[Insight-users] ITK in Python

Gaëtan Lehmann gaetan.lehmann at jouy.inra.fr
Sat Sep 30 11:42:59 EDT 2006 

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
>>>>>>>
>>>>>>
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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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