[ITK-users] Texture pixel by pixel

Francisco López-Franca franciscolopezdelafranca at gmail.com
Thu Feb 11 12:08:12 EST 2016


Hi Dzenan,
The original class is here:

https://github.com/blowekamp/itkTextureAnalysis/blob/master/include/itkTextureFeatureImageFilter.h
https://github.com/blowekamp/itkTextureAnalysis/blob/b3911a8ab891859c50c7e3c8819d1a9fa0eaf4af/include/itkTextureFeatureImageFilter.hxx

I've just added setInput and setMaskImage methods and modify some lines in
the original class as I indicated in the yesterday mail within this thread.
I'm running it on Windows, and there is no error at all, just a crash. I
may have to include exceptions management.
The crash occurs just when calling p3 = maskIter.GetPixel(iter->first)

If you know why it could be or if you need more clarification, please let
me know.
Many thanks

2016-02-11 17:16 GMT+01:00 dzenanz [via ITK Insight Users] <
ml-node+s2283740n7588477h22 at n2.nabble.com>:

> Hi Francisco,
>
> "THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES." What is the error message
> that goes along with the crash? In which file and line does it crash?
>
> Regards
>
> On Thu, Feb 11, 2016 at 4:55 AM, Francisco Lopez de la Franca <[hidden
> email] <http:///user/SendEmail.jtp?type=node&node=7588477&i=0>> wrote:
>
>> Hi,
>> Please, someone that could help me. I'm working in a pre-doctorate
>> project and I need this class to work.
>> I've read the chapter 13 in the ITK Software Guide on how to write a
>> filter and now I see the fact of the threads due to inheritance of
>> ImageToImageFilter.
>> But, I keep on without understanding why the code crashes just when
>> calling
>> *const PixelType p3 = maskIter.GetPixel(iter->first);*
>> It is just a call to read data, not to write.
>>
>> I guess somebody that had worked with creation of filters might see
>> "easily" the problem, but not me.
>>
>> So, again, please, I need someone to help me with this because I'm stuck
>> on this point.
>>
>> Thank you very much.
>> KR.
>> /Francisco
>>
>> 2016-02-10 12:53 GMT+01:00 Francisco Lopez de la Franca <[hidden email]
>> <http:///user/SendEmail.jtp?type=node&node=7588477&i=1>>:
>>
>>> Hi Bradley again.
>>> I'm modifying your class in order to be able to set a mask image (a
>>> binary image) to be used as a limit in the histogram calculations, I mean,
>>> I set an input, a mask and the class should take into account to calculate
>>> the histograms only the voxels that belong to the input and to the mask
>>> image and having the value 1 in the mask image.
>>> The changes seem to be easy but I don´t know why my tests are not
>>> working. It seems that 2 threads are working at the same time and when I
>>> added my mask iterator, the code crashes.
>>>
>>> *** Consider that the input and mask images are the same origin, spacing
>>> and size.
>>>
>>> I attach the main changes I've done, and I would thank you a lot if you
>>> don't mind having a look and help me to find what I'm doing wrong:
>>>
>>> template< class TImageType, class TOutputImage >
>>> void
>>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetInput*(InputImageType
>>> *image)
>>> {
>>>   // Process object is not const-correct so the const_cast is required
>>> here
>>>   this->ProcessObject::SetNthInput( 0,
>>>                                     const_cast< InputImageType * >(
>>> image ) );
>>> }
>>>
>>> template< class TImageType, class TOutputImage >
>>> void
>>> TextureFeatureImageFilterV2< TImageType, TOutputImage >::*SetMaskImage*(InputImageType
>>> *image)
>>> {
>>>   // Process object is not const-correct so the const_cast is required
>>> here
>>>   this->ProcessObject::SetNthInput( 1, const_cast< InputImageType * >(
>>> image ) );
>>>
>>>   _maskImage = image; // _maskImage is a private member
>>> }
>>>
>>> In the *ThreadedGenerateData*(const RegionType& outputRegionForThread,
>>> ThreadIdType threadId ) method:
>>> {
>>>
>>> ...
>>>
>>>   for ( fit = faceList.begin(); fit != faceList.end(); ++fit )
>>>     {
>>>     NeighborhoodIteratorType nIter( radius, input, *fit );
>>>     *NeighborhoodIteratorType maskIter( radius, _maskImage, *fit);*
>>>     OutputIterator           outIter(output, *fit);
>>>
>>>     OutputPixelType out;
>>>     NumericTraits<OutputPixelType>::SetLength( out,
>>> this->GetNumberOfOutputComponents() );
>>>
>>>     while( !nIter.IsAtEnd() )
>>>       {
>>>       this->FillHistogram( *histogram, nIter, *maskIter *);
>>>
>>>       ...
>>>
>>>       ++nIter;
>>>       ++outIter;
>>>      * ++maskIter;*
>>>     ...
>>>
>>> In the *FillHistogram *method:
>>> {
>>>
>>> ...
>>>
>>>   while( iter != m_CooccurenceOffsetVector.end() )
>>>     {
>>>
>>>     const PixelType p1 = niter.GetPixel(iter->first);
>>>     const PixelType p2 = niter.GetPixel(iter->second);
>>>     std::cout << "Before p3" << std::endl;
>>>
>>> *    const PixelType p3 = maskIter.GetPixel(iter->first);    *std::cout
>>> << "After p3: " << p3 << std::endl;
>>>
>>> *    const PixelType p4 = maskIter.GetPixel(iter->second);   *
>>> std::cout << "After p4: " << p4 << std::endl;
>>>
>>>     if (    p1 >= m_Min && p2 >= m_Min && p1 <= m_Max && p2 <= m_Max
>>>             *&& p3 == _insidePixelValue && p4 == _insidePixelValue* )
>>> // The point
>>>       {
>>>
>>> ...
>>>
>>>
>>> *THE CODE PRINTS TWICE "BEFORE P3" AND CRASHES.*
>>>
>>> Thank you so much.
>>> My kind regards.
>>> /Paco
>>>
>>> 2016-01-25 12:50 GMT+01:00 Francisco Lopez de la Franca <[hidden email]
>>> <http:///user/SendEmail.jtp?type=node&node=7588477&i=2>>:
>>>
>>>> Hello Bradley again.
>>>> Sorry but I'd like to re-open this issue because I need your class but
>>>> with some modification.
>>>> I pass to tell you.
>>>>
>>>> As my tests with your external class were not good taking into account
>>>> the performance, I wonder if you could create a variant of it, but in which
>>>> I can set a mask image and your class just return the VectorImage with all
>>>> the features for that region (the masked locations) as
>>>> itk::ScalarImageToTextureFeaturesFilter class does.
>>>> I mean, to get the vector image with all the features but just
>>>> calculate it for the regions belonging to the mask image. Positions not
>>>> belonging to the mask region could have a pixel value of 0, for instance.
>>>>
>>>> I don´t know if it is very costly for you,  but I would thank you so
>>>> much. Otherwise, I could try it but I'd need your suggestions on how to do
>>>> it.
>>>>
>>>> Thanks a lot.
>>>> Best regards.
>>>>
>>>> 2015-09-30 23:38 GMT+02:00 Francisco Lopez de la Franca <[hidden email]
>>>> <http:///user/SendEmail.jtp?type=node&node=7588477&i=3>>:
>>>>
>>>>> Hello Bradley again,
>>>>> I would like to ask you for a couple of favours. In the one hand,
>>>>> could you please send me your 3D image so that I can test on it? And on the
>>>>> other hand, could you test the example I have referenced in the previous
>>>>> email with your image, not changing anything in the code, such as it is,
>>>>> and tell me if the execution time is normal?
>>>>> Thank you very much.
>>>>> Regards,
>>>>> /Francisco
>>>>>
>>>>> PS: All my application trace is printed via standard 'cout' command,
>>>>> not due to a debugging compilation mode.
>>>>>
>>>>>
>>>>> El miércoles, 30 de septiembre de 2015, Bradley Lowekamp <[hidden
>>>>> email] <http:///user/SendEmail.jtp?type=node&node=7588477&i=4>>
>>>>> escribió:
>>>>>
>>>>>> Hello,
>>>>>>
>>>>>> Did you compile TextureFeatureImage in Release mode?
>>>>>>
>>>>>> 1) The filter does not scale well with a large radius. And given by
>>>>>> your initial report of print a very large number of offset you, it sounds
>>>>>> like you are using a large radius with many offsets. I created a
>>>>>> 224x224x300 unsigned short image and ran with the default offset and a
>>>>>> radius of 2 in 5 minutes on my laptop. When I wrote this filter is was ~10x
>>>>>> faster than this example... things change though...
>>>>>>
>>>>>>
>>>>>> 2) I sounds like the boundaries/limits of the histogram may be
>>>>>> clipping you values. I would inspect the co-occurance matrix.
>>>>>>
>>>>>>
>>>>>> HTH,
>>>>>> Brad
>>>>>>
>>>>>> On Sep 30, 2015, at 3:28 AM, Francisco Lopez de la Franca <[hidden
>>>>>> email] <http:///user/SendEmail.jtp?type=node&node=7588477&i=5>>
>>>>>> wrote:
>>>>>>
>>>>>> I've tested with itkTextureFeatureImageFilter, with
>>>>>> itk::ScalarImageToTextureFeaturesFilter and also with the
>>>>>> http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures example,
>>>>>> for a 3D image and here are my comments:
>>>>>>
>>>>>>
>>>>>> 1. I had to interrupt the test after several hours and it kept on
>>>>>> calculating. And this is for only a 3D image (224x224x300). I need to
>>>>>> process around 35 images.
>>>>>> 2. The result (texture features: entropy, energy, correlation, LH,
>>>>>> inertia, CS and CP) for every voxel was: [1, 0, 1, 0, 0, 0, 7.83083e+247].
>>>>>> These values were not what I expected based on my experience on another
>>>>>> application I developed, but in that case, I calculated the texture
>>>>>> features for an image as a whole, not voxel by voxel.
>>>>>>
>>>>>> Regards.
>>>>>>
>>>>>> 2015-09-30 8:46 GMT+02:00 vis <[hidden email]
>>>>>> <http:///user/SendEmail.jtp?type=node&node=7588477&i=6>>:
>>>>>>
>>>>>>> i yes i have tried radius = 3;
>>>>>>> still no luck
>>>>>>>
>>>>>>> On Wed, Sep 30, 2015 at 12:06 PM, Francisco López-Franca [via ITK
>>>>>>> Insight
>>>>>>> Users] <[hidden email]
>>>>>>> <http:///user/SendEmail.jtp?type=node&node=7588477&i=7>> wrote:
>>>>>>>
>>>>>>> > Have you tried with a radius of 3 instead of 1?
>>>>>>> >
>>>>>>> > 2015-09-30 8:26 GMT+02:00 vis <[hidden email]
>>>>>>> > <http:///user/SendEmail.jtp?type=node&node=7587961&i=0>>:
>>>>>>> >
>>>>>>> >> hey Matt,
>>>>>>> >> thanks for ur advice.. it did build successfully... but im not
>>>>>>> able to run
>>>>>>> >> the code for 2D png image... i tried to change the dimension to 2
>>>>>>> and
>>>>>>> >> build
>>>>>>> >> it which it did.. but when i run the code using the command
>>>>>>> >> line itkTextureFeatureImageFilterTest.exe cthead.png putput.png
>>>>>>> 1... i see
>>>>>>> >> this output
>>>>>>> >>
>>>>>>> >> offset: [-1, -1] [0, -1]
>>>>>>> >> offset: [0, -1] [1, -1]
>>>>>>> >> offset: [-1, 0] [0, 0]
>>>>>>> >> offset: [0, 0] [1, 0]
>>>>>>> >> offset: [-1, 1] [0, 1]
>>>>>>> >> offset: [0, 1] [1, 1] and it asks for abort the program... if pls
>>>>>>> tel me
>>>>>>> >> how can i modify this code to work wid 2d image... forgive me if
>>>>>>> my ques
>>>>>>> >> are really silly im trying to learn something..
>>>>>>> >> regards
>>>>>>> >> Vis
>>>>>>> >>
>>>>>>> >> On Wed, Sep 30, 2015 at 2:56 AM, Matt McCormick-2 [via ITK
>>>>>>> Insight Users]
>>>>>>> >> <
>>>>>>> >> [hidden email] <
>>>>>>> http:///user/SendEmail.jtp?type=node&node=7587961&i=1>>
>>>>>>> >> wrote:
>>>>>>> >>
>>>>>>> >> > Hi,
>>>>>>> >> >
>>>>>>> >> > The function:
>>>>>>> >> >
>>>>>>> >> >   itkTextureFeatureImageFilterTest(int argc, char *argv[])
>>>>>>> >> >
>>>>>>> >> > must be renamed to
>>>>>>> >> >
>>>>>>> >> >   main(int argc, char* argv[])
>>>>>>> >> >
>>>>>>> >> > HTH,
>>>>>>> >> > Matt
>>>>>>> >> >
>>>>>>> >> > On Tue, Sep 29, 2015 at 6:08 AM, vis <[hidden email]
>>>>>>> >> > <http:///user/SendEmail.jtp?type=node&node=7587952&i=0>> wrote:
>>>>>>> >> >
>>>>>>> >> > > hi all,
>>>>>>> >> > > im trying to build the itkTextureFeatureImageFilterTest.cxx
>>>>>>> code but
>>>>>>> >> im
>>>>>>> >> > not
>>>>>>> >> > > able to it is showing the following error
>>>>>>> >> > > 1>------ Rebuild All started: Project: ZERO_CHECK,
>>>>>>> Configuration:
>>>>>>> >> Debug
>>>>>>> >> > x64
>>>>>>> >> > > ------
>>>>>>> >> > > 1>  Checking Build System
>>>>>>> >> > > 1>  CMake does not need to re-run because
>>>>>>> >> > >
>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/CMakeFiles/generate.stamp
>>>>>>> >> > is
>>>>>>> >> > > up-to-date.
>>>>>>> >> > > 2>------ Rebuild All started: Project:
>>>>>>> >> itkTextureFeatureImageFilterTest,
>>>>>>> >> > > Configuration: Debug x64 ------
>>>>>>> >> > > 2>  Building Custom Rule
>>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt
>>>>>>> >> > > 2>  CMake does not need to re-run because
>>>>>>> >> > >
>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp
>>>>>>> >> > is
>>>>>>> >> > > up-to-date.
>>>>>>> >> > > 2>  itkTextureFeatureImageFilterTest.cxx
>>>>>>> >> > > 2>C:\Program Files (x86)\Microsoft Visual Studio
>>>>>>> >> > > 11.0\VC\include\xutility(2176): warning C4996:
>>>>>>> 'std::_Copy_impl':
>>>>>>> >> > Function
>>>>>>> >> > > call with parameters that may be unsafe - this call relies on
>>>>>>> the
>>>>>>> >> caller
>>>>>>> >> > to
>>>>>>> >> > > check that the passed values are correct. To disable this
>>>>>>> warning, use
>>>>>>> >> > > -D_SCL_SECURE_NO_WARNINGS. See documentation on how to use
>>>>>>> Visual C++
>>>>>>> >> > > 'Checked Iterators'
>>>>>>> >> > > 2>          C:\Program Files (x86)\Microsoft Visual Studio
>>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of
>>>>>>> 'std::_Copy_impl'
>>>>>>> >> > > 2>
>>>>>>> >> > >
>>>>>>> >>
>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(439) :
>>>>>>> >> > see
>>>>>>> >> > > reference to function template instantiation '_OutIt
>>>>>>> std::copy<const
>>>>>>> >> > > unsigned char*,unsigned char*>(_InIt,_InIt,_OutIt)' being
>>>>>>> compiled
>>>>>>> >> > > 2>          with
>>>>>>> >> > > 2>          [
>>>>>>> >> > > 2>              _OutIt=unsigned char *,
>>>>>>> >> > > 2>              _InIt=const unsigned char *
>>>>>>> >> > > 2>          ]
>>>>>>> >> > > 2>
>>>>>>> >> > >
>>>>>>> >>
>>>>>>> c:\itk\source\modules\io\imagebase\include\itkImageFileReader.hxx(353) :
>>>>>>> >> > > while compiling class template member function 'void
>>>>>>> >> > > itk::ImageFileReader<TOutputImage>::GenerateData(void)'
>>>>>>> >> > > 2>          with
>>>>>>> >> > > 2>          [
>>>>>>> >> > > 2>              TOutputImage=InputImageType
>>>>>>> >> > > 2>          ]
>>>>>>> >> > > 2>
>>>>>>> >> > >
>>>>>>> >> >
>>>>>>> >>
>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\itkTextureFeatureImageFilterTest.cxx(47)
>>>>>>> >> >
>>>>>>> >> > > : see reference to class template instantiation
>>>>>>> >> > > 'itk::ImageFileReader<TOutputImage>' being compiled
>>>>>>> >> > > 2>          with
>>>>>>> >> > > 2>          [
>>>>>>> >> > > 2>              TOutputImage=InputImageType
>>>>>>> >> > > 2>          ]
>>>>>>> >> > > 2>          C:\Program Files (x86)\Microsoft Visual Studio
>>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of
>>>>>>> 'std::_Copy_impl'
>>>>>>> >> > > 2>          C:\Program Files (x86)\Microsoft Visual Studio
>>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of
>>>>>>> 'std::_Copy_impl'
>>>>>>> >> > > 2>          C:\Program Files (x86)\Microsoft Visual Studio
>>>>>>> >> > > 11.0\VC\include\xutility(2157) : see declaration of
>>>>>>> 'std::_Copy_impl'
>>>>>>> >> > > 2>     Creating library
>>>>>>> >> > >
>>>>>>> >> >
>>>>>>> >>
>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.lib
>>>>>>> >> >
>>>>>>> >> > > and object
>>>>>>> >> > >
>>>>>>> >> >
>>>>>>> >>
>>>>>>> D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/bin/Debug/itkTextureFeatureImageFilterTest.exp
>>>>>>> >> >
>>>>>>> >> > > 2>MSVCRTD.lib(crtexe.obj) : error LNK2019: unresolved
>>>>>>> external symbol
>>>>>>> >> > main
>>>>>>> >> > > referenced in function __tmainCRTStartup
>>>>>>> >> > >
>>>>>>> >> >
>>>>>>> >>
>>>>>>> 2>D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\Debug\itkTextureFeatureImageFilterTest.exe
>>>>>>> >> >
>>>>>>> >> > > : fatal error LNK1120: 1 unresolved externals
>>>>>>> >> > > 3>------ Rebuild All started: Project: ALL_BUILD,
>>>>>>> Configuration: Debug
>>>>>>> >> > x64
>>>>>>> >> > > ------
>>>>>>> >> > > 3>  Building Custom Rule
>>>>>>> >> > > D:/ITK_VTK_EX/My_ITK_Ex/seg/Texture/test/CMakeLists.txt
>>>>>>> >> > > 3>  CMake does not need to re-run because
>>>>>>> >> > >
>>>>>>> D:\ITK_VTK_EX\My_ITK_Ex\seg\Texture\test\bin\CMakeFiles\generate.stamp
>>>>>>> >> > is
>>>>>>> >> > > up-to-date.
>>>>>>> >> > > ========== Rebuild All: 2 succeeded, 1 failed, 0 skipped
>>>>>>> ==========
>>>>>>> >> > > im using the follwing CMakeList.txt
>>>>>>> >> > > # This is the root ITK CMakeLists file.
>>>>>>> >> > > cmake_minimum_required(VERSION 2.4)
>>>>>>> >> > > if(COMMAND CMAKE_POLICY)
>>>>>>> >> > >   cmake_policy(SET CMP0003 NEW)
>>>>>>> >> > > endif()
>>>>>>> >> > >
>>>>>>> >> > >
>>>>>>> >> > > # This project is designed to be built outside the Insight
>>>>>>> source
>>>>>>> >> tree.
>>>>>>> >> > > project(HelloWorld)
>>>>>>> >> > >
>>>>>>> >> > > # Find ITK.
>>>>>>> >> > > find_package(ITK REQUIRED)
>>>>>>> >> > > include(${ITK_USE_FILE})
>>>>>>> >> > >
>>>>>>> >> > > add_executable(itkTextureFeatureImageFilterTest
>>>>>>> >> > > itkTextureFeatureImageFilterTest.cxx )
>>>>>>> >> > >
>>>>>>> >> > > target_link_libraries(itkTextureFeatureImageFilterTest
>>>>>>> >> ${ITK_LIBRARIES})
>>>>>>> >> > >
>>>>>>> >> > > please tel me wat the error is??
>>>>>>> >> > >
>>>>>>> >> > >
>>>>>>> >> > >
>>>>>>> >> > > --
>>>>>>> >> > > View this message in context:
>>>>>>> >> >
>>>>>>> >>
>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587935.html
>>>>>>> >> > > Sent from the ITK Insight Users mailing list archive at
>>>>>>> Nabble.com.
>>>>>>> >> > > _____________________________________
>>>>>>> >> > > Powered by www.kitware.com
>>>>>>> >> > >
>>>>>>> >> > > Visit other Kitware open-source projects at
>>>>>>> >> > > http://www.kitware.com/opensource/opensource.html
>>>>>>> >> > >
>>>>>>> >> > > Kitware offers ITK Training Courses, for more information
>>>>>>> visit:
>>>>>>> >> > > http://www.kitware.com/products/protraining.php
>>>>>>> >> > >
>>>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at:
>>>>>>> >> > > http://www.itk.org/Wiki/ITK_FAQ
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>>>>>>> >> >
>>>>>>> >> > Visit other Kitware open-source projects at
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>>>>>>> >> > Kitware offers ITK Training Courses, for more information visit:
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>>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click
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>>>>>>> >> > < > .
>>>>>>> >> > NAML
>>>>>>> >> > <
>>>>>>> >>
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>>>>>>> >> >
>>>>>>> >> >
>>>>>>> >>
>>>>>>> >>
>>>>>>> >>
>>>>>>> >>
>>>>>>> >> --
>>>>>>> >> View this message in context:
>>>>>>> >>
>>>>>>> http://itk-insight-users.2283740.n2.nabble.com/ITK-users-Texture-pixel-by-pixel-tp7587867p7587960.html
>>>>>>> >> Sent from the ITK Insight Users mailing list archive at
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>>>>>>> >> _____________________________________
>>>>>>> >> Powered by www.kitware.com
>>>>>>> >>
>>>>>>> >> Visit other Kitware open-source projects at
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>>>>>>> >
>>>>>>> >
>>>>>>> > _____________________________________
>>>>>>> > Powered by www.kitware.com
>>>>>>> >
>>>>>>> > Visit other Kitware open-source projects at
>>>>>>> > http://www.kitware.com/opensource/opensource.html
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>>>>>>> > Kitware offers ITK Training Courses, for more information visit:
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>>>>>>> >
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>>>>>>> Visit other Kitware open-source projects at
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>>>>>>
>>>>>> _____________________________________
>>>>>> Powered by www.kitware.com
>>>>>>
>>>>>> Visit other Kitware open-source projects at
>>>>>> http://www.kitware.com/opensource/opensource.html
>>>>>>
>>>>>> Kitware offers ITK Training Courses, for more information visit:
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>>>>>>
>>>>>> Please keep messages on-topic and check the ITK FAQ at:
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