Odeint function from scipy.integrate gives wrong result - python-2.7

Question

I use odeint function to solve a coupled differential equations system and plot one of the variables (theta_i) after the system is solved. My variable (theta_i) comes from the equation:
theta_i = np.arctan2(g1,g2)
where g1 ang g2 are variables calculated in the same function. The results have to be between -pi and pi and they are supposed to look like this (plot from matlab simulation):
However, when I try to plot theta_i after odeint has finished I get this(plot from my python code):
which is really weird. When I print the values of theta_i right after its calcumation (still inside the function) they look correct (between -0.2 and 0.5), so it has to be something with the result's storing and my implementation of odeint. All the other variables that come from the odeint solution are correct. I searched similar posts but nobody had the same problem with me. What might be the problem here? I am new to python and I use python 2.7.12. Thank you in advance.
import numpy as np
from scipy.integrate import odeint
import matplotlib.pyplot as plt
added_mass_x = 0.03 # kg
added_mass_y = 0.04
mb = 0.3 # kg
m1 = mb-added_mass_x
m2 = mb-added_mass_y
l1 = 0.07 # m
l2 = 0.05 # m
J = 0.00050797 # kgm^2
Sa = 0.0110 # m^2
Cd = 2.44
Cl = 3.41
Kd = 0.000655 # kgm^2
r = 1000 # kg/m^3
c1 = 0.5*r*Sa*Cd
c2 = 0.5*r*Sa*Cl
c3 = 0.5*mb*(l1**2)
c4 = Kd/J
c5 = (1/(2*J))*(l1**2)*mb*l2
c6 = (1/(3*J))*(l1**3)*mb
theta_0 = 10*(np.pi/180) # rad
theta_A = 20*(np.pi/180) # rad
f = 2 # Hz
t = np.linspace(0,100,8000) # s
def direct(u,t):
vcx = u[0]
vcy = u[1]
wz = u[2]
psi = u[3]
x = u[4]
y = u[5]
vcx_i = u[6]
vcy_i = u[7]
psi_i = u[8]
wz_i = u[9]
theta_i = u[10]
theta_deg_i = u[11]
# Subsystem 1
omega = 2*np.pi*f # rad/s
theta = theta_0 + theta_A*np.sin(omega*t) # rad
theta_deg = (theta*180)/np.pi # deg
thetadotdot = -(omega**2)*theta_A*np.sin(omega*t) # rad/s^2
# Subsystem 2
vcxdot = (m2/m1)*vcy*wz-(c1/m1)*vcx*np.sqrt((vcx**2)+(vcy**2))+(c2/m1)*vcy*np.sqrt((vcx**2)+(vcy**2))*np.arctan2(vcy,vcx)-(c3/m1)*thetadotdot*np.sin(theta)
vcydot = -(m1/m2)*vcx*wz-(c1/m2)*vcy*np.sqrt((vcx**2)+(vcy**2))-(c2/m2)*vcx*np.sqrt((vcx**2)+(vcy**2))*np.arctan2(vcy,vcx)+(c3/m2)*thetadotdot*np.cos(theta)
wzdot = ((m1-m2)/J)*vcx*vcy-c4*wz*wz*np.sign(wz)-c5*thetadotdot*np.cos(theta)-c6*thetadotdot
psidot = wz
# Subsystem 3
xdotdot = vcxdot*np.cos(psi)-vcx*np.sin(psi)*wz+vcydot*np.sin(psi)+vcy*np.cos(psi)*wz # m/s^2
ydotdot = -vcxdot*np.sin(psi)-vcx*np.cos(psi)*wz+vcydot*np.cos(psi)-vcy*np.sin(psi)*wz # m/s^2
xdot = vcx*np.cos(psi)+vcy*np.sin(psi) # m/s
ydot = -vcx*np.sin(psi)+vcy*np.cos(psi) # m/s
# Subsystem 4
vcx_i = xdot*np.cos(psi_i)-ydot*np.sin(psi_i)
vcy_i = ydot*np.cos(psi_i)+xdot*np.sin(psi_i)
psidot_i = wz_i
vcxdot_i = xdotdot*np.cos(psi_i)-xdot*np.sin(psi_i)*psidot_i-ydotdot*np.sin(psi_i)-ydot*np.cos(psi_i)*psidot_i
vcydot_i = ydotdot*np.cos(psi_i)-ydot*np.sin(psi_i)*psidot_i+xdotdot*np.sin(psi_i)+xdot*np.cos(psi_i)*psidot_i
g1 = -(m1/c3)*vcxdot_i+(m2/c3)*vcy_i*wz_i-(c1/c3)*vcx_i*np.sqrt((vcx_i**2)+(vcy_i**2))+(c2/c3)*vcy_i*np.sqrt((vcx_i**2)+(vcy_i**2))*np.arctan2(vcy_i,vcx_i)
g2 = (m2/c3)*vcydot_i+(m1/c3)*vcx_i*wz_i+(c1/c3)*vcy_i*np.sqrt((vcx_i**2)+(vcy_i**2))+(c2/c3)*vcx_i*np.sqrt((vcx_i**2)+(vcy_i**2))*np.arctan2(vcy_i,vcx_i)
A = 12*np.sin(2*np.pi*f*t+np.pi) # eksiswsi tail_frequency apo simulink
if A>=0.1:
wzdot_i = ((m1-m2)/J)*vcx_i*vcy_i-c4*wz_i**2*np.sign(wz_i)-c5*g2-c6*np.sqrt((g1**2)+(g2**2))
elif A<-0.1:
wzdot_i = ((m1-m2)/J)*vcx_i*vcy_i-c4*wz_i**2*np.sign(wz_i)-c5*g2+c6*np.sqrt((g1**2)+(g2**2))
else:
wzdot_i = ((m1-m2)/J)*vcx_i*vcy_i-c4*wz_i**2*np.sign(wz)-c5*g2
if g2>0:
theta_i = np.arctan2(g1,g2)
elif g2<0 and g1>=0:
theta_i = np.arctan2(g1,g2)-np.pi
elif g2<0 and g1<0:
theta_i = np.arctan2(g1,g2)+np.pi
elif g2==0 and g1>0:
theta_i = -np.pi/2
elif g2==0 and g1<0:
theta_i = np.pi/2
elif g1==0 and g2==0:
theta_i = 0
theta_deg_i = (theta_i*180)/np.pi
#print theta_deg_i
return [vcxdot, vcydot, wzdot, psidot, xdot, ydot, vcxdot_i, vcydot_i, psidot_i, wzdot_i, theta_i, theta_deg_i]
# arxikes synthikes
vcx_0 = 0.1257
vcy_0 = 0
wz_0 = 0
psi_0 = 0
x_0 = 0
y_0 = 0
vcx_i_0 = 0.1257
vcy_i_0 = 0
psi_i_0 = 0
wz_i_0 = 0
theta_i_0 = 0.1745
theta_deg_i_0 = 9.866
u0 = [vcx_0, vcy_0, wz_0, psi_0, x_0, y_0, vcx_i_0, vcy_i_0, psi_i_0, wz_i_0, theta_i_0, theta_deg_i_0]
u = odeint(direct, u0, t, tfirst=False)
vcx = u[:,0]
vcy = u[:,1]
wz = u[:,2]
psi = u[:,3]
x = u[:,4]
y = u[:,5]
vcx_i = u[:,6]
vcy_i = u[:,7]
psi_i = u[:,8]
wz_i = u[:,9]
theta_i = u[:,10]
theta_deg_i = u[:,11]
print theta_i
plt.figure(17)
plt.plot(t,theta_i,'r-',linewidth=1,label='theta_i')
plt.xlabel('t [s]')
plt.title('theta_i [rad] (Main body CF)')
plt.legend()
plt.show()

Answer 1

The problem as you stated is that theta_i is not part of the gradient. When you formulate your direct, it should be of the form:
def direct(vector, t):
return vector_dot
The quickest and dirtiest solution (without cleaning the code) is to use the function you already defined:
theta_i = [direct(u_i, t_i)[10] for t_i, u_i in zip(t, u)]
I used a a shorter interval: t = np.linspace(0,10,8000). It yielded this:
EDIT: How to remove your theta from the integrator:
def direct(u, t):
# your original function as it is
def direct2(u,t):
return direct(u,t)[:9]
#now integrate the second function
u = odeint(direct2, u0, t)