[Insight-developers] Develop ITK

[Luis Ibanez]

Hi Nikos,


It looks like the new Transform that you wrote has some
inefficient code in it.


A) Could you post the source code of you  Transform ?
    (to the mailing list)

B) Have you run a profiler on your code ?

    LTProf is a good option,

    kcachegrind is another option for locating bottlenecks
    http://kcachegrind.sourceforge.net/html/Home.html


   Regards,


      Luis



--------------------------
Nikolaos Dikaios wrote:
> Hi Luis,
> 
> The output of  >>grep CMAKE_BUILD_TYPE CMakeCache.txt is
> 
> CMAKE_BUILD_TYPE:STRING=Release
> //Modified flag for variable: CMAKE_BUILD_TYPE
> CMAKE_BUILD_TYPE-MODIFIED:INTERNAL=1
> 
> The code that i use is almost identical to itk3.8 ... i simply renamed
> itkBSplineDeformableTransform to itkBSplineNewTransform and
> itkBSplineInterpolationWeightFunction to
> itkNewBSplineInterpolationWeightFunction
> 
> I kept the rest of the code the same ... I get the same registration
> output (as expected) but its significantly slower when i include the new
> files.
> 
> Regards,
> 
> Nikos
> 
> 
> 
> On Tue, 2009-06-30 at 13:08 -0400, Luis Ibanez wrote:
> 
>>Hi Nikolaos,
>>
>>
>>Please verify the build mode by doing:
>>
>>          ccmake .
>>
>>and checking the content of the CMake variable
>>
>>
>>      CMAKE_BUILD_TYPE
>>
>>
>>It should say "Release"
>>
>>Alternatively, you can also do
>>
>>
>>      grep CMAKE_BUILD_TYPE CMakeCache.txt
>>
>>
>>in the binary directory of your project.
>>
>>
>>If this turned out to be set to Release,
>>then the next option is to start profiling
>>your code...   :-/
>>
>>
>>
>>      Regards,
>>
>>
>>          Luis
>>
>>
>>
>>----------------------
>>Nikolaos Dikaios wrote:
>>
>>>Hi Dan,
>>>
>>>Thanks for your reply.
>>>
>>>I used 
>>>
>>>
>>>
>>>>>cmake -i
>>>
>>>
>>>and then
>>>
>>>
>>>
>>>>>make -release 
>>>
>>>
>>>in order to build in release mode. But it still is significantly slow.
>>>
>>>Regards,
>>>
>>>Nikos
>>> 
>>>
>>>On Mon, 2009-06-29 at 18:08 +0200, Dan Mueller wrote:
>>>
>>>
>>>>Hi Nikos,
>>>>
>>>>Did you build your source in Release mode? Building in release mode
>>>>can have massive speed impact...
>>>>
>>>>Please let us know.
>>>>
>>>>Regards, Dan
>>>>
>>>>2009/6/29 Nikolaos Dikaios <nd301 at wbic.cam.ac.uk>:
>>>>
>>>>
>>>>>Dear all,
>>>>>
>>>>>I tried to develop a transformation function in the ITK similar to the
>>>>>itkBSplineDeformableTransform.h.
>>>>>
>>>>>When i use the the new transformation function, registration becomes
>>>>>extremely slow (compared to the same registration scheme using the
>>>>>BSplineDeformableTransform). Has anybody experienced this problem ?
>>>>>
>>>>>Thank you in advance for your help,
>>>>>
>>>>>Nikos
>>>>>
>>>>>PS. The MakeList that i use to cmake is:
>>>>>
>>>>># Project name
>>>>>PROJECT(itk_aff_p_nr_reg)
>>>>>
>>>>># Find the ITK stuff
>>>>>FIND_PACKAGE(ITK)
>>>>>IF(ITK_FOUND)
>>>>>      INCLUDE(${ITK_USE_FILE})
>>>>>ENDIF(ITK_FOUND)
>>>>>
>>>>># Set a path to the sources
>>>>>SET(SOURCES
>>>>>../Sources
>>>>>)
>>>>>
>>>>>
>>>>>
>>>>># Create a library using different *.cxx
>>>>>SET(myNRR
>>>>>${SOURCES}/itkNewBSplineInterpolationWeightFunction.cxx
>>>>>${SOURCES}/itkBSplineTransform.cxx
>>>>>)
>>>>>ADD_LIBRARY( aff_p_nr_reg ${myNRR} )
>>>>>
>>>>># Location of library include files
>>>>>INCLUDE_DIRECTORIES( ${SOURCES} )
>>>>>
>>>>># Library location for the linker
>>>>>LINK_DIRECTORIES( ${SOURCES} )
>>>>>
>>>>># Add the executable built from *.cxx
>>>>>ADD_EXECUTABLE( itk_aff_p_nr_reg itk_aff_p_nr_reg.cxx )
>>>>>
>>>>># Link the executable with required libraries
>>>>>TARGET_LINK_LIBRARIES( itk_aff_p_nr_reg aff_p_nr_reg ITKCommon
>>>>>ITKAlgorithms ITKBasicFilters ITKIO ITKStatistics ITKNumerics )
>>>>>
>>>>>
>>>>>
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>>>>>
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>>>>>
>>>>>Please keep messages on-topic and check the ITK FAQ at: http://www.itk.org/Wiki/ITK_FAQ
>>>>>
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>>>>>
>>>
>>>
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> 
> 
>