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

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# Conflicts:
#	cara/mc-output.py
#	cara/montecarlo.py
This commit is contained in:
Andrejh 2021-03-01 15:26:49 +01:00
commit 91c07b9e5c
1 changed files with 26 additions and 17 deletions
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43
cara/montecarlo.py
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@ -11,7 +11,7 @@ import matplotlib.pyplot as plt
import matplotlib.patches as patches
import matplotlib.lines as mlines
from sklearn.neighbors import KernelDensity
TIME_STEP = 0.001
TIME_STEP = 0.01
USE_SCOEH = False
@ -687,9 +687,9 @@ def composite_plot_pi_vs_viral_load(baselines: typing.List[MCExposureModel], lab
axs[1, 0].set_xticks([i for i in range(2, 13, 2)])
axs[1, 0].set_xticklabels(['$10^{' + str(i) + '}$' for i in range(2, 13, 2)])
axs[1, 0].set_xlim(2, 12)
axs[1, 0].set_xlabel('Viral load (RNA copies mL$^{-1}$)', fontsize=12)
axs[0, 0].set_ylabel('Probability of infection (%)\n$P(I|qID=60)$', fontsize=12)
plt.suptitle(title, fontsize=12)
axs[1, 0].set_xlabel('Viral load (RNA copies mL$^{-1}$)\n$vl$')
axs[0, 0].set_ylabel('Probability of infection (%)\n$P(I|qID=60)$')
plt.suptitle(title)
axs[0, 0].text(11, -0.01, '$(i)$')
axs[1, 0].text(11, axs[1, 0].get_ylim()[1] * 0.8, '$(ii)$')
@ -704,12 +704,12 @@ def composite_plot_pi_vs_viral_load(baselines: typing.List[MCExposureModel], lab
break
for i, (crit, color) in enumerate(zip(crits, colors)):
axs[0, 0].text(2.5, 0.45 - i * 0.1, f'x $vl_{"{0.95}"}=' + '10^{' + str(np.round(crits[i], 1)) + '}$', fontsize=10, color=color)
axs[0, 0].text(2.5, 0.4 - i * 0.1, f'x $vl_{"{0.95}"}=' + '10^{' + str(np.round(crits[i], 1)) + '}$', fontsize=10, color=color)
axs[0, 0].plot(crits[i], 0.95, 'x', color=color)
if show_lines:
axs[0, 0].hlines([0.5], colors=['lightgrey'], linestyles=['dashed'], xmin=2, xmax=12)
axs[0, 0].text(9.7, 0.52, "$P(I) = 0.5$", color='grey')
axs[0, 0].text(9.7, 0.52, "$P(I) = 0.5$", color='lightgrey')
middle_positions = []
for line in lines:
for i, point in enumerate(line):
@ -1064,7 +1064,6 @@ def compare_concentration_curves(exp_models: typing.List[MCExposureModel], label
ax.legend(loc='upper left')
ax.set_ylim(ax.get_ylim()[0], ax.get_ylim()[1] * 1.2)
ax.spines["right"].set_visible(False)
factors = [0.6 * model.exposed.activity.inhalation_rate * (1 - model.exposed.mask.η_inhale) for model in exp_models]
present_indexes = np.array([exp_models[0].exposed.person_present(t) for t in times])
@ -1076,27 +1075,37 @@ def compare_concentration_curves(exp_models: typing.List[MCExposureModel], label
for c, factor in zip(modified_concentrations, factors)]
plt.suptitle(title)
plt.xlabel("Time ($h$)", fontsize=14)
plt.ylabel("Quantum concentration ($q\;m^{-3}$)\nmean values", fontsize=14)
plt.xlabel("Time ($h$)", fontsize=12)
plt.ylabel("Quantum concentration ($q\;m^{-3}$)\nmean values of $C(t)$", fontsize=12)
if show_qd:
ax1 = ax.twinx()
for qd, label, color in zip(qds, labels, colors):
ax1.plot(times, qd, label='qD - ' + label, color=color, linestyle='dotted')
ax1.spines["right"].set_linestyle("--")
ax1.spines["right"].set_linestyle((0,(1,5)))
ax1.set_ylabel('Dose ($q$)', fontsize=14)
ax1.set_ylabel('Dose ($q$)', fontsize=12)
ax1.set_ylim(ax1.get_ylim()[0], ax1.get_ylim()[1] * 1.2)
ax2 = ax.twinx()
ax2.spines["right"].set_position(("axes", 1.15))
ax2.spines["right"].set_linestyle((0,(1,5)))
ax2.set_ylabel('Dose (RNA copies)\nmean values', fontsize=14)
ax2.spines["right"].set_position(("axes", 1.2))
ax2.set_ylabel('Dose (RNA copies)\nmean values $qD$', fontsize=12)
ax2.set_ylim(tuple(y * exp_models[0].concentration_model.virus.qID for y in ax1.get_ylim()))
#ax1.legend(loc='upper right')
plt.tight_layout()
plt.hlines([60], colors=['lightgrey'], linestyles=['dashed'], xmin=start, xmax=stop)
plt.text(7, 65, "$qID = 60$", color='grey')
plt.text(7, 65, "$qID = 60$", color='lightgrey')
plt.show()
print()
def print_qd_info(model: MCExposureModel) -> None:
qds = model.exposed.activity.inhalation_rate * (1 - model.exposed.mask.η_inhale) * model.quanta_exposure() * 0.6
print(f"----- qD distribution -----\n"
f"Mean:\t{np.mean(qds)}\n"
f"Median:\t{np.median(qds)}\n\n"
f"Percentiles\n"
f"1st:\t{np.percentile(qds, 1)}\n"
f"5th:\t{np.percentile(qds, 5)}\n"
f"10th:\t{np.percentile(qds, 10)}\n"
f"90th:\t{np.percentile(qds, 90)}\n"
f"95th:\t{np.percentile(qds, 95)}\n"
f"99th:\t{np.percentile(qds, 99)}\n")