[Tubetk-developers] itkImageToTubeRigidRegistration2

Wed Jul 25 17:50:05 EDT 2012

On Wed, Jul 25, 2012 at 9:40 PM, Michael Jeulinl
<michael.jeulinl at kitware.com> wrote:
>> Could you please share that document with me?  The link does not work.
>
> Done.

Thanks.  Looks good.

>
>
>> I have attached screenshots from the test outputs on my side.  The
>> translation along the "axial" direction is off in the "2" case.
>
> Indeed, exact same problem.

Good to know.  I'll add a regression test on the output, and start
integrating the "2" version.
>
>> Excellent.  Where is this code currently located?  Would you like to
>> work on this while I address the convergence issues?
>
> I have just started working on it, will start really coding tomorrow and
> push my code and my own Slicer repository first.
> The plan sounds perfect to me otherwise.

Great.  Let's do that, then.  Team break huddle ;-).

Thanks,
Matt

>
> Thank you very much for the quick review.
> Michael.
>
> On Wed, Jul 25, 2012 at 5:29 PM, Matt McCormick <matt.mccormick at kitware.com>
> wrote:
>>
>> Hi Michael,
>>
>> Many thanks for the information.
>>
>>
>> >
>> > From what I remember and what I just checked quickly:
>> >
>> > The "itkImageToTubeRigidRegistration" is the re-factored and cleaned
>> > version
>> > of the initial one given the exact same results while the
>> > "itkImageToTubeRigidRegistration2" is a modified version of this
>> > previous
>> > class.
>> > This last one is supposed to be better as described here:
>> >
>> > (https://docs.google.com/open?id=1psAY1BKx2pEfVPDF4S-xwHOuSP4Mrp7AxQXErgmmQvHthA-LvFauCEdfpQQs).
>>
>> Could you please share that document with me?  The link does not work.
>>
>> > It is the one I would like to be the right one (I may have to go through
>> > an
>> > other clean step however), nevertheless I was waiting for some feedbacks
>> > first and as you are saying:
>> >
>> >> Comparing the output of the tests, the registered tube resampled onto
>> >> an image, the "2" result does not resemble the input image (as far as
>> >> I can tell).
>> >
>> > --> See Image enclosed.
>> >
>> > I just have some trouble to explain this as the performance measurement
>> > on
>> > the second metric seems to be more accurate and following a "more"
>> > coherent
>> > curve and equations compared to the initial one (c.f. previous link &&
>> > enclosed convergence curves). I was thinking about first making the read
>> > of
>> > the ".tre" file to be able to make some visual comparisons; I am really
>> > open
>> > to any explanations/ideas about why the results are that "bad" given the
>> > new
>> > metric.
>>
>> I have attached screenshots from the test outputs on my side.  The
>> translation along the "axial" direction is off in the "2" case.
>>
>> If you would like a second set of eyes, I can work on a piecewise
>> integration of the second class.
>>
>> >
>> > Then, concerning the ability to read a ".tre" file into a viewer, It is
>> > exactly what I am currently working on. I will create a specific module
>> > to
>> > get the reading and representation done as well as the integration with
>> > a
>> > MRML scene.
>> > Thank you to let me know if the plan suits you and do not hesitate for
>> > any
>> > comments/suggestions.
>>
>> Excellent.  Where is this code currently located?  Would you like to
>> work on this while I address the convergence issues?
>>
>> Thanks,
>> Matt
>>
>>
>>
>> >
>> > Regards,
>> > Michael J-L.
>> >
>> >
>> >
>> > On Tue, Jul 24, 2012 at 3:28 PM, Danielle Pace
>> > <danielle.pace at kitware.com>
>> > wrote:
>> >>
>> >> Unfortunately, there's no way to read a .tre into Slicer - that's
>> >> something we've always wanted to do.
>> >>
>> >> Stephen has a program to visualize .tre's - perhaps he can copy it for
>> >> you, or perhaps there's a more generic ITK spatial object viewer.
>> >>
>> >> -Danielle
>> >>
>> >>
>> >> On Tue, Jul 24, 2012 at 2:11 PM, Matt McCormick
>> >> <matt.mccormick at kitware.com> wrote:
>> >>>
>> >>> On Tue, Jul 24, 2012 at 5:44 PM, Stephen Aylward
>> >>> <stephen.aylward at kitware.com> wrote:
>> >>> > Michael extended his vacation by one day.   He should be back in the
>> >>> > office tomorrow.
>> >>>
>> >>> OK, great.
>> >>>
>> >>> >
>> >>> > Thanks for looking at this.   My understanding is that the 2 classes
>> >>> > are the correct ones; however, I really hate the "2" suffix.   If
>> >>> > the
>> >>> > old ones were broken, they should be replaced - instead of using a
>> >>> > numbering system.
>> >>> >
>> >>> > Perhaps beging by looking for the differences in the code and see if
>> >>> > the "" versions can be replaced by the "2" version (nearly the same
>> >>> > APIs, etc).
>> >>>
>> >>> As far as I can tell, the Registration classes are nearly the same
>> >>> apart from some cleanup.  The Metric class underwent refactoring.  The
>> >>> best hint as to what is going on appears to be:
>> >>>
>> >>>  * The improvment implemented here is about
>> >>>  * the precomputation of the internal kernels proposed by Lange et
>> >>> al.:
>> >>>  * \link http://www.zib.de/lamecker/publications/cars2007.pdf
>> >>>
>> >>> Comparing the output of the tests, the registered tube resampled onto
>> >>> an image, the "2" result does not resemble the input image (as far as
>> >>> I can tell).
>> >>>
>> >>> Is there a way to visualize the tube spatial object directly?  It is a
>> >>> MetaIO ".tre" file containing a Scene, Group, and Tube ObjectType.  I
>> >>> assume Slicer should recognize it as a "Model", but it seems to think
>> >>> it is a "Volume".
>> >>>
>> >>> Thanks,
>> >>> Matt
>> >>>
>> >>>
>> >>> >
>> >>> > s
>> >>> >
>> >>> > On Tue, Jul 24, 2012 at 1:04 PM, Matt McCormick
>> >>> > <matt.mccormick at kitware.com> wrote:
>> >>> >> The test output of the "2" classes does not appear to be correct?
>> >>> >>
>> >>> >> On Tue, Jul 24, 2012 at 4:18 PM, Matt McCormick
>> >>> >> <matt.mccormick at kitware.com> wrote:
>> >>> >>> Hi Michael,
>> >>> >>>
>> >>> >>> I am looking at the TubeTK itkImageToTubeRigidRegistration,
>> >>> >>> itkImageToTubeRigidRegistration2, itkImageToTubeRigidMetric,
>> >>> >>> itkImageToTubeRigidMetric2, and I am wondering if we replace the
>> >>> >>> original classes with the "2" version, and concentrate on
>> >>> >>> development
>> >>> >>> there?
>> >>> >>>
>> >>> >>> Thanks,
>> >>> >>> Matt
>> >>> >> _______________________________________________
>> >>> >> 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. - North Carolina Office
>> >>> > http://www.kitware.com
>> >>> > stephen.aylward (Skype)
>> >>> > (919) 969-6990 x300
>> >>> _______________________________________________
>> >>> Tubetk-developers mailing list
>> >>> Tubetk-developers at tubetk.org
>> >>> http://public.kitware.com/cgi-bin/mailman/listinfo/tubetk-developers
>> >>
>> >>
>> >>
>> >>
>> >> --
>> >> Danielle Pace, M.ESc.
>> >> Research and Development Engineer
>> >> Kitware Inc.,
>> >> North Carolina Office
>> >>
>> >> www.kitware.com
>> >> 919-969-6990 X 319
>> >>
>> >
>
>