dolfin team mailing list archive

[A Navaei <axnavaei@xxxxxxxxxxxxxx>]

2009/2/19 Martin Sandve Alnæs <martinal@xxxxxxxxx>:
> Just a note: Images usually assume rectangular cells, dolfin currently
> only supports simplices.

Since a rectangular simplicial mesh and triangulated simplicial mesh
share the nodes, it shouldn't be a problem. There is no link present
in image data structure, only nodes.


-Ali

>
> 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-----
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>>>> >> >>
>>>> >> >> iEYEARECAAYFAkmdMN8ACgkQTuwUCDsYZdGnOQCdFBJSD4FymLnVPbheRt63aJJa
>>>> >> >> yyoAn3KDuOmwd8ZX5YR1KucbafvieNBc
>>>> >> >> =lpyI
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>>>> >> >>
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>>>
>>>
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