dolfin team mailing list archive

["Garth N. Wells" <gnw20@xxxxxxxxx>]

On Fri, 2010-08-06 at 13:37 -0700, Johan Hake wrote:
> On Friday August 6 2010 12:10:34 Anders Logg wrote:
> > On Fri, Aug 06, 2010 at 07:57:52PM +0100, Garth N. Wells wrote:
> > > On Fri, 2010-08-06 at 11:55 -0700, Johan Hake wrote:
> > > > On Friday August 6 2010 11:48:37 Anders Logg wrote:
> > > > > On Wed, Aug 04, 2010 at 05:06:57PM -0700, Johan Hake wrote:
> > > > > > On Wednesday August 4 2010 13:09:47 Riesen Patrick wrote:
> > > > > > > -----Original Message-----
> > > > > > > From: Garth N. Wells [mailto:gnw20@xxxxxxxxx]
> > > > > > > Sent: Wed 04.08.2010 19:07
> > > > > > > To: johan.hake@xxxxxxxxx
> > > > > > > Cc: Riesen  Patrick; dolfin@xxxxxxxxxxxxxxxxxxx
> > > > > > > Subject: Re: [Dolfin] python: xml read for vector / std::vector
> > > > > > > 
> > > > > > > On Wed, 2010-08-04 at 10:03 -0700, Johan Hake wrote:
> > > > > > > > On Wednesday August 4 2010 09:28:22 Patrick Riesen wrote:
> > > > > > > > > Patrick Riesen wrote:
> > > > > > > > > > Johan Hake wrote:
> > > > > > > > > >> Patrick!
> > > > > > > > > >> 
> > > > > > > > > >> On Wednesday August 4 2010 09:13:24 Patrick Riesen wrote:
> > > > > > > > > >>> hello dolfin developers
> > > > > > > > > >>> 
> > > > > > > > > >>> I write out a std::vector in XML file format from cpp.
> > > > > > > > > >>> Can I read the XML file in again in python and construct
> > > > > > > > > >>> a numpy array? I know how to do it with a dolfin Vector,
> > > > > > > > > >>> but is it possible with a std::vector<double>? I could
> > > > > > > > > >>> not figure out the syntax, i tried
> > > > > > > > > >>> 
> > > > > > > > > >>> # this is ok
> > > > > > > > > >>> fn = File("data/norm.xml")
> > > > > > > > > >>> div_vec = d.Vector()
> > > > > > > > > >>> a = n.array((11,1))
> > > > > > > > > >>> 
> > > > > > > > > >>> # fails
> > > > > > > > > >>> fn >> a
> > > > > > > > > >>> # fails
> > > > > > > > > >>> fn >> div_vec.array()
> > > > > > > > > >> 
> > > > > > > > > >> Have you tried:
> > > > > > > > > >>   fn >> div_vec
> > > > > > > > > >>   a = div_vec.array()
> > > > > > > > > > 
> > > > > > > > > > yes, that gives the error:
> > > > > > > > > > *** Error: Handler stack not empty. Something is wrong!
> > > > > > > > 
> > > > > > > > The format is then different for the Vector XML file and the
> > > > > > > > std::vector file?
> > > > > > > > 
> > > > > > > > > if i write out a dolfin::Vector in xml, it's all fine with:
> > > > > > > > > 
> > > > > > > > > fn = File("data/norm.xml")
> > > > > > > > > div_vec = d.Vector()
> > > > > > > > > fn >> div_vec
> > > > > > > > > a = div_vec.array()
> > > > > > > > > 
> > > > > > > > > but if i write out a std::vector<double> in xml, I can't read
> > > > > > > > > it in.
> > > > > > > > 
> > > > > > > > Silly question from a Python user:
> > > > > > > >   How do you write the std::vector to a XML file?
> > > > > > > 
> > > > > > > You don't ;);
> > > > > > > 
> > > > > > > DOLFIN does. It's overloaded in the XMLFile class.
> > > > > > > Well, anyway, i thought if dolfin can write out a std::vector to
> > > > > > > xml via File/XMLFile, pydolfin can also read it in, but
> > > > > > > obviously not.
> > > > > > 
> > > > > > I think you stumble across some unused code there. I am not sure
> > > > > > but I think Ola implemented this for some debugging of the
> > > > > > parallel interface. But I am not sure actually.
> > > > > > 
> > > > > > If we had a typemap for std::vector <-> numpy array (which we could
> > > > > > have, but
> > > > > > 
> > > > > > desided we did not want...) we sould be able to do:
> > > > > >   somefile >> array
> > > > > >   somefile << array
> > > > > > 
> > > > > > Where somefile will be file generated by XMLArray, which probably
> > > > > > define a different XML interfaces than XMLVector.
> > > > > 
> > > > > Input/output is implemented for the Array class so it would be
> > > > > appropriate to use that. It was implemented to handle input/output
> > > > > for parallel mesh data (stored in the data section of a mesh as
> > > > > MeshFunctions, Arrays and maps).
> > > > 
> > > > Ok
> > > > 
> > > > > Can someone remind me of why we don't have a typemap for numpy.array
> > > > > and dolfin::Array? Or what am I missing here?
> > > > 
> > > > We have that, but the XMLArray read and writes  std::vector, which
> > > > typemaps we decided to ditch.
> > > 
> > > The best solution is to use dolfin::Array in XMLArray. It will also
> > > simplify io of dolfin::Vector.
> >
> > Aha. I missed that. I suggest we support input/output for both
> > dolfin::Array and std::vector. It should be possible to implement
> > with a good deal of code reuse.
> 
> Another thing, is it anything that prevent us to harmonize the xml format of 
> an XMLArray and an XMLVector? Any potential issues during parallel? If so one 
> should be able to do what Patrick did in the first place.
> 

Do you mean the structure of the XML file or the code in XMLArray and
XMLVector?  The only real difference between XMLArray and XMLVector is a
call the GenericVector::set/set_local, so it should be possible to
harmonise the two.

I'm modifying XMLArray right now to keep track of the index. This will
allow reading elements in arbitrary orders, and it will permit reading
just chunks of a file (one process handling only a portion of a file) or
a reading a file containing only a portion of a vector.

Garth

> > Speaking of which, would it be possible to add a constructor to
> > dolfin::Array that takes a std::vector?
> > 
> >   std::vector<int> x(10);
> > 
> >   dolfin::Array<int> xx(x);
> > 
> > ?
> > 
> > I have been missing that on a few occasions.
> 
> That should be possible with copying of data of course.
> 
> Johan