[Insight-developers] [Insight-users] Submit ITK modules to Insight Journal

Thu Apr 4 13:22:07 EDT 2013

On Thu, Apr 4, 2013 at 10:12 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:

> OK,
>
> So where is the official recommendation on how to create an IJ article
> with an ITKv4 Submodule?
>
> It sounds like I should get the IJ template just for the text, and just
> create a standard ITKv4 module, and submit that via the git URL?
>
> >> Correct! Give it a  try and let us know how it goes!
Thank you!

> Thanks for the clarifications.
> Brad
>
> On Apr 4, 2013, at 9:54 AM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com> wrote:
>
>  Turns out that  IJ already has the capability of accepting the *git repo
> url* at the time of submission, at the
> *"Upload Source Code"* step. Sorry about my earlier  msg.
>
> Here is an example of :
> http://www.insight-journal.org/browse/publication/852#
>
> On the right side you can see:
> - Download Source code (zip file we saved)
> - Source code repository (shows the git url)
> - Github (link to the cloned repository).
>
>
> On Wed, Apr 3, 2013 at 1:17 PM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com>wrote:
>
>>
>>
>>
>> On Wed, Apr 3, 2013 at 1:04 PM, Bradley Lowekamp <blowekamp at mail.nih.gov>wrote:
>>
>>> Xiaoxiao,
>>>
>>> I was looking at the instructions for the source module:
>>>
>>>
>>> https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/tree/ModularTemplate/Source
>>>
>>> It looks like I need to copy my current ITK Module into this IJ Template
>>> directory, then copy it back into ITK to build it... Seems like too much
>>> coping.
>>>
>>>
>>
>>> Say I have a module I have been using and want to write an IJ article on
>>> it:
>>>
>>> https://github.com/blowekamp/itkOBBLabelMap
>>>
>>> Could I just add a submodule in the Source directory? Do I have to use
>>> the "MyIJSubmission" for the name of my module?
>>>
>>>
>> >> You don't need to copy your ITK module into the IJ template directory.
>> You should be able to just upload the module folder "*itkOBBLabelMap"* as
>> it is, no need to use "MyIJSubmission".  Take a look at the LSTK example<http://www.insight-journal.org/browse/publication/869>,
>> look into the zip file, you will see.   I will update the instructions to
>> make it clear.
>>
>>
>>>  Would something like the following work:
>>> git clone --origin template git at github.com:InsightSoftwareConsortium/InsightJournalTemplate.git
>>> ijOBBLabelMap
>>> cd  ijOBBLabelMap
>>> git submodule add https://github.com/blowekamp/itkOBBLabelMapSource/itkOBBLabelMap
>>>
>>> * >> Why you are using submodule here? Right now, we still require
>> contributors to upload the code tar ball instead of providing a git url. It
>> is an excellent idea though to use a git repo link instead. This will need
>> some extra work on the IJ server end. Let me check how difficult it is and
>> report back.*
>>  * *
>>
>>> Thanks,
>>> Brad
>>>
>>>
>>>
>>> On Apr 3, 2013, at 12:08 PM, Xiaoxiao Liu <xiaoxiao.liu at kitware.com>
>>> wrote:
>>>
>>> Hi All,
>>>
>>> Just want to let you know that our favorite open-source journal the Insight
>>> Journal <http://www.insight-journal.org/>
>>> now supports *ITK module* submissions.
>>>
>>> The modular code template can be found at:
>>> http://www.insight-journal.org/help/submission
>>>
>>> Here is an example of the ITK module submission:
>>>   http://www.insight-journal.org/browse/publication/869
>>> with the dashboard testing results<http://open.cdash.org/viewTest.php?buildid=2837728>shown on the review page.
>>>
>>> Newly submitted  ITK modules will be tested with ITK 4.3.1 for now,  and
>>> hopefully will soon be tested with  latest release version of ITK at the
>>> time of submission.
>>>
>>> The main advantages of organizing your code into a ITK module (using the
>>> itk module macros in the CMake code) for IJ submission are:
>>> 1) Make it easier to integrate your code into ITK proper later. The
>>> modular structure makes you to think about the module dependencies and
>>> categorization of your code earlier on.
>>> 2) Make it easy to share your cool contribution to the community via the ITK
>>> Remote Module distribution mechanism<http://www.itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules> :
>>> other ITK users/developers can fetch your code remotely by switching on a
>>> CMake variable at build time.
>>> 3) Testing is easy when utilizing the testing infrastructure  (providing
>>> image comparisons) in ITK, just follow the example provided in the modular
>>> template.
>>>
>>> Please let me know if you see problems or need help when submitting your
>>> modular ITK code.
>>> Thanks.
>>>
>>> --Best
>>> Xiaoxiao
>>> ---------------------------------------------
>>> *Xiaoxiao Liu*, Ph.D.
>>> R & D Engineer
>>> Kitware Inc <http://www.kitware.com/>.
>>> Clifton Park, NY
>>> Phone: (518) 881-4924  or  (518) 371-3971 x124
>>>
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>>>
>>>
>>
>>
>> --
>>
>>
>> ---------------------------------------------
>> *Xiaoxiao Liu*, Ph.D.
>>  R & D Engineer
>> Kitware Inc <http://www.kitware.com/>.
>> Clifton Park, NY
>> Phone: (518) 881-4924  or  (518) 371-3971 x124
>>
>>
>
>
> --
>
>
> ---------------------------------------------
> *Xiaoxiao Liu*, Ph.D.
> R & D Engineer
> Kitware Inc <http://www.kitware.com/>.
> Clifton Park, NY
> Phone: (518) 881-4924  or  (518) 371-3971 x124
>
>
>

-- 

---------------------------------------------
*Xiaoxiao Liu*, Ph.D.
R & D Engineer
Kitware Inc <http://www.kitware.com/>.
Clifton Park, NY
Phone: (518) 881-4924  or  (518) 371-3971 x124
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