[Numpy-discussion] Advice on converting Numarray C extension?

Charles R Harris charlesr.harris@gmail....
Mon Jun 29 19:10:42 CDT 2009


On Mon, Jun 29, 2009 at 4:17 PM, Russell E. Owen <rowen@u.washington.edu>wrote:

> In article
> <e06186140906291429m3cb339e8ge298f179d811e8a7@mail.gmail.com>,
>  Charles R Harris <charlesr.harris@gmail.com> wrote:
>
> > On Mon, Jun 29, 2009 at 3:03 PM, Russell E. Owen
> > <rowen@u.washington.edu>wrote:
> >
> > > I have an old Numarray C extension (or, rather, a Python package
> > > containing a C extension) that I would like to convert to numpy
> > > (in a way that is likely to be supported long-term).
> > >
> > > Options I have found include:
> > >
> > > - Use the new numpy extension. This seems likely to be fast and
> > > future-proof. But I am finding the documentation slow going. Does
> anyone
> > > know of a simple example (e.g. read in an array, create a new array)?
> > >
> > > - Use the Numarray compatible C API. Simple (and takes advantage of the
> > > nice Numarray tutorial example for documentation), but will this be
> > > supported in the long term?
> > >
> > > - Switch to ctypes. Simple in concept. But I'm wondering if I can get
> > > distutils to build the resulting package.
> > >
> > > - Use SWIG. I have some experience with it, but not with numpy arrays.
> > >
> > > - Use Cython to replace the C code. No idea if this is a long-term
> > > supported package.
> > >
> > > Another option is to try to rewrite in pure python. Perhaps the numpy
> > > indexing is sophisticated enough to allow an efficient solution. The C
> > > extension computes a radial profile from a 2-d masked array:
> > >  radProf(r)= sum of all unmasked pixels at radius r about some
> > > specified center index
> > > I can easily generate (and cache) a 2-d array of radius index, but is
> it
> > > possible to use that to efficiently generate the desired sum?
> > >
> > > Any opinions?
> > >
> >
> > How big is the extension and what does it do?
>
> It basically contains 2 functions:
> 1: radProfile: given a masked image (2d array), a radius and a desired
> center: compute a new 1d array whose value at index r is the sum of all
> unmasked pixels at radius r.
>
> 2: radAsymm: given the same inputs as radProfile, return a (scalar)
> measure of radial asymmetry by computing the variance of unmasked pixels
> at each radius and combining the results.
>
> The original source file is about 1000 lines long, of which 1/3 to 1/2
> is the basic C code and the rest is Python wrapper.
>

It sounds small enough that you should be able to update it to the numpy
interface. What functions do you need? You should also be able to attach a
copy (zipped) if it is small enough, which might help us help you.

Chuck
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