dolfin team mailing list archive

[Johan Hake <johan.hake@xxxxxxxxx>]

On Wednesday 10 March 2010 05:39:21 Chris Richardson wrote:
> New question #103867 on DOLFIN:
> https://answers.launchpad.net/dolfin/+question/103867
> 
> I have a mesh generator, written in C++, which I have now linked with
>  dolfin, using the MeshEditor class to construct a mesh. This works, but I
>  would like to be able to use it from python. 

Cool! Do you link your generator to any particular 
triangulation/tetrahedarlization library? I have written one TriTetMesh which 
wrap Triangle and Tetgen. It is a bit sharp in the edges, but perfectly usable 
both from C++ and Python. Have a look at:

   <https://launchpad.net/tritetmesh>

You should also be able to get some clues of how you can do the linking to 
PyDOLFIN using TriTetMesh, as I also use SWIG. I do not return a mesh during 
runtime, I just saves it to file. It spare me for some nasty SWIG related 
stuff, which I eventually could fix.

>  I have tried to use SWIG to
>  create a module, but I don't know how to tell it that my new class
>  inherits Mesh.

You need to %import the types. PyDOLFIN comes with some handy SWIG import 
files, if you just want to import the types related to Mesh. You should for 
example be able to put:

  %include "dolfin/swig/import/mesh.i"

before your SWIG declarations.

This file %import's  all the types from the dolfin/mesh kernel modules, which 
is probably what you want. 

If you want to return a mesh at runtime you might experience some nasty 
surprises as Mesh is a shared_ptr stored type in PyDOLFIN. This means you need 
to explicitly tell SWIG this. Please ask for more help if you want to do this.

We also have a JIT compiler of DOLFIN code in PyDOLFIN, which (should) 
automagicaly take care of the shared_ptr declarations.

  compile_extension_module(code, module_name="",
                           recompile=False,
                           dolfin_module_import=None,
                           additional_declarations="",
                           additional_system_headers=None,
                           use_numpy_typemaps=True)

This function is unfortunately wrapped by a Python decorator (due to some 
parallel fixes), so the interactive documentation is None. 

Here comes a summary:
  code is a 'str' with your C++ code.
  module_name is an optional name for your module, 
  dolfin_module_import is a list of 'str' with name of the kernel module, 
      in you case 'mesh', 
  the other arguments can be used to fine tune typemaps.

Take a look in

   site-packages/dolfin/compile_modules/__init__.py

where the function is defined and in 

  site-packages/dolfin/compile_modules/{subdomains.py, expression.py}

where the function is used.

The answer might be more than you asked for, but I would really like to have 
users of the compile_extension_module function ;)

Best regards,

Johan

> Here is a summary of my code... but maybe there is a better way to do this?
> 
> Chris
> 
> mymesh.i
> ========
> 
>  %module mymesh
>  %{
>  /* Put header files here or function declarations like below */
> #include "mymesh.h"
>  %}

Put %import/%include statement here.

> /* mymesh.h */
> namespace dolfin{
> 
>   class Mymesh : public Mesh
>   {
>   public:
>     Mymesh();
>   };
> }
> 
> mymesh.cpp
> ==========
> 
> #include "mymesh.h"
> 
> #include <dolfin/mesh/MeshPartitioning.h>
> #include <dolfin/mesh/MeshEditor.h>
> #include <dolfin.h>
> 
> using namespace dolfin;
> .....
> Mymesh::Mymesh() {
>  Mesheditor editor;
> ....
> }
> 
> 
> # swig -c++ -python mymesh.i
> mymesh.i:11: Warning(401): Nothing known about base class 'Mesh'. Ignored.
>