Merge remote-tracking branch 'origin/feature/mc' into feature/mc
# Conflicts: # cara/mc-output.py
This commit is contained in:
markus
commit
7cf31b50df
3 changed files with 124 additions and 38 deletions
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@ -1,7 +1,7 @@
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from cara.montecarlo import *
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from cara.model_scenarios import *
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#classroom_model.infection_probability()
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classroom_model.infection_probability()
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#compare_concentration_curves([classroom_model, classroom_model_with_hepa], ['Just window', 'Window and HEPA'])
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#print(np.mean(chorale_model.infection_probability()))
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@ -12,13 +12,18 @@ from cara.model_scenarios import *
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# #print(np.mean(classroom_model_with_hepa.infection_probability()))
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composite_plot_pi_vs_viral_load([shared_office_worst_model[1], shared_office_model[1],shared_office_better_model[1]],
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labels=['No mask &\nwindows closed', 'Baseline', 'Baseline +\nHEPA filter'],
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colors=['tomato', '#1f77b4', 'limegreen'],
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title='$P(I|qID)$ vs $vl$ - Shared office scenario',
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vl_points=200)
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#plot_pi_vs_viral_load([shared_office_model[1]], labels=['Baseline, qID=60', 'HEPA, qID=60', 'No mask + windows closed, qID=60'],title='$P(I|qID)$ - Shared office scenario')
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print(np.mean(shared_office_model[1].infection_probability()))
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composite_plot_pi_vs_viral_load([shared_office_worst_model[1], shared_office_model[1], shared_office_better_model[1]],
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labels=['No mask &\nwindows closed', 'Baseline', 'Baseline +\nHEPA filter'],
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colors=['tomato', '#1f77b4', 'limegreen'],
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title='$P(I|qID)$ vs $vl$ - Shared office scenario',
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vl_points=200)
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composite_plot_pi_vs_viral_load([classroom_model[1], classroom_model_with_hepa[1]],
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labels=['No mask &\nwindows closed', 'Baseline', 'Baseline +\nHEPA filter'],
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colors=['tomato', '#1f77b4', 'limegreen'],
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title='$P(I|qID)$ vs $vl$ - Shared office scenario',
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vl_points=200)
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#plot_pi_vs_viral_load([shared_office_model[1]], labels=['Baseline'],title='')
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#generate_cdf_curves_vs_qr(masked=False,qid=1000)
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@ -115,7 +115,7 @@ exposure_models_2 = [MCExposureModel(
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)
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) for qid in (100, 60)]
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classroom_model = MCExposureModel(
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classroom_model = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=160),
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ventilation=models.SlidingWindow(
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@ -128,7 +128,7 @@ classroom_model = MCExposureModel(
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number=1,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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masked=False,
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virus=MCVirus(halflife=1.1, qID=60),
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=2,
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samples=200000,
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breathing_category=3,
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@ -140,9 +140,90 @@ classroom_model = MCExposureModel(
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['No mask']
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)
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)
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)for qid in (100, 60)]
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classroom_model_with_hepa = MCExposureModel(
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classroom_model_full_open = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=160),
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ventilation=models.SlidingWindow(
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active=models.PeriodicInterval(period=120, duration=120),
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inside_temp=models.PiecewiseConstant((0, 24), (293,)),
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outside_temp=models.PiecewiseConstant((0, 24), (283,)),
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window_height=1.6, opening_length=0.6,
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),
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infected=MCInfectedPopulation(
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number=1,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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masked=False,
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=2,
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samples=200000,
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breathing_category=3,
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)
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),
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exposed=models.Population(
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number=19,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['No mask']
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)
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)for qid in (100, 60)]
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classroom_model_summer = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=160),
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ventilation=models.SlidingWindow(
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active=models.PeriodicInterval(period=120, duration=10),
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inside_temp=models.PiecewiseConstant((0, 24), (293,)),
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outside_temp=models.PiecewiseConstant((0, 24), (291,)),
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window_height=1.6, opening_length=0.6,
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),
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infected=MCInfectedPopulation(
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number=1,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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masked=False,
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=2,
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samples=200000,
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breathing_category=3,
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)
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),
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exposed=models.Population(
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number=19,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['No mask']
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)
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)for qid in (100, 60)]
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classroom_model_full_open_summer = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=160),
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ventilation=models.SlidingWindow(
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active=models.PeriodicInterval(period=120, duration=120),
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inside_temp=models.PiecewiseConstant((0, 24), (293,)),
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outside_temp=models.PiecewiseConstant((0, 24), (291,)),
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window_height=1.6, opening_length=0.6,
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),
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infected=MCInfectedPopulation(
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number=1,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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masked=False,
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=2,
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samples=200000,
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breathing_category=3,
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)
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),
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exposed=models.Population(
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number=19,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['No mask']
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)
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)for qid in (100, 60)]
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classroom_model_with_hepa = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=160),
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ventilation=models.MultipleVentilation(
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@ -161,7 +242,7 @@ classroom_model_with_hepa = MCExposureModel(
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number=1,
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presence=models.SpecificInterval(((0, 2), (2.5, 4), (5, 7), (7.5, 9))),
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masked=False,
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virus=MCVirus(halflife=1.1, qID=60),
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=2,
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samples=200000,
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breathing_category=3,
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@ -173,7 +254,7 @@ classroom_model_with_hepa = MCExposureModel(
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['No mask']
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)
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)
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)for qid in (100, 60)]
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shared_office_model = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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@ -263,7 +344,7 @@ shared_office_better_model = [MCExposureModel(
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)
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) for qid in (100, 60)]
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ski_cabin_model = MCExposureModel(
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ski_cabin_model = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=10),
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ventilation=models.HVACMechanical(
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@ -274,7 +355,7 @@ ski_cabin_model = MCExposureModel(
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number=1,
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presence=models.SpecificInterval(((0, 0.33),)),
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masked=True,
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virus=MCVirus(halflife=1.1, qID=60),
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=2,
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samples=200000,
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breathing_category=4,
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@ -287,9 +368,9 @@ ski_cabin_model = MCExposureModel(
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activity=models.Activity.types['Moderate activity'],
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mask=models.Mask.types['Type I']
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)
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)
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)for qid in (100, 60)]
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gym_model = MCExposureModel(
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gym_model = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=300),
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ventilation=models.AirChange(
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@ -300,7 +381,7 @@ gym_model = MCExposureModel(
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number=2,
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presence=models.SpecificInterval(((0, 1),)),
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masked=False,
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virus=MCVirus(halflife=1.1, qID=60),
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=1,
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samples=200000,
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breathing_category=5,
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@ -313,9 +394,9 @@ gym_model = MCExposureModel(
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activity=models.Activity.types['Heavy exercise'],
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mask=models.Mask.types['No mask']
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)
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)
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)for qid in (100, 60)]
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waiting_room_model = MCExposureModel(
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waiting_room_model = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=100),
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ventilation=models.AirChange(
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@ -326,7 +407,7 @@ waiting_room_model = MCExposureModel(
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number=1,
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presence=models.SpecificInterval(((0, 2),)),
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masked=False,
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virus=MCVirus(halflife=3.8, qID=60),
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virus=MCVirus(halflife=3.8, qID=qid),
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expiratory_activity=4,
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samples=200000,
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breathing_category=1,
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@ -339,9 +420,9 @@ waiting_room_model = MCExposureModel(
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activity=models.Activity.types['Seated'],
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mask=models.Mask.types['No mask']
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)
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)
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)for qid in (100, 60)]
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chorale_model = MCExposureModel(
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chorale_model = [MCExposureModel(
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concentration_model=MCConcentrationModel(
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room=models.Room(volume=810),
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ventilation=models.AirChange(
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@ -352,7 +433,7 @@ chorale_model = MCExposureModel(
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number=1,
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presence=models.SpecificInterval(((0, 2.5),)),
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masked=False,
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virus=MCVirus(halflife=1.1, qID=100),
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virus=MCVirus(halflife=1.1, qID=qid),
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expiratory_activity=3,
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samples=200000,
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breathing_category=3,
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@ -365,4 +446,4 @@ chorale_model = MCExposureModel(
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activity=models.Activity.types['Moderate activity'],
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mask=models.Mask.types['No mask']
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)
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)
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)for qid in (100, 60)]
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@ -579,8 +579,8 @@ def plot_pi_vs_viral_load(baselines: typing.Union[MCExposureModel, typing.List[M
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plt.vlines(x=(left, right), ymin=0, ymax=1,
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colors=('grey', 'grey'), linestyles='dotted')
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plt.text(left - 1.1, 0.80, '$vl_{crit1}$', fontsize=12,color='black')
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plt.text(right + 0.1, 0.80, '$vl_{crit2}$', fontsize=12,color='black')
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plt.text(left - 1.1, 0.80, '$vl_{0.05}$', fontsize=12,color='black')
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plt.text(right + 0.1, 0.80, '$vl_{0.95}$', fontsize=12,color='black')
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# add 3 shaded areas
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plt.axvspan(3, left, alpha=0.1, color='limegreen')
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plt.axvspan(left, right, alpha=0.1, color='orange')
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@ -589,16 +589,16 @@ def plot_pi_vs_viral_load(baselines: typing.Union[MCExposureModel, typing.List[M
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if labels is not None:
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plt.legend(labels)
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# this is an inset plot inside the main plot
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a = plt.axes([.2, .25, .3, .2], facecolor='lightgrey')
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plt.title('Histogram', fontsize=10)
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# choose between hist or violin plot
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if len(baselines) == 1:
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plt.hist(baselines[0].infection_probability()/100, bins=50)
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plt.xticks([0, 0.5, 1])
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plt.yticks([])
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#a = plt.axes([.2, .25, .3, .2], facecolor='lightgrey')
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#
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#plt.title('Histogram', fontsize=10)
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## choose between hist or violin plot
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#
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#if len(baselines) == 1:
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# plt.hist(baselines[0].infection_probability()/100, bins=50)
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# plt.xticks([0, 0.5, 1])
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# plt.yticks([])
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#
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# parts = plt.violinplot((shared_office_worst_model[1].infection_probability()/100, shared_office_model[1].infection_probability()/100, shared_office_better_model[1].infection_probability()/100), positions = (1, 2, 3), showmeans=True, showmedians=True)
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# for pc in parts['bodies']:
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# pc.set_facecolor('#D43F3A')
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