[SciPy-user] Sparse matrices and weave.inline, f2py or Pyrex

William Hunter willemjagter at gmail.com
Tue Aug 15 03:09:12 CDT 2006

OK, so that's it then. I'll give hacking lil_matrix.__setitem__ a
shot, although it would be my first attempt at hacking. I suppose
looking at the matrix.__setitem__ method is a good starting point, if
there is such an <object.method>?

Has there ever been an attempt at using dictionaries to work with
sparse matrices? I'm exposing my obvious novice status here, but it
seems possible if I look at the two intro texts on Python I have. One
would have to make use of an iterative method like Jacobi or SOR.

Robert Cimrman ones mentioned he'd like to see Tim Davies' CSparse
wrapped. Me too. He mentioned using ctypes. Would that require less
work than, say SWIG.


On 13/08/06, Ed Schofield <schofield at ftw.at> wrote:
> > On 11/08/06, David Grant <davidgrant at gmail.com> wrote:
> >>
> >>
> >> On 8/11/06, William Hunter <willemjagter at gmail.com> wrote:
> >> > List;
> >> >
> >> > Has anyone ever attempted using sparse matrices in combination with
> >> > either one of the following; weave.inline, f2py or Pyrex?
> >> >
> >> > What is the best option? Perhaps a case of personal preference?
> >> >
> >> > Reason I'm asking: I've gotten the solving part of my code to run
> >> > satisfactorily, but building them with Python's for loops takes
> >> a heck
> >> > of a long time, too long.
> >>
> >> Have you tried using vector indexing with numpy first? See if you
> >> can remove
> >> some of those python for loops.
> >>
> On 12/08/2006, at 1:50 PM, William Hunter wrote:
> > Yes, well, my best attempt at it. You'll notice that the sparse
> > matrices doesn't support fancy indexing, unfortunately. (I'm hoping
> > someone can prove me wrong :-)
> >
> > Here's some code you can fiddle with (also attached -
> > sparsefiddle.py), if you want.
> >
> > [code snipped]
> >
> Yeah, sparse fancy indexing is still only partially supported. I
> don't think it'll ever be possible to make sparse support all of
> NumPy's indexing tricks. But I'd like to fill out the sparse indexing
> code so that more NumPy-like indexing operations are supported; this
> would at least improve usability. We could also definitely improve
> performance by a constant factor by taking the loops inside the
> methods such as __setitem__. You could try hacking the
> lil_matrix.__setitem__ method to accept index sequences of the form
> returned by ix_ to avoid all the extra method calls. (And I'd be
> happy to accept a patch!)
> It might be possible to speed up your code somewhat by doing the
> loops in a compiled language, but I expect this would be a complex
> endeavour and the gains would be small. To get speed gains of orders
> of magnitude you'd need to think about the optimal sparse data type
> and find an algorithm that's suitable for your matrix structure. I
> think constructing sparse matrices efficiently is inherently a tricky
> business ...
> -- Ed
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