[SciPy-user] C extension to manipulate sparse lil matrix

[Andy Fraser]

>>>>> "A" == Andy Fraser <afraser at lanl.gov> writes:

    A> I want to move some time critical bits of code for hidden
    A> Markov models from python to C.  [...]

    A> Now, I am trying to figure out how to manipulate lil sparse
    A> matrices.  In particular calling such a matrix "SM", and
    A> supposing that "t" is the index for a row, I want to assign new
    A> arrays to "SM.rows[t]" and "SM.data[t]".

    A> I would be grateful if someone posted C code that interchanged
    A> two rows of a lil sparse matrix.  [...]

I've answered my own question.  I append the code below.  I found that
lil matrices consist of numpy arrays of python lists.  I also found
that I could replace the python lists with numpy arrays.  Here are
some resources that helped:

   http://www.tramy.us/ Oliphant's "Guide to Numpy"
   http://docs.python.org/extending/
   http://docs.python.org/c-api/memory.html
   http://www.scipy.org/Cookbook/C_Extensions/NumPy_arrays
   http://docs.python.org/c-api/arg.html#arg-parsing

Here is code that swaps "rows":

static PyObject *
hmm_test1(PyObject *self, PyObject *args)
/* Python equivalent of:
def test1(A_O # An array of objects like the "rows" of a sparse lil matrix
          ):
    temp = A_O[0]
    A_O[0] = A_O[1]
    A_O[1] = temp
    return
*/
{
  PyObject **object0, **object1, *temp;
  PyArrayObject *A_O;
  if (!PyArg_ParseTuple(args, "O&",
                        PyArray_Converter, &A_O
                        ))
    return NULL;
  object0 = PyArray_GETPTR1(A_O, 0);
  object1 = PyArray_GETPTR1(A_O, 1);
  temp = *object0;
  *object0 = *object1;
  *object1 = temp;
  return Py_BuildValue(""); /* return None */
}