ArrayStruct_and_Pyrex - SciPy wiki dump (original) (raw)

Overview

Pyrex is a language for writing C extensions to Python. Its syntax is very similar to writing Python. A .pyx file is compiled to a .c file, which is then compiled like a standard C extension module for Python. Many people find writing extension modules with Pyrex preferable to writing them in C or using other tools, such as SWIG.

See http://numeric.scipy.org/ for an explanation of the __array_struct__ interface. The following packages support the interface:

NumPy (all versions)
Numeric (>=24.2)
numarray (>=1.5.0)

Here is a Pyrex file which shows how to export its data using the __array_struct__ array interface. This allows various Python types to have a view of the data without actually copying the data itself.

cdef extern from "Python.h": ctypedef int Py_intptr_t void Py_INCREF(object) void Py_DECREF(object) object PyCObject_FromVoidPtrAndDesc( void* cobj, void* desc, void (*destr)(void *, void *))

cdef extern from "stdlib.h": ctypedef int size_t ctypedef long intptr_t void malloc(size_t size) void free(void ptr)

CONTIGUOUS=0x01 FORTRAN=0x02 ALIGNED=0x100 NOTSWAPPED=0x200 WRITEABLE=0x400

ctypedef struct PyArrayInterface: int version
int nd
char typekind
int itemsize
int flags
Py_intptr_t *shape
Py_intptr_t *strides void *data

cdef void free_array_interface( void* ptr, void arr ): cdef PyArrayInterface inter

inter = <PyArrayInterface*>ptr
arrpy = <object>arr
Py_DECREF( arrpy )
free(inter)

ctypedef unsigned char fi ctypedef fi* fiptr cdef class Unsigned8Buf: cdef fiptr data cdef Py_intptr_t shape[2] cdef Py_intptr_t strides[2]

def __init__(self, int width, int height):
    cdef int bufsize
    bufsize = width*height*sizeof(fi)
    self.data=<fiptr>malloc( bufsize )
    if self.data==NULL: raise MemoryError("Error allocating memory")
    self.strides[0]=width
    self.strides[1]=1 
    
    self.shape[0]=height
    self.shape[1]=width

def __dealloc__(self):
        free(self.data)
        
property __array_struct__:
    def __get__(self):
        cdef PyArrayInterface* inter

        cdef Py_intptr_t *newshape   
        cdef Py_intptr_t *newstrides 
        cdef int nd

        nd = 2

        inter = <PyArrayInterface*>malloc( sizeof( PyArrayInterface ) )
        if inter is NULL:
            raise MemoryError()

        inter.version = 2
        inter.nd = nd
        inter.typekind = 'u'[0] 
        inter.itemsize = 1
        inter.flags = NOTSWAPPED | ALIGNED | WRITEABLE
        inter.strides = self.strides
        inter.shape = self.shape
        inter.data = self.data
        Py_INCREF(self)
        obj = PyCObject_FromVoidPtrAndDesc( <void*>inter, <void*>self, free_array_interface)
        return obj

Using data malloced elsewhere with a Pyrex-based extension

One example is the get_data_copy() function of _cam_iface_shm.pyx in the motmot camera utilities software. In this use example, an image is copied from shared memory into an externally malloced buffer supporting the __array_struct__ interface. (The shared memory stuff has only been tested on linux, but the rest should work anywhere.)

ArrayStruct_and_Pyrex - SciPy wiki dump (original) (raw)

Overview

Sharing data malloced by a Pyrex-based extension

Using data malloced elsewhere with a Pyrex-based extension

See also