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Plot animation of spread of COVID 19
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''' | |
Download data from github: https://github.com/CSSEGISandData/COVID-19 | |
Place this file in | |
COVID-19/csse_covid_19_data/csse_covid_19_time_series/plotme.py | |
REQUIRES: | |
matplotlib | |
numpy | |
pillow | |
TO RUN: | |
python plotme.py | |
''' | |
from pylab import * | |
from numpy import * | |
import glob | |
import csv | |
import os.path | |
import os | |
covid = {} | |
n_day = 0 | |
for fn in glob.glob('*.csv'): | |
dat = list(csv.reader(open(fn))) | |
#dates = [d for d in dat[0][4:] + dat[0][4:] + [dat[0][-1]] * 10] | |
dates = [d for d in dat[0][4:]] | |
typ = fn[:-4].split('-')[-1] | |
for l in dat[1:]: | |
city = l[0] + '//', l[1] | |
lat = float(l[2]) | |
lon = float(l[3]) | |
dat = list(map(float, l[4:])) | |
if city not in covid: | |
covid[city] = {} | |
covid[city][typ] = dat | |
covid[city]['lat'] = lat | |
covid[city]['lon'] = lon | |
if len(dat) > n_day: | |
n_day = len(dat) | |
world = [] | |
for ll in open('world.dat.txt').readlines(): | |
ll = ll.strip() | |
if ll: | |
lon, lat = map(float, ll.split()) | |
world.append((lat, lon)) | |
else: | |
world.append((nan, nan)) | |
world = array(world) | |
DEG = pi/180 | |
theta = arange(361) * DEG | |
circ = [cos(theta), sin(theta)] | |
def getr(n): | |
return sqrt(n/pi)/5 | |
def plot_day(day, png): | |
close('all') | |
figure(figsize=(12, 6)) | |
title(dates[day]) | |
axis('equal') | |
xlim(-180, 180) | |
ylim(-90, 90) | |
xticks([]) | |
yticks([]) | |
plot(world[:,1], world[:,0], 'k-', linewidth=.5) | |
for city in covid: | |
if covid[city]['Confirmed'][day] > 0: | |
plot(covid[city]['lon'], covid[city]['lat'], 'k.') | |
if covid[city]['Deaths'][day] > 0: | |
plot(covid[city]['lon'], covid[city]['lat'], 'r.') | |
for city in covid: | |
c = covid[city] | |
confirmed = getr(c['Confirmed'][day]) | |
fill(c['lon'] + circ[0] * confirmed, c['lat'] + circ[1] * confirmed, 'k-', alpha=.3) | |
for city in covid: | |
c = covid[city] | |
deaths = getr(c['Deaths'][day]) | |
fill(c['lon'] + circ[0] * deaths, c['lat'] + circ[1] * deaths, 'k-', color='r', alpha=1) | |
for city in covid: | |
c = covid[city] | |
recovered = getr(c['Recovered'][day]) | |
fill(c['lon'] + circ[0] * recovered, c['lat'] + circ[1] * recovered, color='g', alpha=.3) | |
# show(); here | |
#### legend | |
fill(-180 + 25 * circ[0], -40 + 25 * circ[1], color='k', alpha=.3) | |
fill(-180 + 5 * circ[0], -40 + 5 * circ[1], color='r', alpha=1) | |
fill(-180 + 15 * circ[0], -40 + 15 * circ[1], color='g', alpha=.3) | |
text(-175, -15, 'Confirmed') | |
text(-175, -30, 'Recovered') | |
text(-175, -40, 'Dead') | |
savefig(png) | |
print ('wrote', png) | |
if not os.path.exists('images'): | |
os.mkdir('images') | |
for day in range(n_day): | |
png = 'images/%03d.png' % day | |
if day < n_day - 1 and os.path.exists(png): | |
continue | |
plot_day(day, png) | |
for i in range(30): | |
png = f'images/{n_day+i+1:03d}.png' | |
plot(i, -89, 'k,') | |
savefig(png) | |
print ('wrote', png) | |
### convert images to GIF | |
import PIL.Image as Image | |
pngs = glob.glob('images/*.png') | |
pngs.sort() | |
gif = 'images.gif' | |
imgs = [] | |
for png in pngs: | |
imgs.append(Image.open(png)) | |
print(imgs[-1].filename) | |
size = imgs[-1].size | |
im = imgs[0] | |
print(len(imgs)) | |
im.save(gif, save_all=True, append_images=imgs, loop=False) | |
print('wrote', gif) |
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Also required world.dat.txt form here:
https://raw.githubusercontent.com/gnuplot/gnuplot/master/demo/world.dat