[Insight-developers] Adding and External Module: Lesion Sizing Toolkit

[Xiaoxiao Liu]

Bill,
Thanks for trying this out! LST is the first external module we bring into
ITKv4. Hopefully other external modules could follow the same structure and
migrate smoothly.

Will be working on those test issues soon. There are also some failing
doxygen related test failures in LST that I haven't got a chance to fix yet.

-xiaoxiao
On Mon, Jun 20, 2011 at 11:37 AM, Bill Lorensen <bill.lorensen at gmail.com>wrote:

> I decided to try the instructions to add an external module:
>
> http://itk.org/Wiki/ITK_Release_4/Modularization/Add_an_external_module_%28external_module%29
> and followed further instructions to add the Lesion Sizing Toolkit as
> an external module:
>
> http://public.kitware.com/LesionSizingKit/index.php/Users/Build_LST_as_ITK_module
>
> The process worked great! As instructed I:
> cd ITK/Modules/External
> git clone git://public.kitware.com/LesionSizingToolkit.git
>
> Then I ran cmake and make. The toolkit was discovered and built.
>
> So far, I have found a couple of problems, not with the process, but
> with LST itself.
>
> 1) I think there is an incorrect test dependency.
> SET_TESTS_PROPERTIES(
> itkGeodesicActiveContourLevelSetSegmentationModuleTest1
>  PROPERTIES DEPENDS itkConfidenceConnectedSegmentationModuleTest1)
> should be:
> SET_TESTS_PROPERTIES(
> itkGeodesicActiveContourLevelSetSegmentationModuleTest1
>  PROPERTIES DEPENDS itkConfidenceConnectedSegmentationModuleTest1
> itkGradientMagnitudeSigmoidFeatureGeneratorTest1)
>
> also
> SET_TESTS_PROPERTIES( itkShapeDetectionLevelSetSegmentationModuleTest1
>  PROPERTIES DEPENDS itkConfidenceConnectedSegmentationModuleTest1
> itkGradientMagnitudeSigmoidFeatureGeneratorTest1)
>
> 2) These files do not exist and some tests fail
> LesionSizingToolkit/Data/Baseline/CannyEdgeDetectionImageFilterTest4_1.mha
> LesionSizingToolkit/Data/Baseline/CannyEdgeDetectionImageFilterTest5_1.mha
> LesionSizingToolkit/Data/Baseline/CannyEdgeDetectionImageFilterTest6_1.mha
>
> 3) I found an iterator bug while running this test:
> itkRegionCompetitionImageFilterTest1
> 8:
> /usr/lib/gcc/i686-redhat-linux/4.4.5/../../../../include/c++/4.4.5/debug/safe_iterator.h:175:
> 8:     error: attempt to dereference a past-the-end iterator.
> 8:
> 8: Objects involved in the operation:
> 8: iterator "this" @ 0x0xbfece8a0 {
> 8: type =
> N11__gnu_debug14_Safe_iteratorIN9__gnu_cxx17__normal_iteratorIPKmNSt6__norm6vectorImSaImEEEEENSt7__debug6vectorImS7_EEEE
> (constant iterator);
> 8:   state = past-the-end;
> 8:   references sequence with type `NSt7__debug6vectorImSaImEEE' @
> 0x0xbfece8a0
>
> I'll have to track it down later. My ITK build uses these flags to
> detect stl errors.
> CMAKE_CXX_FLAGS:STRING=-Wall -Wshadow -Wcast-qual -Wno-deprecated
> -D_GLIBCXX_DEBUG -D_GLIBCXX_DEBUG_PEDANTIC -fstack-protector
>
> Finally,
> 4) The test itkFastMarchingSegmentationModuleTest1-PartSolidLesion1
> ran over night and never completed.
>
> Hope this helps,
>
> Bill
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-- 


---------------------------------------------
*Xiaoxiao Liu*, Ph.D.
R & D Engineer
Kitware Inc <http://www.kitware.com/>.
Clifton Park, NY
Phone: (518) 881-4924  or  (518) 371-3971 x124
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