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Zombie pandemic simulation in France
"""
Model of a Zombie outbreak in France, starting in Grenoble
This is a rewrite from this blog post by Max Berrgren:
http://maxberggren.github.io/2014/11/27/model-of-a-zombie-outbreak/
with a different country, a slightly different model, and different
libraries. The map of population density is taken from Wikimedia Commons
Model
------
I use a modified SIR model. "Modified" because I didn't fully understood
SIR when I wrote the code. The population is divided in 3 categories:
S = Sane people
I = People who have been beaten, they are Incubating, soon-to-be Zombies
R = Rampaging Zombies, who bite sane people.
The rules are as follows:
- Sane citizen don't move (the army forbids it) until they get biten
by a zombie
- Biten people move fast (they don't control themselves) and after
some time they are tranformed into zombies. As a consequence, some
cities like Paris will be contaminated by these people, ahead of the
main zombie wave.
- Zombies walk slowly and bite people.
All units are really much arbitrary and tuned to make a sexy animation.
Result
-------
See the resulting animation here:
http://i.imgur.com/BsgBP4g.gif
Blue represents sane citizen, red zombies, and green/yellow infected
people. Looks like Maubeuge, in the north-east, will (finally) be the
place to go.
Requirements:
-------------
Numpy for numerical computations.
Scipy for the convolution that computes the dispersion
MoviePy for the animation (requires FFMPEG installed)
ImageMagick if you want to make a gif
Copyright Zulko 2014, Licence Public Domain (Creative Commons 0)
@NSA, @DGSE => This is just for science. No plans.
"""
import urllib
import numpy as np
from scipy.ndimage.filters import convolve
import moviepy.editor as mpy
#### RETRIEVE THE MAP FROM THE WEB
filename = ("http://upload.wikimedia.org/wikipedia/commons/a/aa/"
"France_-_2011_population_density_-_200_m_%C3%"
"97_200_m_square_grid_-_Dark.png")
urllib.urlretrieve(filename, "france_density.png")
#### PARAMETERS AND CONSTANTS
infection_rate = 0.3
incubation_rate = 0.1
dispersion_rates = [0, 0.07, 0.03] # for S, I, R
# This kernel models how the people/zombies at one position
# spread to the neighboring positions
dispersion_kernel = np.array([[0.5, 1 , 0.5],
[1 , -6, 1],
[0.5, 1, 0.5]])
france = mpy.ImageClip("france_density.png").resize(width=400)
SIR = np.zeros( (3,france.h, france.w), dtype=float)
SIR[0] = france.get_frame(0).mean(axis=2)/255
start = int(0.6*france.h), int(0.737*france.w)
SIR[1,start[0], start[1]] = 0.8 # infection in Grenoble at t=0
dt = 1.0 # one update = one hour of real time
hours_per_second= 7*24 # one second in the video = one week in the model
world = {'SIR':SIR, 't':0}
##### MODEL
def infection(SIR, infection_rate, incubation_rate):
""" Computes the evolution of #Sane, #Infected, #Rampaging"""
S,I,R = SIR
newly_infected = infection_rate*R*S
newly_rampaging = incubation_rate*I
dS = - newly_infected
dI = newly_infected - newly_rampaging
dR = newly_rampaging
return np.array([dS, dI, dR])
def dispersion(SIR, dispersion_kernel, dispersion_rates):
""" Computes the dispersion (spread) of people """
return np.array( [convolve(e, dispersion_kernel, cval=0)*r
for (e,r) in zip(SIR, dispersion_rates)])
def update(world):
""" spread the epidemic for one time step """
infect = infection(world['SIR'], infection_rate, incubation_rate)
disperse = dispersion(world['SIR'], dispersion_kernel, dispersion_rates)
world['SIR'] += dt*( infect + disperse)
world['t'] += dt
# ANIMATION WITH MOVIEPY
def world_to_npimage(world):
""" Converts the world's map into a RGB image for the final video."""
coefs = np.array([2,25,25]).reshape((3,1,1))
accentuated_world = 255*coefs*world['SIR']
image = accentuated_world[::-1].swapaxes(0,2).swapaxes(0,1)
return np.minimum(255, image)
def make_frame(t):
""" Return the frame for time t """
while world['t'] < hours_per_second*t:
update(world)
return world_to_npimage(world)
animation = mpy.VideoClip(make_frame, duration=25)
# You can write the result as a gif (veeery slow) or a video:
#animation.write_gif(make_frame, fps=15)
animation.write_videofile('test.mp4', fps=20)
@Zulko

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Zulko commented Sep 29, 2016

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