dolfin team mailing list archive

[Kent Andre <kent-and@xxxxxxxxx>]

Great, but I get the following problem: 



Traceback (most recent call last):
  File "itk-dolfin.py", line 16, in <module>
    itk2numpy = itk.PyBuffer[inType]
  File "/usr/lib/InsightToolkit/WrapITK/Python/itkLazy.py", line 14, in
__getattribute__
    value = types.ModuleType.__getattribute__(self, attr)
AttributeError: 'LazyITKModule' object has no attribute 'PyBuffer'

On to., 2009-02-05 at 19:18 +0000, A Navaei wrote:
> >
> > Let me know when you have created debian packages. It seems I have to
> > rebuild everything, even cmake. Compilation is in principle no problem,
> > but I already compile a decent number of packages on a regular basis and
> > being non-bleeding edge on packages I don't know well seems tempting.
> >
> > I might download and compile, but not today.
> >
> > Kent
> >
> >
> 
> python-itk debian, based on the new WrapITK, is just published:
> http://code.google.com/p/wrapitk/wiki/WrapITKBinaries .The 32 bit
> version is ready, the 64 bit version is being built on opensuse build
> service and will be available in a few hours.
> 
> I have tried the [itk]->[numpy]->[dolfin] example, and it already
> looks great, here is the output:
> 
> Checking mesh ordering (finished).
> 211 * 212 = 44732 pixels took 246.780 ms transfering from itk to
> dolfin through numpy
> That is 5.516854 us per pixel.
> 
> I am going to add the itk-dolfin interface in c++ in the next few
> days, which should make the conversion even faster leading to more
> reasonable performance for 3D data. Below is an updated version of the
> example. Let me know if there are any problems.
> 
> 
> -Ali
> 
> ----------------------------------------------------------
> # [itk]->[numpy]->[dolfin] test
> 
> from dolfin import *
> from numpy import *
> import itk
> import time
> 
> dim = 2
> inType = itk.Image[itk.D, dim]
> 
> reader = itk.ImageFileReader[inType].New(FileName="/path/to/file.bmp")
> reader.Update()
> 
> t1 = time.time()
> 
> itk2numpy = itk.PyBuffer[inType]
> 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
> 
> t2 = time.time()
> print '%i * %i = %i pixels took %0.3f ms transfering from itk to
> dolfin through numpy'% (shape[0], shape[1], shape[0]*shape[1],
> (t2-t1)*1e3)
> print 'That is %f us per pixel.'% ((t2-t1) * 1e6 / (shape[0]*shape[1]))
> 
> plot(f) # can viper plot 2d images better than this?
> interactive()