dolfin team mailing list archive

[Luca Antiga <luca.antiga@xxxxxxxxx>]

Hey Kent,
 I'm following the thread, good stuff!
I suppose you're using Paul Novotny's binaries. In that case, only the
following pixel types are explicitly instantiated by the Python wrappers
(see http://paulnovo.org/node/3)

• unsigned char
• unsigned short
• RGB unsigned short
• float
• complex float
• vector float
• covariant vector float

In your case, *I suppose* that what happens is that D2 (doubles in 2D)  
are not
available as pixel types.
This means that you'd want to use F2 as the image type, rather than D2.
In case you need doubles, either recompile ITK and WrapITK or complain
with Paul :-)
However, I admit I don't normally use WrapITK, so the suggestion might  
be bogus.

Keep up the good work. There are several potential interesting  
developments
that could stem from this work...

Luca


On Jan 27, 2009, at 9:22 AM, kent-and@xxxxxxxxx wrote:

> 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()
> > --------------------------------
> > _______________________________________________
> > DOLFIN-dev mailing list
> > DOLFIN-dev@xxxxxxxxxx
> > http://www.fenics.org/mailman/listinfo/dolfin-dev
>
>
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--
Luca Antiga, PhD
Head, Medical Imaging Unit,
Biomedical Engineering Department,
Mario Negri Institute.
mail: Villa Camozzi, 24020, Ranica (BG), Italy
phone: +39 035 4535-381
email: antiga@xxxxxxxxxxxxx
web: http://villacamozzi.marionegri.it/~luca