I have been trying to solve integration with riemann sum. My function has 3 arguments a,b,d so a is lower limit b is higher limit and d is the part where a +(n-1)*d < b. This is my code so far but. My output is 28.652667999999572 what I should get is 28.666650000000388. Also if the input b is lower than a it has to calculate but I have solved that problem already.
def integral(a, b, d):
if a > b:
a,b = b,a
delta_x = float((b-a)/1000)
j = abs((b-a)/delta_x)
i = int(j)
n = s = 0
x = a
while n < i:
delta_A = (x**2+3*x+4) * delta_x
x += delta_x
s += delta_A
n += 1
return abs(s)
print(integral(1,3,0.01))
There is no fault here, neither with the algorithm nor with your code (or python). The Riemann sum is an approximation of the integral and per se not "exact". You approximate the area of a (small) stripe of width dx, say between x and x+dx, and f(x) with the area of an rectangle of the same width and the height of f(x) as it's left upper corner. If the function changes it's value when you go from x to x+dx then the area of the rectangle deviates from the true integral.
As you have noticed, you can make the approximation closer by making thinner and thinner slices, at the cost of more computational effort and time.
In your example, the function is f(x) = x^2 + 3*x + 4, and it's exact integral over x in [1.0,3.0) is 28 2/3 or 28.66666...
The approximation by rectangles is a crude one, you cannot change that. But what you could change is the time it takes for your code to evaluate, say, 10^8 steps instead of 10^3. Look at this code:
def riemann(a, b, dx):
if a > b:
a,b = b,a
# dx = (b-a)/n
n = int((b - a) / dx)
s = 0.0
x = a
for i in xrange(n):
f_i = (x + 3.0) * x + 4.0
s += f_i
x += dx
return s * dx
Here, I've used 3 tricks for speedup, and one for greater precision. First, if you write a loop and you know the number of repetions in advance then use a for-loop instead of a while-loop. It's faster. (BTW, loop variables conventionally are i, j, k ... whereas a limit or final value is n). Secondly, using xrange instead of range is faster for users of python 2.x. Thirdly, factorize polynoms when calculating them often. You should see from the code what I mean here. This way, the result is numerically stable. Last trick: operations within the loop which do not depend on the loop variable can be extracted and applied after the loop has ended. Here, the final multiplication with dx.
Related
I tried implementing the forward substitution method, a solving process to solve the problem Lx = b with L being a lower triangle matrix and x,b as vectors.
This was an easy task:
def tri_solve(L,b):
n = len(b)
x = np.zeros(n)
x[0] = b[0]/L[0,0];
for i in range(1,n):
comp = 0;
for k in range(0,i):
index = L[i,k]
preSolution = x[k]
comp = comp + index * preSolution
x[i] = 1/L[i,i] * (b[i] - comp)
return x;
Now I compared my calculation times for different sized matrices several times with linalg.solve from the scipy module and it turns out that it is much faster. This makes sense in some points, since SciPy is written in C and C++, but I still expected similar or better calculation times for matrices up to 10x10 dimension. Beginning with 6x6 matrices, linalg.solves becomes slightly faster on average.
Is there a way to improve my rather simple solution?
You could try solve_triangular
If you want to accelerate your code, what you could do is to vectorize the inner loop.
def tri_solve(L,b):
n = len(b)
x = np.zeros(n)
x[0] = b[0]/L[0,0];
for i in range(1,n):
comp = np.sum(L[i,:i] * x[:i])
x[i] = 1/L[i,i] * (b[i] - comp)
return x;
Edit: How to use it
You have to pass as first argument a square lower triangular matrix and as second argument you can pass a 1D array
N = 20
A = np.tril(np.random.randn(N, N))
b = np.random.randn(N)
assert np.allclose(np.linalg.solve(A, b), tri_solve(A, b))
Of course this is a naive implementation and is not stable, you can't use it to solve very large or ill conditioned systems.
I am currently trying to write some python code to solve an arbitrary system of first order ODEs, using a general explicit Runge-Kutta method defined by the values alpha, gamma (both vectors of dimension m) and beta (lower triangular matrix of dimension m x m) of the Butcher table which are passed in by the user. My code appears to work for single ODEs, having tested it on a few different examples, but I'm struggling to generalise my code to vector valued ODEs (i.e. systems).
In particular, I try to solve a Van der Pol oscillator ODE (reduced to a first order system) using Heun's method defined by the Butcher Tableau values given in my code, but I receive the errors
"RuntimeWarning: overflow encountered in double_scalars f = lambda t,u: np.array(... etc)" and
"RuntimeWarning: invalid value encountered in add kvec[i] = f(t+alpha[i]*h,y+h*sum)"
followed by my solution vector that is clearly blowing up. Note that the commented out code below is one of the examples of single ODEs that I tried and is solved correctly. Could anyone please help? Here is my code:
import numpy as np
def rk(t,y,h,f,alpha,beta,gamma):
'''Runga Kutta iteration'''
return y + h*phi(t,y,h,f,alpha,beta,gamma)
def phi(t,y,h,f,alpha,beta,gamma):
'''Phi function for the Runga Kutta iteration'''
m = len(alpha)
count = np.zeros(len(f(t,y)))
kvec = k(t,y,h,f,alpha,beta,gamma)
for i in range(1,m+1):
count = count + gamma[i-1]*kvec[i-1]
return count
def k(t,y,h,f,alpha,beta,gamma):
'''returning a vector containing each step k_{i} in the m step Runga Kutta method'''
m = len(alpha)
kvec = np.zeros((m,len(f(t,y))))
kvec[0] = f(t,y)
for i in range(1,m):
sum = np.zeros(len(f(t,y)))
for l in range(1,i+1):
sum = sum + beta[i][l-1]*kvec[l-1]
kvec[i] = f(t+alpha[i]*h,y+h*sum)
return kvec
def timeLoop(y0,N,f,alpha,beta,gamma,h,rk):
'''function that loops through time using the RK method'''
t = np.zeros([N+1])
y = np.zeros([N+1,len(y0)])
y[0] = y0
t[0] = 0
for i in range(1,N+1):
y[i] = rk(t[i-1],y[i-1], h, f,alpha,beta,gamma)
t[i] = t[i-1]+h
return t,y
#################################################################
'''f = lambda t,y: (c-y)**2
Y = lambda t: np.array([(1+t*c*(c-1))/(1+t*(c-1))])
h0 = 1
c = 1.5
T = 10
alpha = np.array([0,1])
gamma = np.array([0.5,0.5])
beta = np.array([[0,0],[1,0]])
eff_rk = compute(h0,Y(0),T,f,alpha,beta,gamma,rk, Y,11)'''
#constants
mu = 100
T = 1000
h = 0.01
N = int(T/h)
#initial conditions
y0 = 0.02
d0 = 0
init = np.array([y0,d0])
#Butcher Tableau for Heun's method
alpha = np.array([0,1])
gamma = np.array([0.5,0.5])
beta = np.array([[0,0],[1,0]])
#rhs of the ode system
f = lambda t,u: np.array([u[1],mu*(1-u[0]**2)*u[1]-u[0]])
#solving the system
time, sol = timeLoop(init,N,f,alpha,beta,gamma,h,rk)
print(sol)
Your step size is not small enough. The Van der Pol oscillator with mu=100 is a fast-slow system with very sharp turns at the switching of the modes, so rather stiff. With explicit methods this requires small step sizes, the smallest sensible step size is 1e-5 to 1e-6. You get a solution on the limit cycle already for h=0.001, with resulting velocities up to 150.
You can reduce some of that stiffness by using a different velocity/impulse variable. In the equation
x'' - mu*(1-x^2)*x' + x = 0
you can combine the first two terms into a derivative,
mu*v = x' - mu*(1-x^2/3)*x
so that
x' = mu*(v+(1-x^2/3)*x)
v' = -x/mu
The second equation is now uniformly slow close to the limit cycle, while the first has long relatively straight jumps when v leaves the cubic v=x^3/3-x.
This integrates nicely with the original h=0.01, keeping the solution inside the box [-3,3]x[-2,2], even if it shows some strange oscillations that are not present for smaller step sizes and the exact solution.
I have been trying to create custom calculator for calculating trigonometric functions. Aside from Chebyshev pylonomials and/or Cordic algorithm I have used Taylor series which have been accurate by few places of decimal.
This is what i have created to calculate simple trigonometric functions without any modules:
from __future__ import division
def sqrt(n):
ans = n ** 0.5
return ans
def factorial(n):
k = 1
for i in range(1, n+1):
k = i * k
return k
def sin(d):
pi = 3.14159265359
n = 180 / int(d) # 180 degrees = pi radians
x = pi / n # Converting degrees to radians
ans = x - ( x ** 3 / factorial(3) ) + ( x ** 5 / factorial(5) ) - ( x ** 7 / factorial(7) ) + ( x ** 9 / factorial(9) )
return ans
def cos(d):
pi = 3.14159265359
n = 180 / int(d)
x = pi / n
ans = 1 - ( x ** 2 / factorial(2) ) + ( x ** 4 / factorial(4) ) - ( x ** 6 / factorial(6) ) + ( x ** 8 / factorial(8) )
return ans
def tan(d):
ans = sin(d) / sqrt(1 - sin(d) ** 2)
return ans
Unfortunately i could not find any sources that would help me interpret inverse trigonometric function formulas for Python. I have also tried putting sin(x) to the power of -1 (sin(x) ** -1) which didn't work as expected.
What could be the best solution to do this in Python (In the best, I mean simplest with similar accuracy as Taylor series)? Is this possible with power series or do i need to use cordic algorithm?
The question is broad in scope, but here are some simple ideas (and code!) that might serve as a starting point for computing arctan. First, the good old Taylor series. For simplicity, we use a fixed number of terms; in practice, you might want to decide the number of terms to use dynamically based on the size of x, or introduce some kind of convergence criterion. With a fixed number of terms, we can evaluate efficiently using something akin to Horner's scheme.
def arctan_taylor(x, terms=9):
"""
Compute arctan for small x via Taylor polynomials.
Uses a fixed number of terms. The default of 9 should give good results for
abs(x) < 0.1. Results will become poorer as abs(x) increases, becoming
unusable as abs(x) approaches 1.0 (the radius of convergence of the
series).
"""
# Uses Horner's method for evaluation.
t = 0.0
for n in range(2*terms-1, 0, -2):
t = 1.0/n - x*x*t
return x * t
The above code gives good results for small x (say smaller than 0.1 in absolute value), but the accuracy drops off as x becomes larger, and for abs(x) > 1.0, the series never converges, no matter how many terms (or how much extra precision) we throw at it. So we need a better way to compute for larger x. One solution is to use argument reduction, via the identity arctan(x) = 2 * arctan(x / (1 + sqrt(1 + x^2))). This gives the following code, which builds on arctan_taylor to give reasonable results for a wide range of x (but beware possible overflow and underflow when computing x*x).
import math
def arctan_taylor_with_reduction(x, terms=9, threshold=0.1):
"""
Compute arctan via argument reduction and Taylor series.
Applies reduction steps until x is below `threshold`,
then uses Taylor series.
"""
reductions = 0
while abs(x) > threshold:
x = x / (1 + math.sqrt(1 + x*x))
reductions += 1
return arctan_taylor(x, terms=terms) * 2**reductions
Alternatively, given an existing implementation for tan, you could simply find a solution y to the equation tan(y) = x using traditional root-finding methods. Since arctan is already naturally bounded to lie in the interval (-pi/2, pi/2), bisection search works well:
def arctan_from_tan(x, tolerance=1e-15):
"""
Compute arctan as the inverse of tan, via bisection search. This assumes
that you already have a high quality tan function.
"""
low, high = -0.5 * math.pi, 0.5 * math.pi
while high - low > tolerance:
mid = 0.5 * (low + high)
if math.tan(mid) < x:
low = mid
else:
high = mid
return 0.5 * (low + high)
Finally, just for fun, here's a CORDIC-like implementation, which is really more appropriate for a low-level implementation than for Python. The idea here is that you precompute, once and for all, a table of arctan values for 1, 1/2, 1/4, etc., and then use those to compute general arctan values, essentially by computing successive approximations to the true angle. The remarkable part is that, after the precomputation step, the arctan computation involves only additions, subtractions, and multiplications by by powers of 2. (Of course, those multiplications aren't any more efficient than any other multiplication at the level of Python, but closer to the hardware, this could potentially make a big difference.)
cordic_table_size = 60
cordic_table = [(2**-i, math.atan(2**-i))
for i in range(cordic_table_size)]
def arctan_cordic(y, x=1.0):
"""
Compute arctan(y/x), assuming x positive, via CORDIC-like method.
"""
r = 0.0
for t, a in cordic_table:
if y < 0:
r, x, y = r - a, x - t*y, y + t*x
else:
r, x, y = r + a, x + t*y, y - t*x
return r
Each of the above methods has its strengths and weaknesses, and all of the above code can be improved in a myriad of ways. I encourage you to experiment and explore.
To wrap it all up, here are the results of calling the above functions on a small number of not-very-carefully-chosen test values, comparing with the output of the standard library math.atan function:
test_values = [2.314, 0.0123, -0.56, 168.9]
for value in test_values:
print("{:20.15g} {:20.15g} {:20.15g} {:20.15g}".format(
math.atan(value),
arctan_taylor_with_reduction(value),
arctan_from_tan(value),
arctan_cordic(value),
))
Output on my machine:
1.16288340166519 1.16288340166519 1.16288340166519 1.16288340166519
0.0122993797673 0.0122993797673 0.0122993797673002 0.0122993797672999
-0.510488321916776 -0.510488321916776 -0.510488321916776 -0.510488321916776
1.56487573286064 1.56487573286064 1.56487573286064 1.56487573286064
The simplest way to do any inverse function is to use binary search.
definitions
let assume function
x = g(y)
And we want to code its inverse:
y = f(x) = f(g(y))
x = <x0,x1>
y = <y0,y1>
bin search on floats
You can do it on integer math accessing mantissa bits like in here:
Any Faster RMS Value Calculation in C?
but if you do not know the exponent of the result prior to computation then you need to use floats for bin search too.
so the idea behind binary search is to change mantissa of y from y1 to y0 bit by bit from MSB to LSB. Then call direct function g(y) and if the result cross x revert the last bit change.
In case of using floats you can use variable that will hold approximate value of the mantissa bit targeted instead of integer bit access. That will eliminate unknown exponent problem. So at the beginning set y = y0 and actual bit to MSB value so b=(y1-y0)/2. After each iteration halve it and do as many iterations as you got mantissa bits n... This way you obtain result in n iterations within (y1-y0)/2^n accuracy.
If your inverse function is not monotonic break it into monotonic intervals and handle each as separate binary search.
The function increasing/decreasing just determine the crossing condition direction (use of < or >).
C++ acos example
so y = acos(x) is defined on x = <-1,+1> , y = <0,M_PI> and decreasing so:
double f64_acos(double x)
{
const int n=52; // mantisa bits
double y,y0,b;
int i;
// handle domain error
if (x<-1.0) return 0;
if (x>+1.0) return 0;
// x = <-1,+1> , y = <0,M_PI> , decreasing
for (y= 0.0,b=0.5*M_PI,i=0;i<n;i++,b*=0.5) // y is min, b is half of max and halving each iteration
{
y0=y; // remember original y
y+=b; // try set "bit"
if (cos(y)<x) y=y0; // if result cross x return to original y decreasing is < and increasing is >
}
return y;
}
I tested it like this:
double x0,x1,y;
for (x0=0.0;x0<M_PI;x0+=M_PI*0.01) // cycle all angle range <0,M_PI>
{
y=cos(x0); // direct function (from math.h)
x1=f64_acos(y); // my inverse function
if (fabs(x1-x0)>1e-9) // check result and output to log if error
Form1->mm_log->Lines->Add(AnsiString().sprintf("acos(%8.3lf) = %8.3lf != %8.3lf",y,x0,x1));
}
Without any difference found... so the implementation is working correctly. Of coarse binary search on 52 bit mantissa is usually slower then polynomial approximation ... on the other hand the implementation is so simple ...
[Notes]
If you do not want to take care of the monotonic intervals you can try
approximation search
As you are dealing with goniometric functions you need to handle singularities to avoid NaN or division by zero etc ...
If you're interested here more bin search examples (mostly on integers)
Power by squaring for negative exponents it contains
I'm using x = numpy.random.rand(1) to generate a random number between 0 and 1. How do I make it so that x > .5 is 2 times more probable than x < .5?
That's a fitting name!
Just do a little manipulation of the inputs. First set x to be in the range from 0 to 1.5.
x = numpy.random.uniform(1.5)
x has a 2/3 chance of being greater than 0.5 and 1/3 chance being smaller. Then if x is greater than 1.0, subtract .5 from it
if x >= 1.0:
x = x - 0.5
This is overkill for you, but it's good to know an actual method for generating a random number with any probability density function (pdf).
You can do that by subclassing scipy.stat.rv_continuous, provided you do it correctly. You will have to have a normalized pdf (so that its integral is 1). If you don't, numpy will automatically adjust the range for you. In this case, your pdf has a value of 2/3 for x<0.5, and 4/3 for x>0.5, with a support of [0, 1) (support is the interval over which it's nonzero):
import scipy.stats as spst
import numpy as np
import matplotlib.pyplot as plt
import ipdb
def pdf_shape(x, k):
if x < 0.5:
return 2/3.
elif 0.5 <= x and x < 1:
return 4/3.
else:
return 0.
class custom_pdf(spst.rv_continuous):
def _pdf(self, x, k):
return pdf_shape(x, k)
instance = custom_pdf(a=0, b=1)
samps = instance.rvs(k=1, size=10000)
plt.hist(samps, bins=20)
plt.show()
tmp = random()
if tmp < 0.5: tmp = random()
is pretty easy way to do it
ehh I guess this is 3x as likely ... thats what i get for sleeping through that class I guess
from random import random,uniform
def rand1():
tmp = random()
if tmp < 0.5:tmp = random()
return tmp
def rand2():
tmp = uniform(0,1.5)
return tmp if tmp <= 1.0 else tmp-0.5
sample1 = []
sample2 = []
for i in range(10000):
sample1.append(rand1()>=0.5)
sample2.append(rand2()>=0.5)
print sample1.count(True) #~ 75%
print sample2.count(True) #~ 66% <- desired i believe :)
First off, numpy.random.rand(1) doesn't return a value in the [0,1) range (half-open, includes zero but not one), it returns an array of size one, containing values in that range, with the upper end of the range having nothing to do with the argument passed in.
The function you're probably after is the uniform distribution one, numpy.random.uniform() since this will allow an arbitrary upper range.
And, to make the upper half twice as likely is a relatively simple matter.
Take, for example, a random number generator r(n) which returns a uniformly distributed integer in the range [0,n). All you need to do is adjust the values to change the distribution:
x = r(3) # 0, 1 or 2, # 1/3 probability each
if x == 2:
x = 1 # Now either 0 (# 1/3) or 1 (# 2/3)
Now the chances of getting zero are 1/3 while the chances of getting one are 2/3, basically what you're trying to achieve with your floating point values.
So I would simply get a random number in the range [0,1.5), then subtract 0.5 if it's greater than or equal to one.
x = numpy.random.uniform(high=1.5)
if x >= 1: x -= 0.5
Since the original distribution should be even across the [0,1.5) range, the subtraction should make [0.5,1.0) twice as likely (and [1.0,1.5) impossible), while keeping the distribution even within each section ([0,0.5) and [0.5,1)):
[0.0,0.5) [0.5,1.0) [1.0,1.5) before
<---------><---------><--------->
[0.0,0.5) [0.5,1.0) [0.5,1.0) after
You could take a "mixture model" approach where you split the process into two steps: first, decide whether to take option A or B, where B is twice as likely as A; then, if you chose A, return a random number between 0.0 and 0.5, else if you chose B, return one between 0.5 and 1.0.
In the example, the randint randomly returns 0, 1, or 2, so the else case is twice as likely as the if case.
m = numpy.random.randint(3)
if m==0:
x = numpy.random.uniform(0.0, 0.5)
else:
x = numpy.random.uniform(0.5, 1.0)
This is a little more expensive (two random draws instead of one) but it can generalize to more complicated distributions in a fairly straightforward way.
if you want a more fluid randomness, you can just square the output of the random function
(and subtract it from 1 to make x > 0.5 more probable instead of x < 0.5).
x = 1 - sqr(numpy.random.rand(1))
consider my code
a,b,c = np.loadtxt ('test.dat', dtype='double', unpack=True)
a,b, and c are the same array length.
for i in range(len(a)):
q[i] = 3*10**5*c[i]/100
x[i] = q[i]*math.sin(a)*math.cos(b)
y[i] = q[i]*math.sin(a)*math.sin(b)
z[i] = q[i]*math.cos(a)
I am trying to find all the combinations for the difference between 2 points in x,y,z to iterate this equation (xi-xj)+(yi-yj)+(zi-zj) = r
I use this combination code
for combinations in it.combinations(x,2):
xdist = (combinations[0] - combinations[1])
for combinations in it.combinations(y,2):
ydist = (combinations[0] - combinations[1])
for combinations in it.combinations(z,2):
zdist = (combinations[0] - combinations[1])
r = (xdist + ydist +zdist)
This takes a long time for python for a large file I have and I am wondering if there is a faster way to get my array for r preferably using a nested loop?
Such as
if i in range(?):
if j in range(?):
Since you're apparently using numpy, let's actually use numpy; it'll be much faster. It's almost always faster and usually easier to read if you avoid python loops entirely when working with numpy, and use its vectorized array operations instead.
a, b, c = np.loadtxt('test.dat', dtype='double', unpack=True)
q = 3e5 * c / 100 # why not just 3e3 * c?
x = q * np.sin(a) * np.cos(b)
y = q * np.sin(a) * np.sin(b)
z = q * np.cos(a)
Now, your example code after this doesn't do what you probably want it to do - notice how you just say xdist = ... each time? You're overwriting that variable and not doing anything with it. I'm going to assume you want the squared euclidean distance between each pair of points, though, and make a matrix dists with dists[i, j] equal to the distance between the ith and jth points.
The easy way, if you have scipy available:
# stack the points into a num_pts x 3 matrix
pts = np.hstack([thing.reshape((-1, 1)) for thing in (x, y, z)])
# get squared euclidean distances in a matrix
dists = scipy.spatial.squareform(scipy.spatial.pdist(pts, 'sqeuclidean'))
If your list is enormous, it's more memory-efficient to not use squareform, but then it's in a condensed format that's a little harder to find specific pairs of distances with.
Slightly harder, if you can't / don't want to use scipy:
pts = np.hstack([thing.reshape((-1, 1)) for thing in (x, y, z)])
sqnorms = np.sum(pts ** 2, axis=1)
dists = sqnorms.reshape((-1, 1)) - 2 * np.dot(pts, pts.T) + sqnorms
which basically implements the formula (a - b)^2 = a^2 - 2 a b + b^2, but all vector-like.
Apologies for not posting a full solution, but you should avoid nesting calls to range(), as it will create a new tuple every time it gets called. You are better off either calling range() once and storing the result, or using a loop counter instead.
For example, instead of:
max = 50
for number in range (0, 50):
doSomething(number)
...you would do:
max = 50
current = 0
while current < max:
doSomething(number)
current += 1
Well, the complexity of your calculation is pretty high. Also, you need to have huge amounts of memory if you want to store all r values in a single list. Often, you don't need a list and a generator might be enough for what you want to do with the values.
Consider this code:
def calculate(x, y, z):
for xi, xj in combinations(x, 2):
for yi, yj in combinations(y, 2):
for zi, zj in combinations(z, 2):
yield (xi - xj) + (yi - yj) + (zi - zj)
This returns a generator that computes only one value each time you call the generator's next() method.
gen = calculate(xrange(10), xrange(10, 20), xrange(20, 30))
gen.next() # returns -3
gen.next() # returns -4 and so on