[Insight-users] problems running and incoherent documentation in Chan-Vese segmentation examples

[Dan Mueller]

Hi Juan,

> *once a piece of code finds its way into ITK, what happens to the IJ
> submission? Ideally it should go into the SoftwareGuide, but it also
> seems hard to find a recent version of it (I even tried to get it from
> the Insight Documents in CVS). Is there a place to contribute this
> kind of documentation?

The code contribution procedure is documented here:
    http://www.itk.org/Wiki/ITK_Procedure_for_Contributing_New_Classes_and_Algorithms

The procedure says that while the code is in the review folder/module,
the IJ article remains the master location for documentation (see step
13), not the SoftwareGuide as you suppose. Whenever ITK review code is
changed, ideally the IJ article should be updated, but I too have
experienced this does not always happen. In fact, being the author of
a few IJ articles, I confess I am sometimes the cause of this
situation!

Some advice:
* You can use the follow link to see if an article has been moved to
ITK: http://www.insight-journal.org/publication/status
* Contact the authors (either directly or via the IJ review/comment
process). The IJ review/comment process is probably the preferred
option, because then other users can see the issues you've
experienced. I don't like having negative reviews on my articles, so I
tend to address these :D

I'm sure the Insight Journal editorial/management team will have
further comments.

Hopefully someone else on the list can comment regarding your specific
questions/issues with the Chan-Vese level set filters.

HTH

Cheers, Dan

On 10 May 2011 14:14, Juan Cardelino <juan.cardelino at gmail.com> wrote:
> =Introduction=
>
> As much as I love open source and ITK in particular, this is the third
> time I try to use contributed code to ITK and fail or invest a huge
> amount of time understanding how to make it work.
> I won't just criticize, but also offer my two cents. I'm willing to
> help improving the documentation and the examples. I did this once
> before without much echo from the community so this will be my last
> try.
>
> While I find the examples in the software guide nice and realistic,
> sometimes they are too complex for a person trying to understand an
> algorithm. Even if you deeply understand them (as in my case) case,
> sometimes a very simple example helps you grasp the basics. In
> addition, in simpler cases is clear what is a good result or not (for
> instance in segmentation) while in a realistic case, a good result is
> an elusive concept.
>
> This time my problem is with the Chan-Vese level set filters. The
> information I could find was the following:
> *Insight journal:
> **nice presentation and examples, but outdated code. This is
> important, because the Insight journal code is the first hit you get
> and you tend to download this. Just after you struggle with it you
> realize that it won't work and look in the mailing lists. Then you
> find out that there are examples buried in the Review folder. My
> suggestion: remove all traces of code from IJ.
> **In addition, within the papers there are examples of use that had
> became obsoleted: names of methods and attributed have changed.
> *Doxygen: the doxygen documentation is not complete for the main
> clases involved, it is hard to find out what does each of the many
> parameters of the algorithm exactly does. You have to deduce them from
> the IJ submission (when available) and then translate them into the
> actual names.
> *ITK git code: there are two examples in the code:
> **they only test the single phase scalar case in the dense and sparse versions
> **they don't have any example usage (yes, again you can deduce this from IJ)
> **they don't have any accompanying images.
> *Kitware wiki:
> **After struggling with the examples in the review folder (which
> changed in last git update of the ITK source) I found out that in the
> ITK wiki there were 3 examples of the Chan-Vese algorithm. Two were
> the single phase spare and dense examples that used to be in the ITK
> source tree and the other was the multiphase case (again, no images).
>
> I'm not a newbie in ITK and I still find hard to grasp information
> from 5 or more different sources which could also be potentially
> contradictory.
>
> I hope I'm doing something wrong and someone can point out where my
> problems are. But I spent a lot of time and careful experimentation in
> this, so I think there is something wrong.
>
> I've summarized my whole experience at my wiki:
> http://iie.fing.edu.uy/rs/wiki/ContributedCode:ITKChanVese, I hope
> someone takes the time to read it. There, I will contribute a couple
> of  simple examples just to say how I think they could be presented.
> In addition, I'm posting comments on the existing examples. Finally, I
> have an easy question:
> *once a piece of code finds its way into ITK, what happens to the IJ
> submission? Ideally it should go into the SoftwareGuide, but it also
> seems hard to find a recent version of it (I even tried to get it from
> the Insight Documents in CVS). Is there a place to contribute this
> kind of documentation?
>
> Thanks in advance.
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