Extension types (aka. cdef classes)

Note

This page uses two different syntax variants:

  • Cython specific cdef syntax, which was designed to make type declarations concise and easily readable from a C/C++ perspective.

  • Pure Python syntax which allows static Cython type declarations in pure Python code, following PEP-484 type hints and PEP 526 variable annotations.

    To make use of C data types in Python syntax, you need to import the special cython module in the Python module that you want to compile, e.g.

    import cython
    

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 Cython language 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.

@cython.cclass
class Function:
    @cython.ccall
    def evaluate(self, x: float) -> float:
        return 0

The cpdef command (or @cython.ccall in Python syntax) makes two versions of the method available; one fast for use from Cython and one slower for use from Python.

Now we can add subclasses of the Function class that implement different math functions in the same evaluate() method.

Then:

sin_of_square.py
from cython.cimports.libc.math import sin

@cython.cclass
class Function:
    @cython.ccall
    def evaluate(self, x: float) -> float:
        return 0

@cython.cclass
class SinOfSquareFunction(Function):
    @cython.ccall
    def evaluate(self, x: float) -> float:
        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. This 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 .pxd file with the same name as the module. Note that we are using Cython syntax here, not Python syntax.

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

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

With this way to implement different functions as subclasses with fast, Cython callable methods, we can now pass these Function objects into an algorithm for numeric integration, that evaluates an arbitrary user provided function over a value interval.

Using this, we can now change our integration example:

integrate.py
from cython.cimports.sin_of_square import Function, SinOfSquareFunction

def integrate(f: Function, a: float, b: float, N: cython.int):
    i: cython.int

    if f is None:
        raise ValueError("f cannot be None")

    s: float = 0
    dx: float = (b - a) / N

    for i in range(N):
        s += f.evaluate(a + i * dx)

    return s * dx

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

We can even pass in a new Function defined in Python space, which overrides the Cython implemented method of the base class:

>>> import integrate
>>> class MyPolynomial(integrate.Function):
...     def evaluate(self, x):
...         return 2*x*x + 3*x - 10
...
>>> integrate(MyPolynomial(), 0, 1, 10000)
-7.8335833300000077

Since evaluate() is a Python method here, which requires Python objects as input and output, this is several times slower than the straight C call to the Cython method, but still faster than a plain Python variant. This shows how large the speed-ups can easily be when whole computational 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:

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

import cython

@cython.cclass
class MyClass:
    pass

# Turn off nonecheck locally for the function
@cython.nonecheck(False)
def func():
    obj: MyClass = None
    try:
        # Turn nonecheck on again for a block
        with cython.nonecheck(True):
            print(obj.myfunc())  # Raises exception
    except AttributeError:
        pass
    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

wave_function.py
from cython.cimports.sin_of_square import Function

@cython.cclass
class WaveFunction(Function):

    # Not available in Python-space:
    offset: float

    # Available in Python-space:
    freq = cython.declare(cython.double, visibility='public')

    # Available in Python-space, but only for reading:
    scale = cython.declare(cython.double, visibility='readonly')

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

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