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Merge remote-tracking branch 'origin/feature/mc' into feature/mc

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# Conflicts:
#	cara/montecarlo.py
This commit is contained in:
markus 2021-02-19 19:03:22 +01:00
commit 5a9e95e87a
1 changed files with 40 additions and 6 deletions
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46
cara/montecarlo.py
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@ -670,8 +670,8 @@ def generate_cdf_curves_vs_qr(masked: bool = False, samples: int = 200000, qid:
fig, axs = plt.subplots(3, 1, sharex='all') fig, axs = plt.subplots(3, 1, sharex='all')
# TODO: Insert title and y-label # TODO: Insert title and y-label
plt.suptitle("INSERT TITLE HERE") plt.suptitle("$F(qR|qID=$" + str(qid) + "$)$",fontsize=12, y=0.93)
fig.text(0.02, 0.5, 'INSERT Y-LABEL HERE', va='center', rotation='vertical') fig.text(0.02, 0.5, 'Cumulative Distribution Function', va='center', rotation='vertical',fontsize=12)
scenarios = [MCInfectedPopulation( scenarios = [MCInfectedPopulation(
number=1, number=1,
@ -687,7 +687,7 @@ def generate_cdf_curves_vs_qr(masked: bool = False, samples: int = 200000, qid:
right = max(np.max(qrs) for qrs in qr_values) right = max(np.max(qrs) for qrs in qr_values)
# Colors can be changed here # Colors can be changed here
colors = ['lightgreen', 'lightblue', 'pink'] colors = ['lightgrey', 'grey', 'black']
breathing_rates = ['Seated', 'Light activity', 'Heavy activity'] breathing_rates = ['Seated', 'Light activity', 'Heavy activity']
activities = ['Breathing', 'Speaking', 'Shouting'] activities = ['Breathing', 'Speaking', 'Shouting']
@ -702,7 +702,8 @@ def generate_cdf_curves_vs_qr(masked: bool = False, samples: int = 200000, qid:
axs[i].set_yticklabels(['0.0', '0.5', '1.0']) axs[i].set_yticklabels(['0.0', '0.5', '1.0'])
axs[i].yaxis.set_label_position("right") axs[i].yaxis.set_label_position("right")
axs[i].set_ylabel(activities[i]) axs[i].set_ylabel(activities[i])
axs[i].legend(handles=lines, loc='upper left') axs[i].grid(linestyle='--')
axs[0].legend(handles=lines, loc='upper left')
plt.xlabel('qR [$q\;h^{-1}$]') plt.xlabel('qR [$q\;h^{-1}$]')
tick_positions = np.arange(int(np.ceil(left)), int(np.ceil(right)), 2) tick_positions = np.arange(int(np.ceil(left)), int(np.ceil(right)), 2)
@ -940,7 +941,7 @@ exposure_models = [MCExposureModel(
concentration_model=MCConcentrationModel( concentration_model=MCConcentrationModel(
room=models.Room(volume=45), room=models.Room(volume=45),
ventilation=models.SlidingWindow( ventilation=models.SlidingWindow(
active=models.PeriodicInterval(period=120, duration=10), active=models.PeriodicInterval(period=120, duration=120),
inside_temp=models.PiecewiseConstant((0, 24), (293,)), inside_temp=models.PiecewiseConstant((0, 24), (293,)),
outside_temp=models.PiecewiseConstant((0, 24), (283,)), outside_temp=models.PiecewiseConstant((0, 24), (283,)),
window_height=1.6, opening_length=0.6, window_height=1.6, opening_length=0.6,
@ -953,6 +954,7 @@ exposure_models = [MCExposureModel(
expiratory_activity=1, expiratory_activity=1,
samples=2000000, samples=2000000,
breathing_category=1, breathing_category=1,
expiratory_activity_weights=(0.7, 0.3, 0)
) )
), ),
exposed=models.Population( exposed=models.Population(
@ -963,6 +965,34 @@ exposure_models = [MCExposureModel(
) )
) for qid in (100, 60)] ) for qid in (100, 60)]
exposure_models_2 = [MCExposureModel(
concentration_model=MCConcentrationModel(
room=models.Room(volume=33),
ventilation=models.SlidingWindow(
active=models.PeriodicInterval(period=120, duration=10),
inside_temp=models.PiecewiseConstant((0, 24), (293,)),
outside_temp=models.PiecewiseConstant((0, 24), (283,)),
window_height=1.6, opening_length=0.6,
),
infected=MCInfectedPopulation(
number=1,
presence=models.SpecificInterval(((0, 4), (5, 9))),
masked=True,
virus=MCVirus(halflife=1.1, qID=qid),
expiratory_activity=4,
samples=2000000,
breathing_category=1,
expiratory_activity_weights=(0.7, 0.1, 0)
)
),
exposed=models.Population(
number=2,
presence=models.SpecificInterval(((0, 4), (5, 9))),
activity=models.Activity.types['Seated'],
mask=models.Mask.types['FFP2']
)
) for qid in (100, 60)]
classroom_model = MCExposureModel( classroom_model = MCExposureModel(
concentration_model=MCConcentrationModel( concentration_model=MCConcentrationModel(
room=models.Room(volume=160), room=models.Room(volume=160),
@ -992,7 +1022,11 @@ classroom_model = MCExposureModel(
plot_concentration_curve(classroom_model) plot_concentration_curve(classroom_model)
#generate_cdf_curves_vs_qr(masked=False) #print(np.mean(exposure_models_2[1].infection_probability()))
#print(np.mean(exposure_models_2[1].infection_probability()))
#plot_pi_vs_viral_load([exposure_models[1],exposure_models_2[1]], labels=['B.1.1.7 - Guideline', 'B.1.1.7 - w/o masks'])
generate_cdf_curves_vs_qr(masked=False,qid=1000)
# rs = [model.expected_new_cases() for model in large_population_baselines] # rs = [model.expected_new_cases() for model in large_population_baselines]
# print(f"R0 - original variant:\t{np.mean(rs[0])}") # print(f"R0 - original variant:\t{np.mean(rs[0])}")