[Tubetk-developers] HDCS Enhancing doesn't work

Tue Nov 26 11:49:31 EST 2013

Results are now significantly better!  Thank you!

I am committing now.

Stephen

On Tue, Nov 26, 2013 at 8:10 AM, Stephen Aylward <
stephen.aylward at kitware.com> wrote:

> 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
> ====================================================
>

-- 

====================================================
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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