pythontkinterbioinformaticsode
Solving simple ODE system within tkinter GUI
I have a simple ODE system for an SIR disease model that works fine and produces a graphic plot. However I am trying to use tkinter to create a simple pop up box that takes parameter values instead of having to put them in through the script.
here is the original code.
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
#three compartments, Susceptible S, infected I, recovered R
#dS/dt, dI/dt, dR/dt
#susceptible sees birth rate coming in, deaths leaving and force of infection leaving
#infected sees FOI coming in, deaths leaving and recovery rates
#recovered sees recovery rate coming in, deaths leaving
#beta is tranmission coefficient, FOI is beta * (I/N) where N is total pop
#initially consider a model not accounting for births and deaths
# Total population, N.
N = 1000
# Initial number of infected and recovered individuals, I0 and R0.
I0, R0 = 1, 0
# Everyone else, S0, is susceptible to infection initially.
S0 = N - I0 - R0
# Contact rate, beta, and mean recovery rate, gamma, (in 1/days).
beta, gamma = 2/7, 1/7
# A grid of time points (in days)
t = np.linspace(0, 160, 160)
# The SIR model differential equations.
def deriv(y, t, N, beta, gamma):
S, I, R = y
dS = ((-beta * S * I) / N)
dI = ((beta * S * I) / N) - (gamma * I)
dR = (gamma * I)
return dS, dI, dR
# Initial conditions are S0, I0, R0
# Integrate the SIR equations over the time grid, t.
solve = odeint(deriv, (S0, I0, R0), t, args=(N, beta, gamma))
S, I, R = solve.T
# Plot the data on three separate curves for S(t), I(t) and R(t)
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
ax.plot(t, S/1000, 'b', alpha=1, lw=2, label='Susceptible')
ax.plot(t, I/1000, 'r', alpha=1, lw=2, label='Infected')
ax.plot(t, R/1000, 'black', alpha=1, lw=2, label='Recovered')
ax.set_xlabel('Time in days')
ax.set_ylabel('Number (1000s)')
ax.set_ylim(0,1.1)
#ax.yaxis.set_tick_params(length=0)
#ax.xaxis.set_tick_params(length=0)
ax.grid(b=True, which='major', c='w', lw=2, ls='-')
legend = ax.legend()
legend.get_frame().set_alpha(0.5)
#for spine in ('top', 'right', 'bottom', 'left'):
# ax.spines[spine].set_visible(False)
plt.show()
Now here is the one with some GUI
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
import tkinter as tk
from tkinter import IntVar
###############################################################################
def mainwindow():
mainwindow = tk.Tk()
mainwindow.geometry('350x350')
tk.Label(mainwindow, text="enter parameters below").grid(row=1)
getN = IntVar()
geti0 = IntVar()
getr0 = IntVar()
getbeta = IntVar()
getgamma = IntVar()
tk.Label(mainwindow, text="N").grid(row=2)
tk.Label(mainwindow, text="i0").grid(row=3)
tk.Label(mainwindow, text="r0").grid(row=4)
tk.Label(mainwindow, text="beta").grid(row=5)
tk.Label(mainwindow, text="gamma").grid(row=6)
e1 = tk.Entry(mainwindow,textvariable = getN).grid(row=2, column=1)
e2 = tk.Entry(mainwindow,textvariable = geti0).grid(row=3, column=1)
e3 = tk.Entry(mainwindow,textvariable = getr0).grid(row=4, column=1)
e4 = tk.Entry(mainwindow,textvariable = getbeta).grid(row=5, column=1)
e5 = tk.Entry(mainwindow,textvariable = getgamma).grid(row=6, column=1)
solve = tk.Button(mainwindow, text='solve!', command=lambda: [values()]).grid(row=7, column=1, sticky=tk.W, pady=4)
def values():
readN = getN.get()
readi0 = geti0.get()
readr0 = getr0.get()
readbeta = getbeta.get()
readgamma = getgamma.get()
intN = int(readN)
inti0 = int(readi0)
intr0 = int(readr0)
intbeta = int(readbeta)
intgamma = int(readgamma)
# Total population, N.
N = readN
# Initial number of infected and recovered individuals, I0 and R0.
I0, R0 = readi0, readr0
# Everyone else, S0, is susceptible to infection initially.
S0 = N - I0 - R0
# Contact rate, beta, and mean recovery rate, gamma, (in 1/days).
beta, gamma = readbeta, readgamma
# A grid of time points (in days)
t = np.linspace(0, 160, 160)
# The SIR model differential equations.
def deriv(y, t, N, beta, gamma):
S, I, R = y
dS = ((-beta * S * I) / N)
dI = ((beta * S * I) / N) - (gamma * I)
dR = (gamma * I)
return dS, dI, dR
# Initial conditions are S0, I0, R0
# Integrate the SIR equations over the time grid, t.
solve = odeint(deriv, (S0, I0, R0), t, args=(N, beta, gamma))
S, I, R = solve.T
# Plot the data on three separate curves for S(t), I(t) and R(t)
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
ax.plot(t, S/1000, 'b', alpha=0.5, lw=2, label='Susceptible')
ax.plot(t, I/1000, 'r', alpha=0.5, lw=2, label='Infected')
ax.plot(t, R/1000, 'g', alpha=0.5, lw=2, label='Recovered with immunity')
ax.set_xlabel('Time /days')
ax.set_ylabel('Number (1000s)')
ax.set_ylim(0,1.2)
ax.yaxis.set_tick_params(length=0)
ax.xaxis.set_tick_params(length=0)
ax.grid(b=True, which='major', c='w', lw=2, ls='-')
legend = ax.legend()
legend.get_frame().set_alpha(0.5)
for spine in ('top', 'right', 'bottom', 'left'):
ax.spines[spine].set_visible(False)
plt.show()
mainwindow.mainloop()
mainwindow()
The first gives the expected plot: 
, however with the GUI it gives this: 
Where has my code gone wrong? The code to solve the system hasnt changed, ive just set it so that the parameters take the values I enter in the pop up box. Has something gone wrong in the lambda function?
Solution
hi tried your code with beta and gamma as 2/7 , 1/7 wasnt able to make it work.
using:
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
import tkinter as tk
from tkinter import IntVar,StringVar,DoubleVar
###############################################################################
def mainwindow():
mainwindow = tk.Tk()
mainwindow.geometry('350x350')
tk.Label(mainwindow, text="enter parameters below").grid(row=1)
getN = IntVar()
geti0 = IntVar()
getr0 = IntVar()
# getbeta = StringVar()
# getgamma = StringVar()
getbeta = DoubleVar()
getgamma = DoubleVar()
tk.Label(mainwindow, text="N").grid(row=2)
tk.Label(mainwindow, text="i0").grid(row=3)
tk.Label(mainwindow, text="r0").grid(row=4)
tk.Label(mainwindow, text="beta").grid(row=5)
tk.Label(mainwindow, text="gamma").grid(row=6)
e1 = tk.Entry(mainwindow,textvariable = getN).grid(row=2, column=1)
e2 = tk.Entry(mainwindow,textvariable = geti0).grid(row=3, column=1)
e3 = tk.Entry(mainwindow,textvariable = getr0).grid(row=4, column=1)
e4 = tk.Entry(mainwindow,textvariable = getbeta).grid(row=5, column=1)
e5 = tk.Entry(mainwindow,textvariable = getgamma).grid(row=6, column=1)
solve = tk.Button(mainwindow, text='solve!', command=lambda: [values()]).grid(row=7, column=1, sticky=tk.W, pady=4)
def values():
readN = getN.get()
readi0 = geti0.get()
readr0 = getr0.get()
# readbeta = float(getbeta.get())
# readgamma = float(getgamma.get())
readbeta = (getbeta.get())
readgamma =(getgamma.get())
print('ppppppppppppp', readbeta,readgamma)
intN = int(readN)
inti0 = int(readi0)
intr0 = int(readr0)
intbeta = float(readbeta)
intgamma = float(readgamma)
# Total population, N.
N = readN
# Initial number of infected and recovered individuals, I0 and R0.
I0, R0 = readi0, readr0
# Everyone else, S0, is susceptible to infection initially.
S0 = N - I0 - R0
# Contact rate, beta, and mean recovery rate, gamma, (in 1/days).
beta, gamma = readbeta, readgamma
# A grid of time points (in days)
t = np.linspace(0, 160, 160)
# The SIR model differential equations.
def deriv(y, t, N, beta, gamma):
S, I, R = y
dS = ((-beta * S * I) / N)
dI = ((beta * S * I) / N) - (gamma * I)
dR = (gamma * I)
return dS, dI, dR
# Initial conditions are S0, I0, R0
# Integrate the SIR equations over the time grid, t.
solve = odeint(deriv, (S0, I0, R0), t, args=(N, beta, gamma))
S, I, R = solve.T
# Plot the data on three separate curves for S(t), I(t) and R(t)
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
ax.plot(t, S/1000, 'b', alpha=0.5, lw=2, label='Susceptible')
ax.plot(t, I/1000, 'r', alpha=0.5, lw=2, label='Infected')
ax.plot(t, R/1000, 'g', alpha=0.5, lw=2, label='Recovered with immunity')
ax.set_xlabel('Time /days')
ax.set_ylabel('Number (1000s)')
ax.set_ylim(0,1.2)
ax.yaxis.set_tick_params(length=0)
ax.xaxis.set_tick_params(length=0)
ax.grid(b=True, which='major', c='w', lw=2, ls='-')
legend = ax.legend()
legend.get_frame().set_alpha(0.5)
for spine in ('top', 'right', 'bottom', 'left'):
ax.spines[spine].set_visible(False)
plt.show()
mainwindow.mainloop()
mainwindow()
and 0.28 , 0.14 as beta and gamma I get:
Hope somebody that knows how to use fraction as input will show up,
I tried using getbeta = StringVar() and getgamma = StringVar()
and readbeta = float(getbeta.get()) and readgamma =float(getgamma.get())
or intbeta = float(readbeta) and intgamma = float(readgamma)
but got ValueError: could not convert string to float: '2/7'
for readbeta = float(getbeta.get())
came accross use of eval to allow input of '2/7' and '1/7' as beta and gamma,see How can I get the data from Entry in tkinter that can be used as function?
here the code updated:
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
import tkinter as tk
from tkinter import IntVar,StringVar,DoubleVar
###############################################################################
def mainwindow():
mainwindow = tk.Tk()
mainwindow.geometry('350x350')
tk.Label(mainwindow, text="enter parameters below").grid(row=1)
getN = IntVar()
geti0 = IntVar()
getr0 = IntVar()
getbeta = StringVar()
getgamma = StringVar()
# getbeta = DoubleVar()
# getgamma = DoubleVar()
tk.Label(mainwindow, text="N").grid(row=2)
tk.Label(mainwindow, text="i0").grid(row=3)
tk.Label(mainwindow, text="r0").grid(row=4)
tk.Label(mainwindow, text="beta").grid(row=5)
tk.Label(mainwindow, text="gamma").grid(row=6)
e1 = tk.Entry(mainwindow,textvariable = getN).grid(row=2, column=1)
e2 = tk.Entry(mainwindow,textvariable = geti0).grid(row=3, column=1)
e3 = tk.Entry(mainwindow,textvariable = getr0).grid(row=4, column=1)
e4 = tk.Entry(mainwindow,textvariable = getbeta).grid(row=5, column=1)
e5 = tk.Entry(mainwindow,textvariable = getgamma).grid(row=6, column=1)
solve = tk.Button(mainwindow, text='solve!', command=lambda: [values()]).grid(row=7, column=1, sticky=tk.W, pady=4)
def values():
readN = getN.get()
readi0 = geti0.get()
readr0 = getr0.get()
# readbeta = float(getbeta.get())
# readgamma = float(getgamma.get())
readbeta = eval(getbeta.get(),{"builtins": {}})
readgamma = eval(getgamma.get(), {"builtins": {}})
print('ppppppppppppp', readbeta,readgamma)
intN = int(readN)
inti0 = int(readi0)
intr0 = int(readr0)
intbeta = float(readbeta)
intgamma = float(readgamma)
# Total population, N.
N = readN
# Initial number of infected and recovered individuals, I0 and R0.
I0, R0 = readi0, readr0
# Everyone else, S0, is susceptible to infection initially.
S0 = N - I0 - R0
# Contact rate, beta, and mean recovery rate, gamma, (in 1/days).
beta, gamma = readbeta, readgamma
# A grid of time points (in days)
t = np.linspace(0, 160, 160)
# The SIR model differential equations.
def deriv(y, t, N, beta, gamma):
S, I, R = y
dS = ((-beta * S * I) / N)
dI = ((beta * S * I) / N) - (gamma * I)
dR = (gamma * I)
return dS, dI, dR
# Initial conditions are S0, I0, R0
# Integrate the SIR equations over the time grid, t.
solve = odeint(deriv, (S0, I0, R0), t, args=(N, beta, gamma))
S, I, R = solve.T
# Plot the data on three separate curves for S(t), I(t) and R(t)
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
ax.plot(t, S/1000, 'b', alpha=0.5, lw=2, label='Susceptible')
ax.plot(t, I/1000, 'r', alpha=0.5, lw=2, label='Infected')
ax.plot(t, R/1000, 'g', alpha=0.5, lw=2, label='Recovered with immunity')
ax.set_xlabel('Time /days')
ax.set_ylabel('Number (1000s)')
ax.set_ylim(0,1.2)
ax.yaxis.set_tick_params(length=0)
ax.xaxis.set_tick_params(length=0)
ax.grid(b=True, which='major', c='w', lw=2, ls='-')
legend = ax.legend()
legend.get_frame().set_alpha(0.5)
for spine in ('top', 'right', 'bottom', 'left'):
ax.spines[spine].set_visible(False)
plt.show()
mainwindow.mainloop()
mainwindow()
it uses getbeta = StringVar() and
getgamma = StringVar() and then readbeta = eval(getbeta.get(),{"builtins": {}}) and readgamma = eval(getgamma.get(), {"builtins": {}})
I read somewhere that use of eval is not safe in python so if anybody as a better solution please share it with us
At the end managed to validate input before sending it to eval function so code should be safe (or not ?? please help here) ;
here the new code:
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
import tkinter as tk
from tkinter import IntVar,StringVar,DoubleVar
###############################################################################
def callback_int(input):
if input.isdigit():
print(input)
return True
elif input == "":
print(input)
return True
else:
print(input)
return False
def callback_str(input, typez=None):
if all([s.isdigit() or s =='/' for s in input]) and input.count('/') <= 1:
print([s.isdigit() or s =='/' for s in input])
# print(input)
return True
elif all([s.isdigit() or s =='.' for s in input]) and input.count('.') <= 1:
print([s.isdigit() or s =='.' for s in input])
# print(input)
return True
else:
print('no valid input : ',input)
return False
def mainwindow():
mainwindow = tk.Tk()
mainwindow.geometry('350x350')
tk.Label(mainwindow, text="enter parameters below").grid(row=1)
getN = IntVar()
geti0 = IntVar()
getr0 = IntVar()
getbeta = StringVar(mainwindow, value='0')
getgamma = StringVar(mainwindow, value='0')
# getbeta = DoubleVar()
# getgamma = DoubleVar()
tk.Label(mainwindow, text="N").grid(row=2)
tk.Label(mainwindow, text="i0").grid(row=3)
tk.Label(mainwindow, text="r0").grid(row=4)
tk.Label(mainwindow, text="beta").grid(row=5)
tk.Label(mainwindow, text="gamma").grid(row=6)
e1 = tk.Entry(mainwindow,textvariable = getN)
e1.grid(row=2, column=1)
e2 = tk.Entry(mainwindow,textvariable = geti0)
e2.grid(row=3, column=1)
e3 = tk.Entry(mainwindow,textvariable = getr0)
e3.grid(row=4, column=1)
e4 = tk.Entry(mainwindow,textvariable = getbeta)
e4.grid(row=5, column=1)
e5 = tk.Entry(mainwindow,textvariable = getgamma)
e5.grid(row=6, column=1)
reg_int = mainwindow.register(callback_int)
reg_str = mainwindow.register(callback_str)
print(type(e4))
e1.config(validate ="key", validatecommand =(reg_int, '%P'))
e2.config(validate ="key", validatecommand =(reg_int, '%P'))
e3.config(validate ="key", validatecommand =(reg_int, '%P'))
e4.config(validate ="key", validatecommand =(reg_str, '%P'))
e5.config(validate ="key", validatecommand =(reg_str, '%P'))
solve = tk.Button(mainwindow, text='solve!', command=lambda: [values()]).grid(row=7, column=1, sticky=tk.W, pady=4)
def values():
readN = getN.get()
readi0 = geti0.get()
readr0 = getr0.get()
# readbeta = float(getbeta.get())
# readgamma = float(getgamma.get())
readbeta = eval(getbeta.get(),{"builtins": {}})
readgamma = eval(getgamma.get(), {"builtins": {}})
print('ppppppppppppp', readbeta,readgamma)
intN = int(readN)
inti0 = int(readi0)
intr0 = int(readr0)
intbeta = float(readbeta)
intgamma = float(readgamma)
# Total population, N.
N = readN
# Initial number of infected and recovered individuals, I0 and R0.
I0, R0 = readi0, readr0
# Everyone else, S0, is susceptible to infection initially.
S0 = N - I0 - R0
# Contact rate, beta, and mean recovery rate, gamma, (in 1/days).
beta, gamma = readbeta, readgamma
# A grid of time points (in days)
t = np.linspace(0, 160, 160)
# The SIR model differential equations.
def deriv(y, t, N, beta, gamma):
S, I, R = y
dS = ((-beta * S * I) / N)
dI = ((beta * S * I) / N) - (gamma * I)
dR = (gamma * I)
return dS, dI, dR
# Initial conditions are S0, I0, R0
# Integrate the SIR equations over the time grid, t.
solve = odeint(deriv, (S0, I0, R0), t, args=(N, beta, gamma))
S, I, R = solve.T
# Plot the data on three separate curves for S(t), I(t) and R(t)
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
ax.plot(t, S/1000, 'b', alpha=0.5, lw=2, label='Susceptible')
ax.plot(t, I/1000, 'r', alpha=0.5, lw=2, label='Infected')
ax.plot(t, R/1000, 'g', alpha=0.5, lw=2, label='Recovered with immunity')
ax.set_xlabel('Time /days')
ax.set_ylabel('Number (1000s)')
ax.set_ylim(0,1.2)
ax.yaxis.set_tick_params(length=0)
ax.xaxis.set_tick_params(length=0)
ax.grid(b=True, which='major', c='w', lw=2, ls='-')
legend = ax.legend()
legend.get_frame().set_alpha(0.5)
for spine in ('top', 'right', 'bottom', 'left'):
ax.spines[spine].set_visible(False)
plt.show()
mainwindow.mainloop()
mainwindow()
that allows for beta and gamma to insert float (i.e 0.28) or fractions (i.e. 2/7) as input into Entry widgets box
starting to enjoy Tkinter, here another improved version with RadioButtons controlling type of input allowed:
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
import tkinter as tk
from tkinter import IntVar,StringVar,DoubleVar
###############################################################################
def mainwindow():
def switch():
print(varb.get(), ' ') #,varbR)
# print(varbR)
getbeta.set('0')
getgamma.set('0')
return
def callback(input,typez=None, varb=None):
value = mainwindow.getvar(varb)
print(value)
# varb.get()=varb.get()
# uu = varb.get()
# print(varb, uu)
# print(varb.get())
if typez == "int":
if input.isdigit():
# print(input)
return True
elif input == "":
# print(input)
return True
else:
print(input, 'not allowed !!!!')
return False
if typez == "str":
if value =='frc':
if len(input) >=1 and input[0] == '/':
return False
if all([s.isdigit() or s =='/' for s in input]) and input.count('/') <= 1:
# print([s.isdigit() or s =='/' for s in input])
# print(input)
return True
else:
print('no valid input : ',input)
return False
elif value =='flt':
if all([s.isdigit() or s =='.' for s in input]) and input.count('.') <= 1:
# print([s.isdigit() or s =='.' for s in input])
# print(input)
return True
else:
print('no valid input : ',input)
return False
else:
return False
mainwindow = tk.Tk()
mainwindow.geometry('550x350')
tk.Label(mainwindow, text="enter parameters below").grid(row=1)
getN = IntVar()
geti0 = IntVar()
getr0 = IntVar()
getbeta = StringVar(mainwindow, value='0')
getgamma = StringVar(mainwindow, value='0')
# getbeta = DoubleVar()
# getgamma = DoubleVar()
tk.Label(mainwindow, text="N").grid(row=2)
tk.Label(mainwindow, text="i0").grid(row=3)
tk.Label(mainwindow, text="r0").grid(row=4)
tk.Label(mainwindow, text="beta").grid(row=5)
tk.Label(mainwindow, text="gamma").grid(row=6)
e1 = tk.Entry(mainwindow,textvariable = getN)
e1.grid(row=2, column=1)
e2 = tk.Entry(mainwindow,textvariable = geti0)
e2.grid(row=3, column=1)
e3 = tk.Entry(mainwindow,textvariable = getr0)
e3.grid(row=4, column=1)
e4 = tk.Entry(mainwindow,textvariable = getbeta)
e4.grid(row=5, column=1)
e5 = tk.Entry(mainwindow,textvariable = getgamma)
e5.grid(row=6, column=1)
varb = StringVar(mainwindow, value='flt')
# varbR=varb.get()
rb1 = tk.Radiobutton(mainwindow, borderwidth=8,height=1, text='float ' ,
variable = varb, value='flt', command=switch, justify="left")
rb1.grid(row=5,column =2, rowspan=1, sticky="w")
rb2 = tk.Radiobutton(mainwindow, borderwidth=8,height=1, text='fraction' ,
variable = varb, value='frc', command=switch ,justify="left")
rb2.grid(row=6,column =2, rowspan=1, sticky="w")
rb1.deselect() # finche non attivo radiobutton non prende parametri
reg = mainwindow.register(callback)
# e1.config(validate ="key", validatecommand =(reg, '%P', 'int',varbR))
# e2.config(validate ="key", validatecommand =(reg, '%P', 'int',varbR))
# e3.config(validate ="key", validatecommand =(reg, '%P', 'int',varbR))
# e4.config(validate ="key", validatecommand =(reg, '%P', 'str',varbR))
# e5.config(validate ="key", validatecommand =(reg, '%P', 'str',varbR))
# e1.config(validate ="key", validatecommand =(reg, '%P', 'int',varb.get()))
# e2.config(validate ="key", validatecommand =(reg, '%P', 'int',varb.get()))
# e3.config(validate ="key", validatecommand =(reg, '%P', 'int',varb.get()))
# e4.config(validate ="key", validatecommand =(reg, '%P', 'str',varb.get()))
# e5.config(validate ="key", validatecommand =(reg, '%P', 'str',varb.get()))
e1.config(validate ="key", validatecommand =(reg, '%P', 'int',varb))
e2.config(validate ="key", validatecommand =(reg, '%P', 'int',varb))
e3.config(validate ="key", validatecommand =(reg, '%P', 'int',varb))
e4.config(validate ="key", validatecommand =(reg, '%P', 'str',varb))
e5.config(validate ="key", validatecommand =(reg, '%P', 'str',varb))
solve = tk.Button(mainwindow, text='solve!', command=lambda: [values()]).grid(row=7, column=1, sticky=tk.W, pady=4)
def values():
try:
a = varb.get()
print(a)
readN = getN.get()
readi0 = geti0.get()
readr0 = getr0.get()
# readbeta = float(getbeta.get())
# readgamma = float(getgamma.get())
# readbeta_ = getbeta.get()
# if readbeta_[0] == '/':
# readbeta_ = readbeta_[1:]
# readbeta = eval(readbeta_,{"builtins": {}})
readbeta = eval(getbeta.get(),{"builtins": {}})
readgamma = eval(getgamma.get(), {"builtins": {}})
intN = int(readN)
inti0 = int(readi0)
intr0 = int(readr0)
intbeta = float(readbeta)
intgamma = float(readgamma)
print('varb : ', varb.get(),
'\nN : ', intN,
'\niO : ',inti0,
'\nr0 : ',intr0,
'\nbeta : ',getbeta.get(),
'\ngamma : ',getgamma.get())
# Total population, N.
N = readN
# Initial number of infected and recovered individuals, I0 and R0.
I0, R0 = readi0, readr0
# Everyone else, S0, is susceptible to infection initially.
S0 = N - I0 - R0
# Contact rate, beta, and mean recovery rate, gamma, (in 1/days).
beta, gamma = readbeta, readgamma
# A grid of time points (in days)
t = np.linspace(0, 160, 160)
# The SIR model differential equations.
def deriv(y, t, N, beta, gamma):
S, I, R = y
dS = ((-beta * S * I) / N)
dI = ((beta * S * I) / N) - (gamma * I)
dR = (gamma * I)
return dS, dI, dR
# Initial conditions are S0, I0, R0
# Integrate the SIR equations over the time grid, t.
solve = odeint(deriv, (S0, I0, R0), t, args=(N, beta, gamma))
S, I, R = solve.T
# Plot the data on three separate curves for S(t), I(t) and R(t)
fig = plt.figure(facecolor='w')
ax = fig.add_subplot(111, facecolor='#dddddd', axisbelow=True)
ax.plot(t, S/1000, 'b', alpha=0.5, lw=2, label='Susceptible')
ax.plot(t, I/1000, 'r', alpha=0.5, lw=2, label='Infected')
ax.plot(t, R/1000, 'g', alpha=0.5, lw=2, label='Recovered with immunity')
ax.set_xlabel('Time /days')
ax.set_ylabel('Number (1000s)')
ax.set_ylim(0,1.2)
ax.yaxis.set_tick_params(length=0)
ax.xaxis.set_tick_params(length=0)
ax.grid(b=True, which='major', c='w', lw=2, ls='-')
legend = ax.legend()
legend.get_frame().set_alpha(0.5)
for spine in ('top', 'right', 'bottom', 'left'):
ax.spines[spine].set_visible(False)
plt.show()
return
except:
print('maybe wrong values !!!!!!!!')
return
mainwindow.mainloop()
mainwindow()
