Cython 和 numpy

Question

Try to run Example 7-11 of High Performance Python

cython_np.pyx

#cython_np.pyx
import numpy as np
cimport numpy as np
def calculate_z(int maxiter, double complex[:] zs, double complex[:] cs):
    cdef unsigned int i, n
    cdef double complex z, c
    cdef int[:] output = np.empty(len(zs), dtype = np.int32)
    for i in range(len(zs)):
        n = 0
        z = zs[i]
        c = cs[i]
        while n < maxiter and (z.real * z.real + z.imag * z.imag) < 4:
            z = z * z + c
            n  += 1
        output[i] = n
    return output

setup.py

from distutils.core import setup
from distutils.extension import Extension
from Cython.Distutils import build_ext

setup(
        cmdclass = {'build_ext':build_ext},
        ext_modules = [Extension("calculate", ["cythonfn.pyx"])]
)

In the terminal , ubuntu 16.04

python3 setup.py build_ext --inplace

get some warning

running build_ext
cythoning cythonfn.pyx to cythonfn.c
building 'calculate' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -c cythonfn.c -o build/temp.linux-x86_64-3.5/cythonfn.o
In file included from /usr/include/python3.5m/numpy/ndarraytypes.h:1777:0,
                 from /usr/include/python3.5m/numpy/ndarrayobject.h:18,
                 from /usr/include/python3.5m/numpy/arrayobject.h:4,
                 from cythonfn.c:274:
/usr/include/python3.5m/numpy/npy_1_7_deprecated_api.h:15:2: warning:          #warning "Using deprecated NumPy API, disable it by " "#defining   NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it by " \
  ^
In file included from /usr/include/python3.5m/numpy/ndarrayobject.h:27:0,
                 from /usr/include/python3.5m/numpy/arrayobject.h:4,
                 from cythonfn.c:274:
/usr/include/python3.5m/numpy/__multiarray_api.h:1448:1: warning: ‘_import_array’ defined but not used [-Wunused-function]
 _import_array(void)
 ^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/cythonfn.o -o MY_DIR/calculate.cpython-35m-x86_64-linux-gnu.so

when I try to run use function calculate.calculate.z in Ipython, it says

TypeError: a bytes-like object is required, not 'list'

detail of using calculate.z

Any idea about the warning?

Answer 1

I think, based on examples inhttp://docs.cython.org/en/latest/src/userguide/memoryviews.html

double complex[:] zs

defines a 1d memoryview with double complex dtype. This is similar to a numpy array with that dtype.

Your code passes a list to this function. Lists are Python objects, and can't be accessed as C or Cython native arrays.

Does your source give any information on how to call this function? I don't have access to that book.

Answer 2

The same issue happens in the 2nd edition. While np.asarray() could solve the problem, it may somewhat(based on my own experiment) hurt the code performance. The reason could be that we need to allocate new space for the newly created array).