Passing/returning Cython Memoryviews Vs Numpy Arrays

I am writing Python code to accelerate a region properties function for labeled objects in a binary image. The following code will calculate the number of border pixels of a labele

Solution 1:

Memoryviews are a more recent addition to Cython, designed to be an improvement compared to the original np.ndarray syntax. For this reason they're slightly preferred. It usually doesn't make too much difference which you use though. Here are a few notes:

Speed

For speed it makes very little difference - my experience is that memoryviews as function parameters are marginally slower, but it's hardly worth worrying about.

Generality

Memoryviews are designed to work with any type that has Python's buffer interface (for example the standard library array module). Typing as np.ndarray only works with numpy arrays. In principle memorviews can support an even wider range of memory layouts which can make interfacing with C code easier (in practice I've never actually seen this be useful).

As a return value

When returning an array from Cython to code Python the user will probably be happier with a numpy array than with a memoryview. If you're working with memoryviews you can do either:

return np.asarray(mview)
return mview.base

Ease of compiling

If you're using np.ndarray you have to get the set the include directory with np.get_include() in your setup.py file. You don't have to do this with memoryviews, which often means you can skip setup.py and just use the cythonize command line command or pyximport for simpler projects.

Parallelization

This is the big advantage of memoryviews compared to numpy arrays (if you want to use it). It does not require the global interpreter lock to take slices of a memoryview but it does for a numpy array. This means that the following code outline can work in parallel with a memoryview:

cdef void somefunc(double[:] x) nogil:
     # implementation goes here

cdef double[:,:] 2d_array = np.array(...)
for i in prange(2d_array.shape[0]):
    somefunc(2d_array[i,:])

If you aren't using Cython's parallel functionality this doesn't apply.

cdef classes

You can use memoryviews as attributes of cdef classes but not np.ndarrays. You can (of course) use numpy arrays as untyped object attributes instead.