I am converting a Cython memoryview to a numpy array (to be able to use it in pure Python code):
from libc.stdlib cimport realloc
cimport numpy as np
DTYPE = np.float64
ctypedef np.float64_t DTYPE_t
cpdef np.ndarray[DTYPE_t] compute(DTYPE_t[:,::1] data):
cdef unsigned int Nchannels = data.shape[0]
cdef unsigned int Ndata = data.shape[1]
cdef DTYPE_t* output = NULL
cdef DTYPE_t[::1] mv
output = <DTYPE_t*>realloc(output, Ndata*sizeof(output))
if not output:
raise MemoryError()
mv = <DTYPE_t[:Ndata]>output
mv[10:Ndata-10] = 0.0
# various calculations...
return np.asarray(mv, dtype=DTYPE, order='C')
It compiles, but the compiler gives the following warning:
/Users/vlad/anaconda/lib/python2.7/site-packages/numpy/core/include
/nump/npy_1_7_deprecated_api.h:15:2: warning:
"Using deprecated NumPy API, disable it by #defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
I added the suggested directive in setup.py:
from distutils.core import setup, Extension
from Cython.Build import cythonize
import numpy
filename = 'agents3.pyx'
agents_module = Extension(
'Agents',
sources = [filename],
define_macros = [('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
include_dirs = [numpy.get_include()],
)
setup (name = 'Agents',
ext_modules = cythonize(agents_module)
)
Now it wouldn't compile, it says:
Vlads-MacBook-Pro:program vlad$ python setup.py build_ext --inplace
Compiling agents3.pyx because it changed.
Cythonizing agents3.pyx
running build_ext
building 'Agents' extension
gcc -fno-strict-aliasing -I/Users/vlad/anaconda/include -arch x86_64 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -DNPY_NO_DEPRECATED_API=NPY_1_7_API_VERSION -I/Users/vlad/anaconda/lib/python2.7/site-packages/numpy/core/include -I/Users/vlad/anaconda/include/python2.7 -c agents3.c -o build/temp.macosx-10.5-x86_64-2.7/agents3.o
agents3.c:2273:52: error: use of undeclared identifier 'NPY_C_CONTIGUOUS'
__pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0);
^
agents3.c:2311:52: error: use of undeclared identifier 'NPY_F_CONTIGUOUS'
__pyx_t_1 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0);
^
agents3.c:2474:42: error: no member named 'descr' in 'struct tagPyArrayObject'
__pyx_t_4 = ((PyObject *)__pyx_v_self->descr);
~~~~~~~~~~~~ ^
agents3.c:4026:27: error: no member named 'base' in 'struct tagPyArrayObject'
Py_XDECREF(__pyx_v_arr->base);
~~~~~~~~~~~ ^
/Users/vlad/anaconda/include/python2.7/object.h:823:34: note: expanded from macro 'Py_XDECREF'
#define Py_XDECREF(op) do { if ((op) == NULL) ; else Py_DECREF(op); } while (0)
^
agents3.c:4026:27: error: no member named 'base' in 'struct tagPyArrayObject'
Py_XDECREF(__pyx_v_arr->base);
~~~~~~~~~~~ ^
/Users/vlad/anaconda/include/python2.7/object.h:823:64: note: expanded from macro 'Py_XDECREF'
#define Py_XDECREF(op) do { if ((op) == NULL) ; else Py_DECREF(op); } while (0)
^
/Users/vlad/anaconda/include/python2.7/object.h:772:24: note: expanded from macro 'Py_DECREF'
--((PyObject*)(op))->ob_refcnt != 0) \
^
agents3.c:4026:27: error: no member named 'base' in 'struct tagPyArrayObject'
Py_XDECREF(__pyx_v_arr->base);
~~~~~~~~~~~ ^
/Users/vlad/anaconda/include/python2.7/object.h:823:64: note: expanded from macro 'Py_XDECREF'
#define Py_XDECREF(op) do { if ((op) == NULL) ; else Py_DECREF(op); } while (0)
^
/Users/vlad/anaconda/include/python2.7/object.h:775:34: note: expanded from macro 'Py_DECREF'
_Py_Dealloc((PyObject *)(op)); \
^
/Users/vlad/anaconda/include/python2.7/object.h:762:15: note: expanded from macro '_Py_Dealloc'
(*Py_TYPE(op)->tp_dealloc)((PyObject *)(op)))
^
/Users/vlad/anaconda/include/python2.7/object.h:115:47: note: expanded from macro 'Py_TYPE'
#define Py_TYPE(ob) (((PyObject*)(ob))->ob_type)
^
agents3.c:4026:27: error: no member named 'base' in 'struct tagPyArrayObject'
Py_XDECREF(__pyx_v_arr->base);
~~~~~~~~~~~ ^
/Users/vlad/anaconda/include/python2.7/object.h:823:64: note: expanded from macro 'Py_XDECREF'
#define Py_XDECREF(op) do { if ((op) == NULL) ; else Py_DECREF(op); } while (0)
^
/Users/vlad/anaconda/include/python2.7/object.h:775:34: note: expanded from macro 'Py_DECREF'
_Py_Dealloc((PyObject *)(op)); \
^
/Users/vlad/anaconda/include/python2.7/object.h:762:45: note: expanded from macro '_Py_Dealloc'
(*Py_TYPE(op)->tp_dealloc)((PyObject *)(op)))
^
agents3.c:4035:16: error: no member named 'base' in 'struct tagPyArrayObject'
__pyx_v_arr->base = __pyx_v_baseptr;
~~~~~~~~~~~ ^
agents3.c:4070:30: error: no member named 'base' in 'struct tagPyArrayObject'
__pyx_t_1 = ((__pyx_v_arr->base == NULL) != 0);
~~~~~~~~~~~ ^
agents3.c:4093:44: error: no member named 'base' in 'struct tagPyArrayObject'
__Pyx_INCREF(((PyObject *)__pyx_v_arr->base));
~~~~~~~~~~~ ^
agents3.c:1065:37: note: expanded from macro '__Pyx_INCREF'
#define __Pyx_INCREF(r) Py_INCREF(r)
^
/Users/vlad/anaconda/include/python2.7/object.h:767:18: note: expanded from macro 'Py_INCREF'
((PyObject*)(op))->ob_refcnt++)
^
agents3.c:4094:41: error: no member named 'base' in 'struct tagPyArrayObject'
__pyx_r = ((PyObject *)__pyx_v_arr->base);
~~~~~~~~~~~ ^
11 errors generated.
error: command 'gcc' failed with exit status 1
Vlads-MacBook-Pro:program vlad$
What should I do? Is it OK to leave the deprecated API call as it is? It tries to acces the base field -- but I am not doing it, it's Cython's fault. I simply converted a memoryview to a numpy array. Is there another, cleaner/safer way of doing it?
Just for a further reference, cython online docs says this is because Cython is using a deprecated Numpy API, and for the time being, it's just a warning that we can ignore.