Simple numpy and Cython example

In [1]:

from IPython.core.display import display, HTML
display(HTML("<style>.container { width:50% !important; }</style>"))

In [2]:

%load_ext cython

In [4]:

# Pass compile options to %%cython
# -a means annotate the source code to show sections
# which have Python interaction

In [6]:

%%cython -a
cimport numpy as np


cdef double _dot(double* a, double* b, int n):
    cdef int i
    cdef double sum


    sum = 0
    for i in range(n):
        sum += a[i] * b[i]
    
    return sum


cpdef double cy_dot(np.ndarray a, np.ndarray b):
    cdef int n = a.shape[0]

    cdef double* a_ptr = <double*> a.data
    cdef double* b_ptr = <double*> b.data

    return _dot(a_ptr, b_ptr, n)

Out[6]:

Generated by Cython 0.23.4

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: cimport numpy as np

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 02: 

 03: 

+04: cdef double _dot(double* a, double* b, int n):

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 05:     cdef int i

 06:     cdef double sum

 07: 

 08: 

+09:     sum = 0

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+10:     for i in range(n):

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+11:         sum += a[i] * b[i]

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 12: 

+13:     return sum

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 14: 

 15: 

+16: cpdef double cy_dot(np.ndarray a, np.ndarray b):

static PyObject *__pyx_pw_46_cython_magic_3e017d4f9980d56ce613de0b5ec2e832_1cy_dot(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds); /*proto*/
static double __pyx_f_46_cython_magic_3e017d4f9980d56ce613de0b5ec2e832_cy_dot(PyArrayObject *__pyx_v_a, PyArrayObject *__pyx_v_b, CYTHON_UNUSED int __pyx_skip_dispatch) {
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+17:     cdef int n = a.shape[0]

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 18: 

+19:     cdef double* a_ptr = <double*> a.data

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+20:     cdef double* b_ptr = <double*> b.data

  __pyx_v_b_ptr = ((double *)__pyx_v_b->data);

 21: 

+22:     return _dot(a_ptr, b_ptr, n)

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  goto __pyx_L0;

In [5]:

import numpy as np
a = np.array([-2., 0., 5.])
b = np.array([1., 1., 1.])
print a.dot(b)

3.0

In [8]:

print cy_dot(a, b)

3.0