From 0cb6477cb2b235f7f8e65195c4104964b120460a Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Fri, 26 May 2023 09:44:47 +0200 Subject: [PATCH] modified file name and references. removed unused variables --- .../{DEFAULT_DATA.py => defaults.py} | 73 +++++++++++++------ caimira/apps/calculator/model_generator.py | 4 +- caimira/apps/calculator/report_generator.py | 6 -- 3 files changed, 52 insertions(+), 31 deletions(-) rename caimira/apps/calculator/{DEFAULT_DATA.py => defaults.py} (56%) diff --git a/caimira/apps/calculator/DEFAULT_DATA.py b/caimira/apps/calculator/defaults.py similarity index 56% rename from caimira/apps/calculator/DEFAULT_DATA.py rename to caimira/apps/calculator/defaults.py index f9157b71..a9e9d0f9 100644 --- a/caimira/apps/calculator/DEFAULT_DATA.py +++ b/caimira/apps/calculator/defaults.py @@ -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'} diff --git a/caimira/apps/calculator/model_generator.py b/caimira/apps/calculator/model_generator.py index ce130790..86e098e2 100644 --- a/caimira/apps/calculator/model_generator.py +++ b/caimira/apps/calculator/model_generator.py @@ -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__) diff --git a/caimira/apps/calculator/report_generator.py b/caimira/apps/calculator/report_generator.py index 885c2e8d..7beb5fee 100644 --- a/caimira/apps/calculator/report_generator.py +++ b/caimira/apps/calculator/report_generator.py @@ -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, }