dolfin team mailing list archive

[A Navaei <axnavaei@xxxxxxxxxxxxxx>]

Do you have python-itk-numpy installed?

2009/2/6 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()
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