<div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote">On Thu, Apr 4, 2013 at 10:12 AM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">OK,<div><br></div><div>So where is the official recommendation on how to create an IJ article with an ITKv4 Submodule?</div>
<div><br></div><div>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?</div><div><br></div></div></blockquote><div style>>> Correct! Give it a try and let us know how it goes!<br>
</div><div style>Thank you!</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word"><div></div><div>Thanks for the clarifications.</div>
<div>Brad</div><div><div class="h5"><div><br><div><div><div>On Apr 4, 2013, at 9:54 AM, Xiaoxiao Liu <<a href="mailto:xiaoxiao.liu@kitware.com" target="_blank">xiaoxiao.liu@kitware.com</a>> wrote:</div><br><blockquote type="cite">
<div dir="ltr"> Turns out that IJ already has the capability of accepting the <b>git repo url</b> at the time of submission, at the <div><b>"Upload Source Code"</b> step. Sorry about my earlier msg.</div>
<div><br></div><div><div style="font-family:arial,sans-serif;font-size:12.800000190734863px">Here is an example of :</div><div style="font-family:arial,sans-serif;font-size:12.800000190734863px"><a href="http://www.insight-journal.org/browse/publication/852#" target="_blank">http://www.insight-journal.org/browse/publication/852#</a><br>
</div><div style="font-family:arial,sans-serif;font-size:12.800000190734863px"><br></div><span style="font-family:arial,sans-serif;font-size:12.800000190734863px">On the right side you can see:</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">- Download Source code (zip file we saved)</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px"><span style="font-family:arial,sans-serif;font-size:12.800000190734863px">- Source code repository (shows the git url)</span><br style="font-family:arial,sans-serif;font-size:12.800000190734863px">
<span style="font-family:arial,sans-serif;font-size:12.800000190734863px">- Github (link to the cloned repository).</span><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Apr 3, 2013 at 1:17 PM, Xiaoxiao Liu <span dir="ltr"><<a href="mailto:xiaoxiao.liu@kitware.com" target="_blank">xiaoxiao.liu@kitware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><div class="gmail_extra"><br><br><div class="gmail_quote"><div>On Wed, Apr 3, 2013 at 1:04 PM, Bradley Lowekamp <span dir="ltr"><<a href="mailto:blowekamp@mail.nih.gov" target="_blank">blowekamp@mail.nih.gov</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word">Xiaoxiao,<div><br></div>
<div>I was looking at the instructions for the source module:</div><div><br></div><div><a href="https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/tree/ModularTemplate/Source" target="_blank">https://github.com/InsightSoftwareConsortium/InsightJournalTemplate/tree/ModularTemplate/Source</a></div>
<div><br></div><div>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.</div><div><br></div></div></blockquote><div>
</div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div></div><div>
Say I have a module I have been using and want to write an IJ article on it:</div>
<div><br></div><div><a href="https://github.com/blowekamp/itkOBBLabelMap" target="_blank">https://github.com/blowekamp/itkOBBLabelMap</a></div><div><br></div><div>Could I just add a submodule in the Source directory? Do I have to use the "MyIJSubmission" for the name of my module?</div>
<div><br></div></div></blockquote><br></div><div><span style="font-weight:bold">>> You don't need to copy your ITK module into the IJ template directory. You should be able to just upload the module folder "</span><b>itkOBBLabelMap"</b><span style="font-weight:bold"> as it is, no need to use "MyIJSubmission". Take a look at the <a href="http://www.insight-journal.org/browse/publication/869" target="_blank">LSTK example</a>, look into the zip file, you will see. I will update the instructions to make it clear.</span></div>
<div>
<div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div></div>
<div>
Would something like the following work:</div><div>git clone --origin template git@github.com:InsightSoftwareConsortium/InsightJournalTemplate.git ijOBBLabelMap</div><div>cd ijOBBLabelMap</div><div>git submodule add <a href="https://github.com/blowekamp/itkOBBLabelMap" target="_blank">https://github.com/blowekamp/itkOBBLabelMap</a> Source/itkOBBLabelMap</div>
<div><br></div></div></blockquote></div><div><b> >> 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.</b></div>
<div><div>
<div><b> </b></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div style="word-wrap:break-word"><div>
</div><div>Thanks,</div><div>Brad</div><div><br><div><br></div><div><br><div><div><div>On Apr 3, 2013, at 12:08 PM, Xiaoxiao Liu <<a href="mailto:xiaoxiao.liu@kitware.com" target="_blank">xiaoxiao.liu@kitware.com</a>> wrote:</div>
<br></div><blockquote type="cite"><div><div dir="ltr"><div>Hi All, </div><div><br></div><div>Just want to let you know that our favorite open-source journal the <a href="http://www.insight-journal.org/" target="_blank">Insight Journal</a> </div>
<div>now supports <b>ITK module</b> submissions.</div>
<div><br></div><div>The modular code template can be found at:</div><div><a href="http://www.insight-journal.org/help/submission" target="_blank">http://www.insight-journal.org/help/submission</a></div><div><br></div><div>
Here is an example of the ITK module submission:</div>
<div> <a href="http://www.insight-journal.org/browse/publication/869" target="_blank">http://www.insight-journal.org/browse/publication/869</a></div><div>with the <a href="http://open.cdash.org/viewTest.php?buildid=2837728" target="_blank">dashboard testing results</a> shown on the review page.</div>
<div><br></div><div>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.<br></div><div><br></div><div>
The main advantages of organizing your code into a ITK module (using the itk module macros in the CMake code) for IJ submission are:</div><div>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.</div>
<div>2) Make it easy to share your cool contribution to the community via the <a href="http://www.itk.org/Wiki/ITK/Policy_and_Procedures_for_Adding_Remote_Modules" target="_blank">ITK Remote Module distribution mechanism</a> : other ITK users/developers can fetch your code remotely by switching on a CMake variable at build time.</div>
<div>3) Testing is easy when utilizing the testing infrastructure (providing image comparisons) in ITK, just follow the example provided in the modular template.</div><div><br></div><div>Please let me know if you see problems or need help when submitting your modular ITK code.</div>
<div>Thanks.</div><div><br></div><div>--Best</div><div>Xiaoxiao</div>---------------------------------------------<br><b>Xiaoxiao Liu</b>, Ph.D.<div><div><font face="arial, sans-serif">R & D Engineer</font></div>
<div><a href="http://www.kitware.com/" target="_blank">Kitware Inc</a>.</div><div><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">Clifton Park, NY</span><div><div>Phone: <a href="tel:%28518%29%20881-4924" value="+15188814924" target="_blank">(518) 881-4924</a> or <span style="border-collapse:collapse;color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px"><a href="tel:%28518%29%20371-3971%20x124" value="+15183713971" target="_blank">(518) 371-3971 x124</a></span></div>
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</blockquote></div><br></div></div></div></blockquote></div></div></div><br><br clear="all"><div><br></div>-- <br><div><div><br></div><div><br></div>---------------------------------------------<br><b>Xiaoxiao Liu</b>, Ph.D.<div>
<div><div>
<font face="arial, sans-serif">R & D Engineer</font></div><div><a href="http://www.kitware.com/" target="_blank">Kitware Inc</a>.</div><div><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">Clifton Park, NY</span><div>
<div>Phone: <a href="tel:%28518%29%20881-4924" value="+15188814924" target="_blank">(518) 881-4924</a> or <span style="border-collapse:collapse;color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px"><a href="tel:%28518%29%20371-3971%20x124" value="+15183713971" target="_blank">(518) 371-3971 x124</a></span></div>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div><br></div><div><br></div>---------------------------------------------<br><b>Xiaoxiao Liu</b>, Ph.D.<div><div><font face="arial, sans-serif">R & D Engineer</font></div>
<div><a href="http://www.kitware.com/" target="_blank">Kitware Inc</a>.</div><div><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">Clifton Park, NY</span><div><div>Phone: <a href="tel:%28518%29%20881-4924" value="+15188814924" target="_blank">(518) 881-4924</a> or <span style="border-collapse:collapse;color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px"><a href="tel:%28518%29%20371-3971%20x124" value="+15183713971" target="_blank">(518) 371-3971 x124</a></span></div>
<div><font face="Verdana, Arial, Helvetica, sans-serif"><span style="line-height:31px;font-size:x-small"><br></span></font></div></div></div></div>
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</blockquote></div><br></div></div></div></div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br><div><br></div><div><br></div>---------------------------------------------<br><b>Xiaoxiao Liu</b>, Ph.D.<div>
<div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">R & D Engineer</span></font></div><div><div><a href="http://www.kitware.com/" target="_blank">Kitware Inc</a>.</div></div><div><span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px">Clifton Park, NY</span><div>
<div>Phone: (518) 881-4924 or <span style="border-collapse:collapse;color:rgb(136,136,136);font-family:arial,sans-serif;font-size:13px">(518) 371-3971 x124</span></div><div><font face="Verdana, Arial, Helvetica, sans-serif"><span style="line-height:31px;font-size:x-small"><br>
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