[Insight-users] ITK in Python
Erik Anderson
eranders at sci.utah.edu
Fri Sep 29 18:51:36 EDT 2006
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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