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modified file name and references. removed unused variables

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This commit is contained in:
Luis Aleixo 2023-05-26 09:44:47 +02:00
parent 1171e51f90
commit 0cb6477cb2
3 changed files with 52 additions and 31 deletions
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73
caimira/apps/calculator/DEFAULT_DATA.py → caimira/apps/calculator/defaults.py
View file

@ -79,33 +79,55 @@ DEFAULTS = {
# ------------------ Activities ----------------------
ACTIVITIES: typing.List[typing.Dict[str, typing.Any]] = [
{'name': 'office', 'activity': 'Seated', 'expiration': {'Speaking': 1, 'Breathing': 2}}, # Mostly silent in the office, but 1/3rd of time speaking.
{'name': 'smallmeeting', 'activity': 'Seated', 'expiration': {'Speaking': 1, 'Breathing': None}},
{'name': 'largemeeting', 'activity': 'Standing', 'expiration': {'Speaking': 1, 'Breathing': 2}}, # Each infected person spends 1/3 of time speaking.
# Mostly silent in the office, but 1/3rd of time speaking.
{'name': 'office', 'activity': 'Seated',
'expiration': {'Speaking': 1, 'Breathing': 2}},
{'name': 'smallmeeting', 'activity': 'Seated',
'expiration': {'Speaking': 1, 'Breathing': None}},
# Each infected person spends 1/3 of time speaking.
{'name': 'largemeeting', 'activity': 'Standing',
'expiration': {'Speaking': 1, 'Breathing': 2}},
{'name': 'callcentre', 'activity': 'Seated', 'expiration': 'Speaking'},
{'name': 'controlroom-day', 'activity': 'Seated', 'expiration': {'Speaking': 1, 'Breathing': 1}}, # Daytime control room shift, 50% speaking.
{'name': 'controlroom-night', 'activity': 'Seated', 'expiration': {'Speaking': 1, 'Breathing': 9}}, # Nightshift control room, 10% speaking.
# Daytime control room shift, 50% speaking.
{'name': 'controlroom-day', 'activity': 'Seated',
'expiration': {'Speaking': 1, 'Breathing': 1}},
# Nightshift control room, 10% speaking.
{'name': 'controlroom-night', 'activity': 'Seated',
'expiration': {'Speaking': 1, 'Breathing': 9}},
{'name': 'library', 'activity': 'Seated', 'expiration': 'Breathing'},
{'name': 'lab', 'activity': 'Light activity', 'expiration': {'Speaking': 1, 'Breathing': 1}}, # Model 1/2 of time spent speaking in a lab.
{'name': 'workshop', 'activity': 'Moderate activity', 'expiration': {'Speaking': 1, 'Breathing': 1}}, # Model 1/2 of time spent speaking in a workshop.
# Model 1/2 of time spent speaking in a lab.
{'name': 'lab', 'activity': 'Light activity',
'expiration': {'Speaking': 1, 'Breathing': 1}},
# Model 1/2 of time spent speaking in a workshop.
{'name': 'workshop', 'activity': 'Moderate activity',
'expiration': {'Speaking': 1, 'Breathing': 1}},
{'name': 'training', 'activity': 'Standing', 'expiration': 'Speaking'},
{'name': 'training_attendee', 'activity': 'Seated', 'expiration': 'Breathing'},
{'name': 'gym', 'activity': 'Heavy exercise', 'expiration': 'Breathing'},
{'name': 'household-day', 'activity': 'Light activity', 'expiration': {'Breathing': 5, 'Speaking': 5}},
{'name': 'household-night', 'activity': 'Seated', 'expiration': {'Breathing': 7, 'Speaking': 3}},
{'name': 'primary-school', 'activity': 'Light activity', 'expiration': {'Breathing': 5, 'Speaking': 5}},
{'name': 'secondary-school', 'activity': 'Light activity', 'expiration': {'Breathing': 7, 'Speaking': 3}},
{'name': 'university', 'activity': 'Seated', 'expiration': {'Breathing': 9, 'Speaking': 1}},
{'name': 'restaurant', 'activity': 'Seated', 'expiration': {'Breathing': 1, 'Speaking': 9}},
{'name': 'household-day', 'activity': 'Light activity',
'expiration': {'Breathing': 5, 'Speaking': 5}},
{'name': 'household-night', 'activity': 'Seated',
'expiration': {'Breathing': 7, 'Speaking': 3}},
{'name': 'primary-school', 'activity': 'Light activity',
'expiration': {'Breathing': 5, 'Speaking': 5}},
{'name': 'secondary-school', 'activity': 'Light activity',
'expiration': {'Breathing': 7, 'Speaking': 3}},
{'name': 'university', 'activity': 'Seated',
'expiration': {'Breathing': 9, 'Speaking': 1}},
{'name': 'restaurant', 'activity': 'Seated',
'expiration': {'Breathing': 1, 'Speaking': 9}},
{'name': 'precise', 'activity': None, 'expiration': None},
]
# ------------------ Validation ----------------------
ACTIVITY_TYPES = [ activity['name'] for activity in ACTIVITIES ]
COFFEE_OPTIONS_INT = {'coffee_break_0': 0, 'coffee_break_1': 1, 'coffee_break_2': 2, 'coffee_break_4': 4}
CONFIDENCE_LEVEL_OPTIONS = {'confidence_low': 10, 'confidence_medium': 5, 'confidence_high': 2}
MECHANICAL_VENTILATION_TYPES = {'mech_type_air_changes', 'mech_type_air_supply', 'not-applicable'}
ACTIVITY_TYPES = [activity['name'] for activity in ACTIVITIES]
COFFEE_OPTIONS_INT = {'coffee_break_0': 0, 'coffee_break_1': 1,
'coffee_break_2': 2, 'coffee_break_4': 4}
CONFIDENCE_LEVEL_OPTIONS = {'confidence_low': 10,
'confidence_medium': 5, 'confidence_high': 2}
MECHANICAL_VENTILATION_TYPES = {
'mech_type_air_changes', 'mech_type_air_supply', 'not-applicable'}
MASK_TYPES = {'Type I', 'FFP2', 'Cloth'}
MASK_WEARING_OPTIONS = {'mask_on', 'mask_off'}
MONTH_NAMES = [
@ -113,13 +135,16 @@ MONTH_NAMES = [
'August', 'September', 'October', 'November', 'December',
]
VACCINE_BOOSTER_TYPE = ['AZD1222_(AstraZeneca)', 'Ad26.COV2.S_(Janssen)', 'BNT162b2_(Pfizer)', 'BNT162b2_(Pfizer)_(4th_dose)', 'BNT162b2_(Pfizer)_and_mRNA-1273_(Moderna)',
'BNT162b2_(Pfizer)_or_mRNA-1273_(Moderna)', 'BNT162b2_(Pfizer)_or_mRNA-1273_(Moderna)_(4th_dose)', 'CoronaVac_(Sinovac)', 'Coronavac_(Sinovac)', 'Sinopharm',
'mRNA-1273_(Moderna)', 'mRNA-1273_(Moderna)_(4th_dose)', 'Other']
'BNT162b2_(Pfizer)_or_mRNA-1273_(Moderna)', 'BNT162b2_(Pfizer)_or_mRNA-1273_(Moderna)_(4th_dose)', 'CoronaVac_(Sinovac)', 'Coronavac_(Sinovac)', 'Sinopharm',
'mRNA-1273_(Moderna)', 'mRNA-1273_(Moderna)_(4th_dose)', 'Other']
VACCINE_TYPE = ['Ad26.COV2.S_(Janssen)', 'Any_mRNA_-_heterologous', 'AZD1222_(AstraZeneca)', 'AZD1222_(AstraZeneca)_and_any_mRNA_-_heterologous', 'AZD1222_(AstraZeneca)_and_BNT162b2_(Pfizer)',
'BBIBP-CorV_(Beijing_CNBG)', 'BNT162b2_(Pfizer)', 'BNT162b2_(Pfizer)_and_mRNA-1273_(Moderna)', 'CoronaVac_(Sinovac)', 'CoronaVac_(Sinovac)_and_AZD1222_(AstraZeneca)', 'Covishield',
'mRNA-1273_(Moderna)', 'Sputnik_V_(Gamaleya)', 'CoronaVac_(Sinovac)_and_BNT162b2_(Pfizer)']
VENTILATION_TYPES = {'natural_ventilation', 'mechanical_ventilation', 'no_ventilation'}
VIRUS_TYPES = {'SARS_CoV_2', 'SARS_CoV_2_ALPHA', 'SARS_CoV_2_BETA','SARS_CoV_2_GAMMA', 'SARS_CoV_2_DELTA', 'SARS_CoV_2_OMICRON'}
'BBIBP-CorV_(Beijing_CNBG)', 'BNT162b2_(Pfizer)', 'BNT162b2_(Pfizer)_and_mRNA-1273_(Moderna)', 'CoronaVac_(Sinovac)', 'CoronaVac_(Sinovac)_and_AZD1222_(AstraZeneca)', 'Covishield',
'mRNA-1273_(Moderna)', 'Sputnik_V_(Gamaleya)', 'CoronaVac_(Sinovac)_and_BNT162b2_(Pfizer)']
VENTILATION_TYPES = {'natural_ventilation',
'mechanical_ventilation', 'no_ventilation'}
VIRUS_TYPES = {'SARS_CoV_2', 'SARS_CoV_2_ALPHA', 'SARS_CoV_2_BETA',
'SARS_CoV_2_GAMMA', 'SARS_CoV_2_DELTA', 'SARS_CoV_2_OMICRON'}
VOLUME_TYPES = {'room_volume_explicit', 'room_volume_from_dimensions'}
WINDOWS_OPENING_REGIMES = {'windows_open_permanently', 'windows_open_periodically', 'not-applicable'}
WINDOWS_OPENING_REGIMES = {'windows_open_permanently',
'windows_open_periodically', 'not-applicable'}
WINDOWS_TYPES = {'window_sliding', 'window_hinged', 'not-applicable'}

4
caimira/apps/calculator/model_generator.py
View file

@ -16,7 +16,9 @@ import caimira.monte_carlo as mc
from .. import calculator
from caimira.monte_carlo.data import activity_distributions, virus_distributions, mask_distributions, short_range_distances
from caimira.monte_carlo.data import expiration_distribution, expiration_BLO_factors, expiration_distributions, short_range_expiration_distributions
from .DEFAULT_DATA import *
from .defaults import (NO_DEFAULT, DEFAULT_MC_SAMPLE_SIZE, DEFAULTS, ACTIVITIES, ACTIVITY_TYPES, COFFEE_OPTIONS_INT, CONFIDENCE_LEVEL_OPTIONS,
MECHANICAL_VENTILATION_TYPES, MASK_TYPES, MASK_WEARING_OPTIONS, MONTH_NAMES, VACCINE_BOOSTER_TYPE, VACCINE_TYPE,
VENTILATION_TYPES, VIRUS_TYPES, VOLUME_TYPES, WINDOWS_OPENING_REGIMES, WINDOWS_TYPES)
LOG = logging.getLogger(__name__)

6
caimira/apps/calculator/report_generator.py
View file

@ -123,7 +123,6 @@ def calculate_report_data(form: FormData, model: models.ExposureModel) -> typing
for time in times
]
lower_concentrations = concentrations_with_sr_breathing(form, model, times, short_range_intervals)
highest_const = max(concentrations)
cumulative_doses = np.cumsum([
np.array(model.deposited_exposure_between_bounds(float(time1), float(time2))).mean()
@ -137,8 +136,6 @@ def calculate_report_data(form: FormData, model: models.ExposureModel) -> typing
prob = np.array(model.infection_probability())
prob_dist_count, prob_dist_bins = np.histogram(prob/100, bins=100, density=True)
prob_probabilistic_exposure = np.array(model.total_probability_rule()).mean()
er = np.array(model.concentration_model.infected.emission_rate_per_person_when_present()).mean()
exposed_occupants = model.exposed.number
expected_new_cases = np.array(model.expected_new_cases()).mean()
uncertainties_plot_src = img2base64(_figure2bytes(uncertainties_plot(model))) if form.conditional_probability_plot else None
exposed_presence_intervals = [list(interval) for interval in model.exposed.presence_interval().boundaries()]
@ -151,7 +148,6 @@ def calculate_report_data(form: FormData, model: models.ExposureModel) -> typing
"short_range_expirations": short_range_expirations,
"concentrations": concentrations,
"concentrations_zoomed": lower_concentrations,
"highest_const": highest_const,
"cumulative_doses": list(cumulative_doses),
"long_range_cumulative_doses": list(long_range_cumulative_doses),
"prob_inf": prob.mean(),
@ -160,8 +156,6 @@ def calculate_report_data(form: FormData, model: models.ExposureModel) -> typing
"prob_hist_count": list(prob_dist_count),
"prob_hist_bins": list(prob_dist_bins),
"prob_probabilistic_exposure": prob_probabilistic_exposure,
"emission_rate_per_person": er,
"exposed_occupants": exposed_occupants,
"expected_new_cases": expected_new_cases,
"uncertainties_plot_src": uncertainties_plot_src,
}