[ITK] [ITK-users] Texture pixel by pixel

Dženan Zukić dzenanz at gmail.com
Thu Feb 11 11:16:08 EST 2016 

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 <
franciscolopezdelafranca at gmail.com> 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 <
> franciscolopezdelafranca at gmail.com>:
>
>> 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 <
>> franciscolopezdelafranca at gmail.com>:
>>
>>> 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 <
>>> franciscolopezdelafranca at gmail.com>:
>>>
>>>> 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 <
>>>> blowekamp at mail.nih.gov> 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 <
>>>>> franciscolopezdelafranca at gmail.com> 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 <itkhelpacc at gmail.com>:
>>>>>
>>>>>> 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] <ml-node+s2283740n7587961h47 at n2.nabble.com> 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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>>>>>> >> > To unsubscribe from [ITK-users] Texture pixel by pixel, click
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>>>>>> >> > < > .
>>>>>> >> > NAML
>>>>>> >> > <
>>>>>> >>
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>>>>>> >> Sent from the ITK Insight Users mailing list archive at Nabble.com
>>>>>> .
>>>>>> >> _____________________________________
>>>>>> >> Powered by www.kitware.com
>>>>>> >>
>>>>>> >> Visit other Kitware open-source projects at
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>>>>>> >
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>>>>>> >
>>>>>> > Visit other Kitware open-source projects at
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>>>>>> Sent from the ITK Insight Users mailing list archive at Nabble.com.
>>>>>> _____________________________________
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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
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>>
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