def __init__(self, generateFunc, Yesterday):
self.df = generateFunc[0]
self.stateOfDay = generateFunc[1]
self.MoversList = generateFunc[2]
self.YesterdayPatients = Yesterday
s = States()
self.deathRate = s.returnConfig("Rates", "deathRate", float)
self.daysFromLimbo = s.returnConfig(
"Days", "daysUntilLimboDieDuetoLackOfBeds", int)
self.numberOfBeds = s.returnConfig("SampleDefaults", "numberOfBeds",
int)
self.deathsLackBed = s.returnConfig("Rates", "deathsDueToLackOfBeds",
float)
self.hospitalRate = s.returnConfig("Rates", "hospitalizationRate",
float)
self.hospitalRateICU = s.returnConfig("Rates", "deathRateForICU",
float)
self.dayUntilCuredCovid = s.returnConfig("Days",
"dayUnitlCuredIfPositive",
int)
self.daysUnitlCuredHos = s.returnConfig("Days",
"dayUnitlCuredIfInHospital",
int)
self.xlimit = s.returnConfig("SampleDefaults", "xlimit", int)
self.ylimit = s.returnConfig("SampleDefaults", "ylimit", int)
self.distanceLimit = s.returnConfig("SampleDefaults", "distance",
float)
def __init__(self):
s = States()
self.groupSize = s.returnConfig("SampleDefaults", "groupSize", int)
self.state = s.status
self.colors = s.stateColors
self.sampleSize = s.returnConfig("SampleDefaults", "sampleSize", float)
self.x = s.returnConfig("SampleDefaults", "xLimit", int)
self.y = s.returnConfig("SampleDefaults", "yLimit", int)
class SampleModel:
def __init__(self, day, generateFunc, processFunc, plotFunc, path):
self.day = day
self.path = path
self.s = States()
self.dayLimit = self.s.returnConfig('SampleDefaults', 'dayLimit', int)
self.x = self.s.returnConfig('SampleDefaults', 'xLimit', int)
self.y = self.s.returnConfig('SampleDefaults', 'yLimit', int)
self.groupsize = self.s.returnConfig('SampleDefaults', 'groupSize', int)
self.sampleSize = self.s.returnConfig('SampleDefaults', 'sampleSize', float)
self.distance = self.s.returnConfig('SampleDefaults', 'distance', float)
self.beds = self.s.returnConfig('SampleDefaults', 'numberOfBeds', float)
logfile = f"{self.path}/{self.s.returnConfig('SampleDefaults', 'logfile', str)}"
self.logFile = open(logfile, "w+")
self.distanceLimit = self.s.returnConfig("SampleDefaults", "distance", float)
self.generateData = generateFunc
self.stateOfDay = self.generateData[1]
self.MoversList = self.generateData[2]
self.YesterdayPatients = list(self.generateData[0]['State'])
self.startProcess = processFunc
self.plotData = plotFunc
def write_log(self, *args):
line = ' '.join([str(a) for a in args])
self.logFile.write(line + '\n')
print(line)
return
def infect(self, i):
if rn.random() > 0.25 and self.day > 3:
return
if self.generateData[0].loc[i, "State"] == 0:
self.generateData[0].loc[i, "State"], self.generateData[0].loc[i, "Day"] = 1, self.day
def nextDay(self):
process = self.startProcess
self.day += 1
process.kill(self.day)
process.hospitilize(self.day)
process.cure(self.day)
self.move()
self.interact()
return
def plot(self):
self.plotData.setup_plot(self.day)
return
def count(self):
List = list(self.generateData[0]['State'])
self.stateOfDay.loc[self.day, 'Healthy'] = List.count(0)
self.stateOfDay.loc[self.day, 'Covid-19(+)'] = List.count(1)
self.stateOfDay.loc[self.day, 'Hospitalized'] = List.count(2)
self.stateOfDay.loc[self.day, 'Cured'] = List.count(4)
self.stateOfDay.loc[self.day, 'Dead'] = List.count(3)
self.stateOfDay.loc[self.day, 'Limbo'] = List.count(5)
self.stateOfDay.loc[self.day, 'Self Cured'] = List.count(6)
self.stateOfDay.loc[self.day, 'Total Cured'] = List.count(6) + List.count(4)
return
def run(self):
self.infect(rn.randrange(self.groupsize))
self.plot()
self.count()
self.log(2)
self.nextDay()
self.plot()
self.count()
self.log(2)
return
def interact(self):
for i in range(len(self.generateData[0])):
for j in range(i):
if self.check(i, j):
if (self.generateData[0].loc[i, 'State'] == 0):
self.infect(i)
else:
self.infect(j)
def check(self, i, j):
Dist = math.sqrt((self.generateData[0].loc[i, 'X'] - self.generateData[0].loc[j, 'X'])
** 2 + (self.generateData[0].loc[i, 'Y'] - self.generateData[0].loc[j, 'Y'])**2)
flag = ((self.YesterdayPatients[i] == 1) ^
(self.YesterdayPatients[j] == 1)) and Dist < self.distanceLimit
return flag
def move(self):
for i in self.MoversList:
if (self.generateData[0].loc[i, 'State'] == 2) or (self.generateData[0].loc[i, 'State'] == 3) or (self.generateData[0].loc[i, 'State'] == 5):
self.MoversList.remove(i)
self.generateData[0].loc[i, 'X'], self.generateData[0].loc[i, 'Y'] = (self.generateData[0].loc[i, 'X'] + rn.uniform(
1, self.x / 3)) % self.x , (self.generateData[0].loc[i, 'Y'] + rn.uniform(1, self.y / 3)) % self.y
def log(self, phase):
if phase == 1:
self.write_log(31 * '-')
self.write_log("Here's the Input Data:")
self.write_log(8 * '- - ')
self.write_log('Numper of Sample:', self.groupsize)
self.write_log('X & Y limites: ', self.x, ', ', self.y)
self.write_log('Distance required for Contamination:', self.distance)
self.write_log("Moving Sample", self.sampleSize)
self.write_log("Number Of Beds", self.beds)
x = input("Do you wish to continue? y/n: ")
if x == "y":
pass
elif x == 'n':
sys.exit()
elif phase == 2:
self.write_log(31 * '-')
self.write_log('Day:', self.day)
self.write_log(8 * '- - ')
self.write_log(self.generateData[1].loc[self.day])
return
def end(self):
self.Png_to_gif()
self.stateOfDay.to_excel(f"{self.path}/Stat.xlsx")
self.stateOfDay.plot(title='Statistical Data Vs. Days Passed')
plt.savefig(f"{self.path}/Stat")
self.logFile.close()
def condition(self):
healthy = len(self.generateData[0][self.generateData[0]['State'] == 0])
covid19 = len(self.generateData[0][self.generateData[0]['State'] == 1])
hospitilize = len(self.generateData[0][self.generateData[0]['State'] == 2])
dead = len(self.generateData[0][self.generateData[0]['State'] == 3])
cured = len(self.generateData[0][self.generateData[0]['State'] == 4])
Limbo = len(self.generateData[0][self.generateData[0]['State'] == 5])
selfcured = len(self.generateData[0][self.generateData[0]['State'] == 6])
today = list(self.generateData[1].loc[self.day])
yest = list(self.generateData[1].loc[self.day- 1])
if covid19 == 0 and today == yest and hospitilize == 0:
return 1
else:
return 0
def main(self):
whileBreak = 0
while True:
whileBreak += int(self.condition())
if whileBreak > 2:
self.end()
break
else:
self.whileBreak = 0
self.YesterdayPatients = list(self.generateData[0]['State'])
self.nextDay()
self.plot()
self.count()
self.log(2)
def Png_to_gif(self):
frames = []
inImgs = f"{self.path}/days/*.png"
output = f"{self.path}/png_to_gif.gif"
img, *imgs = [Image.open(i) for i in sorted(glob.glob(inImgs))]
img.save(fp=output, format='GIF', append_images=imgs,
save_all=True, duration=500, loop=0)
class Draw:
def __init__(self, df, path):
self.path = path
self.fig, self.axs = plt.subplots(2, figsize=(10, 8))
self.fig.suptitle('Covid-19 Epidemic Sample Model', fontsize=16)
self.ld = [
'Healthy', 'Covid-19(+)', 'Hospitalized', 'Cured', 'Self Cured',
'Death Toll', 'Limbo', 'Total Cured'
]
self.df = df[0]
self.stateOfDay = df[1]
self.MoversList = df[2]
self.state = States()
self.dayLimit = self.state.returnConfig('SampleDefaults', 'dayLimit',
int)
self.x = self.state.returnConfig('SampleDefaults', 'xLimit', int)
self.y = self.state.returnConfig('SampleDefaults', 'yLimit', int)
self.groupsize = self.state.returnConfig('SampleDefaults', 'groupSize',
int)
self.sampleSize = self.state.returnConfig('SampleDefaults',
'sampleSize', float)
self.distance = self.state.returnConfig('SampleDefaults', 'distance',
float)
self.beds = self.state.returnConfig('SampleDefaults', 'numberOfBeds',
float)
self.distanceLimit = self.state.returnConfig("SampleDefaults",
"distance", float)
def setup_plot(self, day):
self.axs[0].cla()
self.scat = self.axs[0].scatter(self.df['X'],
self.df['Y'],
s=1,
c=self.plt1color())
for i in self.MoversList:
self.axs[0].scatter(self.df.loc[i, 'X'],
self.df.loc[i, 'Y'],
s=6,
facecolors='none',
edgecolors='black')
self.axs[0].text(self.df.loc[i, 'X'] + 0.02,
self.df.loc[i, 'Y'] + 0.02,
str(i),
fontsize=5)
sDay = str(day)
title = f"Day={sDay}, Group Size={self.groupsize}, Movers={self.sampleSize * 100}%, Infection Distance={self.distance}"
self.axs[0].set_title(title, loc='center')
title2 = f"Healthy={len(self.df[self.df['State'] == 0])}, Infected={len(self.df[self.df['State'] == 1])}, Dead={len(self.df[self.df['State'] == 3])}"
self.axs[0].set_xlabel(title2)
self.axs[0].set_yticklabels([])
self.axs[0].set_xticklabels([])
self.axs[0].tick_params(which='both',
bottom=False,
top=False,
right=False,
left=False,
labelbottom=True)
self.axs[1].set_yticklabels([])
self.axs[1].set_xticklabels([])
self.axs[1].cla()
self.axs[1].plot(self.stateOfDay.Healthy,
label=self.ld[0],
color=self.plt2color()[0])
self.axs[1].plot(self.stateOfDay['Covid-19(+)'],
label=self.ld[1],
color=self.plt2color()[1])
self.axs[1].plot(self.stateOfDay.Hospitalized,
label=self.ld[2],
color=self.plt2color()[2])
self.axs[1].plot(self.stateOfDay.Cured,
label=self.ld[3],
color=self.plt2color()[3])
self.axs[1].plot(self.stateOfDay['Self Cured'],
label=self.ld[4],
color=self.plt2color()[4])
self.axs[1].plot(self.stateOfDay.Dead,
label=self.ld[5],
color=self.plt2color()[5])
self.axs[1].plot(self.stateOfDay.Limbo,
label=self.ld[6],
color=self.plt2color()[6])
self.axs[1].plot(self.stateOfDay['Total Cured'],
label=self.ld[7],
color=self.plt2color()[7])
self.axs[1].set_prop_cycle(color=self.plt2color())
self.axs[1].legend(bbox_to_anchor=(0, 1),
loc='upper left',
borderaxespad=0.)
plt.tight_layout(rect=[0, 0.03, 1, 0.95])
plt.ion()
plt.pause(0.5)
plt.xlabel("Days")
if day < 10:
sDay = '0' + sDay
title = f"{self.path}/days/Day{sDay}.png"
plt.savefig(title)
return
def plt1color(self):
cols = []
for l in self.df.index:
if self.df.loc[l, 'State'] == 1: # Infected
cols.append(self.state.stateColors(1))
elif self.df.loc[l, 'State'] == 3: # Dead
cols.append(self.state.stateColors(3))
elif self.df.loc[l, 'State'] == 2: # Hospitalized
cols.append(self.state.stateColors(2))
elif self.df.loc[l, 'State'] == 4: # Cured
cols.append(self.state.stateColors(4))
elif self.df.loc[l, 'State'] == 5: # Limbo
cols.append(self.state.stateColors(5))
elif self.df.loc[l, 'State'] == 100: #Total Cured
cols.append(self.state.stateColors(100))
else:
cols.append('blue') # Healthy
return cols
def plt2color(self):
cols = []
for i in self.stateOfDay.columns:
if i == 'Covid-19(+)': # Infected
cols.append('red')
elif i == 'Dead': # Dead
cols.append('black')
elif i == 'Hospitalized': # Hospitalized
cols.append('orange')
elif i == 'Cured': # Cured
cols.append('green')
elif i == 'Self Cured': # limbo
cols.append('cyan')
elif i == 'Limbo': # limbo
cols.append('yellow')
elif i == 'Total Cured': # limbo
cols.append('lime')
else:
cols.append('blue') # Healthy
return cols
