[Tubetk-developers] itkImageToTubeRigidRegistration2

Wed Jul 25 17:40:07 EDT 2012

>
> Could you please share that document with me?  The link does not work.
>
Done.

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.

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.

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
> >>
> >
>
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