[Insight-users] Re: itk java wrapper on cygwin problem (Progress)

Michael Bell michael.bell at acm.org
Fri Jul 28 10:51:59 EDT 2006 

Gaetan,

I wrapped itkVersorRigid3DTransformOptimizer. No problem, amazingly easy.
Now I need to wrap CenteredTransformInitializer. It has three template classes:
Tansform,Image,Image. How do I do the transformType? (In this case it
is VersorRigid3DTransform).

thanks,
michael

On 7/27/06, Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
>
> I forgot to say that darcs works with http, if you don't need to have a
> write access to the repository. The patches can be sent by email (darcs
> send), or pushed to the repository through ssh.
> Most of the time, the firewalls are not a problem.
>
> Thanks again
>
> Gaetan
>
>
>
> Le Thu, 27 Jul 2006 20:29:38 +0200, Michael Bell <michael.bell at acm.org> a
> écrit:
>
> > Gaetan,
> >
> > Unfortunately, I am behind a firewall, and I can not use darcs or cvs.
> >
> > The attached patch has grammar and spelling fixes, but no content
> > changes. The document is well written, and I will try to add my first
> > class today or tomorrow.
> >
> > thanks,
> > michael
> >
> > On 7/27/06, Gaetan Lehmann <gaetan.lehmann at jouy.inra.fr> wrote:
> >> On Thu, 27 Jul 2006 17:51:28 +0200, Michael Bell <michael.bell at acm.org>
> >> wrote:
> >>
> >> > Gaetan,
> >> >
> >> > I'm reading through the pdf now, and it is very helpful. As a native
> >> > English speaker, may I be of assistance in editing some spelling and
> >> > grammar? Is the document available for changing?
> >>
> >> sure ! any help is welcome :-)
> >> The article is available in article/Article.tex . The best way to record
> >> the changes is to use darcs (usage is partially explained in the
> >> article),
> >> but if don't want to use it, a simple patch would be ok :-)
> >>
> >> Thanks,
> >>
> >> Gaetan
> >>
> >>
> >>
> >> >
> >> > 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
> >>
> >
> >
>
>
>
> --
> Utilisant le client e-mail révolutionnaire d'Opera :
> http://www.opera.com/mail/
>


-- 
michael.bell at acm.org

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