[Insight-users] ITK in Python

[Erik Anderson]

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
>>>>
>>>>
>>>> _______________________________________________
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>>>> Insight-users at itk.org
>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>
>>
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