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use breathing rates

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markus 2021-01-25 16:49:27 +01:00
parent eba70a6580
commit 271e1c8dd8
1 changed files with 14 additions and 3 deletions
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17
cara/montecarlo.py
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@ -72,6 +72,8 @@ class MCInfectedPopulation(models.Population):
viral_load: typing.Optional[float] = None viral_load: typing.Optional[float] = None
breathing_category: typing.Optional[int] = None
def _generate_viral_loads(self) -> np.ndarray: def _generate_viral_loads(self) -> np.ndarray:
kde_model = KernelDensity(kernel='gaussian', bandwidth=0.1) kde_model = KernelDensity(kernel='gaussian', bandwidth=0.1)
kde_model.fit(np.asarray(log_viral_load_frequencies)[0, :][:, np.newaxis], kde_model.fit(np.asarray(log_viral_load_frequencies)[0, :][:, np.newaxis],
@ -99,10 +101,19 @@ class MCInfectedPopulation(models.Population):
mask_efficiency = [0.75, 0.81, 0.81][self.expiratory_activity] if masked else 0 mask_efficiency = [0.75, 0.81, 0.81][self.expiratory_activity] if masked else 0
qr_func = np.vectorize(self._calculate_qr) qr_func = np.vectorize(self._calculate_qr)
# TODO: Add distributions for parameters if self.expiratory_activity == 0:
breathing_rate = 1 assert self.breathing_category is not None, \
"expiratory_activity specified as 0 (breathing) without specified 'breathing_category'"
else:
print("'breathing_category' unused as 0 (breathing) was not chosen as 'expiratory_activity'")
return qr_func(viral_loads, emissions, diameters, mask_efficiency, self.qid) if self.breathing_category is not None:
csi, lamb = lognormal_parameters[self.breathing_category]
breathing_rates = lognormal(csi, lamb, self.samples)
else:
breathing_rates = None
return qr_func(viral_loads, emissions, diameters, mask_efficiency, self.qid, breathing_rates)
@staticmethod @staticmethod
def _calculate_qr(viral_load: float, emission: float, diameter: float, mask_efficiency: float, def _calculate_qr(viral_load: float, emission: float, diameter: float, mask_efficiency: float,