[ITK-users] Texture pixel by pixel
Francisco Lopez de la Franca
franciscolopezdelafranca at gmail.com
Thu Feb 11 04:55:42 EST 2016
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
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>>>>> >> > > Please keep messages on-topic and check the ITK FAQ at:
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>>>>> >> > < > .
>>>>> >> > NAML
>>>>> >> > <
>>>>> >>
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>>>>> >> Sent from the ITK Insight Users mailing list archive at Nabble.com.
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>>>>> >> Powered by www.kitware.com
>>>>> >>
>>>>> >> Visit other Kitware open-source projects at
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>>>>> >
>>>>> > Visit other Kitware open-source projects at
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>>>>
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>>>>
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>
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