Cython: Create Memoryview Without Numpy Array?

Since I found memory-views handy and fast, I try to avoid creating NumPy arrays in cython and work with the views of the given arrays. However, sometimes it cannot be avoided, not

Solution 1:

Didn't know, how to deal with cpython arrays, so I solved this finally by a self made 'memory view', as proposed by fabrizioM. Wouldn't have thought that this would work. Creating a new np.array in a tight loop is pretty expensive, so this gave me a significant speed up. Since I only need a 1 dimensional array, I didn't even had to bother with strides. But even for a higher dimensional arrays, I think this could go well.

cdefclass Vector:
    cdefdouble *data
    cdefpublicint n_ax0

    def__init__(Vector self, int n_ax0):
        self.data = <double*> malloc (sizeof(double) * n_ax0)
        self.n_ax0 = n_ax0

    def__dealloc__(Vector self):
        free(self.data)

...
#@cython.profile(False)@cython.boundscheck(False)
cdefVector my_vec_func(double [:, ::1] a, int [:] v, int cond, int opt):
    # function returning a Vector, which can be hopefully freed by del Vector
    cdefint vecsize
    cdefsize_t i
    # defs..# more stuff...
    vecsize = n
    cdefVector v = Vector(vecsize)

    for i inrange(vecsize):
        # computation
        v[i] = ...

    return v

...
vec = my_vec_func(...
ptr_to_data = vec.data
length_of_vec = vec.n_ax0

Solution 2:

The following thread on the Cython mailing list would probably be of interest to you:

https://groups.google.com/forum/#!topic/cython-users/CwtU_jYADgM

It looks like there are some decent options presented if you are fine with returning a memoryview from your function that gets coerced at some different level where perfomance isn't as much of an issue.

Solution 3:

From http://docs.cython.org/src/userguide/memoryviews.html it follows that memory for cython memory views can be allocated via:

cimport cython
cdeftype [:] cview = cython.view.array(size = size, 
              itemsize = sizeof(type), format = "type", allocate_buffer = True)

or by

from libc.stdlib import malloc, free
cdeftype [:] cview = <type[:size]> malloc(sizeof(type)*size)

Both case works, but in first i have an issues if introduce own type (ctypedef some mytype) because there is no suitable format for it. In second case there is problem with deallocation of memory.

From manual it should work as follows:

cview.callback_memory_free = free

which bind function which free memory to the memoryview, however this code does not compile.