dolfin team mailing list archive

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

Johan Hake wrote:
> On Monday 16 November 2009 22:03:13 DOLFIN wrote:
> > One or more new changesets pushed to the primary dolfin repository.
> > A short summary of the last three changesets is included below.
> >
> > changeset:   7459:739b7539d6eb
> > tag:         tip
> > user:        "Garth N. Wells <gnw20@xxxxxxxxx>"
> > date:        Mon Nov 16 21:02:54 2009 +0000
> > files:       dolfin/swig/numpy_typemaps.i dolfin/swig/std_vector_typemaps.i
> >  site-packages/dolfin/expression.py description:
> > Get typemap(in) for std::vector working.
> >
> > Seems to work but I don't know if it's any good.
>
> (Resending the email as I forgot to send it using the correct email adress...)
>
> I haven't got the time to look at it, but yes the provided typemaps do make a 
> copy, which is not optimal. I have have actually been a bit worried ;) that 
> you might change the interface of eval, and possible other methods too, from 
> double* to std::vector. In most perspectives it is much nicer to pass a 
> std::vector, not least for safety. However std::vector is more difficult to 
> interact with NumPy.

double* is easier, but my impression is that it's not particularly safe.

> SWIG do provide it's own implementation of std::vector which more or less wrap 
> the c++ interface of a vector seamless. We have used this to pass arguments of 
> std:vector previously. However the amount of code that is produced and not 
> used is large (~1MB for DOLFIN version < 9.2). NumPy arrays and lists are also 
> much more convenient structures to work with in Python. 

Does the SWIG implementation of std::vector involve copying? I expect 
that it does because I don't see how one can create a 
std::vector<double> from a list since that would require creating a 
std::vector that points to someone else's (the list's) data. It would 
break the std::vector design.

I see how it could work if one creates a DoubleVector rather than a 
list, but that's ugly.

> I have therefore decided to remove the dependency of std_vector.i by adding 
> our own typemaps for std::vector arguments. Each one of those typemaps do make 
> a copy. For now we have typmaps for primitives and pointers so each copy 
> should not be that bad. But for operations that is performed alot of times, it 
> might be a difference. But I doubt it would for the callback functionality, as 
> I assume just calling the python function would take most of the time.

Agree.

> We could consider creating a NumPy array from the pointer to the first element 
> of the vector, as I have seen you have discussed on the list previously, for 
> other cases. We then have to consider the life time of the vector. 

We need a std::vector that stores a shared_ptr to its data ;).

> For 
> director typemaps that would probably be ok. For other "out" typemaps it might 
> not be ok.

I would be inclined to make a copy. It's safe and we can document it so 
if one sends a NumPy array into a function that takes a 
std::vector<double>&, and that function stores a reference to the 
object, then it 's not the original NumPy array (confusing???).


Do we presently copy data between NumPy arrays and the sub-classes of 
GenericVector?

> Would it be an option to add, in C++, a small template wrapper class for 
> arrays that are supposed to go back and forth to Python via NumPy arrays? 

Maybe. I see that this is what Hans Petter does in a chapter of one of 
his books. Still, there are issues with ownership.

I guess in the end that memory management + pointers is always going to 
be tough in a mixed-language environment.

Garth

> Including basic operations so it will be useful also in C++.
>
> Johan
>
> > changeset:   7458:f9d6aeab7271
> > user:        "Garth N. Wells <gnw20@xxxxxxxxx>"
> > date:        Mon Nov 16 19:06:12 2009 +0000
> > files:       demo/function/eval/python/demo.py
> >  site-packages/dolfin/expression.py description:
> > Comment out some dim checks in expression.py.
> >
> >
> > changeset:   7457:6dc505f97225
> > user:        "Garth N. Wells <gnw20@xxxxxxxxx>"
> > date:        Mon Nov 16 15:13:08 2009 +0000
> > files:       demo/function/eval/python/demo.py dolfin/swig/docstrings.i
> >  dolfin/swig/function_post.i dolfin/swig/function_pre.i
> >  dolfin/swig/std_vector_typemaps.i description:
> > Add empty typemap for NumPy array to std::vector<double>.
> >
> > ----------------------------------------------------------------------
> > For more details, visit http://www.fenics.org/hg/dolfin
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