[Insight-users] Re: WrapITK DemonsRegistration problem

Gaëtan Lehmann gaetan.lehmann at jouy.inra.fr
Sat Aug 19 06:42:54 EDT 2006 

Hi,

I ave just rebuild WrapITK for java, and everything seems to be ok: the  
JNI file is far from empty, the  
itkDemonsRegistrationFilterIF2IF2IVF22_itkDemonsRegistrationFilterIF2IF2IVF22_New  
method is here, ...
I have not tested it though. Can you send me your program, so I can try to  
run it on my system ?

Thanks,

Gaetan

Le Fri, 18 Aug 2006 18:04:44 +0200, Michael Bell <michael.bell at acm.org> a  
écrit:

> Charl,
>
> Have you used DemonsRegistration successfully? I am trying to use it
> today, but I get the error: java.lang.UnsatisfiedLinkError:
> itkDemonsRegistrationFilterIF2IF2IVF22_itkDemonsRegistrationFilterIF2IF2IVF22_New
>
> Then, when I look in itkDemonsRegistrationFilterJNI, the file is very
> small, and it does not include the above function. Most of the other
> registrationJNI files are much longer, and they include the New
> function.
>
> The small JNI file, which does not have the full declarations, is
> common among those cmake files using POINTER_WITH_SUPERCLASS. Do I
> need to create the superclass, itkPDEDeformationRegistrationFilter,
> before I can successfully use the demons class?
>
> thanks,
> michael
>
> On 7/26/06, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
>>
>> Some registration files were added some days ago by Charl P. Botha.
>> It can be a good starting point. See :
>> http://voxel.jouy.inra.fr/darcsweb/darcsweb.cgi?r=WrapITK;a=annotate_shade;h=20060720122257-2fc9d-767d4ccd51a2ea65ac456d70f55b94303c984eb2.gz;f=Modules/Registration/wrap_itkDemonsRegistrationFilter.cmake
>> http://voxel.jouy.inra.fr/darcsweb/darcsweb.cgi?r=WrapITK;a=annotate_shade;h=20060720122257-2fc9d-767d4ccd51a2ea65ac456d70f55b94303c984eb2.gz;f=Modules/Registration/wrap_itkLevelSetMotionRegistrationFilter.cmake
>> http://voxel.jouy.inra.fr/darcsweb/darcsweb.cgi?r=WrapITK;a=annotate_shade;h=20060720122257-2fc9d-767d4ccd51a2ea65ac456d70f55b94303c984eb2.gz;f=Modules/Registration/wrap_itkSymmetricForcesDemonsRegistrationFilter.cmake
>>
>> The WrapITK article also contains some doc - I didn't get feedback about
>> it yet, so I'm not sure it si good enough to write wrappers without  
>> help:
>> http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/WrapITK_-_Enhanced_languages_support_for_the_Insight_Toolkit.pdf
>>
>> Gaetan
>>
>> Le Wed, 26 Jul 2006 18:29:36 +0200, Michael Bell <michael.bell at acm.org>  
>> a
>> écrit:
>>
>> > Gaetan,
>> >
>> > It is the registration tools that I am interested in, so this should
>> > be perfect. I will look into things and come back with questions.
>> >
>> > thanks,
>> > michael
>> >
>> >
>> > On 7/26/06, Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
>> >> On Wed, 26 Jul 2006 16:18:52 +0200, Michael Bell  
>> <michael.bell at acm.org>
>> >> wrote:
>> >>
>> >> > Gaetan,
>> >> >
>> >> > The only issue for me will be the classes that are not wrapped. Why
>> >> > are particular classes not wrapped? Can I help remedy the  
>> situation?
>> >> >
>> >>
>> >> I have tried to wrap as much classes as possible (63% of the filters  
>> are
>> >> wrapped at this time). However, ITK is a large toolkit, and I don't
>> >> always
>> >> have the needed knowledge to choose the revelant template parameters.
>> >> That's the case for example for the registration part which I have  
>> never
>> >> used (and do not plan to use).
>> >> So yes you can help, just by creating the new wrappers with the  
>> revelant
>> >> template parameters.
>> >> The syntax has been made to be easy to use, and I would be pleased to
>> >> help
>> >> to do that.
>> >>
>> >> Let me know if you are interested in adding some new classes
>> >>
>> >> Gaetan
>> >>
>> >>
>> >> > thanks,
>> >> > michael
>> >> >
>> >> > On 7/26/06, Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
>> >> >> On Wed, 26 Jul 2006 15:59:55 +0200, Michael Bell
>> >> <michael.bell at acm.org>
>> >> >> wrote:
>> >> >>
>> >> >> > Gaetan,
>> >> >> >
>> >> >> > I am using ext3 on linux, which has a maximum filesize of 255
>> >> >> > characters. I see that Brad has addressed possible solutions to
>> >> this.
>> >> >> >
>> >> >> > I commented out the MetaDataDictionary, and the rest of the  
>> compile
>> >> >> > finished without errors. Things seem to run well.
>> >> >>
>> >> >> Great !
>> >> >> I'll try to fix that issue when I get some free time.
>> >> >>
>> >> >> > I noticed that some
>> >> >> > classes are named differently than the straight itk wrapping.  
>> For
>> >> >> > example: itkImageMetricIF3 instead of itkImageMetricF3. Does  
>> the I
>> >> >> > stand for Image?
>> >> >>
>> >> >> That's it
>> >> >> Several changes were made in the naming policy, to make it more
>> >> >> expressive, for example, the I for an Image, VI for a VectorImage,
>> >> ...
>> >> >>
>> >> >> Let me know if you found other problems
>> >> >>
>> >> >> Gaetan
>> >> >>
>> >> >> >
>> >> >> > Thanks for your help,
>> >> >> > michael
>> >> >> >
>> >> >> > On 7/25/06, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
>> >> >> >>
>> >> >> >> Hi,
>> >> >> >>
>> >> >> >> I also have the same file with a very long name in my build  
>> tree,
>> >> >> but I
>> >> >> >> don't have any problem to access it. I thought this kind of
>> >> problem
>> >> >> was
>> >> >> >> limited to windows (I say that but André didn't report any  
>> problem
>> >> >> like
>> >> >> >> that). What is you file system ?
>> >> >> >> This kind of problem is already know and has been fixed for  
>> string
>> >> >> lists
>> >> >> >> and vectors in files Module/Base/*SwigExtras*.
>> >> >> >> However, this workaround is inherited from the current ITK
>> >> wrappers,
>> >> >> and
>> >> >> >> has not been modified in WrapITK - I'm not sure how it can be
>> >> used to
>> >> >> >> fix
>> >> >> >> your problem.
>> >> >> >>
>> >> >> >> Brad, can you help on that point ?
>> >> >> >>
>> >> >> >> As a quick fix, I think you should disable the class which use
>> >> this
>> >> >> >> type:
>> >> >> >> MetaDataDictionary.
>> >> >> >> To do that, just comment the line
>> >> >> >>
>> >> >> >>    WRAP_NON_TEMPLATE_CLASS("itk::MetaDataDictionary")
>> >> >> >>
>> >> >> >> in the file Modules/Base/wrap_ITKCommonBase.cmake
>> >> >> >> Taht being said, I think you will have the same problem with  
>> other
>> >> >> types
>> >> >> >> used in more useful classes :-/
>> >> >> >> Let me now if it still fail (or if it work !)
>> >> >> >>
>> >> >> >> Gaetan
>> >> >> >>
>> >> >> >>
>> >> >> >> Le Tue, 25 Jul 2006 15:55:29 +0200, Michael Bell
>> >> >> <michael.bell at acm.org>
>> >> >> >> a
>> >> >> >> écrit:
>> >> >> >>
>> >> >> >> > Gaetan,
>> >> >> >> >
>> >> >> >> > I am trying wrapitk on linux while waiting to receive  
>> VS2003. I
>> >> >> really
>> >> >> >> > like the setup, especially being able to choose what is  
>> wrapped.
>> >> >> >> >
>> >> >> >> > I am getting the following error while compiling  
>> (ITK&CableSwig
>> >> >> 2.8):
>> >> >> >> > Generating wrap_ITKCommonBaseJava.cxx
>> >> >> >> > Unable to open
>> >> >> >> >
>> >> >> >>
>> >> >>
>> >>  
>> /data/WrapITK/Build_Linux/Java/InsightToolkit/SWIGTYPE_p_std___Rb_tree_iteratorTstd__pairTconst_std__basic_stringTchar_std__char_traitsTchar_t_std__allocatorTchar_t_t_itk__SmartPointerTitk__MetaDataObjectBase_t_t_std__pairTconst_std__basic_stringTchar_std__char_traitsTchar_t_std__allocatorTchar_t_t_itk__SmartPointerTitk__MetaDataObjectBase_t_tR_std__pairTconst_std__basic_stringTchar_std__char_traitsTchar_t_std__allocatorTchar_t_t_itk__SmartPointerTitk__MetaDataObjectBase_t_tp_t.java
>> >> >> >> >
>> >> >> >> > The file name is too long. Any ideas on how to correct this?
>> >> >> >> >
>> >> >> >> > thanks,
>> >> >> >> > michael
>> >> >> >> >
>> >> >> >> > On 7/19/06, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>  
>> wrote:
>> >> >> >> >>
>> >> >> >> >> Michael,
>> >> >> >> >>
>> >> >> >> >> André Bongers reported to be able to build WrapITK with the
>> >> .NET
>> >> >> 2003
>> >> >> >> >> c++.
>> >> >> >> >> WrapITK surely still have some bugs on windows plateform,  
>> but
>> >> if
>> >> >> you
>> >> >> >> >> want
>> >> >> >> >> to try it, I will surely be more reactive that official ITK
>> >> >> >> developers.
>> >> >> >> >> WrapITK can be downloaded at
>> >> >> >> >>
>> >> >> >> >>
>> >> >> http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/WrapITK.tar.gz
>> >> >> >> >>
>> >> >> >> >> or directly with darcs
>> >> >> >> >>
>> >> >> >> >>    darcs get --partial
>> >> >> >> >> http://voxel.jouy.inra.fr/darcs/contrib-itk/WrapITK/
>> >> >> >> >>
>> >> >> >> >> and requires ITK 2.8.1
>> >> >> >> >>
>> >> >> >> >> Gaetan
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> Le Wed, 19 Jul 2006 22:10:55 +0200, Michael Bell
>> >> >> >> <michael.bell at acm.org>
>> >> >> >> >> a
>> >> >> >> >> écrit:
>> >> >> >> >>
>> >> >> >> >> > SwigInc.txt is being generated from SwigInc.txt.in, which  
>> has
>> >> >> the
>> >> >> >> >> > extra carriage return character. I suspect this is a  
>> problem
>> >> >> >> because I
>> >> >> >> >> > am using the cygwin recommended unix files, but this file  
>> is
>> >> a
>> >> >> dos
>> >> >> >> >> > file. If I dos2unix SwigInc.txt.in and make, this error  
>> goes
>> >> >> away,
>> >> >> >> and
>> >> >> >> >> > all of the SwigIn.txt files are correct. If I run  
>> dos2unix on
>> >> >> the
>> >> >> >> >> > entire Wrapping directory, many problems are fixed.
>> >> >> >> >> >
>> >> >> >> >> > Which shows the next issue:
>> >> >> >> >> > javac does not understand cygwin paths. This issue can be
>> >> fixed
>> >> >> >> using
>> >> >> >> >> > cygpath.
>> >> >> >> >> >
>> >> >> >> >> > Which shows the next problem:
>> >> >> >> >> > javac VXLNumericsJava.java
>> >> >> >> >> > cannot resolve symbol itkbase
>> >> >> >> >> >
>> >> >> >> >> > I haven't solved that problem, but I am certain it would
>> >> reveal
>> >> >> >> more.
>> >> >> >> >> >
>> >> >> >> >> > It's pretty clear that no one is maintaining the wrappers
>> >> with
>> >> >> >> cygwin.
>> >> >> >> >> > Please make this clear somewhere in the documentation so  
>> the
>> >> >> next
>> >> >> >> >> > person does not waste weeks on this, as I have.
>> >> >> >> >> >
>> >> >> >> >> > So, we know that VS8 does not work. Cygwin does not work.
>> >> What
>> >> >> does
>> >> >> >> >> > work on Windows? I can change compilers, but I can't spend
>> >> time
>> >> >> >> >> > hunting for a platform that does work. Please advise.
>> >> >> >> >> >
>> >> >> >> >> > thanks,
>> >> >> >> >> > michael
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On 7/17/06, Michael Bell <michael.bell at acm.org> wrote:
>> >> >> >> >> >> ITK people,
>> >> >> >> >> >>
>> >> >> >> >> >> I have made some progress tracking down this error:
>> >> >> >> >> >> wrap_vnl_matrix.xml from gccxml_cc1plus:
>> >> >> >> >> >>  error: too many filenames given.  Type gccxml_cc1plus
>> >> --help
>> >> >> for
>> >> >> >> >> usage
>> >> >> >> >> >> make[2]: ***
>> >> [Wrapping/CSwig/VXLNumerics/wrap_vnl_matrix.xml]
>> >> >> >> Error 1
>> >> >> >> >> >>
>> >> >> >> >> >> This is the operation that fails (paths shortened for
>> >> >> >> readability):
>> >> >> >> >> >> gccxml -fxml-start=_cable_ -fxml=wrap_vnl_matrix.xml
>> >> >> >> >> >> --gccxml-gcc-options SwigInc.txt -DCSWIG
>> >> -DCABLE_CONFIGURATION
>> >> >> >> >> >> wrap_vnl_matrix.cxx
>> >> >> >> >> >>
>> >> >> >> >> >> SwigInc.txt contains a list of include paths:
>> >> >> >> >> >>  
>> -I/cygdrive/d/Applications/InsightToolkit-2.8.1/Build_Cygwin
>> >> >> >> >> >>
>> >> -I/cygdrive/d/Applications/InsightToolkit-2.8.1/Code/Algorithms
>> >> >> >> >> >> ...
>> >> >> >> >> >>
>> >> >> -I/cygdrive/d/Applications/InsightToolkit-2.8.1/Code/BasicFilters
>> >> >> >> >> >> ^M
>> >> >> >> >> >>
>> >> >> >> >> >> Then, it has the ^M character at the end. If I remove  
>> this
>> >> >> >> character,
>> >> >> >> >> >> the xml file appears to be created correctly. Does anyone
>> >> know
>> >> >> >> where
>> >> >> >> >> >> this is being created, or why, or how I can prevent it?  
>> Is
>> >> >> this an
>> >> >> >> >> ITK
>> >> >> >> >> >> problem, or a CableSwig problem?
>> >> >> >> >> >>
>> >> >> >> >> >> Please, I'm obviously willing to do the leg work, but it
>> >> will
>> >> >> >> take me
>> >> >> >> >> >> 10 times as long to figure this out than if an ITK  
>> developer
>> >> >> would
>> >> >> >> >> >> step up and help. I've already shown that I was not the
>> >> first
>> >> >> >> person
>> >> >> >> >> >> to deal with this problem, and there are likely others  
>> who
>> >> have
>> >> >> >> not
>> >> >> >> >> >> said anything.
>> >> >> >> >> >>
>> >> >> >> >> >> thanks,
>> >> >> >> >> >> michael
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> --
>> >> >> >> >> >> michael.bell at acm.org
>> >> >> >> >> >>
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> --
>> >> >> >> >> Utilisant le client e-mail révolutionnaire d'Opera :
>> >> >> >> >> http://www.opera.com/mail/
>> >> >> >> >>
>> >> >> >> >
>> >> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> Utilisant le client e-mail révolutionnaire d'Opera :
>> >> >> >> http://www.opera.com/mail/
>> >> >> >>
>> >> >> >
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> 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
>> >> >>
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> 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
>> >>
>> >
>> >
>>
>>
>>
>> --
>> Utilisant le client e-mail révolutionnaire d'Opera :
>> http://www.opera.com/mail/
>>
>
>



-- 
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

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