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Renaming finf in test_full_algorithm

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Nicolas Mounet 2023-12-01 17:37:30 +01:00 committed by Luis Aleixo
parent 1f90d08163
commit d53d62f3f3
4 changed files with 40 additions and 41 deletions
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41
caimira/apps/calculator/static/js/report.js
View file

@ -59,7 +59,7 @@ function draw_plot(svg_id) {
.attr('class', 'y label')
.attr('fill', 'black')
.attr('text-anchor', 'middle')
.text('Mean concentration (virions/m³)');
.text('Mean concentration (IRP/m³)');
// Y cumulative concentration axis declaration.
var yAxisCumEl = vis.append('svg:g')
@ -71,7 +71,7 @@ function draw_plot(svg_id) {
.attr('class', 'y label')
.attr('fill', 'black')
.attr('text-anchor', 'middle')
.text('Mean cumulative dose (infectious virus)');
.text('Mean cumulative dose (IRP)');
// Legend for the plot elements - line and area.
@ -82,8 +82,7 @@ function draw_plot(svg_id) {
.style('fill', '#1f77b4');
// Concentration line text
var legendLineText = vis.append('text')
.text('Mean concentration')
.style('font-size', '15px');
.text('Mean concentration (Infectious Respiratory Particles)')
// Cumulative dose line icon
var legendCumulativeIcon = vis.append('line')
@ -92,8 +91,7 @@ function draw_plot(svg_id) {
.style("stroke", '#1f77b4');
// Cumulative dose line text
var legendCumutiveText = vis.append('text')
.text('Cumulative dose')
.style('font-size', '15px');
.text('Cumulative dose (Infectious Respiratory Particles)')
// Area line icon
var legendAreaIcon = vis.append('rect')
@ -104,7 +102,6 @@ function draw_plot(svg_id) {
// Area line text
var legendAreaText = vis.append('text')
.text('Presence of exposed person(s)')
.style('font-size', '15px');
sr_unique_activities = [...new Set(short_range_expirations)]
if (show_sr_legend) {
@ -142,7 +139,7 @@ function draw_plot(svg_id) {
if (show_sr_legend) legendBBox_height = 68 + 20 * sr_unique_activities.length;
else legendBBox_height = 68;
var legendBBox = vis.append('rect')
.attr('width', 255)
.attr('width', 420)
.attr('height', legendBBox_height)
.attr('stroke', 'lightgrey')
.attr('stroke-width', '2')
@ -310,9 +307,9 @@ function draw_plot(svg_id) {
graph_width = div_width;
graph_height = div_height
var margins = { top: 30, right: 20, bottom: 50, left: 60 };
if (div_width >= 900) { // For screens with width > 900px legend can be on the graph's right side.
div_width = 900;
graph_width = div_width * (2/3);
if (div_width >= 1100) { // For screens with width > 1100px legend can be on the graph's right side.
div_width = 1100;
graph_width = 600;
const svg_margins = {'margin-left': '0rem'};
Object.entries(svg_margins).forEach(([prop,val]) => vis.style(prop,val));
}
@ -361,7 +358,7 @@ function draw_plot(svg_id) {
yAxisCumLabelEl.attr('transform', 'rotate(-90, 0,' + graph_height + ')')
.attr('x', (graph_height + margins.bottom) / 2.1);
if (plot_div.clientWidth >= 900) {
if (plot_div.clientWidth >= 1100) {
yAxisCumLabelEl.attr('y', graph_width * 1.7);
}
else {
@ -373,7 +370,7 @@ function draw_plot(svg_id) {
const space_between_text_icon = 30;
const text_height = 6;
// Legend on right side.
if (plot_div.clientWidth >= 900) {
if (plot_div.clientWidth >= 1100) {
legendLineIcon.attr('x', graph_width + legend_x_start)
.attr('y', margins.top + size);
legendLineText.attr('x', graph_width + legend_x_start + space_between_text_icon)
@ -746,9 +743,9 @@ function draw_generic_concentration_plot(
graph_width = div_width;
graph_height = div_height;
var margins = { top: 30, right: 20, bottom: 50, left: 60 };
if (window_width >= 900) { // For screens with width > 900px legend can be on the graph's right side.
div_width = 900;
graph_width = div_width * (2/3);
if (window_width >= 1100) { // For screens with width > 1100px legend can be on the graph's right side.
div_width = 1100;
graph_width = 600;
const svg_margins = {'margin-left': '0rem'};
Object.entries(svg_margins).forEach(([prop,val]) => vis.style(prop,val));
}
@ -799,7 +796,7 @@ function draw_generic_concentration_plot(
var scenario_index = Object.keys(data_for_scenarios).indexOf(scenario_name)
// Legend on right side.
var size = 20 * (scenario_index + 1);
if (window_width >= 900) {
if (window_width >= 1100) {
label_icons[scenario_name].attr('x', graph_width + legend_x_start)
.attr('y', margins.top + size);
label_text[scenario_name].attr('x', graph_width + legend_x_start + space_between_text_icon)
@ -817,7 +814,7 @@ function draw_generic_concentration_plot(
if (h_lines) {
h_lines.map((line, index) => {
size = 21 * (scenario_index + index + 2); // account for previous legend elements
if (window_width >= 900) {
if (window_width >= 1100) {
h_line_label_icon[line.label].attr("x1", graph_width + legend_x_start)
.attr("x2", graph_width + legend_x_start + 20)
.attr("y1", margins.top + size)
@ -839,7 +836,7 @@ function draw_generic_concentration_plot(
}
// Legend on right side.
if (window_width >= 900) {
if (window_width >= 1100) {
legendBBox.attr('x', graph_width * 1.02)
.attr('y', margins.top * 1.15);
@ -899,10 +896,10 @@ function draw_histogram(svg_id, prob, prob_sd) {
var vis = d3.select(plot_div).append('svg');
// set the dimensions and margins of the graph
if (div_width > 900) {
div_width = 900;
if (div_width > 1100) {
div_width = 1100;
var margins = { top: 30, right: 20, bottom: 50, left: 60 };
var graph_width = div_width * (2/3);
var graph_width = 600;
const svg_margins = {'margin-left': '0rem'};
Object.entries(svg_margins).forEach(([prop,val]) => vis.style(prop,val));
}

16
caimira/apps/expert.py
View file

@ -131,13 +131,13 @@ class ExposureModelResult(View):
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
ax.set_xlabel('Time (hours)')
ax.set_ylabel('Mean concentration ($virions/m^{3}$)')
ax.set_title('Concentration of virions \nand Cumulative dose')
ax.set_ylabel('Mean concentration ($IRP/m^{3}$)')
ax.set_title('Concentration and Cumulative\ndose of Infectious Respiratory Particles')
ax2 = ax.twinx()
ax2.spines['left'].set_visible(False)
ax2.spines['top'].set_visible(False)
ax2.set_ylabel('Mean cumulative dose (infectious virus)')
ax2.set_ylabel('Mean cumulative dose (IRP)')
ax2.spines['right'].set_linestyle((0,(1,4)))
return ax, ax2
@ -193,8 +193,8 @@ class ExposureModelResult(View):
self.ax.set_xlim(left = min(min(infected_presence.boundaries()[0]), min(exposed_presence.boundaries()[0])),
right = max(max(infected_presence.boundaries()[1]), max(exposed_presence.boundaries()[1])))
figure_legends = [mlines.Line2D([], [], color='#3530fe', markersize=15, label='Mean concentration'),
mlines.Line2D([], [], color='#0000c8', markersize=15, ls="dotted", label='Cumulative dose'),
figure_legends = [mlines.Line2D([], [], color='#3530fe', markersize=15, label='Mean concentration (Infectious Respiratory Particles)'),
mlines.Line2D([], [], color='#0000c8', markersize=15, ls="dotted", label='Cumulative dose (Infectious Respiratory Particles)'),
patches.Patch(edgecolor="#96cbff", facecolor='#96cbff', label='Presence of exposed person(s)')]
self.ax.legend(handles=figure_legends)
@ -236,15 +236,15 @@ class ExposureComparisonResult(View):
ax.spines['top'].set_visible(False)
ax.set_xlabel('Time (hours)')
ax.set_ylabel('Mean concentration ($virions/m^{3}$)')
ax.set_title('Concentration of virions \nand Cumulative dose')
ax.set_ylabel('Mean concentration ($IRP/m^{3}$)')
ax.set_title('Concentration and Cumulative\ndose of Infectious Respiratory Particles')
ax2 = ax.twinx()
ax2.spines['left'].set_visible(False)
ax2.spines['top'].set_visible(False)
ax2.spines['right'].set_linestyle((0,(1,4)))
ax2.set_ylabel('Mean cumulative dose (infectious virus)')
ax2.set_ylabel('Mean cumulative dose (IRP)')
return ax, ax2

2
caimira/apps/templates/base/calculator.report.html.j2
View file

@ -277,7 +277,7 @@
var alternative_scenarios = {{ alternative_scenarios.stats | JSONify }}
draw_generic_concentration_plot(
"alternative_scenario_plot",
"Mean concentration (virions/m³)",
"Mean concentration (IRP/m³)",
);
</script>
<br>

22
caimira/tests/test_full_algorithm.py
View file

@ -56,8 +56,8 @@ class SimpleConcentrationModel:
#: Number of infected people
num_infected: int = 1
#: Fraction of infected viruses
finf: _VectorisedFloat = 0.5
#: Fraction of infected viruses (viable to RNA ratio)
viable_to_RNA: _VectorisedFloat = 0.5
#: Host immunity factor (0. for not immune)
HI: _VectorisedFloat = 0.
@ -182,7 +182,8 @@ class SimpleConcentrationModel:
return ( ( (0 if not self.infected_presence.triggered(t)
else self.f(lambda_rate,0))
+ result * np.exp(-lambda_rate*(t-ti)) )
* self.num_infected * self.finf * (1. - self.HI) / self.room_volume)
* self.num_infected * self.viable_to_RNA
* (1. - self.HI) / self.room_volume)
@dataclass(frozen=True)
@ -410,7 +411,8 @@ class SimpleExposureModel(SimpleConcentrationModel):
else self.f_with_fdep(lambda_rate,0,evaporation)*(t2-t1))
+ (primitive(t2) * np.exp(-lambda_rate*(t2-ti)) -
primitive(t1) * np.exp(-lambda_rate*(t1-ti)) ) )
* self.num_infected * self.finf * (1. - self.HI) / self.room_volume)
* self.num_infected * self.viable_to_RNA
* (1. - self.HI) / self.room_volume)
@method_cache
def integrated_shortrange_concentration(self) -> _VectorisedFloat:
@ -528,7 +530,7 @@ def simple_c_model() -> SimpleConcentrationModel:
room_volume = 50.,
lambda_ventilation= 1.,
BLO_factors = expiration_BLO_factors['Breathing'],
finf = models.Virus.types['SARS_CoV_2_DELTA'].viable_to_RNA_ratio,
viable_to_RNA = models.Virus.types['SARS_CoV_2_DELTA'].viable_to_RNA_ratio,
HI = 0.,
)
@ -576,7 +578,7 @@ def simple_expo_sr_model(simple_sr_models) -> SimpleExposureModel:
room_volume = 50.,
lambda_ventilation= 1.,
BLO_factors = expiration_BLO_factors['Breathing'],
finf = models.Virus.types['SARS_CoV_2_DELTA'].viable_to_RNA_ratio,
viable_to_RNA = models.Virus.types['SARS_CoV_2_DELTA'].viable_to_RNA_ratio,
HI = 0.,
ID50 = models.Virus.types['SARS_CoV_2_DELTA'].infectious_dose,
transmissibility = models.Virus.types['SARS_CoV_2_DELTA'].transmissibility_factor,
@ -624,7 +626,7 @@ def simple_expo_sr_model_distr() -> SimpleExposureModel:
room_volume = 50.,
lambda_ventilation= 1.,
BLO_factors = expiration_BLO_factors['Breathing'],
finf = virus_distributions['SARS_CoV_2_DELTA'
viable_to_RNA = virus_distributions['SARS_CoV_2_DELTA'
].build_model(SAMPLE_SIZE).viable_to_RNA_ratio,
HI = 0.,
ID50 = virus_distributions['SARS_CoV_2_DELTA'
@ -685,7 +687,7 @@ def test_longrange_exposure(c_model):
room_volume = 50.,
lambda_ventilation= 1.,
BLO_factors = expiration_BLO_factors['Breathing'],
finf = models.Virus.types['SARS_CoV_2_DELTA'].viable_to_RNA_ratio,
viable_to_RNA = models.Virus.types['SARS_CoV_2_DELTA'].viable_to_RNA_ratio,
HI = 0.,
ID50 = models.Virus.types['SARS_CoV_2_DELTA'].infectious_dose,
transmissibility = models.Virus.types['SARS_CoV_2_DELTA'].transmissibility_factor,
@ -726,7 +728,7 @@ def test_longrange_concentration_with_distributions(c_model_distr,time):
room_volume = 50.,
lambda_ventilation= 1.,
BLO_factors = expiration_BLO_factors['Breathing'],
finf = virus_distributions['SARS_CoV_2_DELTA'
viable_to_RNA = virus_distributions['SARS_CoV_2_DELTA'
].build_model(SAMPLE_SIZE).viable_to_RNA_ratio,
HI = 0.,
)
@ -746,7 +748,7 @@ def test_longrange_exposure_with_distributions(c_model_distr):
room_volume = 50.,
lambda_ventilation= 1.,
BLO_factors = expiration_BLO_factors['Breathing'],
finf = virus_distributions['SARS_CoV_2_DELTA'
viable_to_RNA = virus_distributions['SARS_CoV_2_DELTA'
].build_model(SAMPLE_SIZE).viable_to_RNA_ratio,
HI = 0.,
ID50 = virus_distributions['SARS_CoV_2_DELTA'