iGyne - Add extension

[xjchen]

Gynecologic malignancies – including cervical, endometrial, and vaginal/vulvar cancers – are with 83,750 new cases in 2010 and 26,930 deaths per year, the 4th leading cause of death in women in the US. Treatment consists of concurrent chemotherapy and external beam radiation followed by interstitial gynecologic brachytherapy, which is the placement of radioactive isotopes directly into a cancer of the uterine cervix or vagina. In order to eradicate the cancer, precise insertion of hollow catheters with introducers into the tumor is required. In this contribution, we investigate a software solution to assist interstitial gynecologic brachytherapy. The software has been implemented as module under 3D Slicer, a free open source software platform for biomedical research. This research module enables on-time processing of the intra-operative MRI data via a DICOM connection to the scanner followed by a multi-stage registration of CAD models of the template and the obturator to the patient images. This allows the virtual placement of interstitial needles during the intervention to assist the physician positioning decision.

[fedorov]

Xiaojun, is there a documentation page for this module? I think it is expected that every extension should have a documentation (user guide) page.

[xjchen]

Hi, Andrey,currently, please refer to http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne
for the relevant documentation. Tina also discussed with us about this issue days ago, and we are planning to create a new website regarding iGyne on NCIGT. Hopefully it will be released soon. Thanks!

[fedorov]

Xiaojun, I leave it to JC and Steve who are the administrators of this
project to decide if this is acceptable.

The page you reference does not contain user level documentation, so it is
not clear how a user would be able to learn how to use your module.

The documentation page referenced from your s4ext file is empty:
http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Extensions/Igyne

Please see instructions how to document an extension here:
http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/DocumentExtension

If JC/Steve decide it is ok to add your extension without documentation, I
let them do it.

On Thu, Aug 30, 2012 at 10:34 AM, Xiaojun Chen notifications@github.comwrote:

Hi, Andrey,currently, please refer to
http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne
for the relevant documentation. Tina also discussed with us about this
issue days ago, and we are planning to create a new website regarding iGyne
on NCIGT. Hopefully it will be released soon. Thanks!

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-8161294.

[pieper]

Andrey is right - it's very important to have user documentation for your
extension that follows the conventions. Using the versioning conventions
will help us all keep the documentation current as new releases are cut.

-Steve

On Thu, Aug 30, 2012 at 10:41 AM, Andrey Fedorov
notifications@github.comwrote:

Xiaojun, I leave it to JC and Steve who are the administrators of this
project to decide if this is acceptable.

The page you reference does not contain user level documentation, so it is
not clear how a user would be able to learn how to use your module.

The documentation page referenced from your s4ext file is empty:

http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Extensions/Igyne

Please see instructions how to document an extension here:

http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/DocumentExtension

If JC/Steve decide it is ok to add your extension without documentation, I
let them do it.

On Thu, Aug 30, 2012 at 10:34 AM, Xiaojun Chen notifications@github.comwrote:

Hi, Andrey,currently, please refer to
http://www.na-mic.org/Wiki/index.php/2012_Summer_Project_Week:iGyne
for the relevant documentation. Tina also discussed with us about this
issue days ago, and we are planning to create a new website regarding
iGyne
on NCIGT. Hopefully it will be released soon. Thanks!

—
Reply to this email directly or view it on GitHub<
https://github.com/Slicer/ExtensionsIndex/issues/67#issuecomment-8161294>.

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-8161487.

[xjchen]

Hi, Andrey and Steve, I have already made the documentation page:
http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Extensions/Igyne
Thank you so much for your comments!

[jcfr]

Hi Xiaojun,

Since your extension will probably be available with the coming release
(4.2) instead of (4.1), I renamed the page into
http://www.slicer.org/slicerWiki/index.php?title=Documentation/Nightly/Extensions/Igyne

Would be great if you could update the tutorial section adding one or two
lines describing what the tutorial is about, how many pages, and how long
it takes to do.

Looking at the extension description file
(2ec68dhttps://github.com/xjchen/ExtensionsIndex/commit/2ec68d671f6015c26fec4fb36fbe32349203138d#L0R10),
seems the revision is incorrect.

Would be great if you could make sure to check that the description file
works as expected. See
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Tutorials/BuildTestPackageDistributeExtensions

Thanks
Jc

On Fri, Aug 31, 2012 at 5:01 PM, Xiaojun Chen notifications@github.comwrote:

Hi, Andrey and Steve, I have already made the documentation page:

http://www.slicer.org/slicerWiki/index.php/Documentation/4.1/Extensions/Igyne
Thank you so much for your comments!

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-8204865.

+1 919 869 8849

[xjchen]

Hi, JC,
I have already updated the tutorial section and extension description file as you suggested. Thank you so much!

Best regards,
Xiaojun

[jcfr]

Consider also updating the scmrevision in the description file and testing it following the instruction reported above. Thanks
Jc

[xjchen]

Hi, JC,
I have already updated ‘scmrevision’ as 06cc4ef (https://github.com/xjchen/ExtensionsIndex/blob/67-add-iGyne/Igyne.s4ext) according to the commit log of the igyne github (https://github.com/xjchen/igyne, my last commit is 06cc4ef ), does it work? If not, can I just remove (or comment) this code line in the description file? Thanks!

[jcfr]

Hi Xiaojun,

Revision number is valid. Was probably looking at an older topic.
Could you create a topic and submit a pull request with the correct
description file.

To clarify, how should the extension be named: iGyne, IGyne or Igyne ?

I think IGyne should the name since all extension name starts with an
upercase letter. Let me know what you think ?

Thanks
Jc

On Wed, Sep 5, 2012 at 1:28 PM, Xiaojun Chen notifications@github.comwrote:

Hi, JC,
I have already updated ‘scmrevision’ as 06cc4ef (
https://github.com/xjchen/ExtensionsIndex/blob/67-add-iGyne/Igyne.s4ext)
according to the commit log of the igyne github (
https://github.com/xjchen/igyne, my last commit is 06cc4ef ), does it
work? If not, can I just remove (or comment) this code line in the
description file? Thanks!

—
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[xjchen]

Hi, JC,
I have already created a new topic named “iGyne1.0 - Add extension”(see issue 110).
According to Tina’s suggestion, the extension should be named as iGyne, just like “iPhone”, “iPad”, etc. Further, the letter “i” here not only means “information”, but also means “image-guided”. We are sorry for that it may cause some confusion since all the other extension name starts with an upercase letter,just as you mentioned.
Thank you so much!

Best,
-Xiaojun

[jcfr]

Hi Xiaojun,

Having "IGyne" is good. What matters is to be consistent when referencing
the extension :)

Seems there are no commit referenced in issue 110. See
#110

Could you add anote with the topic/commit that you would like to see
integrated into Nightly extensions build ?
Would you also like to see the extension integrated into 4.2 release ?

Thanks
Jc

On Mon, Nov 5, 2012 at 7:26 AM, Xiaojun Chen notifications@github.comwrote:

Hi, JC,
I have already created a new topic named “iGyne1.0 - Add extension”(see
issue 110).
According to Tina’s suggestion, the extension should be named as iGyne,
just like “iPhone”, “iPad”, etc. Further, the letter “i” here not only
means “information”, but also means “image-guided”. We are sorry for that
it may cause some confusion since all the other extension name starts with
an upercase letter,just as you mentioned.
Thank you so much!

Best,
-Xiaojun

—
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+1 919 869 8849

[xjchen]

Hi, JC,
Sorry for my late reply. I have already add a note for it, and I would be more than happy to see it could be integrated into 4.2 release. Thanks!

Xiaojun

[jcfr]

Hi Xiaojun,

Make sure to sync with Guillaume (CC'ed) regarding the iGyne extension.
Seems both of you were talking about the same extension.

Hth
Jc

On Wed, Nov 14, 2012 at 4:33 AM, Xiaojun Chen notifications@github.comwrote:

Hi, JC,
Sorry for my late reply. I have already add a note for it, and I would be
more than happy to see it could be integrated into 4.2 release. Thanks!

Xiaojun

—
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[jcfr]

Hi Jc,

Actually, it is two different extensions, iGyne v1 (c++ loadable module) and iGyne v2 (qt scripted module)
Thanks,

Guillaume

On Nov 16, 2012, at 9:42 AM, Jean-Christophe Fillion-Robin jchris.fillionr@kitware.com wrote:

Hi Xiaojun,

Make sure to sync with Guillaume (CC'ed) regarding the iGyne extension. Seems both of you were talking about the same extension.

Hth
Jc

On Wed, Nov 14, 2012 at 4:33 AM, Xiaojun Chen notifications@github.com wrote:
Hi, JC,
Sorry for my late reply. I have already add a note for it, and I would be more than happy to see it could be integrated into 4.2 release. Thanks!

Xiaojun

—
Reply to this email directly or view it on GitHub.

+1 919 869 8849

[jcfr]

Hi Guillaume,

Thanks for clarifying. I understand better now.

That said from a user perspective since functionality matters more than
implementation details. Should we just give up on adding the iGyne v1 to
avoid confusion ?

Where is the code base for iGyne v2 ?

Out of curiosity, what was the motivation for converting an entire code
base from C++ to python ?

Thanks
Jc

On Fri, Nov 16, 2012 at 9:46 AM, Guillaume Pernelle gpernelle@gmail.comwrote:

Hi Jc,

Actually, it is two different extensions, iGyne v1 (c++ loadable module)
and iGyne v2 (qt scripted module)
Thanks,

Guillaume

On Nov 16, 2012, at 9:42 AM, Jean-Christophe Fillion-Robin <
jchris.fillionr@kitware.com> wrote:

Hi Xiaojun,

Make sure to sync with Guillaume (CC'ed) regarding the iGyne extension.
Seems both of you were talking about the same extension.

Hth
Jc

On Wed, Nov 14, 2012 at 4:33 AM, Xiaojun Chen notifications@github.comwrote:

Hi, JC,
Sorry for my late reply. I have already add a note for it, and I would be
more than happy to see it could be integrated into 4.2 release. Thanks!

Xiaojun

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/67#issuecomment-10360037.

+1 919 869 8849

+1 919 869 8849

[jcfr]

Hi Jc,

you can find the code here.
We moved to python for the advantage of using ctkworklowwidget as it has been done in ChangeTracker.
iGyne v1 is just now one step of iGyne v2 (iGyneNeedlePlanningStep.py) and there is now a workflow that doesn't require the user to navigate between different modules (but it is internally still depending on them).

I am not sure about continuing or giving up on adding iGyne v1 as an extension as well. We will talk about that with Tina on monday

Thanks,
Guillaume

On Nov 16, 2012, at 9:51 AM, Jean-Christophe Fillion-Robin jchris.fillionr@kitware.com wrote:

Hi Guillaume,

Thanks for clarifying. I understand better now.

That said from a user perspective since functionality matters more than implementation details. Should we just give up on adding the iGyne v1 to avoid confusion ?

Where is the code base for iGyne v2 ?

Out of curiosity, what was the motivation for converting an entire code base from C++ to python ?

Thanks
Jc

On Fri, Nov 16, 2012 at 9:46 AM, Guillaume Pernelle gpernelle@gmail.com wrote:
Hi Jc,

Actually, it is two different extensions, iGyne v1 (c++ loadable module) and iGyne v2 (qt scripted module)
Thanks,

Guillaume

On Nov 16, 2012, at 9:42 AM, Jean-Christophe Fillion-Robin jchris.fillionr@kitware.com wrote:

Hi Xiaojun,

Make sure to sync with Guillaume (CC'ed) regarding the iGyne extension. Seems both of you were talking about the same extension.

Hth
Jc

On Wed, Nov 14, 2012 at 4:33 AM, Xiaojun Chen notifications@github.com wrote:
Hi, JC,
Sorry for my late reply. I have already add a note for it, and I would be more than happy to see it could be integrated into 4.2 release. Thanks!

Xiaojun

—
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+1 919 869 8849

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[jcfr]

sorry i forgot the link: https://github.com/gpernelle/iGynePy

On Nov 16, 2012, at 10:52 AM, Guillaume Pernelle gpernelle@gmail.com wrote:

Hi Jc,

you can find the code here.
We moved to python for the advantage of using ctkworklowwidget as it has been done in ChangeTracker.
iGyne v1 is just now one step of iGyne v2 (iGyneNeedlePlanningStep.py) and there is now a workflow that doesn't require the user to navigate between different modules (but it is internally still depending on them).

I am not sure about continuing or giving up on adding iGyne v1 as an extension as well. We will talk about that with Tina on monday

Thanks,
Guillaume

On Nov 16, 2012, at 9:51 AM, Jean-Christophe Fillion-Robin jchris.fillionr@kitware.com wrote:

Hi Guillaume,

Thanks for clarifying. I understand better now.

That said from a user perspective since functionality matters more than implementation details. Should we just give up on adding the iGyne v1 to avoid confusion ?

Where is the code base for iGyne v2 ?

Out of curiosity, what was the motivation for converting an entire code base from C++ to python ?

Thanks
Jc

On Fri, Nov 16, 2012 at 9:46 AM, Guillaume Pernelle gpernelle@gmail.com wrote:
Hi Jc,

Actually, it is two different extensions, iGyne v1 (c++ loadable module) and iGyne v2 (qt scripted module)
Thanks,

Guillaume

On Nov 16, 2012, at 9:42 AM, Jean-Christophe Fillion-Robin jchris.fillionr@kitware.com wrote:

Hi Xiaojun,

Make sure to sync with Guillaume (CC'ed) regarding the iGyne extension. Seems both of you were talking about the same extension.

Hth
Jc

On Wed, Nov 14, 2012 at 4:33 AM, Xiaojun Chen notifications@github.com wrote:
Hi, JC,
Sorry for my late reply. I have already add a note for it, and I would be more than happy to see it could be integrated into 4.2 release. Thanks!

Xiaojun

—
Reply to this email directly or view it on GitHub.

+1 919 869 8849

+1 919 869 8849

[jcfr]

Since there is now a newer version of the module captured by issue #150. Closing this issue.