C[omp]ute

From: andrew cooke <andrew@...>

Date: Sat, 4 Apr 2015 17:27:31 -0300

An example I made this morning for work.  We allocate an array on the heap
(with malloc) and then pass it into a numpy array that's returned to the
Python level.  Because we set the OWNDATA flag, numpy will free the array when
it's no longer needed.

Andrew


andrew@...:~/project/numpy-c> cat example.c

#include <Python.h>
// i think this means we're using the 1.9 api
// http://docs.scipy.org/doc/numpy/reference/c-api.deprecations.html
#define NPY_NO_DEPRECATED_API NPY_1_9_API_VERSION
#include <numpy/arrayobject.h>

static PyObject *new_vec(PyObject *self, PyObject *args);

static PyMethodDef module_methods[] = {
  {"new_vec", new_vec, METH_VARARGS,
   "create a new vector with n entries, numbered 0 to n-1"},
  {NULL, NULL, 0, NULL}};

PyMODINIT_FUNC initexample(void) {
  if (!(Py_InitModule3("example", module_methods, 
                       "an exmaple module"))) return;
  // something to do with numpy
  import_array();
}

static PyObject *new_vec(PyObject *self, PyObject *args) {
  // expect a single integer argument
  int i, n;
  if (!(PyArg_ParseTuple(args, "i", &n))) return NULL;
  // create the array in C on the heap
  int *array = NULL;
  if (!(array = malloc(n * sizeof(int)))) return NULL;
  for (i = 0; i < n; ++i) array[i] = i;
  // return the array as a numpy array (numpy will free it later)
  npy_intp dims[1] = {n};
  PyObject *narray = PyArray_SimpleNewFromData(1, dims, NPY_INT, array);
  // this is the critical line - tell numpy it has to free the data
  PyArray_ENABLEFLAGS((PyArrayObject*)narray, NPY_ARRAY_OWNDATA);
  return narray;
}


andrew@...:~/project/numpy-c> cat setup.py 

from distutils.core import setup, Extension
from numpy.distutils.misc_util import get_numpy_include_dirs

setup(ext_modules=[Extension("example", ["example.c"])],
      include_dirs=get_numpy_include_dirs())


andrew@...:~/project/numpy-c> cat test.py 

import numpy as np
import example as e

print(e.new_vec(5))


andrew@...:~/project/numpy-c> cat build.sh

#!/bin/bash

rm -fr build
rm -f example.so
python2 setup.py build_ext --inplace
python2 test.py


andrew@...:~/project/numpy-c> ./build.sh

running build_ext
building 'example' extension
C compiler: gcc -pthread -fno-strict-aliasing -fmessage-length=0
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
-funwind-tables -fasynchronous-unwind-tables -g -DNDEBUG -fmessage-length=0
-grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector
-funwind-tables -fasynchronous-unwind-tables -g -DOPENSSL_LOAD_CONF -fPIC

creating build
creating build/temp.linux-x86_64-2.7
compile options: '-I/usr/lib64/python2.7/site-packages/numpy/core/include
-I/usr/include/python2.7 -c'
gcc: example.c
gcc -pthread -shared build/temp.linux-x86_64-2.7/example.o -L/usr/lib64
-lpython2.7 -o /home/andrew/project/numpy-c/example.so
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