dolfin team mailing list archive

[Martin Sandve Alnæs <martinal@xxxxxxxxx>]

Just a note: Images usually assume rectangular cells, dolfin currently
only supports simplices.

Martin



On Thu, Feb 19, 2009 at 1:57 PM, A Navaei <axnavaei@xxxxxxxxxxxxxx> wrote:
> 2009/2/19 Johan Hake <hake@xxxxxxxxx>:
>> The previous email was sent a bit premature...
>>
>> [snip]
>>
>>> > I have also thought of this :)
>>> >
>>> > Then you can take an ordered mesh, iterate over the vertices, and use the
>>> > present implementation of the eval function (which in its present shape
>>> > is a piecewise constant interpolator isn't it?), to fill the new _vector,
>>> > all done in the constructor. Then you have a discrete function in the
>>> > first place :)
>>>
>>> Is it possible to set the pointer to _vector data directly where we
>>> can pass the pointer to image data? If this works, no loop will be
>>> involve in data conversion and it will be super fast.
>>
>> Yes but you do not know how the mesh is ordered.
>
> Consider a 2D image data mapped on a structured grid, with size
> (number of nodes in each direction) of (sx, sy), the value of image
> brightness at coordinate (i, j) is given by I(k), where:
>
> k = i + sx * j
>
> Is this not enough information to create the mesh?
>
>>
>>> It seems _vector.set()
>>> (http://www.fenics.org/pub/documents/dolfin/dolfin-progr-reference/d6/da4/c
>>>lassdolfin_1_1GenericVector.html#bc4ecede55f2846ecadae02426df8f63) accepts
>>> the pointer to each row, is that right?
>>
>> There is no such thing as a row in a vector. It stores the data in a
>> contigouos way (if not distributed).
>
> No idea why it says rows: virtual void dolfin::GenericVector::set
> (const double *block, const uint *num_rows, const uint *const *
>        rows).
>
>>
>>> Is there a better way of assigning the whole data at once?
>>
>> Maybe but you then have to be sure that your data is arrange in exact same
>> manner as the mesh.
>
> As long as we work with complete rectangular images, which is the
> frequently used case, it should be fine. Given this, how is it
> possible to directly assign the image data pointer to _vector?
>
>>
>>> > Note that this will only work for a piecewise linear lagrange
>>> > FunctionSpace.
>>>
>>> It should be ok, it would be equivalent of having the image function
>>> initialised with Lagrange element, but much more faster.
>>>
>>> > But haveing this in place you can always interpolate to other
>>> > FunctionSpaces. However these interpolations will only be linear of
>>> > course.
>>>
>>> It is not possible to interpolate a function to another space using
>>> non-linear interpolators?
>>
>> If your raw image data is represented by a linear FunctionSpace any
>> interpolation using this space would be linear.
>
> Right, that's yet another problem.
>
>
> -Ali
>
>>
>> Johan
>>
>>> To Anders: Do you think if this is more practical and efficient than
>>> the other discussed approach? Would this be general enough to work
>>> with an arbitrary PDE of any finite element type?
>>>
>>>
>>> -Ali
>>>
>>> > Johan
>>> >
>>> >> -Ali
>>> >>
>>> >> > -Ali
>>> >> >
>>> >> >>> >> Another way of doing this could be by the use of an existing
>>> >> >>> >> FunctionSpace:
>>> >> >>> >>
>>> >> >>> >>   UnitSquare dummy_mesh(1, 1);
>>> >> >>> >>   PoissonFunctionSpace V(dummy_mesh);
>>> >> >>> >>   ImageFunction v(image, V);
>>> >> >>> >>
>>> >> >>> >> Then, in the constructor of ImageFunction, V.element and V.dofmap
>>> >> >>> >> can be used to create another FunctionSpace which has a mesh
>>> >> >>> >> created using image:
>>> >> >>> >>
>>> >> >>> >>   ImageToFunction(Image image, const FunctionSpace& V)
>>> >> >>> >>   {
>>> >> >>> >>     // Create the function space
>>> >> >>> >>     UnitSquare mesh(image.get_size()[0] - 1, image.get_size()[1]
>>> >> >>> >> - 1); FunctionSpace IV(mesh, V.element(), V.dofmap());
>>> >> >>> >>
>>> >> >>> >>     // ...
>>> >> >>> >>   };
>>> >> >>> >>
>>> >> >>> >> The problem with this approach is that it involves the use of a
>>> >> >>> >> dummy mesh.
>>> >> >>> >>
>>> >> >>> >> A mesh-independent constructor added to FunctionSpace could help.
>>> >> >>> >> Alternatively, if a (protected) default (empty) constructor is
>>> >> >>> >> added to FunctionSpace, ImageFunctionSpace:FunctionSpace can have
>>> >> >>> >> a mesh-independent constructor. However, the FFC-generated
>>> >> >>> >> function spaces, eg PoissonFunctionSpace, still need a mesh.
>>> >> >>> >>
>>> >> >>> >> Hope this makes the problem more clear now.
>>> >> >>> >
>>> >> >>> > Create the mesh and the FunctionSpace subclass inside the
>>> >> >>> > ImageFunction constructor. Neither the mesh nor the function space
>>> >> >>> > need to be visible outside.
>>> >> >>>
>>> >> >>> Again, there is no mesh-free ctor for FunctionSpace, and it doesn't
>>> >> >>> come with a default ctor so that the subclass can implement a
>>> >> >>> mesh-free ctor. I quote the above again:
>>> >> >>
>>> >> >> You don't need a mesh-free constructor for FunctionSpace, see above.
>>> >> >>
>>> >> >>> ' A mesh-independent constructor added to FunctionSpace could help.
>>> >> >>>  Alternatively, if a (protected) default (empty) constructor is
>>> >> >>> added to FunctionSpace, ImageFunctionSpace:FunctionSpace can have a
>>> >> >>> mesh-independent constructor.'
>>> >> >>
>>> >> >> It's not needed if you do as I suggest.
>>> >> >>
>>> >> >> --
>>> >> >> Anders
>>> >> >>
>>> >> >> -----BEGIN PGP SIGNATURE-----
>>> >> >> Version: GnuPG v1.4.9 (GNU/Linux)
>>> >> >>
>>> >> >> iEYEARECAAYFAkmdMN8ACgkQTuwUCDsYZdGnOQCdFBJSD4FymLnVPbheRt63aJJa
>>> >> >> yyoAn3KDuOmwd8ZX5YR1KucbafvieNBc
>>> >> >> =lpyI
>>> >> >> -----END PGP SIGNATURE-----
>>> >> >>
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>>
>>
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