Extension types (aka. cdef classes)

To support object-oriented programming, Cython supports writing normal Python classes exactly as in Python:

class MathFunction(object):
    def __init__(self, name, operator):
        self.name = name
        self.operator = operator

    def __call__(self, *operands):
        return self.operator(*operands)

Based on what Python calls a “built-in type”, however, Cython supports a second kind of class: extension types, sometimes referred to as “cdef classes” due to the keywords used for their declaration. They are somewhat restricted compared to Python classes, but are generally more memory efficient and faster than generic Python classes. The main difference is that they use a C struct to store their fields and methods instead of a Python dict. This allows them to store arbitrary C types in their fields without requiring a Python wrapper for them, and to access fields and methods directly at the C level without passing through a Python dictionary lookup.

Normal Python classes can inherit from cdef classes, but not the other way around. Cython requires to know the complete inheritance hierarchy in order to lay out their C structs, and restricts it to single inheritance. Normal Python classes, on the other hand, can inherit from any number of Python classes and extension types, both in Cython code and pure Python code.

So far our integration example has not been very useful as it only integrates a single hard-coded function. In order to remedy this, with hardly sacrificing speed, we will use a cdef class to represent a function on floating point numbers:

cdef class Function:
    cpdef double evaluate(self, double x) except *:
        return 0

The directive cpdef makes two versions of the method available; one fast for use from Cython and one slower for use from Python. Then:

from libc.math cimport sin

cdef class Function:
    cpdef double evaluate(self, double x) except *:
        return 0

cdef class SinOfSquareFunction(Function):
    cpdef double evaluate(self, double x) except *:
        return sin(x ** 2)

This does slightly more than providing a python wrapper for a cdef method: unlike a cdef method, a cpdef method is fully overridable by methods and instance attributes in Python subclasses. It adds a little calling overhead compared to a cdef method.

To make the class definitions visible to other modules, and thus allow for efficient C-level usage and inheritance outside of the module that implements them, we define them in a sin_of_square.pxd file:

cdef class Function:
    cpdef double evaluate(self, double x) except *

cdef class SinOfSquareFunction(Function):
    cpdef double evaluate(self, double x) except *

Using this, we can now change our integration example:

from sin_of_square cimport Function, SinOfSquareFunction

def integrate(Function f, double a, double b, int N):
    cdef int i
    cdef double s, dx
    if f is None:
        raise ValueError("f cannot be None")
    s = 0
    dx = (b - a) / N
    for i in range(N):
        s += f.evaluate(a + i * dx)
    return s * dx

print(integrate(SinOfSquareFunction(), 0, 1, 10000))

This is almost as fast as the previous code, however it is much more flexible as the function to integrate can be changed. We can even pass in a new function defined in Python-space:

>>> import integrate
>>> class MyPolynomial(integrate.Function):
...     def evaluate(self, x):
...         return 2*x*x + 3*x - 10
>>> integrate(MyPolynomial(), 0, 1, 10000)

This is about 20 times slower, but still about 10 times faster than the original Python-only integration code. This shows how large the speed-ups can easily be when whole loops are moved from Python code into a Cython module.

Some notes on our new implementation of evaluate:

  • The fast method dispatch here only works because evaluate was declared in Function. Had evaluate been introduced in SinOfSquareFunction, the code would still work, but Cython would have used the slower Python method dispatch mechanism instead.
  • In the same way, had the argument f not been typed, but only been passed as a Python object, the slower Python dispatch would be used.
  • Since the argument is typed, we need to check whether it is None. In Python, this would have resulted in an AttributeError when the evaluate method was looked up, but Cython would instead try to access the (incompatible) internal structure of None as if it were a Function, leading to a crash or data corruption.

There is a compiler directive nonecheck which turns on checks for this, at the cost of decreased speed. Here’s how compiler directives are used to dynamically switch on or off nonecheck:

# cython: nonecheck=True
#        ^^^ Turns on nonecheck globally

import cython

cdef class MyClass:

# Turn off nonecheck locally for the function
def func():
    cdef MyClass obj = None
        # Turn nonecheck on again for a block
        with cython.nonecheck(True):
            print(obj.myfunc())  # Raises exception
    except AttributeError:
    print(obj.myfunc())  # Hope for a crash!

Attributes in cdef classes behave differently from attributes in regular classes:

  • All attributes must be pre-declared at compile-time
  • Attributes are by default only accessible from Cython (typed access)
  • Properties can be declared to expose dynamic attributes to Python-space
from sin_of_square cimport Function

cdef class WaveFunction(Function):

    # Not available in Python-space:
    cdef double offset

    # Available in Python-space:
    cdef public double freq

    # Available in Python-space, but only for reading:
    cdef readonly double scale

    # Available in Python-space:
    def period(self):
        return 1.0 / self.freq

    def period(self, value):
        self.freq = 1.0 / value