[Insight-developers] Moving Insight Journal Paper 176

Tue May 12 10:54:20 EDT 2009

Excellent.  Thanks for the pointer.
- Wes

2009/5/12 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>

>
> Le 12 mai 09 à 15:27, Wes Turner a écrit :
>
>  ITK Developers,
>>
>> I am starting to move the components of paper 176
>> http://hdl.handle.net/1926/584  or
>> http://www.insight-journal.org/browse/publication/176 into the Review
>> directory I will be doing this file-by-file over the next several days so as
>> to minimize disruption to testing.
>>
>> Gaetan: The first class I will be moving is the itkLabelObject.  In doing
>> this, I will need to generate a .txx and write a class-only test program.
>>
>
> The very first class is itk::LabelObjectLine, which is used in
> itk::LabelObject.
>
> In my opinion, the order should be:
>
>  itk::LabelObjectLine
>  itk::LabelObject
>  itk::LabelMap
>
> which are the base classes, and then
>
>  itk::LabelImageToLabelMapImageFilter
>  itk::LabelMapToLabelImageFilter
>
> because they are very simple classes to convert from/to standard
> itk::Image.
>
> Gaëtan
>
>
>
>>
>> - Wes
>>
>> 2009/5/12 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>>
>> Le 12 mai 09 à 14:31, Wes Turner a écrit :
>>
>>
>> Gaetan,
>>
>> 2009/5/11 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>>
>> Hi Wes,
>>
>> Le 11 mai 09 à 22:20, Wes Turner a écrit :
>>
>>
>> Gaetan,
>>
>> Two quick issues.
>>
>>      • If we try to configure the system with CMAKE_BUILD_TYPE set to
>> Release, the compiler crashes (error message is below).  System is Ubuntu,
>> gcc-4.2.4 oor 4.3.2.
>>
>> I had this kind of problem on mandriva 2009.0 rc1 last year. A compiler
>> upgrade fixed the problem.
>> Now that I see that code, it recall me that et should be moved to an
>> helper function, because, IIRC, msvc 6 doesn't like too much the templated
>> method. This small change may help with your compiler issue as well :-)
>>
>> It's not clear.  Is this something you can help with, or are you proposing
>> that I move this out?
>>
>> I can't help with the compiler issue.
>> But the method where your compiler fail needs a small refactoring to build
>> with older compilers. This refactoring may help with the compiler crash
>> you're experimenting.
>>
>> I hope that's much clear.
>>
>>
>>
>>
>>
>>
>>      • The test AttributeValues2 is failing - same system,
>> CMAKE_BUILD_TYPE not specidfied.  The log file is attached.
>>
>> This one may be caused by my lack of knowledge on how to compare floats in
>> a portable way: the test is ok only on one of my hosts, so I'm not too
>> surprised that it fails for you.
>> I really need a clean way to check those values.
>>
>> I made a change that solves this at least for now.  The issue was that you
>> are scaling the difference by the expected value -- which is good for
>> reasonable values.  For the particular case that was failing, the comparison
>> value  was on the order of e-28 (effectively zero) which is unstable and
>> blows up for even small absolute differences.  I added an additional check
>> of the absolute difference against vnl_math::eps and the test passes. You
>> can review the addition when I check this in, hopefully later today.
>>
>> Great!
>>
>> Gaëtan
>>
>>
>>
>>
>>
>>
>> - Wes
>>
>> Gaëtan
>>
>>
>>
>> Any chance you can try and resolve these issues?
>>
>> Thanks much!
>>
>> - Wes
>>
>> [ 14%] Building CXX object
>> CMakeFiles/binary_fillhole.dir/binary_fillhole.o
>> /home/wesley/Packages/InsightJournal/Insight_journal_176_8/binaryAttributeMorphology/itkLabelMapMaskImageFilter.txx:
>> In member function ‘void itk::LabelMapMaskImageFilter<TInputImage,
>> TOutputImage>::ThreadedGenerateData(typename TInputImage::LabelObjectType*)
>> [with TInputImage = itk::LabelMap<itk::AttributeLabelObject<long unsigned
>> int, 2u, bool> >, TOutputImage = itk::Image<unsigned char, 2u>]’:
>> /home/wesley/Packages/InsightJournal/Insight_journal_176_8/binaryAttributeMorphology/itkLabelMapMaskImageFilter.txx:419:
>> internal compiler error: in get_biv_step, at loop-iv.c:774
>> Please submit a full bug report,
>> with preprocessed source if appropriate.
>> See <URL:http://gcc.gnu.org/bugs.html> for instructions.
>> For Debian GNU/Linux specific bug reporting instructions,
>> see <URL:file:///usr/share/doc/gcc-4.2/README.Bugs>.
>> make[2]: *** [CMakeFiles/binary_fillhole.dir/binary_fillhole.o] Error 1
>> make[1]: *** [CMakeFiles/binary_fillhole.dir/all] Error 2
>> make: *** [all] Error 2
>>
>>
>> <wes.turner at kitware.com> wrote:
>> Thanks.  I will grab your new code and will keep in touch during the
>> process.
>>
>> - Wes
>>
>> 2009/5/8 Gaëtan Lehmann <gaetan.lehmann at jouy.inra.fr>
>>
>>
>> Hi Wes,
>>
>> Thanks a lot for taking this task: that's a quite important amount of
>> work.
>>
>> Le 6 mai 09 à 21:23, Wes Turner a écrit :
>>
>>
>> Gaetan:
>> Your paper 176, Label object representation and manipulation with ITK,
>> looks like a good candidate to be moved into the review directory.  Does the
>> current submission to the IJ represent the current state of the code?
>>
>> No. There are some changes since the last submission, that I didn't have
>> time to submit to the IJ.
>> There are available at
>> http://voxel.jouy.inra.fr/darcs/contrib-itk/binaryAttributeMorphology/binaryAttributeMorphology.tar.gz
>>
>> The new code include many style fixes that I'm quite sure you would be
>> pleased to not have to fix :-)
>>
>>
>>  Anything else I should know before taking the plunge?
>>
>>
>> I'm not a native english speaker, and I'm not so good at choosing names.
>> So if you have suggestions on names, I would be pleased to discuss them :-)
>>
>>
>> ITK developers:
>> This submission is fairly large (around 65 classes).
>>
>> I'm afraid I've added a few more - I see 71 .h files in my repository.
>>
>>
>>  I will send out a warning before I commit anything to Review and will
>> work to minimize the extent and duration of any breakages, but I thought it
>> would be a good idea to keep you informed before taking any steps.  Your
>> comments and pointers are appreciated.  The reference submission is
>> http://hdl.handle.net/1926/584 if you want to check it out.
>>
>>
>> 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.mandriva.org
>> http://www.itk.org  http://www.clavier-dvorak.org
>>
>>
>>
>>
>> --
>> Wesley D. Turner, Ph.D.
>> Kitware, Inc.
>> R&D Engineer
>> 28 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-371-3971 x120
>>
>>
>>
>> --
>> Wesley D. Turner, Ph.D.
>> Kitware, Inc.
>> R&D Engineer
>> 28 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-371-3971 x120
>> <LastTest.log>
>>
>> --
>> 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.mandriva.org
>> http://www.itk.org  http://www.clavier-dvorak.org
>>
>>
>>
>>
>> --
>> Wesley D. Turner, Ph.D.
>> Kitware, Inc.
>> R&D Engineer
>> 28 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-371-3971 x120
>>
>> --
>> 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.mandriva.org
>> http://www.itk.org  http://www.clavier-dvorak.org
>>
>>
>>
>>
>> --
>> Wesley D. Turner, Ph.D.
>> Kitware, Inc.
>> R&D Engineer
>> 28 Corporate Drive
>> Clifton Park, NY 12065-8662
>> Phone: 518-371-3971 x120
>>
>
> --
> 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.mandriva.org
> http://www.itk.org  http://www.clavier-dvorak.org
>
>


-- 
Wesley D. Turner, Ph.D.
Kitware, Inc.
R&D Engineer
28 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-371-3971 x120
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