Getting started with Cython

Cython is a subset of python language which allows you to write faster c code. Using cython one can write code with speed comparable to C using simplicity of Python. You write your code in a file with extension .pyx and compile it either one by one manually or using a setup.py file whose code is shared below.

I thought to check the speedup gained using cython so I wrote two files. First one was a pure python.py file while other one was a cython (cython.pyx file). The results I got were pretty amazing:

Contents of python.py file:-

def aman(t):
print "Normal Python functions"
sum = 0
for i in range(t):
for j in range(t):
sum = sum + i*j

Running this code in IPython with t = 5000 took almost 2.37 seconds to complete.

Contents of cython.pyx file :-

def pyfun(t):
        print "Normal Python functions"
        sum = 0
        for i in range(t):
                for j in range(t):
                        sum = sum + i*j
        return sum

def m_fun(int t):
        print "Python function with Static Typing"
        cdef int sum = 0, i, j
        for i in range(t):
                for j in range(t):
                        sum = sum + i*j
        return sum
        
cdef fun(int t):
                print "Cython function"
        cdef:
                int sum =0
                int i = 0
                int j = 0
        for i in range(t):
                for j in range(t):
                        sum = sum + i*j
        return sum

def cfun(a):
        return _aman(a)
        

cpdef int cpfun(int t):
        print "Cpdef function c type:"
        cdef:
                int sum =0
                int i = 0
                int j = 0
        for i in range(t):
                for j in range(t):
                        sum = sum + i*j
        return sum

cpdef cppfun(t):
        sum = 0
        print "Cpdef function python:"
        for i in range(t):
                for j in range(t):
                        sum = sum + i*j
        return sum

The running time of  these functions were quite interesting:-

1st:- pyfun():- Same python code copied as it is in cython:- Took 1.72 seconds.

2nd:- m_fun():- The python code with static types defined. Took 0.0222 seconds

3rd:- cfun():- The cdef fun with a python wrapper function:- Took 0.02279 seconds

4th:-  cpfun():- Pure c code just defined as cpdef. Took 1.7299 seconds

5th:- cppfun():- The pyton code written using static pyhon declarations everyehre. Took almot 0.021 seconds to run.

This table shows the correct time taken by different cython functions :

No	Versions	Time taken	Speedup
1	Pure Python in .py file	2.37	1
2	Pure Python in .pyx file	1.72	1.377906977
3	python def function with static variable declarations	0.0222	106.7567568
4	cdef function	0.019	124.7368421
5	cpdef function without static declaration	1.7299	1.370021389
6	cpdef function with static declaration	0.02099	81.94378275

P.S. The content of setup.py file are:-

from distutils.core import setup, Extension
import numpy
from Cython.Distutils import build_ext

setup(
    cmdclass={'build_ext': build_ext},
    ext_modules=[Extension("aman",
                 sources=["aman.pyx"],
                 include_dirs=[numpy.get_include()])])

The command required to automatically convert .pyx file to .so extension is:

>>>  python setup.py build_ext –inplace

For time calculation in IPython the following commands can be used:-

>>> import timeit

>>> a = timeit.Timer(“python.aman(5000)”, “import python”)

>>>a = a.timeit(num)  #num defines how many times you want to run the loop.

>>> print a

</Keep Coding>