caimira/apps/calculator/__init__.py b/caimira/apps/calculator/__init__.py
@@ -42,7 +42,7 @@
 # calculator version. If the calculator needs to make breaking changes (e.g. change
 # form attributes) then it can also increase its MAJOR version without needing to
 # increase the overall CAiMIRA version (found at ``caimira.__version__``).
-__version__ = "4.15.1"
+__version__ = "4.15.2"
 
 LOG = logging.getLogger("Calculator")
 

diff --git a/caimira/apps/calculator/defaults.py b/caimira/apps/calculator/defaults.py
@@ -73,6 +73,7 @@
     'sensor_in_use': '',
     'short_range_option': 'short_range_no',
     'short_range_interactions': '[]',
+    'short_range_occupants': 0,
 }
 
 # ------------------ Activities ----------------------

diff --git a/caimira/apps/calculator/model_generator.py b/caimira/apps/calculator/model_generator.py
@@ -72,6 +72,7 @@ class VirusFormData(FormData):
     sensor_in_use: str
     short_range_option: str
     short_range_interactions: list
+    short_range_occupants: int
 
     _DEFAULTS: typing.ClassVar[typing.Dict[str, typing.Any]] = DEFAULTS
 
@@ -182,6 +183,13 @@ def validate(self):
 
             if total_percentage != 100:
                 raise ValueError(f'The sum of all respiratory activities should be 100. Got {total_percentage}.')
+
+        # Validate number of people with short-range interactions
+        max_occupants_for_sr = self.total_people - self.infected_people
+        if self.short_range_occupants > max_occupants_for_sr:
+            raise ValueError(
+                f'The total number of occupants having short-range interactions ({self.short_range_occupants}) should be lower than the exposed population ({max_occupants_for_sr}).'
+            )
 
     def initialize_room(self) -> models.Room:
         # Initializes room with volume either given directly or as product of area and height
@@ -206,7 +214,6 @@ def build_mc_model(self) -> mc.ExposureModel:
         room = self.initialize_room()
         ventilation: models._VentilationBase = self.ventilation()
         infected_population = self.infected_population()
-
         short_range = []
         if self.short_range_option == "short_range_yes":
             for interaction in self.short_range_interactions:
@@ -234,6 +241,7 @@ def build_mc_model(self) -> mc.ExposureModel:
                 geographic_cases=self.geographic_cases,
                 ascertainment_bias=CONFIDENCE_LEVEL_OPTIONS[self.ascertainment_bias],
             ),
+            exposed_to_short_range=self.short_range_occupants,
         )
 
     def build_model(self, sample_size=None) -> models.ExposureModel:

diff --git a/caimira/apps/calculator/report_generator.py b/caimira/apps/calculator/report_generator.py
@@ -431,7 +431,7 @@ def manufacture_alternative_scenarios(form: VirusFormData) -> typing.Dict[str, m
             scenarios['Neither ventilation nor masks'] = without_mask_or_vent.build_mc_model()
 
     else:
-        no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[])
+        no_short_range_alternative = dataclass_utils.replace(form, short_range_interactions=[], total_people=form.total_people - form.short_range_occupants)
         scenarios['Base scenario without short-range interactions'] = no_short_range_alternative.build_mc_model()
 
     return scenarios

diff --git a/caimira/apps/calculator/static/js/form.js b/caimira/apps/calculator/static/js/form.js
@@ -869,7 +869,7 @@ function validate_sr_parameter(obj, error_message) {
   if ($(obj).val() == "" || $(obj).val() == null) {
     if (!$(obj).hasClass("red_border") && !$(obj).prop("disabled")) {
       var parameter = document.getElementById($(obj).attr('id'));
-      insertErrorFor(parameter, error_message)
+      insertErrorFor(parameter, error_message);
       $(parameter).addClass("red_border");
     }
     return false;
@@ -880,6 +880,22 @@ function validate_sr_parameter(obj, error_message) {
   }
 }
 
+function validate_sr_people(obj) {
+  let sr_total_people = document.getElementById($(obj).attr('id'));
+  let max = document.getElementById("total_people").valueAsNumber - document.getElementById("infected_people").valueAsNumber;
+  if ($(obj).val() == "" || $(obj).val() == null || sr_total_people.valueAsNumber > max) {
+    if (!$(obj).hasClass("red_border")) {
+      insertErrorFor(sr_total_people, "Value must be less or equal than the number of exposed people.");
+      $(sr_total_people).addClass("red_border");
+    }
+    return false;
+  } else {
+    removeErrorFor($(obj));
+    $(obj).removeClass("red_border");
+    return true;
+  }
+}
+
 function parseValToNumber(val) {
   return parseInt(val.replace(':',''), 10);
 }
@@ -1084,7 +1100,6 @@ $(document).ready(function () {
   validateMaxInfectedPeople();
   $("#total_people").change(validateMaxInfectedPeople);
   $("#activity_type").change(validateMaxInfectedPeople);
-  $("#total_people").change(validateMaxInfectedPeople);
   $("#infected_people").change(validateMaxInfectedPeople);
 
   //Validate all non zero values
@@ -1253,7 +1268,8 @@ $(document).ready(function () {
     let activity = validate_sr_parameter('#sr_expiration_no_' + String(index)[0], "Required input.");
     let start = validate_sr_parameter('#sr_start_no_' + String(index)[0], "Required input.");
     let duration = validate_sr_parameter('#sr_duration_no_' + String(index)[0], "Required input.");
-    if (activity && start && duration) {
+    let total_people = validate_sr_people('#short_range_occupants');
+    if (activity && start && duration && total_people) {
       if (validate_sr_time('#sr_start_no_' + String(index)) && validate_sr_time('#sr_duration_no_' + String(index))) {
         document.getElementById('sr_expiration_no_' + String(index)).disabled = true;
         document.getElementById('sr_start_no_' + String(index)).disabled = true;

diff --git a/caimira/apps/templates/base/calculator.form.html.j2 b/caimira/apps/templates/base/calculator.form.html.j2
@@ -584,6 +584,16 @@
             <div class="col-md-12 p-0 form-group" id="dialog_sr"></div>
             <div class="text-center"><button type="button" class="add_node_btn_frm_field btn btn-primary btn-sm">Add row</button></div>
             <input type="text" class="form-control d-none" name="short_range_interactions">
+            <br />
+            <div class="form-group row">
+              <div class="col-sm-4">
+                <label class="col-form-label col-form-label-sm">Total people with short-range interactions:</label>
+              </div>
+              <div class="col-sm-2">
+                <input type="number" id="short_range_occupants" name="short_range_occupants" class="form-control form-control-sm" min="0" value="1" tabindex="-1" onchange="validate_sr_people(this)" required>
+              </div>
+              <div class="col-sm-6"></div>
+            </div>
           </div>
 
           <div class="modal-footer">

diff --git a/caimira/apps/templates/base/calculator.report.html.j2 b/caimira/apps/templates/base/calculator.report.html.j2
@@ -54,13 +54,20 @@
 	<div class="tab-content" style="border-top: #dee2e6 1px solid; margin-top: -1px" >
 
 		<div class="tab-pane show active" id="results" role="tabpanel" aria-labelledby="results-tab" style="padding: 1%">
+			{% set long_range_prob_inf = prob_inf %}
+			{% set long_range_expected_cases = expected_new_cases %}
 
+			{# Update values if short range option is "short_range_yes" #}
 			{% if form.short_range_option == "short_range_yes" %}
 				{% set scenario = alternative_scenarios.stats.values() | first %}
+				{# Probability of infection values #}
 				{% set long_range_prob_inf = scenario.probability_of_infection %}
-				{% set long_range_prob_probabilistic_exposure = scenario.prob_probabilistic_exposure if form.exposure_option == 'p_probabilistic_exposure' %}
-			{% else %}
-				{% set long_range_prob_inf = prob_inf %}
+				{# Expected new case values #}
+				{% set long_range_expected_cases = scenario.expected_new_cases %}
+
+				{% if form.exposure_option == 'p_probabilistic_exposure' %}
+					{% set long_range_prob_probabilistic_exposure = scenario.prob_probabilistic_exposure %}
+				{% endif %}
 			{% endif %}
 
 			{% block report_results %}
@@ -97,6 +104,7 @@
 														</div>
 													{% endblock long_range_warning_animation %}
 												</div>
+												<h6><b>Expected new cases:</b> {{ long_range_expected_cases | float_format }}</h6>
 											</div>
 											<br>
 											{% if form.short_range_option == "short_range_yes" %}
@@ -118,18 +126,19 @@
 														</div>
 														{% endblock warning_animation %}
 													</div>
+													<h6><b>Expected new cases:</b> {{ expected_new_cases | float_format }}</h6>
 												</div>
 											{% endif %}
 										<div class="d-flex">
 											{% block report_summary %}
 											<div class="flex-row align-self-center">
 												<div class="align-self-center alert alert-dark mb-0" role="alert">
-													Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the <b>probability of one exposed occupant getting infected is {{ long_range_prob_inf | non_zero_percentage }}</b> and the <b>expected number of new cases is {{ expected_new_cases | float_format }}</b>*.
+													Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the <b>probability of one exposed occupant getting infected is {{ long_range_prob_inf | non_zero_percentage }}</b> and the <b>expected number of new cases is {{ long_range_expected_cases | float_format }}</b>*.
 												</div>
 												{% if form.short_range_option == "short_range_yes" %}
 													<br>
 													<div class="align-self-center alert alert-dark mb-0" role="alert">
-														In this scenario, assuming <b>short-range interactions</b> occur, the <b>probability of one exposed occupant getting infected can go as high as {{ prob_inf | non_zero_percentage }}</b>.
+														In this scenario, the <b>probability the occupant(s) exposed to short-range interactions get infected can go as high as {{ prob_inf | non_zero_percentage }}</b> and the <b>expected number of new cases increases to {{ expected_new_cases | float_format }}</b>.
 													</div>
 												{% endif %}
 												{% block probabilistic_exposure_probability %}
@@ -601,14 +610,16 @@
 							{% endif %}
 							</p></li>
 							{% if form.short_range_option == "short_range_yes" %}
-							<li><p class="data_text">
-							Short-range interactions: {{ form.short_range_interactions|length }}
-							</p></li>
+							<li><p class="data_text">Total number of occupants having short-range interactions: {{ form.short_range_occupants }}</p></li>
 							<ul>
 							{% for interaction in form.short_range_interactions %}
-								<li>Expiratory activity {{ loop.index if form.short_range_interactions|length > 1 }}: {{ "Shouting/Singing" if interaction.expiration == "Shouting" else interaction.expiration }} </li>
-								<li>Start time {{ loop.index if form.short_range_interactions|length > 1 }}: {{ interaction.start_time }} </li>
-								<li>Duration {{ loop.index if form.short_range_interactions|length > 1 }}: {{ interaction.duration }} {{ "minutes" if interaction.duration|float > 1 else "minute" }}</li>
+							<li>Interaction no. {{ loop.index }}:
+							<ul>
+								<li>Expiratory activity: {{ "Shouting/Singing" if interaction.expiration == "Shouting" else interaction.expiration }} </li>
+								<li>Start time: {{ interaction.start_time }} </li>
+								<li>Duration: {{ interaction.duration }} {{ "minutes" if interaction.duration|float > 1 else "minute" }}</li>
+							</ul>
+							</li>
 							{% endfor %}
 							</ul>
 							{% endif %}

diff --git a/caimira/apps/templates/cern/calculator.report.html.j2 b/caimira/apps/templates/cern/calculator.report.html.j2
@@ -70,7 +70,7 @@
         <div class="alert alert-success mb-0" role="alert">
           <strong>Acceptable:</strong>
       {% endif %}
-        Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the <b>probability of one exposed occupant getting infected is {{long_range_prob_inf | non_zero_percentage}}</b> and the <b>expected number of new cases is {{expected_new_cases | float_format}}</b>*.
+        Taking into account the uncertainties tied to the model variables, in this scenario and assuming all occupants are exposed equally (i.e. without short-range interactions), the <b>probability of one exposed occupant getting infected is {{long_range_prob_inf | non_zero_percentage}}</b> and the <b>expected number of new cases is {{ long_range_expected_cases | float_format }}</b>*.
       </div>
       {% if form.short_range_option == "short_range_yes" %} 
         <br>
@@ -84,7 +84,7 @@
           <div class="alert alert-success mb-0" role="alert">
             <strong>Acceptable:</strong>
         {% endif %}
-        In this scenario, assuming <b>short-range interactions</b> occur, the <b>probability of one exposed occupant getting infected can go as high as {{prob_inf | non_zero_percentage}}</b>.
+        In this scenario, the <b>probability the occupant(s) exposed to short-range interactions get infected can go as high as {{ prob_inf | non_zero_percentage }}</b> and the <b>expected number of new cases increases to {{ expected_new_cases | float_format }}</b>.
         </div>
       {% endif %}
 

diff --git a/caimira/models.py b/caimira/models.py
@@ -1579,6 +1579,9 @@ class ExposureModel:
     #: Geographical data
     geographical_data: Cases
 
+    #: Total people with short-range interactions
+    exposed_to_short_range: int = 0
+
     #: The number of times the exposure event is repeated (default 1).
     @property
     def repeats(self) -> int:
@@ -1814,10 +1817,15 @@ def expected_new_cases(self) -> _VectorisedFloat:
                     "with dynamic occupancy")
 
         """
-        The expect_new_cases should always take the long-range infection_probability and multiply by the occupants exposed to long-range.
+        The expected_new_cases may provide one or two different outputs:
+            1) Long-range exposure: take the infection_probability and multiply by the occupants exposed to long-range. 
+            2) Short- and long-range exposure: take the infection_probability of long-range multiplied by the occupants exposed to long-range only, 
+               plus the infection_probability of short- and long-range multiplied by the occupants exposed to short-range only.
         """
+
         if self.short_range != ():
-            return nested_replace(self, {'short_range': ()}).infection_probability() * self.exposed.number / 100
+            new_cases_long_range = nested_replace(self, {'short_range': (),}).infection_probability() * (self.exposed.number - self.exposed_to_short_range)
+            return (new_cases_long_range + (self.infection_probability() * self.exposed_to_short_range)) / 100
 
         return self.infection_probability() * self.exposed.number / 100
 

diff --git a/caimira/tests/apps/calculator/conftest.py b/caimira/tests/apps/calculator/conftest.py
@@ -11,3 +11,12 @@ def baseline_form_data():
 @pytest.fixture
 def baseline_form(baseline_form_data, data_registry):
     return model_generator.VirusFormData.from_dict(baseline_form_data, data_registry)
+
+
+@pytest.fixture
+def baseline_form_with_sr(baseline_form_data, data_registry):
+    form_data_sr = baseline_form_data
+    form_data_sr['short_range_option'] = 'short_range_yes'
+    form_data_sr['short_range_interactions'] = '[{"expiration": "Shouting", "start_time": "10:30", "duration": "30"}]'
+    form_data_sr['short_range_occupants'] = 5
+    return model_generator.VirusFormData.from_dict(form_data_sr, data_registry)
diff --git a/caimira/tests/apps/calculator/test_report_generator.py b/caimira/tests/apps/calculator/test_report_generator.py
@@ -7,7 +7,9 @@
 import pytest
 
 from caimira.apps.calculator import make_app
-from caimira.apps.calculator.report_generator import ReportGenerator, readable_minutes
+from caimira.apps.calculator.model_generator import VirusFormData
+from caimira.apps.calculator.report_generator import (ReportGenerator, readable_minutes, calculate_report_data,
+    manufacture_alternative_scenarios, interesting_times, comparison_report)
 import caimira.apps.calculator.report_generator as rep_gen
 
 
@@ -90,3 +92,26 @@ def test_interesting_times_w_temp(exposure_model_w_outside_temp_changes):
         5., 5.4, 5.8, 6.2, 6.6, 7., 7.4, 7.8, 8.
     ]
     np.testing.assert_allclose(result, expected)
+
+
+def test_expected_new_cases(baseline_form_with_sr: VirusFormData):   
+    model = baseline_form_with_sr.build_model()
+
+    executor_factory = partial(
+        concurrent.futures.ThreadPoolExecutor, 1,
+    )
+
+    # Short- and Long-range contributions
+    report_data = calculate_report_data(baseline_form_with_sr, model, executor_factory)
+    sr_lr_expected_new_cases = report_data['expected_new_cases']
+    sr_lr_prob_inf = report_data['prob_inf']/100
+
+    # Long-range contributions alone
+    scenario_sample_times = interesting_times(model)
+    alternative_scenarios = manufacture_alternative_scenarios(baseline_form_with_sr)
+    alternative_statistics = comparison_report(
+        baseline_form_with_sr, report_data, alternative_scenarios, scenario_sample_times, executor_factory=executor_factory,
+    )
+
+    lr_expected_new_cases = alternative_statistics['stats']['Base scenario without short-range interactions']['expected_new_cases']
+    np.testing.assert_almost_equal(sr_lr_expected_new_cases, lr_expected_new_cases + sr_lr_prob_inf * baseline_form_with_sr.short_range_occupants, 2)