[Tubetk-developers] HDCS Enhancing doesn't work

Stephen Aylward stephen.aylward at kitware.com
Tue Nov 26 08:10:50 EST 2013 

Again you have found a bug.

I am testing and then will commit the fix you suggested.

Thank you!
Stephen


On Mon, Nov 25, 2013 at 6:33 PM, kenichiro yoshimi
<rccm.kyoshimi at gmail.com> wrote:
> Hi Stephen,
>
> Probably In my case, HDCS enhancing might work well with the modification to
> itktubeAnisotropicHybridDiffusionImageFilter.hxx as described below. But, I
> don't know whether this change is valid or not.
>
> l. 327
>  EigenVectorMatrixType eigenVectorMatrix;
>   ==>
>  EigenVectorMatrixType eigenVectorMatrix = eigenVectorImageIterator.Get();
>
> Thanks a lot,
> yoshimi
>
>
> 2013/11/25 kenichiro yoshimi <rccm.kyoshimi at gmail.com>
>>
>> Hi Stephen,
>>
>> Today, I could confirm that HDCS enhancing works, by setting the
>> particular parameters (EED Contrast (1.0), CED Contrast (1.0) and Hybrid
>> Contrast(1.0)) to testing case. Now I'm trying in my cases. Then I meet the
>> failure to sort eigenvalues in
>> "itktubeAnisotropicHybridDiffusionImageFilter.hxx". The following codes may
>> be wrong:
>>
>> l. 216:
>> if(  vnl_math_abs( eigenValue[i] > largest ) )
>>   ==> if(  vnl_math_abs( eigenValue[i] ) > largest )
>>
>> l.226:
>> if( eigenValue[i] != smallest && eigenValue[i] != largest )
>>   ==> if( vnl_math_abs( eigenValue[i] ) != smallest &&
>>              vnl_math_abs( eigenValue[i] ) != largest )
>>
>> Could you please confirm this?
>>
>> Thanks,
>> yoshimi
>>
>>
>> 2013/11/21 kenichiro yoshimi <rccm.kyoshimi at gmail.com>
>>>
>>> Hi Stephen,
>>>
>>> Thank you for your kind advice.
>>>
>>> Following your instructions, I build a "Experimental" project, but the
>>> tests may not run. Then I obtain the build log as:
>>>
>>> 1>------ Build : Project: Experimental, Release x64 ------
>>> 1>   Site: YOSHIMI
>>> 1>   Build name: Win32-vs9
>>> 1>Create new tag: 20131120-2346 - Experimental
>>> 1>Configure project
>>> 1>   Each . represents 1024 bytes of output
>>> 1>    . Size of output: 0K
>>> 1>Build project
>>> 1>   Each symbol represents 1024 bytes of output.
>>> 1>   '!' represents an error and '*' a warning.
>>> 1>    ......... Size of output: 8K
>>> 1>   0 Compiler errors
>>> 1>   0 Compiler warnings
>>> 1>Test project G:/work/kitware/build/TubeTK
>>> 1>No tests were found!!!
>>> 1>Performing coverage
>>> 1> Cannot find any coverage files. Ignoring Coverage request.
>>> 1>Submit files (using http)
>>> 1>   Using HTTP submit method
>>> 1>   Drop site:http://open.cdash.org/submit.php?project=TubeTK
>>> 1>   Uploaded:
>>> G:/work/kitware/build/TubeTK/Testing/20131120-2346/Build.xml
>>> 1>   Uploaded:
>>> G:/work/kitware/build/TubeTK/Testing/20131120-2346/Configure.xml
>>> 1>   Uploaded:
>>> G:/work/kitware/build/TubeTK/Testing/20131120-2346/Test.xml
>>> 1>   Submission successful
>>>
>>> I am attaching the CMakeCache.txt file for the building TubeTK. I
>>> appreciate if you would point out what I was doing wrong.
>>>
>>> Thanks,
>>> yoshimi
>>>
>>>
>>> 2013/11/20 Stephen Aylward <stephen.aylward at kitware.com>
>>>>
>>>> Hi,
>>>>
>>>> Sorry that you are having troubles.
>>>>
>>>> When you build using windows, there should be a build target/project
>>>> called "Experimental" that you can build from within Visual Studio
>>>> 2008. Please try building that project.  It should cause all of the
>>>> tests to run.  Please let me know if there are failures.
>>>>
>>>> Thanks,
>>>> Stephen
>>>>
>>>>
>>>> On Wed, Nov 20, 2013 at 6:36 AM, kenichiro yoshimi
>>>> <rccm.kyoshimi at gmail.com> wrote:
>>>> > Hi Stephen,
>>>> >
>>>> > Thanks for your reply.
>>>> > I build TubeTK with Visual Studio 2008, but I don't know the way to
>>>> > run the
>>>> > tests. So, I write the program that is  the same  as
>>>> > "itktubeAnisotropicHybridDiffusionImageFilterTest.cxx" and run with
>>>> > the
>>>> > testing data. The result has no error, but the output image data is
>>>> > the same
>>>> > as input data just like using Slicer plugin.
>>>> >
>>>> > My Slicer versioin is 4.3.1-2013-11-07 r22692 64 bit. My system is
>>>> > Windows 8
>>>> > 64bit.
>>>> >
>>>> > Best regards,
>>>> > yoshimi
>>>> >
>>>> >
>>>> > 2013/11/19 Stephen Aylward <stephen.aylward at kitware.com>
>>>> >>
>>>> >> Hi Kenichiro,
>>>> >>
>>>> >> Thank you for trying TubeTK.
>>>> >>
>>>> >> How did you install the TubeTK extensions?  If you compiled them,
>>>> >> then
>>>> >> I would like you to run the tests on your local build, and see if
>>>> >> they
>>>> >> pass.  As you said, we use that data in testing, and so if the tests
>>>> >> pass, then the integration into Slicer is the problem.  If the tests
>>>> >> fail, then the build of TubeTK is the problem.
>>>> >>
>>>> >> Also, what version of Slicer are you using?
>>>> >>
>>>> >> Thanks,
>>>> >> Stephen
>>>> >>
>>>> >>
>>>> >> On Mon, Nov 11, 2013 at 6:31 AM, kenichiro yoshimi
>>>> >> <rccm.kyoshimi at gmail.com> wrote:
>>>> >> > Dear all,
>>>> >> >
>>>> >> > I'm trying to use the Slicer plugin filter named "Hybrid Enhancing
>>>> >> > Anisotropic Diffusion with Continuous Switch (TubeTK)". But it does
>>>> >> > not
>>>> >> > reflect even if I specify various parameters. I try to apply it to
>>>> >> > CroppedWholeLungCTScan.mhd which is used for testing framework.
>>>> >> >
>>>> >> > Can someone help me in getting this to work?
>>>> >> >
>>>> >> > Cheers,
>>>> >> > yoshimi
>>>> >> >
>>>> >> > _______________________________________________
>>>> >> > Tubetk-developers mailing list
>>>> >> > Tubetk-developers at tubetk.org
>>>> >> >
>>>> >> > http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers
>>>> >> >
>>>> >>
>>>> >>
>>>> >>
>>>> >> --
>>>> >>
>>>> >> ====================================================
>>>> >> Stephen R. Aylward, Ph.D.
>>>> >> Senior Director of Operations, North Carolina, Kitware, Inc.
>>>> >> http://www.kitware.com
>>>> >> http://www.aylward.org
>>>> >> (919) 969-6990 x300
>>>> >> ====================================================
>>>> >
>>>> >
>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> ====================================================
>>>> Stephen R. Aylward, Ph.D.
>>>> Senior Director of Operations, North Carolina, Kitware, Inc.
>>>> http://www.kitware.com
>>>> http://www.aylward.org
>>>> (919) 969-6990 x300
>>>> ====================================================
>>>
>>>
>>
>



-- 

====================================================
Stephen R. Aylward, Ph.D.
Senior Director of Operations, North Carolina, Kitware, Inc.
http://www.kitware.com
http://www.aylward.org
(919) 969-6990 x300
====================================================

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