Interfacing C code with Cython
As Cython code compiles down to C code, it is relatively straightforward to utilize also Cython for interfacing with C.
In order to use C functions and variables from the library, one must provide
external declarations for them in the Cython .pyx file. While normal
declarations refer to functions and variables that are defined in the same
file, by adding
extern keyword one can specify that they are defined
elsewhere. As an example, by having in a .pyx file the statement
cdef extern void add(double *a, double *b, double *c, int n)
one could call
add function within that file. In addition, the actual
library or source implementing the function needs to be included in setup.py when building the
extension module with Cython.
With the above construct, Cython will add the declaration to the generated .c file. However, when using libraries it is preferable to have the actual library header included in the generated file. This can be achieved with the following construct:
cdef extern from "mylib.h" void add(double *a, double *b, double *c, int n) void subtract(double *a, double *b, double *c, int n)
Now, mylib.h header is included in the generated .c file, while the
statements in the following block specify that functions
can be used within the .pyx file. It is important to understand that Cython
does not itself read the C header file, so you still need to provide
declarations from it that you use.
Including the library in setup.py
Compared to building simple pure Cython modules, one has to provide some extra information in the setup.py. If the code to be interfaced is in a library (i.e. .so) one can use the following type of setup.py:
from distutils.core import setup, Extension from Cython.Build import cythonize ext = Extension("module_name", sources=["cython_source.pyx",], libraries=["name",], # Cython module is linked against library_dirs=[".",]) # libname.so, looked in "." setup(ext_modules=cythonize(ext))
One can also use direct C source files if more appropriate:
from distutils.core import setup, Extension from Cython.Build import cythonize # Specify all sources in Extension object ext = Extension("module_name", sources=["cython_source.pyx", "c_source.c"]) setup(ext_modules=cythonize(ext))
Passing NumPy arrays from Cython to C
Similarly as when using CFFI to pass NumPy arrays into C, also in the case of
Cython one needs to be able to pass a pointer to the “data area” of an array.
For arrays that are declared as type of
ndarray, Cython supports similar
& syntax as in C:
import numpy as np cimport numpy as np cdef extern from "myclib.h": void add(double *a, double *b, double *c, int n) void subtract(double *a, double *b, double *c, int n) def add_py(np.ndarray[cnp.double_t,ndim=1] a, np.ndarray[cnp.double_t,ndim=1] b): add(&a, &b, &c, len(a))
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