Enhancements for Dynamic and Static Occupancy Handling

- Added default 'static' keyword to single group with static occupancy
- Added default values for 'dynamic_exposed_occupancy' and 'dynamic_infected_occupancy'
- Adapted default model to use ExposureModelGroup instance when static occupancy is defined
- Updated JS methods to generate multiple plots when dynamic occupancy is defined
- Handled the alternative scenario generation when dynamic occupancy is defined
- Improved results generation for exposure groups
- Updated HTML report for visualising results across multiple groups
- Enhanced model representations

Author: lrdossan

caimira/src/caimira/api/controller/virus_report_controller.py

@@ -4,7 +4,6 @@
 
 from caimira.calculator.validators.virus.virus_validator import VirusFormData
 from caimira.calculator.store.data_registry import DataRegistry
-from caimira.calculator.models.models import ExposureModel
 import caimira.calculator.report.virus_report_data as rg
 
 
@@ -33,5 +32,6 @@ def submit_virus_form(form_data: typing.Dict, report_generation_parallelism: typ
 
     # Handle model representation
     if report_data['model']: report_data['model'] = repr(report_data['model'])
+    for single_group_output in report_data['groups'].values(): del single_group_output['model'] # Model representation per group not needed
 
     return report_data

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

@@ -666,7 +666,7 @@ def fraction_deposited(self, evaporation_factor: float=0.3) -> _VectorisedFloat:
             # deposition fraction depends on aerosol particle diameter.
             d = (self.diameter * evaporation_factor)
             IFrac = 1 - 0.5 * (1 - (1 / (1 + (0.00076*(d**2.8)))))
-            fdep = IFrac * (0.0587
+            fdep = IFrac * (0.0587 # type: ignore
                     + (0.911/(1 + np.exp(4.77 + 1.485 * np.log(d))))
                     + (0.943/(1 + np.exp(0.508 - 2.58 * np.log(d)))))
         return fdep
@@ -1642,6 +1642,9 @@ class ExposureModel:
     #: Total people with short-range interactions
     exposed_to_short_range: int = 0
 
+    #: Unique group identifier
+    identifier: str = 'static'
+
     #: The number of times the exposure event is repeated (default 1).
     @property
     def repeats(self) -> int:

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

@@ -6,7 +6,6 @@
 import json
 import re
 
-from collections import defaultdict
 import numpy as np
 
 from .defaults import DEFAULTS, NO_DEFAULT, COFFEE_OPTIONS_INT

caimira/src/caimira/calculator/validators/form_validator.py

@@ -245,7 +245,7 @@ def initialize_room(self) -> models.Room:
 
         return models.Room(volume=volume, inside_temp=models.PiecewiseConstant((0, 24), (inside_temp,)), humidity=humidity) # type: ignore
 
-    def build_mc_model(self) -> typing.Union[mc.ExposureModel, mc.ExposureModelGroup]:
+    def build_mc_model(self) -> mc.ExposureModelGroup:
         size = self.data_registry.monte_carlo['sample_size']
 
         room: models.Room = self.initialize_room()
@@ -295,30 +295,31 @@ def build_mc_model(self) -> typing.Union[mc.ExposureModel, mc.ExposureModelGroup
                     exposed=exposed_population,
                     geographical_data=geographical_data,
                     exposed_to_short_range=self.short_range_occupants,
+                    identifier=exposure_group,
                 )
                 exposure_model_set.append(exposure_model)
 
-            if len(list(self.dynamic_exposed_occupancy.keys())) == 1:
-                return exposure_model_set[0]
-            else:
-                return mc.ExposureModelGroup(
-                    data_registry=self.data_registry,
-                    exposure_models=[individual_model.build_model(size) for individual_model in exposure_model_set]
-                )
+            return mc.ExposureModelGroup(
+                data_registry=self.data_registry,
+                exposure_models=[individual_model.build_model(size) for individual_model in exposure_model_set]
+            )
 
         elif self.occupancy_format == 'static':
             exposed_population = self.exposed_population()
             short_range_tuple = tuple(item for sublist in short_range.values() for item in sublist)
-            return mc.ExposureModel(
+            return mc.ExposureModelGroup(
                 data_registry=self.data_registry,
-                concentration_model=concentration_model,
-                short_range=short_range_tuple,
-                exposed=exposed_population,
-                geographical_data=geographical_data,
-                exposed_to_short_range=self.short_range_occupants,
+                exposure_models = [mc.ExposureModel(
+                    data_registry=self.data_registry,
+                    concentration_model=concentration_model,
+                    short_range=short_range_tuple,
+                    exposed=exposed_population,
+                    geographical_data=geographical_data,
+                    exposed_to_short_range=self.short_range_occupants,
+                ).build_model(size)]
             )
 
-    def build_model(self, sample_size=None) -> typing.Union[models.ExposureModel, models.ExposureModelGroup]:
+    def build_model(self, sample_size=None) -> models.ExposureModelGroup:
         size = self.data_registry.monte_carlo['sample_size'] if not sample_size else sample_size
         return self.build_mc_model().build_model(size=size)
 

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

@@ -17,7 +17,7 @@
 
 def test_model_from_dict(baseline_form_data, data_registry):
     form = virus_validator.VirusFormData.from_dict(baseline_form_data, data_registry)
-    assert isinstance(form.build_model(), models.ExposureModel)
+    assert isinstance(form.build_model(), models.ExposureModelGroup)
 
 
 def test_model_from_dict_invalid(baseline_form_data, data_registry):

caimira/tests/apps/calculator/test_model_generator.py

@@ -123,8 +123,8 @@ def prepare_context(
         data_registry_version: typing.Optional[str] = f"v{model.data_registry.version}" if model.data_registry.version else None
 
         # Alternative scenarios data
-        alternative_scenarios: typing.Dict[str,typing.Any] = alternative_scenarios_data(form, report_data, executor_factory)
-        context.update(alternative_scenarios)
+        if form.occupancy_format == 'static':
+            context.update(alternative_scenarios_data(form, report_data, executor_factory)) 
 
         # Alternative viral load data
         if form.conditional_probability_viral_loads:

cern_caimira/src/cern_caimira/apps/calculator/report/virus_report.py

@@ -126,13 +126,13 @@ p.notes {
         padding: 15px; 
         page-break-inside: avoid;
     }
-    #button_full_exposure, #button_hide_high_concentration {
+    #button_full_exposure-group_static, #button_hide_high_concentration-group_static {
         display: none!important;
     }
-    #long_range_cumulative_checkbox, #lr_cumulative_checkbox_label {
+    #long_range_cumulative_checkbox-group_static, #lr_cumulative_checkbox_label-group_static {
         display: none!important;
     }
-    #button_alternative_full_exposure, #button_alternative_hide_high_concentration {
+    #button_alternative_full_exposure-group_static, #button_alternative_hide_high_concentration-group_static {
         display: none!important;
     }
     #export-csv {

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

@@ -301,6 +301,7 @@ function displayFittingData(json_response) {
   // Not needed for the form submission
   delete json_response["CO2_plot_img"];
   delete json_response["predictive_CO2"];
+  delete json_response["CO2_plot_data"];
   // Convert nulls to empty strings in the JSON response
   if (json_response["room_capacity"] === null) json_response["room_capacity"] = '';
   if (json_response["ventilation_lsp_values"] === null) json_response["ventilation_lsp_values"] = '';

cern_caimira/src/cern_caimira/apps/calculator/static/js/co2_form.js

@@ -4,13 +4,18 @@ function on_report_load(conditional_probability_viral_loads) {
 }
 
 /* Generate the concentration plot using d3 library. */
-function draw_plot(svg_id) {
+function draw_plot(svg_id, group_id, times, concentrations_zoomed, 
+                concentrations, cumulative_doses, long_range_cumulative_doses, 
+                exposed_presence_intervals, short_range_interactions) {
 
     // Used for controlling the short-range interactions 
-    let button_full_exposure = document.getElementById("button_full_exposure");
-    let button_hide_high_concentration = document.getElementById("button_hide_high_concentration");
-    let long_range_checkbox = document.getElementById('long_range_cumulative_checkbox')
-    let show_sr_legend = short_range_expirations?.length > 0;
+    let button_full_exposure = document.getElementById(`button_full_exposure-group_${group_id}`);
+    let button_hide_high_concentration = document.getElementById(`button_hide_high_concentration-group_${group_id}`);
+    let long_range_checkbox = document.getElementById(`long_range_cumulative_checkbox-group_${group_id}`);
+    let show_sr_legend = short_range_interactions.length > 0;
+
+    let short_range_intervals = short_range_interactions.map((interaction) => interaction["presence_interval"]);
+    let short_range_expirations = short_range_interactions.map((interaction) => interaction["expiration"]);
 
     var data_for_graphs = {
         'concentrations': [],
@@ -521,12 +526,12 @@ function draw_plot(svg_id) {
     }
 
     // Draw for the first time to initialize.
-    redraw();
+    redraw(svg_id);
     update_concentration_plot(concentrations, cumulative_doses);
 
     // Redraw based on the new size whenever the browser window is resized.
     window.addEventListener("resize", e => {
-        redraw();
+        redraw(svg_id);
         if (button_full_exposure && button_full_exposure.disabled) update_concentration_plot(concentrations, cumulative_doses);
         else update_concentration_plot(concentrations_zoomed, long_range_cumulative_doses)
     });
@@ -536,12 +541,13 @@ function draw_plot(svg_id) {
 // 'list_of_scenarios' is a dictionary with all the scenarios 
 // 'times' is a list of times for all the scenarios
 function draw_generic_concentration_plot(
-        plot_svg_id,
+        svg_id,
+        times,
         y_axis_label,
         h_lines,
     ) {
 
-    if (plot_svg_id === 'CO2_concentration_graph') {
+    if (svg_id === 'CO2_concentration_graph') {
         list_of_scenarios = {'CO₂ concentration': {'concentrations': CO2_concentrations}};
         min_y_axis_domain = 400;
     }
@@ -575,7 +581,7 @@ function draw_generic_concentration_plot(
     var first_scenario = Object.values(data_for_scenarios)[0]
 
     // Add main SVG element
-    var plot_div = document.getElementById(plot_svg_id);
+    var plot_div = document.getElementById(svg_id);
     var vis = d3.select(plot_div).append('svg');
 
     var xRange = d3.scaleTime().domain([first_scenario[0].hour, first_scenario[first_scenario.length - 1].hour]);
@@ -706,7 +712,7 @@ function draw_generic_concentration_plot(
     }
 
     function update_concentration_plot(concentration_data) {
-        list_of_scenarios = (plot_svg_id === 'CO2_concentration_graph') ? {'CO₂ concentration': {'concentrations': CO2_concentrations}} : alternative_scenarios
+        list_of_scenarios = (svg_id === 'CO2_concentration_graph') ? {'CO₂ concentration': {'concentrations': CO2_concentrations}} : alternative_scenarios
         var highest_concentration = 0.
 
         for (scenario in list_of_scenarios) {
@@ -739,11 +745,11 @@ function draw_generic_concentration_plot(
     var graph_width;
     var graph_height;
 
-    function redraw() {
+    function redraw(svg_id) {
         // Define width and height according to the screen size. Always use an already defined
-        var window_width = document.getElementById('concentration_plot').clientWidth;
+        var window_width = document.getElementById(svg_id).clientWidth;
         var div_width = window_width;
-        var div_height = document.getElementById('concentration_plot').clientHeight;
+        var div_height = document.getElementById(svg_id).clientHeight;
         graph_width = div_width;
         graph_height = div_height;
         var margins = { top: 30, right: 20, bottom: 50, left: 60 };
@@ -882,12 +888,12 @@ function draw_generic_concentration_plot(
     }
 
     // Draw for the first time to initialize.
-    redraw();
+    redraw(svg_id);
     update_concentration_plot('concentrations');
 
     // Redraw based on the new size whenever the browser window is resized.
     window.addEventListener("resize", e => {
-        redraw();
+        redraw(svg_id);
         update_concentration_plot('concentrations');
     });
 }

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

@@ -455,8 +455,8 @@
     </div><br>
 
     <input type="text" class="form-control d-none" name="occupancy_format" value="static" required> {# "static" vs. "dynamic" #}
-    <input type="text" class="form-control d-none" name="dynamic_exposed_occupancy">
-    <input type="text" class="form-control d-none" name="dynamic_infected_occupancy">
+    <input type="text" class="form-control d-none" name="dynamic_exposed_occupancy" value="{}">
+    <input type="text" class="form-control d-none" name="dynamic_infected_occupancy" value="[]">
 
     <div class="form-group row">
       <div class="col-sm-4"><label class="col-form-label">Total number of occupants:</label></div>