Merge branch 'master' into 'user-guide-update-1'

# Conflicts:
#   cara/apps/calculator/templates/report.html.j2

cara/apps/calculator/model_generator.py

@@ -403,7 +403,7 @@ def baseline_raw_form_data():
         'mask_type': 'Type I',
         'mask_wearing': 'removed',
         'mechanical_ventilation_type': '',
-        'model_version': 'BetaV1.1.0',
+        'model_version': 'v1.1.0',
         'opening_distance': '0.2',
         'recurrent_event_month': 'January',
         'room_number': '123',

cara/apps/calculator/report_generator.py

@@ -3,6 +3,7 @@ import dataclasses
 from datetime import datetime
 import io
 from pathlib import Path
+import typing
 
 import jinja2
 import matplotlib
@@ -21,14 +22,18 @@ class RepeatEvents:
     expected_new_cases: float
 
 
-def calculate_report_data(model: models.ExposureModel):
-    resolution = 600
-
+def model_start_end(model: models.ExposureModel):
     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])
+    return t_start, t_end
 
+
+def calculate_report_data(model: models.ExposureModel):
+    resolution = 600
+
+    t_start, t_end = model_start_end(model)
     times = list(np.linspace(t_start, t_end, resolution))
     concentrations = [model.concentration_model.concentration(time) for time in times]
     highest_const = max(concentrations)
@@ -99,6 +104,93 @@ def minutes_to_time(minutes: int) -> str:
     return f"{hour_string}:{minute_string}"
 
 
+def manufacture_alternative_scenarios(form: FormData) -> typing.Dict[str, models.ExposureModel]:
+    scenarios = {}
+
+    # Two special option cases - HEPA and/or FFP2 masks.
+    FFP2_being_worn = bool(form.mask_wearing == 'continuous' and form.mask_type == 'FFP2')
+    if FFP2_being_worn and form.hepa_option:
+        scenarios['Base scenario with HEPA and FFP2 masks'] = form.build_model()
+    elif FFP2_being_worn:
+        scenarios['Base scenario with FFP2 masks'] = form.build_model()
+    elif form.hepa_option:
+        scenarios['Base scenario with HEPA filter'] = form.build_model()
+
+    # The remaining scenarios are based on Type I masks (possibly not worn)
+    # and no HEPA filtration.
+    form = dataclasses.replace(form, mask_type='Type I')
+    if form.hepa_option:
+        form = dataclasses.replace(form, hepa_option=False)
+
+    with_mask = dataclasses.replace(form, mask_wearing='continuous')
+    without_mask = dataclasses.replace(form, mask_wearing='removed')
+
+    if form.ventilation_type == 'mechanical':
+        scenarios['Mechanical ventilation with Type I masks'] = with_mask.build_model()
+        scenarios['Mechanical ventilation without masks'] = without_mask.build_model()
+
+    elif form.ventilation_type == 'natural':
+        scenarios['Windows open with Type I masks'] = with_mask.build_model()
+        scenarios['Windows open without masks'] = without_mask.build_model()
+
+    # No matter the ventilation scheme, we include scenarios which don't have any ventilation.
+    with_mask_no_vent = dataclasses.replace(with_mask, ventilation_type='no-ventilation')
+    without_mask_or_vent = dataclasses.replace(without_mask, ventilation_type='no-ventilation')
+    scenarios['No ventilation with Type I masks'] = with_mask_no_vent.build_model()
+    scenarios['Neither ventilation nor masks'] = without_mask_or_vent.build_model()
+
+    return scenarios
+
+
+def comparison_plot(scenarios: typing.Dict[str, models.ExposureModel]):
+    fig = plt.figure()
+    ax = fig.add_subplot(1, 1, 1)
+
+    resolution = 350
+    times = None
+
+    dash_styled_scenarios = [
+        'Base scenario with FFP2 masks',
+        'Base scenario with HEPA filter',
+        'Base scenario with HEPA and FFP2 masks',
+    ]
+
+    for name, model in scenarios.items():
+        if times is None:
+            t_start, t_end = model_start_end(model)
+            times = np.linspace(t_start, t_end, resolution)
+        concentrations = [model.concentration_model.concentration(time) for time in times]
+
+        if name in dash_styled_scenarios:
+            ax.plot(times, concentrations, label=name, linestyle='--')
+        else:
+            ax.plot(times, concentrations, label=name, linestyle='-', alpha=0.5)
+
+    # Place a legend outside of the axes itself.
+    ax.legend(bbox_to_anchor=(1.05, 1), loc='upper left')
+    ax.spines['right'].set_visible(False)
+    ax.spines['top'].set_visible(False)
+
+    ax.set_xlabel('Time (hour of day)')
+    ax.set_ylabel('Concentration ($q/m^3$)')
+    ax.set_title('Concentration of infectious quanta')
+
+    return fig
+
+
+def comparison_report(scenarios: typing.Dict[str, models.ExposureModel]):
+    statistics = {}
+    for name, model in scenarios.items():
+        statistics[name] = {
+            'probability_of_infection': model.infection_probability(),
+            'expected_new_cases': model.expected_new_cases(),
+        }
+    return {
+        'plot': embed_figure(comparison_plot(scenarios)),
+        'stats': statistics,
+    }
+
+
 def build_report(model: models.ExposureModel, form: FormData):
     now = datetime.now()
     time = now.strftime("%d/%m/%Y %H:%M:%S")
@@ -112,6 +204,8 @@ def build_report(model: models.ExposureModel, form: FormData):
     }
 
     context.update(calculate_report_data(model))
+    alternative_scenarios = manufacture_alternative_scenarios(form)
+    context['alternative_scenarios'] = comparison_report(alternative_scenarios)
 
     cara_templates = Path(__file__).parent.parent / "templates"
     calculator_templates = Path(__file__).parent / "templates"

cara/apps/calculator/static/css/report.css

@@ -39,11 +39,15 @@ p.result_title {
 	font-size: 15pt;
 }
 
-.image {
+p.image {
 	text-align: center;
 	font-size: 13pt;
 }
 
-.discalimer {
+p.disclaimer {
 	font-size: 12pt;
 }
+
+p.notes {
+	font-size: 10pt;
+}

cara/apps/calculator/templates/report.html.j2

@@ -19,9 +19,12 @@
 
 	<p class=subtitle> Created {{ creation_date }} using model version {{ form.model_version }}</p><br>
 
+  <p><strong>Applicable rules: <br>
+  Please ensure that this scenario conforms to current <a href="https://hse.cern/covid-19-information"> CERN HSE rules<a> (minimum ventilation requirements, mask wearing and the maximum number of people permitted in a space).</strong></p>
+
 	<p>Simulation Name: {{ form.simulation_name }}</p>
 	<p>Room Number: {{ form.room_number }}</p>
-
+	
 	<p class="data_title">Input data:</p>
 	<ul>
 		<li><p class="data_text">Room Volume: {{ model.concentration_model.room.volume }} m³</p></li>
@@ -166,7 +169,40 @@
             {% endfor %}
             </tbody>
         </table>
-    <p>
+    </p>
+
+    <p class="data_title">Alternative scenarios:</p>
+    <p class="data_text">
+    <img id="scenario_concentration_plot" src="{{ alternative_scenarios.plot }}" align="left" />
+        <table class="table table-striped w-auto">
+            <thead class="thead-light">
+                <tr>
+                    <th>Scenario</th>
+                    <th>P(i)</th>
+                    <th>Expected new cases</th>
+                </tr>
+            </thead>
+            <tbody>
+            {% for scenario_name, scenario_stats in alternative_scenarios.stats.items() %}
+                <tr>
+                    <td>{{ scenario_name }}</td>
+                    <td>{{ scenario_stats.probability_of_infection | int_format }}%</td>
+                    <td style="text-align:right">{{ scenario_stats.expected_new_cases | float_format }}</td>
+                </tr>
+            {% endfor %}
+            </tbody>
+        </table>
+
+    </p>
+    <div style="clear: both;">
+
+    <p class="notes"> <strong> Notes for alternative scenarios: </strong><br>
+    1) This graph shows the concentration of infectious quanta in the air. The filtration of Type I and FFP2 masks, if worn, applies not only to the emission rate but also to the individual exposure (i.e. inhalation ).<br>
+    For this reason, scenarios with different types of mask will show the same concentration on the graph but have different Pi values.<br>
+    2) If you have selected more sophisticated options, such as HEPA filtration or FFP2 masks, this will be indicated in the plot as the "base scenario", representing the inputs inserted in the form.<br>
+    The other alternative scenarios shown for comparison will not include either HEPA filtration or FFP2 masks. <br>
+    <br>
+		</p>
 
 	<br><br><br>
 	<div style="border: 2px solid black; padding: 15px;">