dolfin team mailing list archive

[A Navaei <axnavaei@xxxxxxxxxxxxxx>]

Kent: Luca is right about the lack of wrapping for double type. I was
not aware that you were using the debian package available in ubuntu,
that binary (which has been nicely packaged) is now a bit out of date
and uses an old design of wrapitk while only the types that Luca
mentioned are wrapped. If you have access to a fast server, compiling
wrapitk is not that bad, simply turn python wrapping and double type
supporting on in the cmake gui, and you're good to go. If you turn the
cpack debian option on, it will also automatically generate a ready to
use debian package.

Luca: Your work on vmtk is interesting, does it use the available
limited support of finite-elements in itk for image registration, or
does it use fenics?


-Ali

2009/1/27  <kent-and@xxxxxxxxx>:
>
> Does this code require a particular version ? I get:
>
>  ~/tmp >python image_read.py
> [kent-and-laptop:08136] mca: base: component_find: unable to open osc
> pt2pt: file not found (ignored)
> Traceback (most recent call last):
>  File "image_read.py", line 8, in <module>
>    reader = itk.ImageFileReader[inType].New(FileName="bowling.jpg")
>  File "/usr/lib/WrapITK/Python/itkTemplate.py", line 215, in __getitem__
>    raise KeyError, 'itkTemplate : No template %s for the %s class' %
> (str(parameters), self.__name__)
> KeyError: "itkTemplate : No template [<class 'itkImage.itkImageD2'>] for
> the itk::ImageFileRead
>
>
> Kent
>
>
>>>
>>>I agree with Anders.
>>>
>>>The dof_map does of course have a very simple structure in this case,
>>> which
>>>can be written as an explicit formula. This is an advantage we usually
>>> don't
>>>have when working on unstructured meshes. Still, I think the cpu time and
>>>memory
>>>will not be dominated by the dof_map so it might be smart to wait about
>>>taking
>>>advantage of this until after profiling.
>>>
>>>Can you store the images eg as a numpy array?
>>
>> Do you want to perform the profiling with numpy as a bridge between
>> itk and dolfin? There is an external project in wrapitk called
>> PyBuffer which generates the numpy interface. You must have wrappring
>> for double type on. I don't have access to python itk binaries right
>> now, but I guess the following untested script should allow you to
>> start such profiling. This is written for 2D images and generalisation
>> to nD is trivial.
>>
>>
>> -Ali
>>
>>
>> -------------------------------
>> from dolfin import *
>> from numpy import *
>> import itk
>>
>> dim = 2
>> inType = itk.Image[itk.D, dim]
>>
>> reader = itk.ImageFileReader[inType].New(FileName="/path/to/file.bmp")
>> reader.Update()
>>
>> itk2numpy = itkPyBufferD2_New()
>> numpy_arr = itk2numpy.GetArrayFromImage( reader.GetOutput() )
>> shape = numpy_arr.shape
>>
>> mesh = UnitSquare(shape[0]-1, shape[1]-1)
>>
>> class ImageFunction(Function):
>>     def eval(self, value, x):
>>         i = int((self.A.shape[0]-1)*x[0])
>>         j = int((self.A.shape[1]-1)*x[1])
>>         print i,j
>>         value[0] = self.A[(i,j)]
>>
>> V = FunctionSpace(mesh, "CG", 1)
>> f = ImageFunction(V)
>> f.A = numpy_arr
>>
>> plot(f) # can viper plot 2d images better than this?
>> interactive()
>> --------------------------------
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>>
>
>
>