[Insight-users] Problem with wrapping itk with python 2.3
Gaëtan Lehmann
gaetan.lehmann at jouy.inra.fr
Wed Nov 18 12:40:55 EST 2009
Le 18 nov. 09 à 17:45, alex sando a écrit :
> hi Gaëtan , currently I am trying the registration function of ITK
> under python :), Here is my Code:
>
> 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
> .ImageRegistrationMethod
> [itk.Image.US2,itk.Image.US2].TranslationTransform[itk.D,
> 2].TransformParametersType(transformer.GetNumberOfParameters())
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~this line failed
> as i previous mentioned...
>
> #parameters = [0.0, 0.0]
> ~~~~~~~~~~~~~~~~~~~~~~~~using parameters just as list seems
> works ,but it will cause "registration_object.Update()" finished
> with last_para = [0.0,0.0] and optimizer.GetValue() = 1, which
> definitely means the registration failed... My problem is what
> should i do to set the parameters correctly.... thanks again in
> advance...
>
> registration_object.SetInitialTransformParameters(parameters)
ok, so since ParametersType is not available in python, you have to
figure out what real type it is. With wrapitk 0.3, I can look at the
method docstring, and I get that (in IPython):
3> registration_object.SetInitialTransformParameters?
Type: instancemethod
Base Class: <type 'instancemethod'>
String Form: <bound method
itkImageRegistrationMethodIUS2IUS2
.itkImageRegistrationMethodIUS2IUS2_SetInitialTra <...> odIUS2IUS2;
proxy of <Swig Object of type 'itkImageRegistrationMethodIUS2IUS2 *'
at 0x2b05e70> >>
Namespace: Interactive
Docstring:
itkImageRegistrationMethodIUS2IUS2_SetInitialTransformParameters
(itkImageRegistrationMethodIUS2IUS2 self, itkArrayD param)
Set/Get the initial transformation parameters.
You can also use help() in python interpreter, if you don't use ipython:
7> help(registration_object.SetInitialTransformParameters)
Help on method
itkImageRegistrationMethodIUS2IUS2_SetInitialTransformParameters in
module _itkImageRegistrationMethodPython:
itkImageRegistrationMethodIUS2IUS2_SetInitialTransformParameters(...)
method of
itkImageRegistrationMethodPython.itkImageRegistrationMethodIUS2IUS2
instance
itkImageRegistrationMethodIUS2IUS2_SetInitialTransformParameters
(itkImageRegistrationMethodIUS2IUS2 self, itkArrayD param)
Set/Get the initial transformation parameters.
So parameters must be of type itkArrayD, that you can instantiate with
itk.Array.D()
I don't remember exactly what you can find in the docstring with
wrapitk 0.2 - it will be different for sure, but you should find the
information you need anyway.
HTH,
Gaëtan
> optimizer.SetMaximumStepLength(4.00)
> optimizer.SetMinimumStepLength(0.01)
> optimizer.SetNumberOfIterations(200)
> try:
> registration_object.Update()
> except itkError:
> print itkError
> last_para = registration_object.GetLastTransformParameters()
> print last_para.GetElement(0), last_para.GetElement(1)
> print optimizer.GetCurrentIteration(), optimizer.GetValue()
>
> Regards,
>
> Alex
>
> 2009/11/19 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>
> 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
>
>
--
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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