Using Cython to wrap a c++ template to accept any numpy array

Question

I'm trying to wrap a parallel sort written in c++ as a template, to use it with numpy arrays of any numeric type. I'm trying to use Cython to do this.

My problem is that I don't know how to pass a pointer to the numpy array data (of a correct type) to a c++ template. I believe I should use fused dtypes for this, but I don't quite understand how.

The code in .pyx file is below

# importing c++ template
cdef extern from "test.cpp":
    void inPlaceParallelSort[T](T* arrayPointer,int arrayLength)

def sortNumpyArray(np.ndarray a):
    # This obviously will not work, but I don't know how to make it work. 
    inPlaceParallelSort(a.data, len(a))

In the past I did similar tasks with ugly for-loops over all possible dtypes, but I believe there should be a better way to do this.

IanH · Accepted Answer · 2015-02-21 22:12:30Z

7

Yes, you want to use a fused type to have Cython call the sorting template for the appropriate specialization of the template. Here's a working example for all non-complex data types that does this with std::sort.

# cython: wraparound = False
# cython: boundscheck = False

cimport cython

cdef extern from "<algorithm>" namespace "std":
    cdef void sort[T](T first, T last) nogil

ctypedef fused real:
    cython.char
    cython.uchar
    cython.short
    cython.ushort
    cython.int
    cython.uint
    cython.long
    cython.ulong
    cython.longlong
    cython.ulonglong
    cython.float
    cython.double

cpdef void npy_sort(real[:] a) nogil:
    sort(&a[0], &a[a.shape[0]-1])

answered Feb 21, 2015 at 22:12

IanH

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2 Comments

Maxim Imakaev Over a year ago

This did not compile as is, the compiler complained a lot about nogil. I had to kill it, but parallelization worked without it.

IanH Over a year ago

@MaximImakaev Yep, the nogil is really only necessary if you want to call the Cython function inside a parallel loop. The parallization inside your sorting function should be fine without it. It's odd that it wouldn't compile with it there though. There's probably some difference in Cython versions. I have a recent development version (pretty similar to 0.22) and it worked fine for me.

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