[ITK] [ITK-users] Python wrapping issue

Wed Oct 14 12:36:05 EDT 2015

Hi,

Yes, Sami make good points.  It is important to check that

  PYTHON_EXECUTABLE
  PYTHON_INCLUDE_DIR
  PYTHON_LIBRARY

are set to consistent values in ITK's CMake build configuration.

To see what types available for different objects, which depends on
the CMake configuration, use the GetTypes() method.  For example

  import itk
  print(itk.Image.GetTypes())
  print(itk.HistogramMatchingImageFilter.GetTypes())

The HistogramMatchingImageFilter can also be called in SimpleITK:

  import SimpleITK as sitk
  result = sitk.HistogramMatching(image1, image2)
  # or, the object oriented interface
  histogramMatching = sitk.HistogramMatchingImageFilter()

Hope this helps,
Matt

On Wed, Oct 14, 2015 at 11:32 AM, Sami Koho <sami.koho at gmail.com> wrote:
> Hi Paolo,
>
> a couple of thoughts from my own experiences on various platforms. I haven’t
> had any problems with ITK on Ubuntu, when used with the standard system
> Python 2.7, so some of these might not apply:
>
> Do you happen to have several different Python distributions on your
> computer? I have seen such crashing when the ITK was built against one
> distribution and then used in another. I have also had some difficulties
> with using ITK Python wrapping on Anaconda. It might also be a compiler
> compatibility problem, ie. if the Python distribution has been compiled with
> a different compiler than ITK, but I wouldn’t expect this on Ubuntu, as
> everything is built with the same GNU compilers.
>
> Best,
>
> Sami
>
>
> On 14 Oct 2015, at 17:17, Paolo Zaffino <p.zaffino at yahoo.it> wrote:
>
> Hi Matt and hi all,
> thank you very much for your help.
> Unfortunately python crashes (segmentation fault) at the final phase of
> these three examples (basically when I try to create an image):
>
> import itk
> Dimension = 3
> PixelType = itk.F
> ImageType = itk.Image[PixelType, Dimension]
>
> import itk
> img = itk.Image.F3.New()
>
> import itk
> pixelType = itk.UC
> imageType = itk.Image[pixelType, 2]
>
> Any idea?
> Thank you very much again.
>
> Best.
> Paolo
>
>
>
> On 14/10/2015 16:48, Matt McCormick wrote:
>
> Hi Paolo,
>
> Lassi has some good suggestions. Some additional information:
>
> If you use ITK Git master [1], the Python wrapping builds in half the
> time as ITK 4.8.
>
> To create a histogram matching filter, the preferred syntax is:
>
>   import itk
>   Dimension = 3
>   PixelType = itk.F
>   ImageType = itk.Image[PixelType, Dimension]
>   histogramMatching = itk.HistogramMatchingImageFilter[ImageType,
> ImageType].New()
>
> Hope this helps,
> Matt
>
> [1] http://www.itk.org/Wiki/ITK/Git
>
> On Wed, Oct 14, 2015 at 5:27 AM, Paavolainen, Lassi
> <lassi.paavolainen at jyu.fi> wrote:
>
> Hi Paolo,
>
> Why you want to import itkImagePython instead of just itk?
>
> import itk
> img = itk.Image.F3.New()
>
> should work as previously. Notice that
> itk.HistogramMatchingImageFilter()
> would not work in any case since you need to define the types as well.
>
> The modular design of ITK 4 should not have effected the interface of ITK
> Python wrappings in anyway. If I'm wrong then maybe someone can correct me.
>
> So I would first check that you are able to import itk and load some filter.
> If not, then check that all shared libs are in search path.
>
> Cheers,
> Lassi
>
> ________________________________
> From: Insight-users [insight-users-bounces at itk.org] on behalf of Paolo
> Zaffino [p.zaffino at yahoo.it]
> Sent: Wednesday, October 14, 2015 11:51
> To: insight-users at itk.org
> Subject: [ITK-users] Python wrapping issue
>
> Dear ITK community,
> I compiled ITK 4.8 into an Ubuntu 14.04 machine enabling also the python
> wrapping.
> Compiling the code took really a while and I had to restart the make phase
> more than one time since it crashed without any apparently reason.
> Finally when the make step was over I executed the make install command.
>
> If I open ipython and I type "import itkImagePython" it returns
>
> ---------------------------------------------------------------------------
> ImportError                               Traceback (most recent call last)
> <ipython-input-1-dfd82b0a3e37> in <module>()
> ----> 1 import itkImagePython
>
> /usr/local/lib/ITK-4.8/Python/itkImagePython.py in <module>()
>      30                 fp.close()
>      31             return _mod
> ---> 32     _itkImagePython = swig_import_helper()
>      33     del swig_import_helper
>      34 else:
>
> /usr/local/lib/ITK-4.8/Python/itkImagePython.py in swig_import_helper()
>      22             fp, pathname, description =
> imp.find_module('_itkImagePython', [dirname(__file__)])
>      23         except ImportError:
> ---> 24             import _itkImagePython
>      25             return _itkImagePython
>      26         if fp is not None:
>
> ImportError: No module named _itkImagePython
>
> but if I run "import ITKRegionGrowingPython" it works.
> In addition, after importing ITKRegionGrowingPython also itkImagePython
> works!
>
> I think the path is correctly set, since I see
> /usr/local/lib/ITK-4.8/Python.
> I also noted that in the "compiledFolder/lib" I see:
>
> ITKRegionGrowingPython.py and _ITKRegionGrowingPython.so
> itkImagePython.py but NOT _itkImagePython.so
>
>
> Do you have any idea?
>
> Furthermore, is it the syntax itk.something still valid or it has been
> replaced by separate submodules?
> Because if I run
> hm=itk.HistogramMatchingImageFilter()
> I get
> UnboundLocalError: local variable 'module' referenced before assignment
>
> Thank you very much.
> Regards.
>
> Paolo
>
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