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

Wed Jul 26 12:29:36 EDT 2006

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
>

-- 
michael.bell at acm.org