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Changed label on short range activity and added BR on dilution factor

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This commit is contained in:
Luis Aleixo 2022-03-28 15:41:55 +02:00
parent b51848b755
commit 5720f0340a
7 changed files with 126 additions and 83 deletions
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28
cara/apps/calculator/model_generator.py
View file

@ -13,7 +13,7 @@ from cara import data
import cara.data.weather
import cara.monte_carlo as mc
from .. import calculator
from cara.monte_carlo.data import activity_distributions, virus_distributions, mask_distributions, dilution_factor
from cara.monte_carlo.data import activity_distributions, virus_distributions, mask_distributions, short_range_distances
from cara.monte_carlo.data import expiration_distribution, expiration_BLO_factors, expiration_distributions, short_range_expiration_distributions
@ -245,29 +245,31 @@ class FormData:
else:
humidity = 0.5
room = models.Room(volume=volume, humidity=humidity)
infected_population = self.infected_population()
if self.short_range_option == "short_range_yes":
short_range_expirations = tuple(short_range_expiration_distributions[interaction['expiration']] for interaction in self.short_range_interactions)
short_range_activities = tuple([infected_population.activity for _ in self.short_range_interactions])
sr_presence=self.short_range_intervals()
sr_activities=self.short_range_activities()
short_range_expirations = tuple(short_range_expiration_distributions[activity] for activity in sr_activities)
dilutions=dilution_factor(activities=sr_activities)
else:
sr_presence=()
short_range_expirations=()
dilutions=()
short_range_activities=()
sr_presence=()
# Initializes and returns a model with the attributes defined above
return mc.ExposureModel(
concentration_model=mc.ConcentrationModel(
room=room,
ventilation=self.ventilation(),
infected=self.infected_population(),
infected=infected_population,
evaporation_factor=0.3,
),
short_range = mc.ShortRangeModel(
presence=sr_presence,
expirations=short_range_expirations,
dilutions=dilutions,
activities=short_range_activities,
presence=sr_presence,
distances=short_range_distances,
),
exposed=self.exposed_population(),
)
@ -655,7 +657,7 @@ class FormData:
for interaction in self.short_range_interactions:
start_time = time_string_to_minutes(interaction['start_time'])
duration = float(interaction['duration'])
short_range_intervals.append((interaction['activity'], models.SpecificInterval((start_time/60, (start_time + duration)/60))))
short_range_intervals.append((interaction['expiration'], models.SpecificInterval((start_time/60, (start_time + duration)/60))))
return tuple(short_range_intervals)
@ -665,10 +667,6 @@ class FormData:
breaks=self.exposed_lunch_break_times() + self.exposed_coffee_break_times(),
)
def short_range_activities(self) -> typing.List[str]:
return ([interaction['activity'] for interaction in self.short_range_interactions]
if self.short_range_interactions else [])
def build_expiration(expiration_definition) -> mc._ExpirationBase:
if isinstance(expiration_definition, str):

44
cara/apps/calculator/static/js/form.js
View file

@ -408,7 +408,7 @@ function validate_form(form) {
$(".form_field_outer_row").each(function (index, element){
let obj = {};
const $element = $(element);
obj.activity = $element.find("[name='short_range_activity']").val();
obj.expiration = $element.find("[name='short_range_expiration']").val();
obj.start_time = $element.find("[name='short_range_start_time']").val();
obj.duration = $element.find("[name='short_range_duration']").val();
short_range_interactions.push(JSON.stringify(obj));
@ -656,8 +656,8 @@ $(document).ready(function () {
let index = 1;
for (const interaction of JSON.parse(value)) {
$("#dialog_sr").append(inject_sr_interaction(index, value = interaction, is_validated="row_validated"))
$('#sr_activity_no_' + String(index)).val(interaction.activity).change();
document.getElementById('sr_activity_no_' + String(index)).disabled = true;
$('#sr_expiration_no_' + String(index)).val(interaction.expiration).change();
document.getElementById('sr_expiration_no_' + String(index)).disabled = true;
document.getElementById('sr_start_no_' + String(index)).disabled = true;
document.getElementById('sr_duration_no_' + String(index)).disabled = true;
document.getElementById('edit_row_no_' + String(index)).style.cssText = 'display:inline !important';
@ -838,35 +838,35 @@ $(document).ready(function () {
function inject_sr_interaction(index, value, is_validated) {
return `<div class="col-md-12 form_field_outer p-0">
<div class="form_field_outer_row split ${is_validated}">
<div class="split" style="flex: 3">
<div class="form_field_outer_row ${is_validated} split">
<div class='form-group row'>
<div class="col-sm-4"><label class="col-form-label"> Activity: </label></br></div>
<div class="col-sm-7"><select id="sr_activity_no_${index}" name="short_range_activity" class="form-control" onchange="validate_sr_parameter(this)" form="not-submitted">
<div class="col-sm-4"><label class="col-form-label col-form-label-sm"> Expiration: </label><br></div>
<div class="col-sm-8"><select id="sr_expiration_no_${index}" name="short_range_expiration" class="form-control form-control-sm" onchange="validate_sr_parameter(this)" form="not-submitted">
<option value="" selected disabled>Select type</option>
<option value="Breathing">Breathing</option>
<option value="Speaking">Speaking</option>
<option value="Shouting">Shouting</option>
</select></br>
</select><br>
</div>
</div>
<div class='form-group row'>
<div class="col-sm-4"><label class="col-form-label"> Start: </label></div>
<div class="col-sm-7"><input type="time" class="form-control short_range_option" name="short_range_start_time" id="sr_start_no_${index}" value="${value.start_time}" onchange="validate_sr_time(this)" form="not-submitted"></br></div>
</div>
</div>
<div class="split" style="flex: 2">
<div class='form-group row' style="flex: 2">
<div class="col-sm-4"><label class="col-form-label"> Duration:</label></div>
<div class="col-sm-8"><input type="number" id="sr_duration_no_${index}" value="${value.duration}" class="form-control short_range_option" name="short_range_duration" min=1 placeholder="Minutes" onchange="validate_sr_time(this)" form="not-submitted"></br></div>
<div class='form-group row'>
<div class="col-sm-4"><label class="col-form-label col-form-label-sm"> Start: </label></div>
<div class="col-sm-8"><input type="time" class="form-control form-control-sm short_range_option" name="short_range_start_time" id="sr_start_no_${index}" value="${value.start_time}" onchange="validate_sr_time(this)" form="not-submitted"><br></div>
</div>
<div class="form-group mt-1" style="flex: 1">
<div class='form-group row'>
<div class="col-sm-4"><label class="col-form-label col-form-label-sm"> Duration:</label></div>
<div class="col-sm-8"><input type="number" id="sr_duration_no_${index}" value="${value.duration}" class="form-control form-control-sm short_range_option" name="short_range_duration" min=1 placeholder="Minutes" onchange="validate_sr_time(this)" form="not-submitted"><br></div>
</div>
<div class="form-group" style="max-width: 8rem">
<button type="button" id="edit_row_no_${index}" class="edit_node_btn_frm_field btn btn-success btn-sm d-none">Edit</button>
<button type="button" id="validate_row_no_${index}" class="validate_node_btn_frm_field btn btn-success btn-sm">Save</button>
<button type="button" class="remove_node_btn_frm_field btn btn-danger btn-sm">Delete</button>
</div>
</div>
</div>
</div>`
}
@ -889,12 +889,12 @@ $(document).ready(function () {
// Validate row button (Save button)
$("body").on("click", ".validate_node_btn_frm_field", function() {
var index = $(this).attr('id').split('_').slice(-1)[0];
let activity = validate_sr_parameter('#sr_activity_no_' + String(index)[0], "Required input.");
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) {
if (validate_sr_time('#sr_start_no_' + String(index)) && validate_sr_time('#sr_start_no_' + String(index))) {
document.getElementById('sr_activity_no_' + String(index)).disabled = true;
document.getElementById('sr_expiration_no_' + String(index)).disabled = true;
document.getElementById('sr_start_no_' + String(index)).disabled = true;
document.getElementById('sr_duration_no_' + String(index)).disabled = true;
document.getElementById('edit_row_no_' + String(index)).style.cssText = 'display:inline !important';
@ -915,7 +915,7 @@ $(document).ready(function () {
$("body").on("click", ".edit_node_btn_frm_field", function() {
$(this).hide();
let id = $(this).attr('id').split('_').slice(-1)[0];
document.getElementById('sr_activity_no_' + String(id)).disabled = false;
document.getElementById('sr_expiration_no_' + String(id)).disabled = false;
document.getElementById('sr_start_no_' + String(id)).disabled = false;
document.getElementById('sr_duration_no_' + String(id)).disabled = false;
document.getElementById('validate_row_no_' + String(id)).style.cssText = 'display:inline !important';

5
cara/apps/expert.py
View file

@ -504,9 +504,10 @@ baseline_model = models.ExposureModel(
evaporation_factor=0.3,
),
short_range=models.ShortRangeModel(
presence=(),
expirations=(),
dilutions=(),
activities=(),
presence=(),
distances=(),
),
exposed=models.Population(
number=10,

5
cara/apps/templates/base/calculator.form.html.j2
View file

@ -391,11 +391,12 @@
<h5 class="modal-title" id="short_range_dialogTitle">Short-range interactions</h5>
</div>
<div class="modal-body">
<div class="col-md-12 p-0 form-group" id="dialog_sr">
</div>
<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">
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary dismiss_btn_frm_field" data-dismiss="modal">Clear all</button>
<button type="button" class="btn btn-primary close_btn_frm_field">Save all</button>

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

@ -335,7 +335,7 @@
</p></li>
<ul>
{% for interaction in form.short_range_interactions %}
<li>Expiratory activity {{ loop.index if form.short_range_interactions|length > 1 }}: {{ interaction.activity }} </li>
<li>Expiratory activity {{ loop.index if form.short_range_interactions|length > 1 }}: {{ 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>
{% endfor %}

58
cara/models.py
View file

@ -1074,14 +1074,52 @@ class ConcentrationModel:
@dataclass(frozen=True)
class ShortRangeModel:
#: Short-range activities and respective interactions
presence: typing.Tuple[typing.Tuple[str, SpecificInterval], ...]
#: Expiration types
expirations: typing.Tuple[_ExpirationBase, ...]
#: The dilution factors for each of the expiratory activity
dilutions: typing.Tuple[_VectorisedFloat, ...]
#: Activity types
activities: typing.Tuple[Activity, ...]
#: Short-range expirtory activities and respective interactions
presence: typing.Tuple[typing.Tuple[str, SpecificInterval], ...]
#: Interpersonal distances
distances: _VectorisedFloat
def dilution_factor(self, BR: _VectorisedFloat) -> _VectorisedFloat:
'''
The dilution factor for the respective expiratory activity type.
'''
# Average mouth diameter
D = 0.02
# Convert Breathing rate from m3/h to m3/s
BR_s = BR/3600
# Area of the mouth assuming a perfect circle
Am = np.pi*(D**2)/4
# Initial velocity from the division of the Breathing rate with the area
u0 = BR_s/Am
tstar = 2.0
Cr1 = 0.18
Cr2 = 0.2
Cx1 = 2.4
# The expired flow rate during the expiration period, m^3/s
Q0 = u0 * np.pi/4*D**2
# Parameters in the jet-like stage
x01 = D/2/Cr1
# Time of virtual origin
t01 = (x01/Cx1)**2 * (Q0*u0)**(-0.5)
# The transition point, m
xstar = np.mean(Cx1*(Q0*u0)**0.25*(tstar + t01)**0.5 - x01)
# Dilution factor at the transition point xstar
Sxstar = np.mean(2*Cr1*(xstar+x01)/D)
return np.piecewise(self.distances, [self.distances < xstar, self.distances >= xstar],
[
lambda distance: 2*Cr1*(distance + x01)/D,
lambda distance: Sxstar*(1 + Cr2*(distance - xstar)/Cr1/(xstar + x01))**3
])
def _normed_concentration(self, concentration_model: ConcentrationModel, time: float) -> _VectorisedFloat:
"""
@ -1095,16 +1133,18 @@ class ShortRangeModel:
start, stop = tuple(period.boundaries())
# Verifies if the given time falls within a short-range interaction
if start < time <= stop:
dilution = self.dilutions[index]
dilution = self.dilution_factor(self.activities[index].exhalation_rate)
jet_origin_concentration = self.expirations[index].jet_origin_concentration()
# Long-range concentration normalized by the virus viral load
long_range_normed_concentration = concentration_model.concentration(time) / concentration_model.virus.viral_load_in_sputum
long_range_normed_concentration = (concentration_model.concentration(time) /
concentration_model.virus.viral_load_in_sputum)
# The long-range concentration values are then approximated using interpolation:
# The set of points where we want the interpolated values are the short-range particle diameters (given the current expiration);
# The set of points with a known value are the long-range particle diameters (given the initial expiration);
# The set of known values are the long-range concentration values normalized by the viral load.
long_range_normed_concentration_interpolated=np.interp(self.expirations[index].particle.diameter, concentration_model.infected.particle.diameter, long_range_normed_concentration)
long_range_normed_concentration_interpolated=np.interp(self.expirations[index].particle.diameter,
concentration_model.infected.particle.diameter, long_range_normed_concentration)
# Short-range concentration formula. The long-range concentration is added in the concentration method (ExposureModel).
return ((1/dilution)*(jet_origin_concentration - long_range_normed_concentration_interpolated))
@ -1146,7 +1186,7 @@ class ShortRangeModel:
start_bound, stop_bound = start, stop
jet_origin_integrated = self.expirations[index].jet_origin_concentration()
dilution = self.dilutions[index]
dilution = self.dilution_factor(self.activities[index].exhalation_rate)
total_normed_concentration = -(concentration_model.integrated_concentration(start_bound, stop_bound)/concentration_model.virus.viral_load_in_sputum/dilution)
total_normed_concentration_interpolated = np.interp(self.expirations[index].particle.diameter, concentration_model.infected.particle.diameter, total_normed_concentration)

67
cara/monte_carlo/data.py
View file

@ -182,39 +182,39 @@ def expiration_distribution(
)
def dilution_factor(activities):
D = 0.02
# From https://www.mdpi.com/1660-4601/17/4/1445/htm
distance = LogNormal(0.8542127255693238, 0.42755967248106513).generate_samples(250_000)
# def dilution_factor(activities):
# D = 0.02
# # Fit from Fig 8 a) "stand-stand" in https://www.mdpi.com/1660-4601/17/4/1445/htm
# distance = LogNormal(-0.269359136417347, 0.4728300188814934).generate_samples(250_000)
factors = []
for activity in activities:
u0 = 0.98 if activity == "Breathing" else 3.9
tstar = 2.0
Cr1 = 0.18
Cr2 = 0.2
Cx1 = 2.4
# The expired flow rate during the expiration period, m^3/s
Q0 = u0 * np.pi/4*D**2
# Parameters in the jet-like stage
x01 = D/2/Cr1
# Time of virtual origin
t01 = (x01/Cx1)**2 * (Q0*u0)**(-0.5)
# The transition point, m
xstar = Cx1*(Q0*u0)**0.25*(tstar + t01)**0.5 - x01
# Dilution factor at the transition point xstar
Sxstar = 2*Cr1*(xstar+x01)/D
factors.append(
np.piecewise(
distance,
[distance < xstar, distance >= xstar],
[
lambda distance: 2*Cr1*(distance + x01)/D,
lambda distance: Sxstar*(1 + Cr2*(distance - xstar)/Cr1/(xstar + x01))**3
]
)
)
return factors
# factors = []
# for activity in activities:
# u0 = 0.98 if activity == "Breathing" else 3.9
# tstar = 2.0
# Cr1 = 0.18
# Cr2 = 0.2
# Cx1 = 2.4
# # The expired flow rate during the expiration period, m^3/s
# Q0 = u0 * np.pi/4*D**2
# # Parameters in the jet-like stage
# x01 = D/2/Cr1
# # Time of virtual origin
# t01 = (x01/Cx1)**2 * (Q0*u0)**(-0.5)
# # The transition point, m
# xstar = Cx1*(Q0*u0)**0.25*(tstar + t01)**0.5 - x01
# # Dilution factor at the transition point xstar
# Sxstar = 2*Cr1*(xstar+x01)/D
# factors.append(
# np.piecewise(
# distance,
# [distance < xstar, distance >= xstar],
# [
# lambda distance: 2*Cr1*(distance + x01)/D,
# lambda distance: Sxstar*(1 + Cr2*(distance - xstar)/Cr1/(xstar + x01))**3
# ]
# )
# )
# return factors
expiration_BLO_factors = {
@ -235,3 +235,6 @@ short_range_expiration_distributions = {
exp_type: expiration_distribution(BLO_factors, d_max=100)
for exp_type, BLO_factors in expiration_BLO_factors.items()
}
short_range_distances = LogNormal(-0.269359136417347, 0.4728300188814934)