I am trying to solve a function in an annular domain that has a change of phase with respect to the angular direction of the annulus.
My attempt to solve it is the following:
import numpy as np
from scipy import integrate
def f(x0, y0):
r = np.sqrt(x0**2 + y0**2)
if r >= rIn and r <= rOut:
theta = np.arctan(y0 / x0)
R = np.sqrt((x - x0)**2 + (y - y0)**2 + z**2)
integrand = (np.exp(-1j * (k*R + theta))) / R
return integrand
else:
return 0
# Test
rIn = 0.5
rOut = 1.5
x = 1
y = 1
z = 1
k = 3.66
I = integrate.dblquad(f, -rOut, rOut, lambda x0: -rOut, lambda x0: rOut)
My problem is that I don't know how to get rid of the division by zero occuring when I evaluate theta.
Any help will be more than appreciated!
Use numpy.arctan2 instead, it will have problems only if both x and y are zero, in which case the angle is undetermined.
Also I see you that your integrand is complex, in this case you will probably have to handle real and imaginary part separately, as done here.
Related
I am trying to solve a system of nonlinear equations in Python. The equations have the form:
(1) x^2 + y^2 = a
(2)(x-b)^2 + y^2 = c
where x and y are the variables and a,b,c are parameters. I would like to have a function which i can pass the parameters a,b,c to and it returns me the values for x and y. How can I do that ?
What i currently have is
from scipy.optimize import fsolve
def equation(var, *data):
a,b,c = data
x,y = var
eq1 = x**2 + y**2 - a**2
eq2 = (x - b)**2 + y**2 - c**2
return [eq1, eq2]
x,y = fsolve(equation, args=data)
But this does not quite work. Can someone help?
I think it is just missing the initialized values
from scipy.optimize import fsolve
def equation(var, *data):
a,b,c = data
x,y = var
eq1 = x**2 + y**2 - a**2
eq2 = (x - b)**2 + y**2 - c**2
return [eq1, eq2]
x,y = fsolve(equation,[1,1], args=(1,1,1))
print(x,y)
Taking inspiration from geometrical interpretation of Thierry Lathuille, there is maybe no real need to use a nonlinear solver.
First, Eq. (1) requires y^2=a^2-x^2 and thus (x-b)^2+a^2-x^2=c^2 according to Eq. (2). The latter equality simplifies to b^2-2bx+a^2=c^2 with xSol=(a^2+b^2-c^2)/(2b) as the possible solution for x (the symmetry suggest that there'll be only one solution for x). With this solution for x, we can check the sign of a^2-xSol^2. If negative, then there is no solution. If non-negative, then the solutions are (xSol,+ySol) and (xSol,-ySol) with ySol=np.sqrt(a^2-xSol^2).
Based on some testing with the code below, the solution above seems to work (but correct me if I'm wrong).
from scipy.optimize import fsolve
import numpy as np
abc = (1,1,4)
# Nonlinear optimizer
def equation(var, *data):
a,b,c = data
x,y = var
eq1 = x**2 + y**2 - a**2
eq2 = (x - b)**2 + y**2 - c**2
return [eq1, eq2]
x,y = fsolve(equation,[1,1], args=abc)
print(x,y)
# Geometric solution
a = abc[0]; b = abc[1]; c = abc[2]
xSol = (a**2+b**2-c**2)/(2*b)
if a**2-xSol**2<0:
print("No solution")
else:
ySol = np.sqrt(a**2-xSol**2)
print(xSol,ySol)
print(xSol,-ySol)
Using MATLAB, I am trying to solve the equation using Newtons Method but keep printing the result "None". I am not sure where the mistake is as I do not want to tamper with the formula.
def newt(p):
maxIt = 1000
tol = 10^(-5)
for i in range(maxIt):
fp = 2*p**3 + p**2 - p + 1 #double * for exponent
fprimep = 6*p**2 + 2*p - 1 #f'p
p_new = p - fp/fprimep
if abs (p - p_new) < tol:
return p
p = p_new
#initial values
p0 = -1.2
p = newt(p0)
print(p)
The error in your code is due to a partial conversion from Matlab. You define tol = 10^(-5), but this is not exponentiation in Python, it is bitwise xor. Correcting that, you get the proper result:
def newt(p):
maxIt = 1000
tol = 1e-5 # Error was here
for i in range(maxIt):
fp = 2*p**3 + p**2 - p + 1 #double * for exponent
fprimep = 6*p**2 + 2*p - 1 #f'p
p_new = p - fp/fprimep
if abs (p - p_new) < tol:
return p
p = p_new
#initial values
p0 = -1.2
p = newt(p0)
print(p)
# -1.23375
As for the return value, your function returns None when the method does not converge. I'm not sure this was a intentional decision, but it is a good convention anyway, since it allows the user to know the method did not converge. A more robust method would be to throw an exception, maybe adding the guess at the time the iteration stopped and the convergence ratio.
Let (0,0) and (Xo,Yo) be two points on a Cartesian plane. We want to determine the parabolic curve, Y = AX^2 + BX + C, which passes from these two points and has a given arc length equal to S. Obviously, S > sqrt(Xo^2 + Yo^2). As the curve must pass from (0,0), it should be C=0. Hence, the curve equation reduces to: Y = AX^2 + BX. How can I determine {A,B} knowing {Xo,Yo,S}? There are two solutions, I want the one with A>0.
I have an analytical solution (complex) that gives S for a given set of {A,B,Xo,Yo}, though here the problem is inverted... I can proceed by solving numerically a complex system of equations... but perhaps there is a numerical routine out there that does exactly this?
Any useful Python library? Other ideas?
Thanks a lot :-)
Note that the arc length (line integral) of the quadratic a*x0^2 + b*x0 is given by the integral of sqrt(1 + (2ax + b)^2) from x = 0 to x = x0. On solving the integral, the value of the integral is obtained as 0.5 * (I(u) - I(l)) / a, where u = 2ax0 + b; l = b; and I(t) = 0.5 * (t * sqrt(1 + t^2) + log(t + sqrt(1 + t^2)), the integral of sqrt(1 + t^2).
Since y0 = a * x0^2 + b * x0, b = y0/x0 - a*x0. Substituting the value of b in u and l, u = y0/x0 + a*x0, l = y0/x0 - a*x0. Substituting u and l in the solution of the line integral (arc length), we get the arc length as a function of a:
s(a) = 0.5 * (I(y0/x0 + a*x0) - I(y0/x0 - a*x0)) / a
Now that we have the arc length as a function of a, we simply need to find the value of a for which s(a) = S. This is where my favorite root-finding algorithm, the Newton-Raphson method, comes into play yet again.
The working algorithm for the Newton-Raphson method of finding roots is as follows:
For a function f(x) whose root is to be obtained, if x(i) is the ith guess for the root,
x(i+1) = x(i) - f(x(i)) / f'(x(i))
Where f'(x) is the derivative of f(x). This process is continued till the difference between two consecutive guesses is very small.
In our case, f(a) = s(a) - S and f'(a) = s'(a). By simple application of the chain rule and the quotient rule,
s'(a) = 0.5 * (a*x0 * (I'(u) + I'(l)) + I(l) - I(u)) / (a^2)
Where I'(t) = sqrt(1 + t^2).
The only problem that remains is calculating a good initial guess. Due to the nature of the graph of s(a), the function is an excellent candidate for the Newton-Raphson method, and an initial guess of y0 / x0 converges to the solution in about 5-6 iterations for a tolerance/epsilon of 1e-10.
Once the value of a is found, b is simply y0/x0 - a*x0.
Putting this into code:
def find_coeff(x0, y0, s0):
def dI(t):
return sqrt(1 + t*t)
def I(t):
rt = sqrt(1 + t*t)
return 0.5 * (t * rt + log(t + rt))
def s(a):
u = y0/x0 + a*x0
l = y0/x0 - a*x0
return 0.5 * (I(u) - I(l)) / a
def ds(a):
u = y0/x0 + a*x0
l = y0/x0 - a*x0
return 0.5 * (a*x0 * (dI(u) + dI(l)) + I(l) - I(u)) / (a*a)
N = 1000
EPSILON = 1e-10
guess = y0 / x0
for i in range(N):
dguess = (s(guess) - s0) / ds(guess)
guess -= dguess
if abs(dguess) <= EPSILON:
print("Break:", abs((s(guess) - s0)))
break
print(i+1, ":", guess)
a = guess
b = y0/x0 - a*x0
print(a, b, s(a))
Run the example on CodeSkulptor.
Note that due to the rational approximation of the arc lengths given as input to the function in the examples, the coefficients obtained may ever so slightly differ from the expected values.
I am trying to compute the fresnel integral over a grid of coordinates using dblquad. But its taking very long and finally it's not giving any result.
Below is my code. In this code I integrated only over a 10 x 10 grid but I need to integrate at least over a 500 x 500 grid.
import time
st = time.time()
import pylab
import scipy.integrate as inte
import numpy as np
print 'imhere 0'
def sinIntegrand(y,x, X , Y):
a = 0.0001
R = 2e-3
z = 10e-3
Lambda = 0.5e-6
alpha = 0.01
k = np.pi * 2 / Lambda
return np.cos(k * (((x-R)**2)*a + (R-(x**2 + y**2)) * np.tan(np.radians(alpha)) + ((x - X)**2 + (y - Y)**2) / (2 * z)))
print 'im here 1'
def cosIntegrand(y,x,X,Y):
a = 0.0001
R = 2e-3
z = 10e-3
Lambda = 0.5e-6
alpha = 0.01
k = np.pi * 2 / Lambda
return np.sin(k * (((x-R)**2)*a + (R-(x**2 + y**2)) * np.tan(np.radians(alpha)) + ((x - X)**2 + (y - Y)**2) / (2 * z)))
def y1(x,R = 2e-3):
return (R**2 - x**2)**0.5
def y2(x, R = 2e-3):
return -1*(R**2 - x**2)**0.5
points = np.linspace(-1e-3,1e-3,10)
points2 = np.linspace(1e-3,-1e-3,10)
yv,xv = np.meshgrid(points , points2)
#def integrate_on_grid(func, lo, hi,y1,y2):
# """Returns a callable that can be evaluated on a grid."""
# return np.vectorize(lambda n,m: dblquad(func, lo, hi,y1,y2,(n,m))[0])
#
#intensity = abs(integrate_on_grid(sinIntegrand,-1e-3 ,1e-3,y1, y2)(yv,xv))**2 + abs(integrate_on_grid(cosIntegrand,-1e-3 ,1e-3,y1, y2)(yv,xv))**2
Intensity = []
print 'im here2'
for i in points:
row = []
for j in points2:
print 'im here'
intensity = abs(inte.dblquad(sinIntegrand,-1e-3 ,1e-3,y1, y2,(i,j))[0])**2 + abs(inte.dblquad(cosIntegrand,-1e-3 ,1e-3,y1, y2,(i,j))[0])**2
row.append(intensity)
Intensity.append(row)
Intensity = np.asarray(Intensity)
pylab.imshow(Intensity,cmap = 'gray')
pylab.show()
print str(time.time() - st)
I would really appreciate if you could tell any better way of doing this.
Using a scipy.integrate.dblquad to calculate every pixel of your image is going to be slow in any case.
You should try rewriting your mathematical problem so you can use some classical function in scipy.special instead. For instance, scipy.special.fresnel might work, although it is 1D and your problem seems to be in 2D. Otherwise, that there is a relationship between the Fresnel integral and the incomplete Gamma function (scipy.special.gammainc), if that helps.
If none of this work, as a last resort you can spend time optimizing your code and adapting it to Cython. This it will probably give a speed up of a factor of 10 to 100 (see this answer). Though this wouldn't be sufficient to go from a grid 10x10 to a grid 500x500.
I've written some Python code to do some image processing work, but it takes a huge amount of time to run. I've spent the last few hours trying to optimize it, but I think I've reached the end of my abilities.
Looking at the outputs from the profiler, the function below is taking a large proportion of the overall time of my code. Is there any way that it can be speeded up?
def make_ellipse(x, x0, y, y0, theta, a, b):
c = np.cos(theta)
s = np.sin(theta)
a2 = a**2
b2 = b**2
xnew = x - x0
ynew = y - y0
ellipse = (xnew * c + ynew * s)**2/a2 + (xnew * s - ynew * c)**2/b2 <= 1
return ellipse
To give the context, it is called with x and y as the output from np.meshgrid with a fairly large grid size, and all of the other parameters as simple integer values.
Although that function seems to be taking a lot of the time, there are probably ways that the rest of the code can be speeded up too. I've put the rest of the code at this gist.
Any ideas would be gratefully received. I've tried using numba and autojiting the main functions, but that doesn't help much.
Let's try to optimize make_ellipse in conjunction with its caller.
First, notice that a and b are the same over many calls. Since make_ellipse squares them each time, just have the caller do that instead.
Second, notice that np.cos(np.arctan(theta)) is 1 / np.sqrt(1 + theta**2) which seems slightly faster on my system. A similar trick can be used to compute the sine, either from theta or from cos(theta) (or vice versa).
Third, and less concretely, think about short-circuiting some of the final ellipse formula evaluations. For example, wherever (xnew * c + ynew * s)**2/a2 is greater than 1, the ellipse value must be False. If this happens often, you can "mask" out the second half of the (expensive) calculation of the ellipse at those locations. I haven't planned this thoroughly, but see numpy.ma for some possible leads.
It won't speed up things for all cases, but if your ellipses don't take up the whole image, you should limit your search for points inside the ellipse to its bounding rectangle. I am lazy with the math, so I googled it and reused #JohnZwinck neat cosine of an arctangent trick to come up with this function:
def ellipse_bounding_box(x0, y0, theta, a, b):
x_tan_t = -b * np.tan(theta) / a
if np.isinf(x_tan_t) :
x_cos_t = 0
x_sin_t = np.sign(x_tan_t)
else :
x_cos_t = 1 / np.sqrt(1 + x_tan_t*x_tan_t)
x_sin_t = x_tan_t * x_cos_t
x = x0 + a*x_cos_t*np.cos(theta) - b*x_sin_t*np.sin(theta)
y_tan_t = b / np.tan(theta) / a
if np.isinf(y_tan_t):
y_cos_t = 0
y_sin_t = np.sign(y_tan_t)
else:
y_cos_t = 1 / np.sqrt(1 + y_tan_t*y_tan_t)
y_sin_t = y_tan_t * y_cos_t
y = y0 + b*y_sin_t*np.cos(theta) + a*y_cos_t*np.sin(theta)
return np.sort([-x, x]), np.sort([-y, y])
You can now modify your original function to something like this:
def make_ellipse(x, x0, y, y0, theta, a, b):
c = np.cos(theta)
s = np.sin(theta)
a2 = a**2
b2 = b**2
x_box, y_box = ellipse_bounding_box(x0, y0, theta, a, b)
indices = ((x >= x_box[0]) & (x <= x_box[1]) &
(y >= y_box[0]) & (y <= y_box[1]))
xnew = x[indices] - x0
ynew = y[indices] - y0
ellipse = np.zeros_like(x, dtype=np.bool)
ellipse[indices] = ((xnew * c + ynew * s)**2/a2 +
(xnew * s - ynew * c)**2/b2 <= 1)
return ellipse
Since everything but x and y are integers, you can try to minimize the number of array computations. I imagine most of the time is spent in this statement:
ellipse = (xnew * c + ynew * s)**2/a2 + (xnew * s - ynew * c)**2/b2 <= 1
A simple rewriting like so should reduce the number of array operations:
a = float(a)
b = float(b)
ellipse = (xnew * (c/a) + ynew * (s/a))**2 + (xnew * (s/b) - ynew * (c/b))**2 <= 1
What was 12 array operations is now 10 (plus 4 scalar ops). I'm not sure if numba's jit would have tried this. It might just do all the broadcasting first, then jit the resulting operations. In this case, reordering so common operations are done at once should help.
Furthering along, you can rewrite this again as
ellipse = ((xnew + ynew * (s/c)) * (c/a))**2 + ((xnew * (s/c) - ynew) * (c/b))**2 <= 1
Or
t = numpy.tan(theta)
ellipse = ((xnew + ynew * t) * (b/a))**2 + (xnew * t - ynew)**2 <= (b/c)**2
Replacing one more array operation with a scalar, and eliminating other scalar ops to get 9 array operations and 2 scalar ops.
As always, be aware of what the range of inputs are to avoid rounding errors.
Unfortunately there's no way good way to do a running sum and bail early if either of the two addends is greater than the right hand side of the comparison. That would be an obvious speed-up, but one you'd need cython (or c/c++) to code.
You can speed it up considerably by using Cython. There is a very good documentation on how to do this.