[Insight-developers] Moving Insight Journal Paper 176

Tue May 12 11:23:14 EDT 2009

We want to group the files being added for paper 176 in Doxygen.  I propose
adding:
\ingroup LabeledImageObject
\ingroup LabeledImageFilter

For the objects and filters respectively.

Any comments?

- Wes

On Tue, May 12, 2009 at 10:54 AM, Wes Turner <wes.turner at kitware.com> wrote:

> 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
>

-- 
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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