[Insight-users] Problem with wrapping itk with python 2.3

Gaëtan Lehmann gaetan.lehmann at jouy.inra.fr
Wed Nov 18 11:35:17 EST 2009


Le 18 nov. 09 à 17:28, alex sando a écrit :

> hi Gaëtan ,
> the RegistrationType should be ImageRegistrationMethod :) But when i  
> tried:
>
> parameters =  
> itk 
> .ImageRegistrationMethod 
> [itk 
> .Image 
> .US2 
> ,itk.Image.US2].ParametersType(transformer.GetNumberOfParameters())
>
> it gave me the error:
> AttributeError: type object 'itkImageRegistrationMethodIUS2IUS2' has  
> no attribute 'ParametersType'
>
> And in ITK's source file, i found that:
>
> typedef  typename MetricType::TransformParametersType     
> ParametersType;

ParametersType is a typedef, so it is not available in python

>
> So I guess that the correct invoke maybe like:
>
> parameters =  
> itk 
> .ImageRegistrationMethod 
> [itk.Image.US2,itk.Image.US2].TranslationTransform[itk.D,  
> 2].TransformParametersType(transformer.GetNumberOfParameters())
>
> But it failed with:
>
> AttributeError: type object 'itkImageRegistrationMethodIUS2IUS2' has  
> no attribute 'TranslationTransform'
>

I'm not sure what you're trying to do there. What is  
TranslationTransform?

> Would you give me any suggestion about this issue?.... thanks:)
>
> Alex
>
>
>
> 2009/11/18 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 18 nov. 09 à 16:17, alex sando a écrit :
>
>
> hi Gaëtan, it works again:). But i got two new questions:)
>
>        transformer = itk.TranslationTransform[itk.D, 2].New()
>        optimizer = itk.RegularStepGradientDescentOptimizer.New()
>        interpolator =  
> itk.LinearInterpolateImageFunction[itk.Image.US2, itk.D].New()
>        metric =  
> itk.MeanSquaresImageToImageMetric[itk.Image.US2,itk.Image.US2].New()
>        registration_object =  
> itk.ImageRegistrationMethod[itk.Image.US2,itk.Image.US2].New()
>        registration_object.SetMetric(metric.GetPointer())
>        registration_object.SetOptimizer(optimizer.GetPointer())
>        registration_object.SetTransform(transformer.GetPointer())
>        registration_object.SetInterpolator(interpolator.GetPointer())
>        registration_object.SetFixedImage(convertor.GetOutput())
>        registration_object.SetMovingImage(convertor1.GetOutput())
>         
> registration_object 
> .SetFixedImageRegion(convertor.GetOutput().GetBufferedRegion())
>
>        #parameters =  
> itk 
> .RegistrationType.ParametersType(transformer.GetNumberOfParameters())
>                                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~this  
> failed in the python, what should i do to construct a ParametersType  
> object in python?
>
> typedefs available in c++ are not available in python.
> What type ParametersType is supposed to be?
>
>
>
>
>        parameters = [0.0, 0.0]
>        ~~~~~~~~~~~~~~~~~just treat parameters as a list seems works,  
> am i correct?
>
>        registration_object.SetInitialTransformParameters(parameters)
>        optimizer.SetMaximumStepLength(4.00)
>        optimizer.SetMinimumStepLength(0.01)
>        optimizer.SetNumberOfIterations(200)
>
>        try:
>            registration_object.Update()
>        except itkError:
>            print itkError
>
>        last_para = registration_object.GetLastTransformParameters()
>        ~~~~~~~this returns a itkArray pointer and it seems   
> unindexable, cause it failed when i using "last_para[0]" how can i  
> access the actual transform parameters? thanks in advance again;)
>
> Usually, there is a SetElement() and GetElement() method for this  
> kind of class. It seems to be the case as well for itk::Array :-)
>
>
> Gaëtan
>
>
>
> Regards,
>
> Alex
>
> 2009/11/18 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 18 nov. 09 à 14:17, alex sando a écrit :
>
>
> Great! It works! thank you Gaëtan :)
>
> But i got an error when i tried to use ITK python to finish some  
> Registration work....Here is my code:
>
>       transformer = itk.TranslationTransform[itk.D, 3].New()
>       optimizer = itk.RegularStepGradientDescentOptimizer.New()
>       interpolator =  
> itk.LinearInterpolateImageFunction[itk.Image.US3, itk.D].New()
>       metric =  
> itk.MeanSquaresImageToImageMetric[itk.Image.US3,itk.Image.US3].New()
>       registration_object =  
> itk.ImageRegistrationMethod[itk.Image.US3,itk.Image.US3].New()
>       registration_object.SetMetric(metric)
>       ~~~~~~~~~~~~~~~~~~~~~~~~~~~ I got an error from this
> TypeError: Type error. Got  
> _p_itk__SmartPointerTitk__MeanSquaresImageToImageMetricTitk__ImageTunsigned_short_3u_t_itk__ImageTunsigned_short_3u_t_t_t 
> , expected  
> _p_itk__SmartPointerTitk__ImageToImageMetricTitk__ImageTunsigned_short_3u_t_itk__ImageTunsigned_short_3u_t_t_t
>
> Is there something i do wrong when invorking the method? The error  
> may indicate the SetMetric function requires a base class... could  
> you tell how to solve it.... many many thanks
>
>
> Usually, when a base class is requested, you have to pass a raw  
> pointer instead of a smart pointer. You can get it with the method  
> GetPointer()
>
>  registration_object.SetMetric(metric.GetPointer())
>
> may work.
>
>
> Gaëtan
>
>
> Alex
>
>
>
> 2009/11/18 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 18 nov. 09 à 09:30, alex sando a écrit :
>
>
> hi Gaëtan, my wrapITK is installed in:
>
> C:\Program Files\WrapITK
>
> itkvtkGlue is installed in:
>
> C:\Program Files\ItkVtkGlue
>
> Do you mean that i should copy ItkVtkGlue into the WrapITK directory?
>
>
> I was thinking to change the base path in CMAKE_INSTALL_PREFIX with  
> cmake gui, and to rebuild and reinstall ItkVtkGlue.
>
>
>
> Regards,
>
> Alex
>
>
> 2009/11/18 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 18 nov. 09 à 09:11, alex sando a écrit :
>
>
> Thanks Gaëtan,  I built itkvtkglue project successfully:
>
> 1>------ Build started: Project: INSTALL, Configuration: Release  
> Win32 ------
> 1>
> 1>Performing Post-Build Event...
> 1>-- Install configuration: "Release"
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/include/InsightToolkit/ 
> BasicFilters/itkImageToVTKImageFilter.h
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/include/InsightToolkit/ 
> BasicFilters/itkImageToVTKImageFilter.txx
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/include/InsightToolkit/ 
> BasicFilters/itkVTKImageToImageFilter.h
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/include/InsightToolkit/ 
> BasicFilters/itkVTKImageToImageFilter.txx
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/ClassIndex/ItkVtkGlue.mdx
> 1>-- Installing: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/lib/_ItkVtkGluePython.pyd
> 1>-- Installing: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/ClassIndex/wrap_ItkVtkGluePython.idx
> 1>-- Installing: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/lib/ItkVtkGluePython.py
> 1>-- Installing: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/ClassIndex/wrap_itkImageToVTKImageFilter.idx
> 1>-- Installing: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/lib/itkImageToVTKImageFilter.py
> 1>-- Installing: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/ClassIndex/wrap_itkVTKImageToImageFilter.idx
> 1>-- Installing: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/lib/itkVTKImageToImageFilter.py
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/SWIG/ItkVtkGlue.swg
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/Python/Configuration/ItkVtkGlueConfig.py
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/Python/ItkVtkGlue.py
> 1>-- Installing external project  into the WrapITK installation  
> directory.
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/Python/itkvtk.py
> 1>-- Up-to-date: C:/Program Files/ItkVtkGlue/lib/InsightToolkit/ 
> WrapITK/Python/itkExtras/itkvtkExtras.py
> 1>Build log was saved at "file://d:\ITKVTKBuild\INSTALL.dir\Release 
> \BuildLog.htm"
> 1>INSTALL - 0 error(s), 0 warning(s)
> ========== Build: 1 succeeded, 0 failed, 4 up-to-date, 0 skipped  
> ==========
>
> But i still get error message when import the module:
>
> import ItkvtkGlue
> ImportError: No module named ItkvtkGlue
> or
> import itkvtk
> ImportError: No module named itkvtk
>
> So I guess VTKImageToImageFilter may be built into the itk module,  
> so i try the filter directly in the source code without the extra  
> "import" expressions:
>
> print "Start to OpenFile"
> convertor = itk.VTKImageToImageFilter[itk.Image.US3].New(imageData)
> img = convertor.GetOutput()
> convertor.Update();
> print "Finished OpenFile"
>
> , but only get:
>
> AttributeError: 'LazyITKModule' object has no attribute  
> 'VTKImageToImageFilter'
>
> How can i fix this.... many many thanks for suggestions...
>
> Hi Alex,
>
> The base path for the installation must be the same than the one  
> used for WrapITK. I don't think that WrapITK is installed in C:/ 
> Program Files/ItkVtkGlue.
> Can you try to install ItkVtkGlue in the same dir than WrapITK?
>
> Gaëtan
>
>
>
>
> Alex
>
>
> 2009/11/18 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 17 nov. 09 à 07:59, alex sando a écrit :
>
>
> hi, currently i want to import a vtkImageData to itkImage so that  
> the data could be processed using some ITK filters, but when i  
> execute the following code:
>
>    imageData = reader.GetOutput()
>    print "Start to OpenFile"
>    convertor = itk.VTKImageToImageFilter[itk.Image.S3].New(imageData)
>    img = convertor.GetOutput()
>    convertor.Update();
>    print "Finished OpenFile"
>
> always get the following error message:
>  File "D:\Lab Affairs\src\control\Common.py", line 448, in  
> _simpleProcess
>  convertor = itk.VTKImageToImageFilter[...].New(imageData)
>  File "C:\Program Files\WrapITK\lib\InsightToolkit\WrapITK\Python 
> \itkLazy.py", line 14, in __getattribute__
>  value = types.ModuleType.__getattribute__(self, attr)
> AttributeError: 'LazyITKModule' object has no attribute  
> 'VTKImageToImageFilter'
>
> VTKImageToImageFilter is not wrapped in the WrapITK? how can i  
> convert the image from & to between vtkImageData and itkImage?  
> thanks...
>
> It is in WrapITK, but in an external project.
> See Wrapping/WrapITK/ExternalProjects/ItkVtkGlue
>
> Gaëtan
>
>
>
> Regards,
>
> Alex
>
> On Tue, Nov 17, 2009 at 1:20 PM, alex sando <yejun.alex at gmail.com>  
> wrote:
> Thanks Gaëtan! It seems work well on my platform:). Some little  
> issues i encountered in the progress, just a record for later's  
> reference :).
> 1. _BasePython project in WrapITK failed because /bigobj compile  
> flag is not set defaultly.
> 2. Dont forget to add path which contains SwigRuntimePython.dll to  
> PATH
>
> Regards,
>
> Alex
>
> 2009/11/17 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
>
> Le 16 nov. 09 à 19:14, alex sando a écrit :
>
>
> hello Gaëtan
>
> Currently i use itk 3.14 and Cableswig 3.14 and wrapitk0.2 in the  
> source of itk 3.14. But when i build wrapitk, it failed with a lot  
> of "itkFlatStructuringElement.h: No such file or directory"  
> error.... can you give me any suggestion to solve this? many thanks,  
> my platform is xp with vs2005 and cmake 2.8.
>
> Sure: turning on ITK_USE_REVIEW in cmake gui should help.
> Please let me know if that fix your problem.
>
> Regards,
>
> Gaëtan
>
>
>
>
> Regards,
>
> Alex
>
> 2009/11/16 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> Le 16 nov. 09 à 13:32, alex sando a écrit :
>
>
> hi all,
>  I am currently working on an legacy system which is composed under  
> python 2.3. Is there any method that could help me to create the itk  
> python wrap under python 2.3? I search for a while on the internet  
> and find the wrapitk is a great tool for using itk under python  
> environment, but its requirement for  the version of python is at  
> least 2.4...I also tried to compile the wrap using cmake, but failed  
> with
>
>
> CMake Warning at CMakeLists.txt:173 (FIND_PACKAGE):
> Could not find module FindCableSwig.cmake or a configuration file for
> package CableSwig.
> Adjust CMAKE_MODULE_PATH to find FindCableSwig.cmake or set  
> CableSwig_DIR
> to the directory containing a CMake configuration file for  
> CableSwig. The
> file will have one of the following names:
> CableSwigConfig.cmake
> cableswig-config.cmake
> CMake Error at CMakeLists.txt:185 (MESSAGE):
> CableSwig is required for CSwig Wrapping.
> Configuring incomplete, errors occurred!
>
> But in fact i set the CableSwig_DIR directory correctly... Is there  
> any suggestion to get itk work under python 2.3.....great  
> appreciate....
>
>
> Hi Alex,
>
> I think that WrapITK 0.2 - in ITK sources - *should* work with  
> python 2.3.
>
> Can you give more informations on your system? OS, cmake version,  
> compiler, ITK version, CableSwig version, …
>
>
> Regards,
>
> Gaëtan
>
>
> -- 
> 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  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>
>
> -- 
> 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  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>
>
>
> -- 
> 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  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>
>
> -- 
> 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  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>
>
> -- 
> 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  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>
>
> -- 
> 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  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>
>
> -- 
> 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  http://www.itk.org
> http://www.mandriva.org  http://www.bepo.fr
>
>

-- 
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  http://www.itk.org
http://www.mandriva.org  http://www.bepo.fr

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