# Cython¶

Christian Elsasser (che@physik.uzh.ch)

The content of this lecture might be distributed under CC by-sa.

## An introductionnary example - Fibonacci numbers¶

Plain python version

In [1]:

    def fib0(n):
        a,b = 1,1
        for i in range(n):
            a,b=a+b,a
        return a

In [2]:

    fib0(5)

Out[2]:

    13

In [3]:

    fib0(6)

Out[3]:

    21

In [5]:

    %timeit fib0(10000)

    1.86 ms ± 11.3 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

In [6]:

    import cython

In [7]:

    cython.__version__

Out[7]:

    '0.29.19'

In [8]:

    %load_ext Cython

Hello, Cython

In [9]:

    %%cython
    def helloWorld():
        print("Hello, Cython!")

In [10]:

    helloWorld

Out[10]:

    <function _cython_magic_d55d0d78aaf5722976e35d5b029bdf83.helloWorld>

In [11]:

    helloWorld()

    Hello, Cython!

Pure python in Cython

In [12]:

    %%cython
    def fib1(n):
        a,b = 1,1
        for i in range(n):
            a,b=a+b,a
        return a

In [13]:

    fib1

Out[13]:

    <function _cython_magic_c7b2b79161369470b419d69e14fd8c7f.fib1>

In [14]:

    fib1(5)

Out[14]:

    13

In [15]:

    %timeit fib1(10000)

    1.69 ms ± 36.8 µs per loop (mean ± std. dev. of 7 runs, 1000 loops each)

C-code enhanced Python

In [16]:

    %%cython
    def fib2(int n):
        cdef int i,a,b
        a,b = 1,1
        for i in range(n):
            a,b = a+b,a
        return a

In [17]:

    fib2

Out[17]:

    <function _cython_magic_e7de6ac7b507cb5c9be41b44460ce6fa.fib2>

In [18]:

    fib2(5)

Out[18]:

    13

In [19]:

    %timeit fib2(10000)

    2.69 µs ± 189 ns per loop (mean ± std. dev. of 7 runs, 100000 loops each)

## Second Example - Numerical integration¶

First try to integrate a function

In [24]:

    %%cython -a

    from math import sin,exp

    def f0(double x):
        return sin(x)*exp(-x)

    def integrate0(double a,double b,int N):
        cdef double s,dx
        cdef int i
        s = 0
        dx = (b-a)/N
        for i in range(N):
            s += f0(a+(i+0.5)*dx)
        return s*dx

Out[24]:
Cython: _cython_magic_570567440a824602d71ac19c2bf356d8.pyx

Generated by Cython 0.29.19

Yellow lines hint at Python interaction.
Click on a line that starts with a "`+`" to see the C code that Cython generated for it.

     01:

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In [26]:

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In [27]:

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In [31]:

    f2(5)

Out[31]:

    -0.006461180938816702

Improvement iteration 2

In [35]:

    %%cython

    from libc.math cimport sin,exp

    cpdef double f3(double x):
        return sin(x)*exp(-x)

    def integrate3(double a,double b,int N):
        cdef double dx,s
        cdef int i
        dx = (b-a)/N
        s = 0.0
        for i in range(N):
            s+=f3(a+(i+0.5)*dx)
        return s*dx

In [36]:

    f3(5)

Out[36]:

    -0.006461180938816702

In [37]:

    %timeit integrate3(0.0,pi,1000000)

    13.7 ms ± 160 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

In [40]:

    import numpy as np

    def f4(x):
        return np.sin(x)*np.exp(-x)

    def integrate4(a,b,N):
        dx = (b-a)/N
        x = (np.arange(N)+0.5)*dx+a
        return np.sum(f4(x))*dx

In [42]:

    %timeit integrate4(0.0,pi,1000000)

    28.3 ms ± 284 µs per loop (mean ± std. dev. of 7 runs, 10 loops each)

## Cython and STL containers¶

In [43]:

    %%cython -+
    #distutils: language = c++
    from libcpp.vector cimport vector
    def manipulateVector(vector[double] v):
        v.push_back(42.0) # Equivalent to append for list in python
        return v

In [44]:

    manipulateVector([1,2,3,4])

Out[44]:

    [1.0, 2.0, 3.0, 4.0, 42.0]

## Cython and exceptions¶

Python Errors in Cython

In [45]:

    %%cython
    cpdef int raiseError():
        raise RuntimeError("A problem!")
        return 1

    warning: /Users/che/.ipython/cython/_cython_magic_14462e3e19cc337c50c4347922e844d0.pyx:3:4: Unreachable code

In [46]:

    raiseError()

    ---------------------------------------------------------------------------
    RuntimeError                              Traceback (most recent call last)
    RuntimeError: A problem!

    Exception ignored in: '_cython_magic_14462e3e19cc337c50c4347922e844d0.raiseError'
    RuntimeError: A problem!

Out[46]:

    0

In [47]:

    %%cython
    cpdef int raiseErrorBetter() except *:
        raise RuntimeError("A problem!")
        return 1

    warning: /Users/che/.ipython/cython/_cython_magic_870d2bad77c520fa5a606110565cf636.pyx:3:4: Unreachable code

In [48]:

    raiseErrorBetter()

    ---------------------------------------------------------------------------
    RuntimeError                              Traceback (most recent call last)
    <ipython-input-48-9e77aa258386> in <module>
    ----> 1 raiseErrorBetter()

    _cython_magic_870d2bad77c520fa5a606110565cf636.pyx in _cython_magic_870d2bad77c520fa5a606110565cf636.raiseErrorBetter()

    _cython_magic_870d2bad77c520fa5a606110565cf636.pyx in _cython_magic_870d2bad77c520fa5a606110565cf636.raiseErrorBetter()

    RuntimeError: A problem!

In [49]:

    try:
        raiseErrorBetter()
    except RuntimeError:
        print("Error caught")

    Error caught

C Error codes in Cython

In [50]:

    %%cython
    cpdef int raiseException(int n) except -1:
        # Assuming C function returning an integer; if -1 --> Error appeared
        return n

In [51]:

    raiseException(1)

Out[51]:

    1

In [52]:

    raiseException(-1)

    ---------------------------------------------------------------------------
    SystemError                               Traceback (most recent call last)
    <ipython-input-52-f1e17eec89ff> in <module>
    ----> 1 raiseException(-1)

    SystemError: <built-in function raiseException> returned NULL without setting an error

## Back to integration - Cython and Classes¶

In [56]:

    %%cython

    from libc.math cimport sin,exp

    cdef class Integrand(object):
        cpdef double evaluate(self,double x):
            raise NotImplementedError()

    cdef class SinExpFunction(Integrand):
        cpdef double evaluate(self,double x):
            return sin(x)*exp(-x)

    def integrate(Integrand f, double a, double b, int N):
        cdef int i
        cdef double dx,s
        dx = (b-a)/N
        s = 0.0
        for i in range(N):
            s += f.evaluate(a+(i+0.5)*dx)
        return s*dx

In [54]:

    f = SinExpFunction()

In [55]:

    import math

In [57]:

    %timeit integrate(f,0,math.pi,1000000)

    16.8 ms ± 147 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

In [58]:

    class Poly(Integrand):
        def evaluate(self,x):
            return 3*x-x**3

In [59]:

    g = Poly()
    integrate(g,0,math.pi,10000)

Out[59]:

    -9.5478660351052

In [60]:

    %timeit integrate(g,0,math.pi,1000000)

    185 ms ± 4.46 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)