[Insight-users] ITK in Python

[Zachary Pincus]

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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