zpoint zpoint - 1 year ago 146
Python Question

Cython and numpy

Try to run Example 7-11 of High Performance Python


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


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

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]
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 Source

I think, based on examples in http://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.