Python Forum

#!/usr/bin/python3

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation


#function to fit: L/(1+np.exp(-k*(x-x0))) + b
#which is a logistic curve


#derivatives over a given variable
def ddk(x, y, L, k, x0, b):
    return -L*(x0-x)*np.exp(k*x0-k*x)*(L/(np.exp(k*x0-k*x)+1)+b-y)/(np.exp(k*x0-k*x)+1)**2

def ddl(x, y, L, k, x0, b):
    return (L/(np.exp(x0*k-k*x)+1)+b-y)/(np.exp(k*x0-k*x)+1)

def ddx0(x, y, L, k, x0, b):
    return -k*L*np.exp(x0*k-k*x)*(L/(np.exp(x0*k-k*x)+1)+b-y)/(np.exp(x0*k-k*x)+1)**2

def ddb(x, y, L, k, x0, b):
    return (L/(np.exp(x0*k-k*x)+1)+b-y)

def funcValue(x, L, k, x0, b):
    return L/(1+np.exp(-k*(x-x0))) + b

def errValue(x, y, L, k, x0, b):
    return (funcValue(x, L, k, x0, b) - y)**2

def standardize(X):
    avg = np.average(X)
    std = np.std(X)
    return (X-avg)/std


vector_ddk = np.vectorize(ddk,  excluded=['L','k','x0','b'])
vector_ddb = np.vectorize(ddb, excluded=['L','k','x0','b'])
vector_ddl = np.vectorize(ddl,  excluded=['L','k','x0','b'])
vector_ddx0= np.vectorize(ddx0, excluded=['L','k','x0','b'])
vector_err = np.vectorize(errValue, excluded=['K', 'k', 'x0','b'])

def update_params(X, y, param_vector, learningRate=1):
    count = np.size(X, axis=0)
    theta1 = param_vector[0] #L
    theta2 = param_vector[1] #k
    theta3 = param_vector[2] #x0
    theta4 = param_vector[3] #b
    theta1mdf = learningRate / count * np.sum(vector_ddk(X, y, theta1, theta2, theta3, theta4))
    theta2mdf = learningRate / count * np.sum(vector_ddl(X, y, theta1, theta2, theta3, theta4))
    theta3mdf = learningRate / count * np.sum(vector_ddx0(X, y, theta1, theta2, theta3, theta4))
    theta4mdf = learningRate / count * np.sum(vector_ddb(X, y, theta1, theta2, theta3, theta4))
    param_vector[0] -= theta1mdf
    param_vector[1] -= theta2mdf
    param_vector[2] -= theta3mdf
    param_vector[3] -= theta4mdf

X = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13] #params
y = [1, 1.2, 1.3, 4, 7, 9, 11, 12, 14, 14.5, 16, 16, 16]

#the regression part
#=========================================================

X = standardize(X)

X = np.matrix(X).reshape(-1).T
y = np.matrix(y).reshape(-1).T

param_vector = [16, 4, 1, 1] #L, k, x0, b

params = []
errors = []

learning_iterations = 500

for i in range(0, learning_iterations):
    params.append(param_vector[:])
    update_params(X, y, param_vector, 0.02)
    errors.append(1/(2*np.size(X,axis=0))*np.sum(vector_err(X, y, *param_vector)))


#==========================================================
#the plotting part

figure = plt.figure()
ax = figure.add_subplot(211)
erax = figure.add_subplot(212)
ln, = ax.plot([], [])
erln, = erax.plot([], [])
erax.set_ylim(ymin=0, ymax=1)
erax.set_xlim(xmin=0, xmax=learning_iterations)
ax.scatter(np.ravel(X), np.ravel(y))

def animate(frame):
    global X, y, params, errors, ln, erln, erax
    _x = np.linspace(X[0,0]-1, X[-1,0]+1, num=100)
    _y = [funcValue(m, *params[frame]) for m in _x]
    ln.set_data(_x, _y)
    _ex = list(range(0, frame+1))
    _ey = [errors[m] for m in _ex]
    erln.set_data(_ex, _ey)
    erax.set_xlabel("Error: " + str(errors[frame]))
    return ln
    

anim = animation.FuncAnimation(figure, animate, frames=learning_iterations, interval=50, repeat=False, repeat_delay=1000)

plt.show()