[ITK] [ITK-users] Python wrapping issue

Sami Koho sami.koho at gmail.com
Wed Oct 14 11:32:39 EDT 2015 

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 <http://www.itk.org/Wiki/ITK/Git>
>> 
>> On Wed, Oct 14, 2015 at 5:27 AM, Paavolainen, Lassi
>> <lassi.paavolainen at jyu.fi> <mailto: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 <mailto:insight-users-bounces at itk.org>] on behalf of Paolo
>>> Zaffino [p.zaffino at yahoo.it <mailto:p.zaffino at yahoo.it>]
>>> Sent: Wednesday, October 14, 2015 11:51
>>> To: insight-users at itk.org <mailto: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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> 
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