How do I use scipy.weave.inline together with external C libraries?

Question

I am trying to understand weave.inline to wrap C code in my Python programs. The code below simply takes the Numpy array and multiplicates all of its elements by 2.

inl.py

import numpy
import scipy.weave

a = numpy.array([1.0, 2.0, 3.0])
N = a.shape[0]

print a
code = \
  """
  int i;
  for(i = 0; i < N; i++)
  {
    a[i] = a[i] * 2;
  }
  """

scipy.weave.inline(code, ['a','N'])
print a

Then I want to carry some functions from inline code to external libraries. Let it be the trivial multiplication by 2. So I create two files:

mult.c

#include "mult.h"

float mult(float n)
{
  return n * 2;
}

mult.h

float inc(float n);

Now I want to use function mult in my inline code. But I don't know how do I link my C files with Python inline code. I tried to compile C files as shared library and pass them as headers and libraries in weave, but that was in vain. Any suggestions?

Answer 1

I have successfully done this, calling math functions from R via weave.inline() code (under Ubuntu Linux).

First, compile your C functions as a shared library. In my case, I grabbed a recent release of R from CRAN, and did

./configure --enable-R-static-lib --enable-static --with-readline=no
cd src/nmath/standalone/
make

You should now have a file called libRmath.so . If libpath is a string with the directory that holds libRmath.so , you can do something like

code = 'return_val = pbinom(100, 20000, 100./20000., 0, 1);'
support_code = 'extern "C" double pbinom(double x, double n, double p, int lower_tail, int log_p);'
weave.inline(code, support_code=support_code,
    library_dirs=[libpath], libraries=["Rmath"], runtime_library_dirs=[libpath])

Note a couple things. The header declarations have to go in support_code , not code (I don't know why), and they have to be prefixed with extern "C" because they're C code, not C++ (this is standard). It should be possible to include headers files instead of using support_code (check the docs for weave.inline), but I haven't tried it. The library name is Rmath , but the shared library file is libRmath.so , in the usual Unix convention. And the path to the library is specified twice, once for linking, and once for execution.

Hope this helps!

Answer 2

put the source of mult.c and mult.h in a string object called extra_code, then add the following line in your .weave invocation

support_code=extra_code,

there is also the option to include standard libraries as follows:

headers = ["<math.h>"]

enjoy