[Insight-users] ITK in Python

Zachary Pincus zpincus at stanford.edu
Sat Sep 30 14:44:41 EDT 2006 

OK, there's now a "README-MACOSX" file in WrapITK that documents this.

Zach

On Sep 30, 2006, at 8:42 AM, Gaëtan Lehmann wrote:

>
> Hi,
>
> Le Sat, 30 Sep 2006 07:45:55 +0200, Zachary Pincus  
> <zpincus at stanford.edu> a écrit:
>
>> Oh dear, this reminds me that I really need to make a README file  
>> for WrapITK and Mac OS X. I've been terribly behind with all of  
>> this due to the minor problem of having to write my thesis right now!
>>
>> The situation is that there is a bug (sort of) in Python 2.4 and  
>> below that makes it not interact with the dynamic loader properly  
>> on OS X, which only manifests when you start passing objects  
>> between different libraries, and then casting them to different  
>> types. And even then, only when a recent version of GCC is in use.  
>> Apparently, WrapITK is the first thing that pressed all of these  
>> buttons at the same time.
>>
>> The short story is that for WrapITK to work correctly on macs,  
>> you'll need to get Python 2.5 (or custom-build a patched 2.4 with  
>> patches that I can point you to). Also, I think (Gaëtan, can you  
>> chime in here?) that you'll have to build WrapITK with the - 
>> fpermissive CPPFLAG to deal with some errors that would otherwise  
>> arise thanks to some low-level changes in Python2.5 that cableswig  
>> isn't caught up on.
>
> Python 2.5 is out - just install it, and set CMAKE_CXX_FLAGS to - 
> fpermissive in cmake.
> You will also have to give the right path for python (python 2.5 is  
> not managed properly by the stable cmake)
>
> On my macbook, I have:
>
>  CMAKE_CXX_FLAGS                  -fpermissive
>  PYTHON_DEBUG_LIBRARY             -framework Python
>  PYTHON_EXECUTABLE                /Library/Frameworks/ 
> Python.framework/Versions/Current/bin/python
>  PYTHON_INCLUDE_PATH              /Library/Frameworks/ 
> Python.framework/Versions/Current/include/python2.5
>  PYTHON_LIBRARY                   -framework Python
>
>>
>> I am tremendously sorry that WrapITK is such a pain on the Mac --  
>> after all, it's what I develop on... please let me know if I can  
>> help in any other way.
>
> nothing really difficult :-)
> It just lack some documentation
>
> Gaetan
>
>>
>> Zach
>>
>>
>>
>>
>> On Sep 29, 2006, at 3:51 PM, Erik Anderson wrote:
>>
>>> Zach,     I got everything working finally (on Suse 10.1) but a  
>>> colleague of mine sent me the following error when she tried to  
>>> run the exact same thing on a Mac:
>>>
>>> RuntimeError: /Users/emanuele/code/Insight/Code/Common/ 
>>> itkImageBase.txx:252:
>>> itk::ERROR: Image(0x271717b0): itk::ImageBase::CopyInformation()  
>>> cannot cast PKN3itk10DataObjectE to PKN3itk9ImageBaseILj2EEE
>>>
>>> I did a little digging and saw the following post by you a couple  
>>> years ago:
>>>
>>> http://public.kitware.com/pipermail/insight-users/2005-July/ 
>>> 014144.html
>>>
>>> However, I can't find a solution to this.  Do you remember how  
>>> this was resolved?
>>>
>>> Thanks a lot,
>>> Erik
>>>
>>> Zachary Pincus wrote:
>>>> Strange that it took so long to get everything working properly  
>>>> together! I'm glad it's working now.
>>>>
>>>> Unfortunately, as to getting the input and output types there's  
>>>> no simple way that I know of. (Perhaps others have some  
>>>> suggestions?) I'm not sure how the vtk wrappers are set up and  
>>>> the docstrings created -- maybe we could look into that for  
>>>> WrapITK.
>>>>
>>>> Options you might pursue could include:
>>>> (1) Doing something with doxygen-generated information. Doxygen  
>>>> can, I think, spit out east-to-parse descriptions of public  
>>>> class methods. There are hooks in WrapITK to link up doxygen  
>>>> files with the corresponding WrapITK classes.
>>>>
>>>> (2) Parsing through the gcc-xml output that is an intermediate  
>>>> step in the wrapping. There are python libraries for reading gcc- 
>>>> xml output, and this should contain all of the information about  
>>>> the signatures of all of the wrapped methods. This is probably  
>>>> the most direct method, especially since the xml files are  
>>>> already there in your build tree.
>>>>
>>>> Zach
>>>>
>>>>
>>>> On Sep 25, 2006, at 4:14 PM, Erik Anderson wrote:
>>>>
>>>>> Zach,
>>>>>    I have gotten to the point where itk is working in Python  
>>>>> (after 2 more rebuilds and a fresh checkout from CVS) but I am  
>>>>> running into another problem that may or may not be able to be  
>>>>> solved.
>>>>>
>>>>>    As I mentioned earlier, I'm trying to get at a full  
>>>>> description of a class.  Currently, I'm able to extract a  
>>>>> proper class hierarchy, but in order to finish everything, I  
>>>>> need to get a prototype for the class' methods.  Really, I just  
>>>>> need a way to get the input and output types for a given class  
>>>>> in ITK.  Is this possible using any sort of wrapping  
>>>>> mechanism?  I know in VTK this can be done via  
>>>>> vtk.SomeClass.SomeMethod.__doc__
>>>>>
>>>>> Thanks again,
>>>>> Erik
>>>>>
>>>>> Zachary Pincus wrote:
>>>>>> Oh no, I think we're a step backwards.
>>>>>>
>>>>>> It looks like now WrapITK can't find any of the configuration  
>>>>>> information, and happily loads nothing at all into the itk  
>>>>>> module when imported.
>>>>>>
>>>>>> Please send the contents of
>>>>>> /usr/local/itk/Wrapping/WrapITK/Python/itkConfig.py
>>>>>> so that we can have a look at it and see where the problem is.
>>>>>>
>>>>>> As to your end goal, I think that the itk loading machinery  
>>>>>> (which I mentioned earlier) already does most of what you  
>>>>>> need. You'll want to look over itk.py, itkBase.py and  
>>>>>> itkConfig.py, but basically what happens is that itkBase.py  
>>>>>> loads all of the configuration files in
>>>>>> /usr/local/itk/Wrapping/WrapITK/Python/Configuration
>>>>>> (and potentially elsewhere). These files describe all of the  
>>>>>> classes in each module, along with the module dependencies, so  
>>>>>> that we can load them in a sane manner.
>>>>>>
>>>>>> This information is stored in itkBase.module_data, which is a  
>>>>>> dict. The keys are module names, and the values are dicts with  
>>>>>> two keys: 'depends' (a list of modules that need to be loaded  
>>>>>> before that module), and 'templates' which is a tuple.
>>>>>> Each element of 'templates' is itself a tuple containing  
>>>>>> either three or four elements.
>>>>>>
>>>>>> If four, then that element describes a particular template  
>>>>>> instantiation of a class:
>>>>>>  (pyClassName, cppClassName, swigClassName, templateParams)
>>>>>> where 'pyClassName' is the python-friendly name of the class  
>>>>>> (no enclosing namespace or template params), 'cppClassName' is  
>>>>>> the fully-qualified name (again less the template params),  
>>>>>> swigClassName is the name of the exact template instantiation  
>>>>>> that SWIG generated, and templateParams is the c++ template  
>>>>>> parameters. This information lets us store all template  
>>>>>> instances together in a python dict so you can say:
>>>>>> Image[US, 2]
>>>>>> as a shortcut for
>>>>>> itkImageUS2
>>>>>> which is the SWIG name for
>>>>>> 'itk::Image<unsigned char, 2>'
>>>>>>
>>>>>> If three, then that element describes a non-template  
>>>>>> instantiation:
>>>>>> (pyClassName, cppClassName, swigClassName)
>>>>>> as above.
>>>>>>
>>>>>> So you could grab the module_data dict from itkBase and churn  
>>>>>> through that to get all the information you need. But first  
>>>>>> you'll need to get the loading working right! So, let's see  
>>>>>> what's in itkConfig.py and whether that reflects what's going  
>>>>>> on in your filesystem.
>>>>>>
>>>>>> Zach
>>>>>>
>>>>>>
>>>>>>
>>>>>> On Sep 25, 2006, at 1:05 PM, Erik Anderson wrote:
>>>>>>
>>>>>>> Zach,
>>>>>>>    Thanks for the quick reply.  I rebuilt everything and now,  
>>>>>>> when I perform the following commands:
>>>>>>> import itk
>>>>>>> dir(itk)
>>>>>>>
>>>>>>> I get something totally different than just a list of the  
>>>>>>> classes I expect.  Instead, I now get the following:
>>>>>>>
>>>>>>> >>> dir(itk)
>>>>>>> ['B', 'D', 'F', 'LD', 'PyCommand', 'PyImageFilter', 'SC',  
>>>>>>> 'SI', 'SL', 'SS', 'SmartPointer', 'UC', 'UI', 'UL', 'US',  
>>>>>>> '_LazyITKModule__lazy_attributes', '__doc__', '__name__',  
>>>>>>> 'auto_progress', 'class_', 'clrLine', 'ctype', 'echo',  
>>>>>>> 'force_load', 'image', 'index', 'physical_size', 'pipeline',  
>>>>>>> 'range', 'show', 'show2D', 'simple_import_callback',  
>>>>>>> 'simple_progress_callback', 'size', 'spacing', 'strel',  
>>>>>>> 'template', 'terminal_import_callback',  
>>>>>>> 'terminal_progress_callback', 'write']
>>>>>>>
>>>>>>> Is this what I should be expecting?  I tried to instantiate a  
>>>>>>> filter (itk.AcosImageFilter) and get the LazyITKModule object  
>>>>>>> has no attribute 'AcosImageFilter'  I guess my real question  
>>>>>>> is, did I just take a step forward or a step backwards?  The  
>>>>>>> end goal here is to be able to capture a list or dictionary  
>>>>>>> of itk modules and the callable functions on those modules.
>>>>>>>
>>>>>>> Thanks a lot,
>>>>>>> Erik
>>>>>>>
>>>>>>> Zachary Pincus wrote:
>>>>>>>> So the general deal here is that the WrapITK Python libs  
>>>>>>>> have tricky dependencies, and are slow to load fully. So  
>>>>>>>> 'import itk' just gives you a bunch of proxy objects, that  
>>>>>>>> when you try to use them, call some code (which can be a bit  
>>>>>>>> brittle, as you've seen), to load the actual ITK libraries  
>>>>>>>> that are needed.
>>>>>>>>
>>>>>>>> It would appear that somehow, this loading is getting  
>>>>>>>> confused about where to find the files it needs to load.  
>>>>>>>> This information should be in (on your system)
>>>>>>>> /usr/local/itk/Wrapping/WrapITK/Python/itkConfig.py
>>>>>>>>  Could you send the contents of this file?
>>>>>>>>
>>>>>>>> In general, the python files you need would be in:
>>>>>>>> /usr/local/itk/Wrapping/WrapITK/lib
>>>>>>>> (I think...). Do you have a file VXLNumericsPython.py in  
>>>>>>>> that directory?
>>>>>>>>
>>>>>>>> Zach
>>>>>>>>
>>>>>>>>
>>>>>>>> On Sep 25, 2006, at 11:55 AM, Erik Anderson wrote:
>>>>>>>>
>>>>>>>>> Hi all,
>>>>>>>>>    I have successfully built ITK and WrapITK with (I think)  
>>>>>>>>> the proper CMake options set.  In a Python shell, I am able  
>>>>>>>>> to successfully import itk via
>>>>>>>>>
>>>>>>>>> import itk
>>>>>>>>>
>>>>>>>>> using dir on the module gives me a list of all the  
>>>>>>>>> wrappings I would expect, however, upon instantiation of a  
>>>>>>>>> class I get the following type of error:
>>>>>>>>>
>>>>>>>>> >>> f = itk.AcosImageFilter
>>>>>>>>> Traceback (most recent call last):
>>>>>>>>>  File "<stdin>", line 1, in ?
>>>>>>>>>  File "/scratch/eranders/env/itk/Wrapping/WrapITK/Python/ 
>>>>>>>>> itkLazy.py", line 18, in __getattribute__
>>>>>>>>>    itkBase.LoadModule(module, namespace)
>>>>>>>>>  File "/scratch/eranders/env/itk/Wrapping/WrapITK/Python/ 
>>>>>>>>> itkBase.py", line 77, in LoadModule
>>>>>>>>>    LoadModule(dep, namespace)
>>>>>>>>>  File "/scratch/eranders/env/itk/Wrapping/WrapITK/Python/ 
>>>>>>>>> itkBase.py", line 77, in LoadModule
>>>>>>>>>    LoadModule(dep, namespace)
>>>>>>>>>  File "/scratch/eranders/env/itk/Wrapping/WrapITK/Python/ 
>>>>>>>>> itkBase.py", line 85, in LoadModule
>>>>>>>>>    if not swigModuleName in sys.modules: module =  
>>>>>>>>> loader.load(swigModuleName)
>>>>>>>>>  File "/scratch/eranders/env/itk/Wrapping/WrapITK/Python/ 
>>>>>>>>> itkBase.py", line 191, in load
>>>>>>>>>    fp, pathname, description = imp.find_module(name)
>>>>>>>>> ImportError: No module named VXLNumericsPython
>>>>>>>>>
>>>>>>>>> My environment is as follows:
>>>>>>>>>
>>>>>>>>> Python 2.4 on Suse 10.1
>>>>>>>>> itk 2.8 built from CVS with WrapITK
>>>>>>>>>
>>>>>>>>> Environment variables set:
>>>>>>>>> LD_LIBRARY_PATH = /usr/local/itk/bin
>>>>>>>>> PYTHONPATH=/usr/local/itk/Wrapping/WrapITK/Python
>>>>>>>>>
>>>>>>>>> Any help would be great.
>>>>>>>>>
>>>>>>>>> Thansk,
>>>>>>>>> Erik Anderson
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Insight-users mailing list
>>>>>>>>> Insight-users at itk.org
>>>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Insight-users mailing list
>>>>>>> Insight-users at itk.org
>>>>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>>>>
>>>>>
>>>>
>>>
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>>
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>
>
>
> -- 
> Gaëtan Lehmann
> Biologie du Développement et de la Reproduction
> INRA de Jouy-en-Josas (France)
> tel: +33 1 34 65 29 66    fax: 01 34 65 29 09
> http://voxel.jouy.inra.fr

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