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

Francisco Lopez de la Franca franciscolopezdelafranca at gmail.com
Wed Sep 30 10:51:17 EDT 2015 

Hi Brad,
I think I've always compiled in Release mode when working with ITK.
The low performance is not only with your filter; the same happens with the
itk::Statistics::ScalarImageToTextureFeaturesFilter and I've also tested
(copy-paste-test) the example
http://itk.org/Wiki/ITK/Examples/Statistics/TextureFeatures, and it takes a
long time.
My image is float-pixel-typed, I donot know if it has something to do. I'll
try to define it as short-typed.

The radius I'm using is 3x3x3 and 13 offsets (default in 3D).
Any suggestion is very welcome.
Thank you very much.
Regards.
/Francisco


2015-09-30 14:55 GMT+02:00 Bradley Lowekamp <blowekamp at mail.nih.gov>:

> 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:
>> >> >
>> >>
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>> .
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