[ITK] [ITK-users] Texture pixel by pixel
Francisco Lopez de la Franca
franciscolopezdelafranca at gmail.com
Mon Jan 25 06:50:35 EST 2016
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.
>>> >> > > _____________________________________
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>>> >> > <
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>>> >>
>>> >>
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>>> >>
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>>
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>>
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