476 lines
15 KiB
Python
476 lines
15 KiB
Python
from caimira.enums import ViralLoads, InfectiousDoses, ViableToRNARatios
|
|
|
|
|
|
class DataRegistry:
|
|
"""Registry to hold data values."""
|
|
|
|
version = None
|
|
|
|
BLOmodel = {
|
|
"cn": {
|
|
"B": 0.06,
|
|
"L": 0.2,
|
|
"O": 0.0010008,
|
|
},
|
|
"mu": {
|
|
"B": 0.989541,
|
|
"L": 1.38629,
|
|
"O": 4.97673,
|
|
},
|
|
"sigma": {
|
|
"B": 0.262364,
|
|
"L": 0.506818,
|
|
"O": 0.585005,
|
|
},
|
|
}
|
|
activity_distributions = {
|
|
"Seated": {
|
|
"inhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": -0.6872121723362303,
|
|
"lognormal_standard_deviation_gaussian": 0.10498338229297108,
|
|
},
|
|
},
|
|
"exhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": -0.6872121723362303,
|
|
"lognormal_standard_deviation_gaussian": 0.10498338229297108,
|
|
},
|
|
},
|
|
},
|
|
"Standing": {
|
|
"inhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": -0.5742377578494785,
|
|
"lognormal_standard_deviation_gaussian": 0.09373162411398223,
|
|
},
|
|
},
|
|
"exhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": -0.5742377578494785,
|
|
"lognormal_standard_deviation_gaussian": 0.09373162411398223,
|
|
},
|
|
},
|
|
},
|
|
"Light activity": {
|
|
"inhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": 0.21380242785625422,
|
|
"lognormal_standard_deviation_gaussian": 0.09435378091059601,
|
|
},
|
|
},
|
|
"exhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": 0.21380242785625422,
|
|
"lognormal_standard_deviation_gaussian": 0.09435378091059601,
|
|
},
|
|
},
|
|
},
|
|
"Moderate activity": {
|
|
"inhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": 0.551771330362601,
|
|
"lognormal_standard_deviation_gaussian": 0.1894616357138137,
|
|
},
|
|
},
|
|
"exhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": 0.551771330362601,
|
|
"lognormal_standard_deviation_gaussian": 0.1894616357138137,
|
|
},
|
|
},
|
|
},
|
|
"Heavy exercise": {
|
|
"inhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": 1.1644665696723049,
|
|
"lognormal_standard_deviation_gaussian": 0.21744554768657565,
|
|
},
|
|
},
|
|
"exhalation_rate": {
|
|
"associated_distribution": "Log-normal",
|
|
"parameters": {
|
|
"lognormal_mean_gaussian": 1.1644665696723049,
|
|
"lognormal_standard_deviation_gaussian": 0.21744554768657565,
|
|
},
|
|
},
|
|
},
|
|
}
|
|
symptomatic_vl_frequencies = {
|
|
"log_variable": [
|
|
2.46032,
|
|
2.67431,
|
|
2.85434,
|
|
3.06155,
|
|
3.25856,
|
|
3.47256,
|
|
3.66957,
|
|
3.85979,
|
|
4.09927,
|
|
4.27081,
|
|
4.47631,
|
|
4.66653,
|
|
4.87204,
|
|
5.10302,
|
|
5.27456,
|
|
5.46478,
|
|
5.6533,
|
|
5.88428,
|
|
6.07281,
|
|
6.30549,
|
|
6.48552,
|
|
6.64856,
|
|
6.85407,
|
|
7.10373,
|
|
7.30075,
|
|
7.47229,
|
|
7.66081,
|
|
7.85782,
|
|
8.05653,
|
|
8.27053,
|
|
8.48453,
|
|
8.65607,
|
|
8.90573,
|
|
9.06878,
|
|
9.27429,
|
|
9.473,
|
|
9.66152,
|
|
9.87552,
|
|
],
|
|
"frequencies": [
|
|
0.001206885,
|
|
0.007851618,
|
|
0.008078144,
|
|
0.01502491,
|
|
0.013258014,
|
|
0.018528495,
|
|
0.020053765,
|
|
0.021896167,
|
|
0.022047184,
|
|
0.018604005,
|
|
0.01547796,
|
|
0.018075445,
|
|
0.021503523,
|
|
0.022349217,
|
|
0.025097721,
|
|
0.032875078,
|
|
0.030594727,
|
|
0.032573045,
|
|
0.034717482,
|
|
0.034792991,
|
|
0.033267721,
|
|
0.042887485,
|
|
0.036846816,
|
|
0.03876473,
|
|
0.045016819,
|
|
0.040063473,
|
|
0.04883754,
|
|
0.043944602,
|
|
0.048142864,
|
|
0.041588741,
|
|
0.048762031,
|
|
0.027921732,
|
|
0.033871788,
|
|
0.022122693,
|
|
0.016927718,
|
|
0.008833228,
|
|
0.00478598,
|
|
0.002807662,
|
|
],
|
|
"kernel_bandwidth": 0.1,
|
|
}
|
|
covid_overal_vl_data = {
|
|
"shape_factor": 3.47,
|
|
"scale_factor": 7.01,
|
|
"start": 0.01,
|
|
"stop": 0.99,
|
|
"num": 30.0,
|
|
"min_bound": 2,
|
|
"max_bound": 10,
|
|
"interpolation_fp_left": 0,
|
|
"interpolation_fp_right": 0,
|
|
"max_function": 0.2,
|
|
}
|
|
viable_to_RNA_ratio_distribution = {
|
|
"low": 0.01,
|
|
"high": 0.6,
|
|
}
|
|
infectious_dose_distribution = {
|
|
"low": 10,
|
|
"high": 100,
|
|
}
|
|
virus_distributions = {
|
|
"SARS_CoV_2": {
|
|
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
|
|
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
|
|
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
|
|
"transmissibility_factor": 1,
|
|
"infectiousness_days": 14,
|
|
},
|
|
"SARS_CoV_2_ALPHA": {
|
|
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
|
|
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
|
|
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
|
|
"transmissibility_factor": 0.78,
|
|
"infectiousness_days": 14,
|
|
},
|
|
"SARS_CoV_2_BETA": {
|
|
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
|
|
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
|
|
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
|
|
"transmissibility_factor": 0.8,
|
|
"infectiousness_days": 14,
|
|
},
|
|
"SARS_CoV_2_GAMMA": {
|
|
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
|
|
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
|
|
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
|
|
"transmissibility_factor": 0.72,
|
|
"infectiousness_days": 14,
|
|
},
|
|
"SARS_CoV_2_DELTA": {
|
|
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
|
|
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
|
|
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
|
|
"transmissibility_factor": 0.51,
|
|
"infectiousness_days": 14,
|
|
},
|
|
"SARS_CoV_2_OMICRON": {
|
|
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
|
|
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
|
|
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
|
|
"transmissibility_factor": 0.2,
|
|
"infectiousness_days": 14,
|
|
},
|
|
"SARS_CoV_2_Other": {
|
|
"viral_load_in_sputum": ViralLoads.COVID_OVERALL.value,
|
|
"infectious_dose": InfectiousDoses.DISTRIBUTION.value,
|
|
"viable_to_RNA_ratio": ViableToRNARatios.DISTRIBUTION.value,
|
|
"transmissibility_factor": 0.1,
|
|
"infectiousness_days": 14,
|
|
},
|
|
}
|
|
mask_distributions = {
|
|
"Type I": {
|
|
"η_inhale": {
|
|
"associated_distribution": "Uniform",
|
|
"parameters": {
|
|
"low": 0.25,
|
|
"high": 0.80,
|
|
},
|
|
},
|
|
"Known filtration efficiency of masks when exhaling?": "No",
|
|
"factor_exhale": 1,
|
|
},
|
|
"FFP2": {
|
|
"η_inhale": {
|
|
"associated_distribution": "Uniform",
|
|
"parameters": {
|
|
"low": 0.83,
|
|
"high": 0.91,
|
|
},
|
|
},
|
|
"Known filtration efficiency of masks when exhaling?": "No",
|
|
"factor_exhale": 1,
|
|
},
|
|
"Cloth": {
|
|
"η_inhale": {
|
|
"associated_distribution": "Uniform",
|
|
"parameters": {
|
|
"low": 0.05,
|
|
"high": 0.40,
|
|
},
|
|
},
|
|
"Known filtration efficiency of masks when exhaling?": "Yes",
|
|
"η_exhale": {
|
|
"associated_distribution": "Uniform",
|
|
"parameters": {
|
|
"low": 0.20,
|
|
"high": 0.50,
|
|
},
|
|
},
|
|
"factor_exhale": 1,
|
|
},
|
|
}
|
|
expiration_BLO_factors = {
|
|
"Breathing": {
|
|
"B": 1.0,
|
|
"L": 0.0,
|
|
"O": 0.0,
|
|
},
|
|
"Speaking": {
|
|
"B": 1.0,
|
|
"L": 1.0,
|
|
"O": 1.0,
|
|
},
|
|
"Singing": {
|
|
"B": 1.0,
|
|
"L": 5.0,
|
|
"O": 5.0,
|
|
},
|
|
"Shouting": {
|
|
"B": 1.0,
|
|
"L": 5.0,
|
|
"O": 5.0,
|
|
},
|
|
}
|
|
long_range_expiration_distributions = {
|
|
"minimum_diameter": 0.1,
|
|
"maximum_diameter": 30,
|
|
}
|
|
short_range_expiration_distributions = {
|
|
"minimum_diameter": 0.1,
|
|
"maximum_diameter": 100,
|
|
}
|
|
short_range_distances = {
|
|
"minimum_distance": 0.5,
|
|
"maximum_distance": 2.0,
|
|
}
|
|
|
|
####################################
|
|
|
|
room = {
|
|
"defaults": {
|
|
"inside_temp": 293,
|
|
"humidity_with_heating": 0.3,
|
|
"humidity_without_heating": 0.5,
|
|
},
|
|
}
|
|
ventilation = {
|
|
"natural": {
|
|
"discharge_factor": {
|
|
"sliding": 0.6,
|
|
},
|
|
},
|
|
"infiltration_ventilation": 0.25,
|
|
}
|
|
particle = {
|
|
"evaporation_factor": 0.3,
|
|
}
|
|
population_with_virus = {
|
|
"fraction_of_infectious_virus": 1,
|
|
}
|
|
concentration_model = {
|
|
"min_background_concentration": 0.0,
|
|
"CO2_concentration_model": {
|
|
"CO2_atmosphere_concentration": 440.44,
|
|
"CO2_fraction_exhaled": 0.042,
|
|
},
|
|
}
|
|
short_range_model = {
|
|
"dilution_factor": {
|
|
"mouth_diameter": 0.02,
|
|
"exhalation_coefficient": 2,
|
|
"tstar": 2,
|
|
"penetration_coefficients": {
|
|
"𝛽r1": 0.18,
|
|
"𝛽r2": 0.2,
|
|
"𝛽x1": 2.4,
|
|
},
|
|
},
|
|
}
|
|
exposure_model = {
|
|
"repeats": 1,
|
|
}
|
|
conditional_prob_inf_given_viral_load = {
|
|
"lower_percentile": 0.05,
|
|
"upper_percentile": 0.95,
|
|
"min_vl": 2,
|
|
"max_vl": 10,
|
|
}
|
|
monte_carlo_sample_size = 250000
|
|
population_scenario_activity = {
|
|
"office": {"placeholder": "Office", "activity": "Seated", "expiration": {"Speaking": 1, "Breathing": 2}},
|
|
"smallmeeting": {
|
|
"placeholder": "Small meeting (<10 occ.)",
|
|
"activity": "Seated",
|
|
"expiration": {"Speaking": 1},
|
|
},
|
|
"largemeeting": {
|
|
"placeholder": "Large meeting (>= 10 occ.)",
|
|
"activity": "Standing",
|
|
"expiration": {"Speaking": 1, "Breathing": 2},
|
|
},
|
|
"callcenter": {"placeholder": "Call Center", "activity": "Seated", "expiration": {"Speaking": 1}},
|
|
"controlroom-day": {
|
|
"placeholder": "Control Room - Day shift",
|
|
"activity": "Seated",
|
|
"expiration": {"Speaking": 1, "Breathing": 1},
|
|
},
|
|
"controlroom-night": {
|
|
"placeholder": "Control Room - Night shift",
|
|
"activity": "Seated",
|
|
"expiration": {"Speaking": 1, "Breathing": 9},
|
|
},
|
|
"library": {"placeholder": "Library", "activity": "Seated", "expiration": {"Breathing": 1}},
|
|
"lab": {
|
|
"placeholder": "Lab",
|
|
"activity": "Light activity",
|
|
"expiration": {"Speaking": 1, "Breathing": 1},
|
|
},
|
|
"workshop": {
|
|
"placeholder": "Workshop",
|
|
"activity": "Moderate activity",
|
|
"expiration": {"Speaking": 1, "Breathing": 1},
|
|
},
|
|
"training": {"placeholder": "Conference/Training (speaker infected)", "activity": "Standing", "expiration": {"Speaking": 1}},
|
|
"training_attendee": {"placeholder": "Conference/Training (attendee infected)", "activity": "Seated", "expiration": {"Breathing": 1}},
|
|
"gym": {"placeholder": "Gym", "activity": "Heavy exercise", "expiration": {"Breathing": 1}},
|
|
"household-day": {
|
|
"placeholder": "Household (day time)",
|
|
"activity": "Light activity",
|
|
"expiration": {"Breathing": 5, "Speaking": 5},
|
|
},
|
|
"household-night": {
|
|
"placeholder": "Household (evening and night time)",
|
|
"activity": "Seated",
|
|
"expiration": {"Breathing": 7, "Speaking": 3},
|
|
},
|
|
"primary-school": {
|
|
"placeholder": "Primary school",
|
|
"activity": "Light activity",
|
|
"expiration": {"Breathing": 5, "Speaking": 5},
|
|
},
|
|
"secondary-school": {
|
|
"placeholder": "Secondary school",
|
|
"activity": "Light activity",
|
|
"expiration": {"Breathing": 7, "Speaking": 3},
|
|
},
|
|
"university": {
|
|
"placeholder": "University",
|
|
"activity": "Seated",
|
|
"expiration": {"Breathing": 9, "Speaking": 1},
|
|
},
|
|
"restaurant": {
|
|
"placeholder": "Restaurant",
|
|
"activity": "Seated",
|
|
"expiration": {"Breathing": 1, "Speaking": 9},
|
|
},
|
|
"precise": {"placeholder": "Precise", "activity": "", "expiration": {}},
|
|
}
|
|
|
|
def to_dict(self):
|
|
# Filter out methods, special attributes, and non-serializable objects
|
|
data_dict = {
|
|
key: value
|
|
for key, value in self.__class__.__dict__.items()
|
|
if not key.startswith("__") and not callable(value) and not isinstance(value, (type, classmethod, staticmethod))
|
|
}
|
|
return data_dict
|
|
|
|
def update(self, data, version=None):
|
|
"""Update local cache with data provided as argument."""
|
|
for attr_name, value in data.items():
|
|
setattr(self, attr_name, value)
|
|
|
|
if version:
|
|
self.version = version
|