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

[Juan Cardelino]

Hi Arnaud,
    Good to know that. I'm currently using 3 different algorithms from
the Level Set framework. Two of them are used as is (Chan-Vese and
Geodesic Active Countours (GAC) with shape guidance) and I only wrote
wrapper code to perform tracking with them and to parse command line
arguments. For the third (classic GAC), I've specialized some of the
classed to perform semi-interactive (user assisted) segmentation.
Essentially, I'm adding a magnet term (minimizing the distance to
given points) that attracts the contour to the user specified points.
Maybe I could contribute that, but I think it is too silly to be
contributed.
But I'm certainly interested in contributing examples. In addition, I
think the examples in the way I'm thinking them could be written with
some independence of the implementation (apart from the code). I think
providing a good explanation, images and results is as important as
the code itself

On Wed, May 11, 2011 at 12:31 PM, Arnaud Gelas
<arnaud_gelas at hms.harvard.edu> wrote:
> Hi Juan,
>
> As part of the ITKv4 effort, we are in the process of refactoring the whole
> level set framework.
> We try to make the new framework as generic, and as flexible as possible to
> mix any kind of
> terms. One of the first implementation to validate the framework is this
> one.
>
> In short term, we won't be make any change on any of these classes in
> Review; and it
> is already planed to get rid of these classes (to relocate them into the
> deprecated module),
> but also to provide an equivalent with the new framework in long-term.
>
> You can contribute patches, documentation based on existing classes; but
> most likely will be deprecated.
> Writing examples is an excellent idea, it will force developers like us to
> modify the example to make it works
> with new API. Note that examples are tested every night!!
>
> You can also contribute in the development of the new level set framework
> itself, and we could discuss offline
> about it on how you could contribute.
>
> Best,
> Arnaud
>
> On May 11, 2011, at 7:57 AM, Juan Cardelino wrote:
>
>> Thanks for the answer guys. I know it takes work, but I think examples
>> of the quality of those in the software guide (or the IJ) are a
>> valuable resource for learning. And I feel it is a pity that they are
>> somehow frozen. In particular, I will I could take the Chan Vese
>> submission, get the source (easily) and update it or re-submit it. You
>> can't rely on the original authors for that, because as we all do,
>> they are probably working in other stuff at the moment and don't have
>> time to update their code.
>> The wiki format could make the update easier, but I think the
>> presentation quality will be lower than the papers on the IJ. At least
>> that's what my experiments with mediawiki show.
>> I have a few questions still open:
>> * whats the link between the gitorious examples and the wiki? if one
>> updates git it reflects on wiki or the other way round?
>> *do you guys want to have the wiki examples in the current format? I
>> mean, plain code pasted in a page? Do you see room for examples like
>> those I made? If there is, where should they go?
>> Thanks again for the great work, ITK is great!
>> Best regards,
>>                Juan
>>
>> On Tue, May 10, 2011 at 5:08 PM, robert tamburo
>> <robert.tamburo at gmail.com> wrote:
>>>
>>> Fair enough. Understandable. I think it's also understandable that a ~6
>>> year
>>> old reference document might frustrate/deter new/old
>>> users/developers. Perhaps the guide is an antiquated form of
>>> documentation
>>> (without dedicated resources for updates) and should be abandoned, or the
>>> model for updating the Software Guide should be revisited. I recall the
>>> Software Guide being 'doxygenated'. Should the downloadable PDF be
>>> updated
>>> to at least reflect changes in functions, variables, code snippets,
>>> comments, etc?
>>> On Tue, May 10, 2011 at 1:37 PM, Bill Lorensen <bill.lorensen at gmail.com>
>>> wrote:
>>>>
>>>> It is the same response. It takes a lot of work to update the book.
>>>> Especially with a changing toolkit.
>>>>
>>>> On Tue, May 10, 2011 at 12:34 PM, robert tamburo
>>>> <robert.tamburo at gmail.com> wrote:
>>>>>
>>>>> I think Juan was referring to the downloadable Software Guide.
>>>>>
>>>>> On Tue, May 10, 2011 at 12:06 PM, Bill Lorensen
>>>>> <bill.lorensen at gmail.com>
>>>>> wrote:
>>>>>>
>>>>>> Juan,
>>>>>>
>>>>>> In general, we don't want to duplicate examples in the ITK
>>>>>> distribution
>>>>>> and the ITK wiki. Wiki examples are intended to be simple examples
>>>>>> that
>>>>>> illustrate a single concept. Also, the user community can contribute
>>>>>> wiki
>>>>>> examples with minimal effort. There have been exceptions I guess.
>>>>>>
>>>>>> As for the book, my guess is that it takes a lot of work to update the
>>>>>> book and that's why it has not been updated for a while. I don't think
>>>>>> it
>>>>>> has to do with book sales.
>>>>>>
>>>>>> Bill
>>>>>>
>>>>>>
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>>>>>
>>>>
>>>
>>>
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