From d2164383e5fd73c358ca32c76b74168de8325068 Mon Sep 17 00:00:00 2001 From: Luis Aleixo Date: Tue, 8 Feb 2022 09:55:51 +0000 Subject: [PATCH] Removed unused code --- cara/apps/calculator/model_generator.py | 9 ------ cara/apps/calculator/report_generator.py | 32 +------------------ cara/models.py | 8 +---- cara/tests/conftest.py | 2 -- cara/tests/models/test_concentration_model.py | 4 --- cara/tests/models/test_exposure_model.py | 6 ---- cara/tests/test_infected_population.py | 2 -- cara/tests/test_known_quantities.py | 8 ----- cara/tests/test_monte_carlo.py | 2 -- cara/tests/test_monte_carlo_full_models.py | 16 ---------- 10 files changed, 2 insertions(+), 87 deletions(-) diff --git a/cara/apps/calculator/model_generator.py b/cara/apps/calculator/model_generator.py index 893144a4..d0b1aaaa 100644 --- a/cara/apps/calculator/model_generator.py +++ b/cara/apps/calculator/model_generator.py @@ -418,13 +418,6 @@ class FormData: infected_occupants = self.infected_people - if self.short_range_option == "short_range_no": - sr_presence=[] - sr_activities=[] - else: - sr_presence=self.short_range_intervals() - sr_activities=self.short_range_activities() - infected = mc.InfectedPopulation( number=infected_occupants, virus=virus, @@ -433,8 +426,6 @@ class FormData: activity=activity, expiration=expiration, host_immunity=0., - short_range_presence=sr_presence, - short_range_activities=sr_activities, ) return infected diff --git a/cara/apps/calculator/report_generator.py b/cara/apps/calculator/report_generator.py index c6205519..258ed6bf 100644 --- a/cara/apps/calculator/report_generator.py +++ b/cara/apps/calculator/report_generator.py @@ -12,9 +12,8 @@ import jinja2 import numpy as np from cara import models -from cara.monte_carlo.data import initial_concentrations_mouth, dilution_factor from ... import monte_carlo as mc -from .model_generator import FormData, _DEFAULT_MC_SAMPLE_SIZE, build_expiration +from .model_generator import FormData, _DEFAULT_MC_SAMPLE_SIZE from ... import dataclass_utils @@ -97,41 +96,13 @@ def interesting_times(model: models.ExposureModel, approx_n_pts=100) -> typing.L return nice_times -def short_range_interesting_times(model: models.ExposureModel, times: typing.List[float]) -> typing.List[float]: - short_range_times : typing.List[float] = [] - for period in model.concentration_model.infected.short_range_presence: - start, finish = tuple(period.boundaries()) - short_range_times = short_range_times + [time for time in times if time > start and time < finish] - return short_range_times - - -def jet_origin_concentrations(model: models.ExposureModel) -> typing.List[float]: - return [initial_concentrations_mouth[activity] for activity in model.concentration_model.infected.short_range_activities] - - -def short_range_initial_concentrations(model: models.ExposureModel, time: float): - dilution = dilution_factor(distance=np.linspace(0.1, 2., 1000)) - jet_origin_initial_concentrations = jet_origin_concentrations(model) - for index, interaction in enumerate(model.concentration_model.infected.short_range_presence): - start, finish = tuple(interaction.boundaries()) - if start <= time <= finish: - concentration = model.concentration_model.concentration(float(time)) - jet_origin_concentration = jet_origin_initial_concentrations[index] * model.concentration_model.infected.virus.viral_load_in_sputum - return concentration + ((1/dilution)*(jet_origin_concentration - concentration)) - - def calculate_report_data(model: models.ExposureModel): times = interesting_times(model) - times_short_range = short_range_interesting_times(model, times) concentrations = [ np.array(model.concentration_model.concentration(float(time))).mean() for time in times ] - short_range_concentrations = [ - np.array(short_range_initial_concentrations(model, float(time))).mean() - for time in times_short_range - ] highest_const = max(concentrations) prob = np.array(model.infection_probability()).mean() er = np.array(model.concentration_model.infected.emission_rate_when_present()).mean() @@ -147,7 +118,6 @@ def calculate_report_data(model: models.ExposureModel): "exposed_presence_intervals": [list(interval) for interval in model.exposed.presence.boundaries()], "cumulative_doses": list(cumulative_doses), "concentrations": concentrations, - "short_range_concentrations": short_range_concentrations, "highest_const": highest_const, "prob_inf": prob, "emission_rate": er, diff --git a/cara/models.py b/cara/models.py index 6b5e6540..f667ba1f 100644 --- a/cara/models.py +++ b/cara/models.py @@ -32,7 +32,7 @@ or length N arrays, where N is the number of parameterisations to run; N must be the same for all parameters of a single model. """ -from dataclasses import dataclass, field +from dataclasses import dataclass import typing import numpy as np @@ -762,12 +762,6 @@ class _PopulationWithVirus(Population): #: The virus with which the population is infected. virus: Virus - #: Short range interactions - short_range_presence: typing.List[SpecificInterval] - - #: The type of expiractory activities in the short range interactions - short_range_activities: typing.List[str] - @method_cache def fraction_of_infectious_virus(self) -> _VectorisedFloat: """ diff --git a/cara/tests/conftest.py b/cara/tests/conftest.py index 45cdbef4..27ce9f1d 100644 --- a/cara/tests/conftest.py +++ b/cara/tests/conftest.py @@ -23,8 +23,6 @@ def baseline_model(): host_immunity=0., # superspreading event, where ejection factor is fixed based # on Miller et al. (2020) - 50 represents the infectious dose. - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) diff --git a/cara/tests/models/test_concentration_model.py b/cara/tests/models/test_concentration_model.py index 16d5b5b0..432b4d80 100644 --- a/cara/tests/models/test_concentration_model.py +++ b/cara/tests/models/test_concentration_model.py @@ -47,8 +47,6 @@ def test_concentration_model_vectorisation(override_params): ), expiration=models._ExpirationBase.types['Breathing'], host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -71,8 +69,6 @@ def simple_conc_model(): virus=models.Virus.types['SARS_CoV_2'], expiration=models.Expiration.types['Breathing'], host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) diff --git a/cara/tests/models/test_exposure_model.py b/cara/tests/models/test_exposure_model.py index 15d20986..238e2316 100644 --- a/cara/tests/models/test_exposure_model.py +++ b/cara/tests/models/test_exposure_model.py @@ -66,8 +66,6 @@ def known_concentrations(func): virus=models.Virus.types['SARS_CoV_2_ALPHA'], expiration=models.Expiration.types['Speaking'], host_immunity=0., - short_range_presence=[], - short_range_activities=[], ) normed_func = lambda x: func(x) / dummy_infected_population.emission_rate_when_present() return KnownNormedconcentration(dummy_room, dummy_ventilation, @@ -166,8 +164,6 @@ def conc_model(): # superspreading event, where ejection factor is fixed based # on Miller et al. (2020) - 50 represents the infectious dose. host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -211,8 +207,6 @@ def test_infectious_dose_vectorisation(): ), expiration=models.Expiration.types['Speaking'], host_immunity=0., - short_range_presence=[], - short_range_activities=[], ) cm = known_concentrations(lambda t: 1.2) cm = replace(cm, infected=infected_population) diff --git a/cara/tests/test_infected_population.py b/cara/tests/test_infected_population.py index 66714f96..8856d312 100644 --- a/cara/tests/test_infected_population.py +++ b/cara/tests/test_infected_population.py @@ -37,8 +37,6 @@ def test_infected_population_vectorisation(override_params): ), expiration=cara.models._ExpirationBase.types['Breathing'], host_immunity=0., - short_range_presence=[], - short_range_activities=[], ) emission_rate = infected.emission_rate(10) assert isinstance(emission_rate, np.ndarray) diff --git a/cara/tests/test_known_quantities.py b/cara/tests/test_known_quantities.py index b94e6acd..2ab80fc8 100644 --- a/cara/tests/test_known_quantities.py +++ b/cara/tests/test_known_quantities.py @@ -76,8 +76,6 @@ def build_model(interval_duration): host_immunity=0., # superspreading event, where ejection factor is fixed based # on Miller et al. (2020) - 50 represents the infectious dose. - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -240,8 +238,6 @@ def build_hourly_dependent_model( activity=models.Activity.types['Light activity'], known_individual_emission_rate=970 * 50, host_immunity=0, - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -265,8 +261,6 @@ def build_constant_temp_model(outside_temp, intervals_open=((7.5, 8.5),)): activity=models.Activity.types['Light activity'], known_individual_emission_rate=970 * 50, host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -297,8 +291,6 @@ def build_hourly_dependent_model_multipleventilation(month, intervals_open=((7.5 activity=models.Activity.types['Light activity'], known_individual_emission_rate=970 * 50, host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) diff --git a/cara/tests/test_monte_carlo.py b/cara/tests/test_monte_carlo.py index 339612df..8a8b0271 100644 --- a/cara/tests/test_monte_carlo.py +++ b/cara/tests/test_monte_carlo.py @@ -55,8 +55,6 @@ def baseline_mc_model() -> cara.monte_carlo.ConcentrationModel: activity=cara.models.Activity.types['Light activity'], expiration=cara.models.Expiration.types['Breathing'], host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) diff --git a/cara/tests/test_monte_carlo_full_models.py b/cara/tests/test_monte_carlo_full_models.py index 4a68b9e1..b4aa247d 100644 --- a/cara/tests/test_monte_carlo_full_models.py +++ b/cara/tests/test_monte_carlo_full_models.py @@ -67,8 +67,6 @@ def shared_office_mc(): activity=activity_distributions['Seated'], expiration=build_expiration({'Speaking': 0.33, 'Breathing': 0.67}), host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -111,8 +109,6 @@ def classroom_mc(): activity=activity_distributions['Light activity'], expiration=build_expiration('Speaking'), host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -146,8 +142,6 @@ def ski_cabin_mc(): activity=activity_distributions['Moderate activity'], expiration=build_expiration('Speaking'), host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -187,8 +181,6 @@ def skagit_chorale_mc(): activity=activity_distributions['Moderate activity'], expiration=build_expiration('Shouting'), host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -228,8 +220,6 @@ def bus_ride_mc(): activity=activity_distributions['Seated'], expiration=build_expiration('Speaking'), host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -264,8 +254,6 @@ def gym_mc(): activity=activity_distributions['Heavy exercise'], expiration=expiration_distributions['Breathing'], host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -300,8 +288,6 @@ def waiting_room_mc(): activity=activity_distributions['Seated'], expiration=build_expiration({'Speaking': 0.3, 'Breathing': 0.7}), host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, ) @@ -379,8 +365,6 @@ def test_small_shared_office_Geneva(mask_type, month, expected_pi, activity=activity_distributions['Seated'], expiration=build_expiration({'Speaking': 0.33, 'Breathing': 0.67}), host_immunity=0., - short_range_presence=[], - short_range_activities=[], ), evaporation_factor=0.3, )