dolfin team mailing list archive

[Johan Hake <hake@xxxxxxxxx>]

On Saturday 14 February 2009 13:48:05 A Navaei wrote:
> It seems that the error can be re-produced even without sub-classing
> and using existing dolfin classes in pure c++. Based on the itk-dolfin
> interface code, the below minimal code should generate the error (note
> that I use the binary distribution which uses std::tr1, replacing it
> with boost shared pointer should not have any effect).

Not in c++ but swig only support std::tr1::shared_ptr from version 1.3.37. But 
if you intend to use shared_ptr only internally there whould not be any 
problems. 

> After wrapping in python:
>
> (1) Calling FunctionTest.CreateFunction(), which returns by value,
> results this error:
>
> RuntimeError: *** Error: Unable to assign to function, missing
> coefficients (user-defined function).

You cannot assign another user-defined function to another Function. It must 
be a discrete function, which has an initialized _vector. This is probably a 
feature that other developers should answer for. 

However this means that you cannot copy a userdefined function, with the side 
effect of not beeing able to return a user-defined Function by value.

> Since dolfin::Function does come with the required copy ctors, the
> problem cannot be stemmed from this.

This use the assignment operator which requires the Function to be a discrete 
and not a user-defined Function.

I consider this to be a bug in the library. Any other comments from the C++ 
DOLFIN developers (I am mostly dealing with the python interface)?

> (2) Calling FunctionTest.CreateFunctionPtr(), which returns the shared
> pointer, does not generate any errors. 

This should be expected, as the copy constructors is not called. When you get 
all this to work, eventually ;), I would suggest using shared_ptr types for 
the return argument, as shared_ptrs are much nicer to deal with in both c++ 
and python. But then you probably need the development version of DOLFIN. We 
do consider a release soon, which you can switch to when this is out.

The support for shared_ptr in PyDOLFIN is lately added, but has more or less 
stabilized now, I think.

> However, there are problems 
> with handling the shared pointer in python. I used this in my swig
> interface file (or in an implicit way you can include dolfin.i
> defining the right flags):
>
> #define SWIG_SHARED_PTR_NAMESPACE std // comment out if it's boost
> #define SWIG_SHARED_PTR_SUBNAMESPACE tr1 // comment out if it's boost
> %include "boost_shared_ptr.i"
> # if defined(SWIG_SHARED_PTR_QNAMESPACE)
> SWIG_SHARED_PTR(Function, dolfin::Function)
> #endif

Which version of swig do you have, refering to the comment above. You need 
swig version >= 1.3.35 to be able to use shared_ptr in the first place and >= 
1.3.37 to be able to use std::str1::shared_ptr.

> Having this, in python, FunctionTest.CreateFunctionPtr() returns a
> proxy to the shared pointer object which is not useful. Are there any
> steps missed in the wrapping process?

Strictly speaking it does _not_ return a proxy but rather a raw pointer to the 
object. The proxy is the python wrapper class that swig creates for us when 
it have the correct type knowledge, which in this case, swig does not have.

> c++ test code:
> -----------------------------
> class FunctionTest
> {
> public:
> 	typedef std::tr1::shared_ptr<const dolfin::Mesh> MeshConstPointerType;
> 	typedef std::tr1::shared_ptr<const dolfin::FiniteElement>
> ElementConstPointerType;
> 	typedef std::tr1::shared_ptr<const dolfin::DofMap> DofMapConstPointerType;
> 	typedef std::tr1::shared_ptr<const dolfin::FunctionSpace>
> FSConstPointerType; typedef std::tr1::shared_ptr<dolfin::Function>
> FPointerType;
>
> 	static dolfin::Function CreateFunction()
> 	{
> 		dolfin::Mesh mesh = dolfin::UnitSquare(100, 100);
> 		std::string elemSig("FiniteElement('Lagrange', 'triangle', 1)");
> 		std::string dofSig("FFC dof map for FiniteElement('Lagrange',
> 'triangle', 1)");
>
> 		FSConstPointerType fs(new dolfin::FunctionSpace(
> 		typename IFSType::MeshConstPointerType(&mesh,
> dolfin::NoDeleter<const dolfin::Mesh>()),
> 		typename IFSType::ElementConstPointerType(new
> dolfin::FiniteElement(elemSig)), typename
> IFSType::DofMapConstPointerType(new dolfin::DofMap(dofSig, mesh))) );
>
> 		dolfin::Function func(fs);
> 		return func;
> 	};
>
> 	static FPointerType CreateFunctionPtr()
> 	{
> 		dolfin::Mesh mesh = dolfin::UnitSquare(100, 100);
> 		std::string elemSig("FiniteElement('Lagrange', 'triangle', 1)");
> 		std::string dofSig("FFC dof map for FiniteElement('Lagrange',
> 'triangle', 1)");
>
> 		FSConstPointerType fs(new dolfin::FunctionSpace(
> 		typename IFSType::MeshConstPointerType(&mesh,
> dolfin::NoDeleter<const dolfin::Mesh>()),
> 		typename IFSType::ElementConstPointerType(new
> dolfin::FiniteElement(elemSig)), typename
> IFSType::DofMapConstPointerType(new dolfin::DofMap(dofSig, mesh))) );
>
> 		FPointerType funcp = FPointerType(new dolfin::Function(fs));
> 		return funcp;
> 	};
> };
> ----------------------------
> > Yes, I can call wrapped DolfinImageFunction in python with no problem,
> > but when using it in pure c++ (itk::ImageToDolfinFunction) an then
> > calling ImageToDolfinFunction after wrapped in python generated the
> > error:
> >
> > RuntimeError: *** Error: Unable to assign to function, missing
> > coefficients (user-defined function).

I think we sorted out this problem above: do not return by value.

> > why v._vector is not null in the first case? I also tried the shared
> > pointer ctors and ended up with the same result. Moreover, I tried
> > sub-classing FunctionSpace (see
> > http://code.google.com/p/wrapitk/source/browse/trunk/ExternalProjects/Itk
> >Dolfin/src/itkDolfinImageFunctionSpace.h), with and without shared pointer
> > ctors, again the same error.
> >
> >> First I assume that you properly instantiate the templates somewhere
> >> else in your build script, as itkDolfin.swg does not define any such
> >> templates.
> >
> > That's correct, wrapitk instantiates the templates automatically.

Ok. Is this done in some of the SMake macros? I am really not familiar to 
CMake

> >> 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.
> >
> > I've tried a simple copy ctor like this:
> >
> >        DolfinImageFunction(const DolfinImageFunction &v)
> >        {
> >                 *this = v;
> >        }
> >
> > which does get called, but didn't help.

Again, bug in copy constructor. You should be able to return a raw pointer to 
the function, but make sure you use the %newobject directive mentioned above, 
to till swig that it should take ownership to the returned object.

> > Just to mention that one problem with c++ dolfin classes is that their
> > member variables are mostly private, causing restrictions on the
> > sub-classes. 

This should others answer.

> > Is there a specific reason for having private variables 
> > instead of protected? For instance, DolfinImageFunction ctors are not
> > able to initialise _function_space or _vector.

This should not be any problems in the ordinary constructor as you can just 
pass the function_space to the super constructor, and a properly working copy 
constructor should also fix this for any derived copy constructors. 

The _vector is created by calling init(). But you do not want to do this as 
the Function will then change status from a user-defined to a discrete 
function, making it impossible to reach the eval function. 

Again hope this helps.

Johan