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Merge branch 'feature/virions_plot' of https://gitlab.cern.ch/cara/cara into feature/virions_plot

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This commit is contained in:
Luis Aleixo 2021-09-08 15:35:30 +02:00
commit fe00584c89
3 changed files with 19 additions and 18 deletions
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18
cara/model_scenarios_paper.py
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@ -29,7 +29,7 @@ yann_er = [8396.78166, 45324.55964, 400054.0827]
######### Standard exposure models ###########
######### Breathing model ###########
def breathing_exposure():
def breathing_exposure(activity: str):
exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel(
room=models.Room(volume=100, humidity=0.5),
@ -45,21 +45,21 @@ def breathing_exposure():
),
presence=mc.SpecificInterval(((0, 2),)),
mask=models.Mask.types["No mask"],
activity=activity_distributions['Seated'],
activity=activity_distributions[activity],
expiration=models.Expiration.types['Breathing'],
),
),
exposed=mc.Population(
number=14,
presence=mc.SpecificInterval(((0, 2),)),
activity=models.Activity.types['Seated'],
activity=models.Activity.types[activity],
mask=models.Mask.types["No mask"],
),
)
return exposure_mc
######### Speaking model ###########
def speaking_exposure():
def speaking_exposure(activity: str):
exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel(
room=models.Room(volume=100, humidity=0.5),
@ -75,21 +75,21 @@ def speaking_exposure():
),
presence=mc.SpecificInterval(((0, 2),)),
mask=models.Mask.types["No mask"],
activity=activity_distributions['Seated'],
activity=activity_distributions[activity],
expiration=models.Expiration.types['Talking'],
),
),
exposed=mc.Population(
number=14,
presence=mc.SpecificInterval(((0, 2),)),
activity=models.Activity.types['Seated'],
activity=models.Activity.types[activity],
mask=models.Mask.types["No mask"],
),
)
return exposure_mc
######### Shouting model ###########
def shouting_exposure():
def shouting_exposure(activity: str):
exposure_mc = mc.ExposureModel(
concentration_model=mc.ConcentrationModel(
room=models.Room(volume=100, humidity=0.5),
@ -105,14 +105,14 @@ def shouting_exposure():
),
presence=mc.SpecificInterval(((0, 2),)),
mask=models.Mask.types["No mask"],
activity=activity_distributions['Seated'],
activity=activity_distributions[activity],
expiration=models.Expiration.types['Shouting'],
),
),
exposed=mc.Population(
number=14,
presence=mc.SpecificInterval(((0, 2),)),
activity=models.Activity.types['Seated'],
activity=models.Activity.types[activity],
mask=models.Mask.types["No mask"],
),
)

7
cara/plot_output.py
View file

@ -29,11 +29,12 @@ print('\n<<<<<<<<<<< Vlout for Breathing, seated with chosen Cn,B >>>>>>>>>>>')
#exposure_model_from_vl_breathing_cn()
print('\n')
############ Plots with viral loads and emission rates ############
#present_vl_er_histograms()
############ Plots with viral loads and emission rates + statistical data ############
present_vl_er_histograms(activity='Seated')
present_vl_er_histograms(activity='Light activity')
############ CDFs for comparing the QR-Values in different scenarios ############
generate_cdf_curves()
#generate_cdf_curves()
############ Used for testing ############
#exposure_model_from_vl_talking_new_points()

12
cara/results_paper.py
View file

@ -257,9 +257,9 @@ def exposure_model_from_vl_talking_cn():
############ Statistical Data ############
def get_statistical_data():
def get_statistical_data(activity: str):
############ Breathing model ############
exposure_mc = breathing_exposure()
exposure_mc = breathing_exposure(activity)
exposure_model = exposure_mc.build_model(size=SAMPLE_SIZE)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present(
cn_B=0.06, cn_L=0.2)
@ -268,7 +268,7 @@ def get_statistical_data():
print_er_info(emission_rate, breathing_er)
############ Speaking model ############
exposure_mc = speaking_exposure()
exposure_mc = speaking_exposure(activity)
exposure_model = exposure_mc.build_model(size=SAMPLE_SIZE)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present(
cn_B=0.06, cn_L=0.2)
@ -277,7 +277,7 @@ def get_statistical_data():
print_er_info(emission_rate, speaking_er)
############ Shouting model ############
exposure_mc = shouting_exposure()
exposure_mc = shouting_exposure(activity)
exposure_model = exposure_mc.build_model(size=SAMPLE_SIZE)
emission_rate = exposure_model.concentration_model.infected.emission_rate_when_present(
cn_B=0.06, cn_L=0.2)
@ -290,8 +290,8 @@ def get_statistical_data():
return viral_load_in_sputum, breathing_er, speaking_er, shouting_er
def present_vl_er_histograms():
viral_load_in_sputum, breathing_er, speaking_er, shouting_er = get_statistical_data()
def present_vl_er_histograms(activity: str):
viral_load_in_sputum, breathing_er, speaking_er, shouting_er = get_statistical_data(activity)
fig, axs = plt.subplots(1, 2, sharex=False, sharey=False)
fig.set_figheight(5)