dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Friday 13 February 2009 16:54:20 A Navaei wrote:
> 2009/2/13 Kent Andre <kent-and@xxxxxxxxx>:
> > On fr., 2009-02-13 at 15:01 +0000, A Navaei wrote:
> >> 2009/2/13 Kent Andre <kent-and@xxxxxxxxx>:
> >> > On fr., 2009-02-13 at 13:12 +0000, A Navaei wrote:
> >> >> his error in python:
> >> >>
> >> >>   File
> >> >> "/usr/lib/InsightToolkit/WrapITK/lib/itkImageToDolfinFunctionPython.p
> >> >>y", line 273, in Convert
> >> >>     return
> >> >> _itkImageToDolfinFunctionPython.itkImageToDolfinFunctionID2_Convert(*
> >> >>args) RuntimeError: *** Error: Unable to assign to function, missing
> >> >> coefficients (user-defined function).
> >> >
> >> > This is caused by the following:
> >>
> >> Yes, I've noticed this. But why doesn't this error happen when calling
> >> the sub-class from python? Why should v._vector be null when the
> >> cub-class is called from c++?
> >
> > There are some magic that goes on in the python version of Function.
> > Hake is the master of this function, so I cc him.
>
> Johan: Why the extensions in dolfin/site-packages/function.py are not
> implemented in c++ and then wrapped in python? It seems focusing some
> parts of the development in the python layer has caused some stuff to
> be missed in the c++ core. For reference I copy the previous
> communication with Kent:

I fell that I am jumping into a discussion I do not have the beginning of, but 
first of all:

The thing we do in dolfin/site-packages/function.py is to be able to 
dynamically create python function classes that inherits both cpp.Function, 
i.e., the c++ version _and_ ffc.Function. Having this in place we are now 
able to define a Function like:

  V = FunctionSpace(UnitSquare(10,10),"CG",1)
  f = Function(V,"sin(x[0])")

where f can be used both to define variational forms, and efficiently be used 
in the assemble loop, where the compiled c++ version of the function is used. 
This means that you can e.g. write

  a = assembe(f*dx)

What we are doing in dolfin/site-packages/function.py is however probably 
_not_ causing your error, as it should still be possible to use pure 
cpp.Functions or subclasses of such, in PyDOLFIN. 

To assemble a form using such function you have to instantiate a ffc.Function 
and a DolfinImageFunction, where the former is used defining the form and the 
latter is passed to

   assemble(...,coefficients=[your_dolfin_image_function])

> ----------------------------
> There are some issues with coding dolfin under c++, a code which works
> with python is difficult, if not impossible, to re-produce in c++. I
> tried sub-classing
> dolfin::Function as itk::DolfinImageFunction:
>
> http://code.google.com/p/wrapitk/source/browse/trunk/ExternalProjects/ItkDo
>lfin/src/itkDolfinImageFunction.h
>
> After wrapping in python, using wrapped itk::DolfinImageFunction works fine
> in python, but the same procedure fails when implemented in c++, as
> demonstrated here:

I am not quite sure I understand this, but are you saying that you are able 
to:

  V = FunctionSpace(UnitSquare(10,10),"Lagrange",1)
  f = DolfinImageFunction(V,someimage)

but not by calling your wrapped ImageToDolfinFunction.DolfinImageFunction()?

First I assume that you properly instantiate the templates somewhere else in 
your build script, as itkDolfin.swg does not define any such templates.

Second you should probably return a pointer to the created function in 
DolfinImageFunction(), and set 

  %newobject itk::ImageToDolfinFunction<YourImageTypes>.DolfinImageFunction;

or define a copy constructor to your DolfinImageFunction, as you are returning 
by value now.

Hope this helps!

Johan

> http://code.google.com/p/wrapitk/source/browse/trunk/ExternalProjects/ItkDo
>lfin/src/itkImageToDolfinFunction.h#56
>
> which generates this error in python:
>
>  File
> "/usr/lib/InsightToolkit/WrapITK/lib/itkImageToDolfinFunctionPython.py",
> line 273, in Convert
>    return
> _itkImageToDolfinFunctionPython.itkImageToDolfinFunctionID2_Convert(*args)
> RuntimeError: *** Error: Unable to assign to function, missing
> coefficients (user-defined function).
>
> Here is the python test generating the above error:
>
> http://code.google.com/p/wrapitk/source/browse/trunk/ExternalProjects/ItkDo
>lfin/tests/test-01.py