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[5.2] Add QuickModelAlign extension #1940

Closed
wants to merge 34 commits into from
Closed

[5.2] Add QuickModelAlign extension #1940

wants to merge 34 commits into from

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seanchoi0519
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New extension

  • Extension has a reasonable name (not too general, not too narrow, suggests what the extension is for)
  • Repository name is Slicer+ExtensionName
  • Repository is associated with 3d-slicer-extension GitHub topic so that it is listed here. To edit topics, click the settings icon in the right side of "About" section header and enter 3d-slicer-extension in "Topics" and click "Save changes". To learn more about topics, read https://help.github.com/en/articles/about-topics
  • Extension description summarizes in 1-2 sentences what the extension is usable (should be understandable for non-experts)
  • Any known related patents must be mentioned in the extension description.
  • LICENSE.txt is present in the repository root. MIT (https://choosealicense.com/licenses/mit/) or Apache (https://choosealicense.com/licenses/apache-2.0/) license is recommended. If source code license is more restrictive for users than MIT, BSD, Apache, or 3D Slicer license then the name of the used license must be mentioned in the extension description.
  • Extension URL and revision (scmurl, scmrevision) is correct, consider using a branch name (main, release, ...) instead of a specific git has to avoid re-submitting pull request whenever the extension is updated
  • Extension icon URL is correct (do not use the icon's webpage but the raw data download URL that you get from the download button - it should look something like this: https://raw.githubusercontent.com/user/repo/main/SomeIcon.png)
  • Screenshot URLs (screenshoturls) are correct, contains at least one
  • Homepage URL points to valid webpage containing the following:
    • Extension name
    • Short description: 1-2 sentences, which summarizes what the extension is usable for
    • At least one nice, informative image, that illustrates what the extension can do. It may be a screenshot.
    • Description of contained modules: at one sentence for each module
    • Tutorial: step-by-step description of at least the most typical use case, include a few screenshots, provide download links to sample input data set
    • Publication: link to publication and/or to PubMed reference (if available)
    • License: We suggest you use a permissive license that includes patent and contribution clauses. This will help protect developers and ensure the code remains freely available. We suggest you use the Slicer License or the Apache 2.0. Always mention in your README file the license you have chosen. If you choose a different license, explain why to the extension maintainers. Depending on the license we may not be able to host your work. Read here to learn more about licenses.
    • Content of submitted s4ext file is consistent with the top-level CMakeLists.txt file in the repository (description, URLs, dependencies, etc. are the same)
  • Hide unused features in the repository to reduce noise/irrelevant information:
    • Click Settings and in repository settings uncheck Wiki, Projects, and Discussions (if they are currently not used)
    • Click the settings icon next to About in the top-right corner of the repository main page and uncheck Releases and Packages (if they are currently not used)

lassoan and others added 30 commits November 23, 2022 18:22
@lassoan
Update PULL_REQUEST_TEMPLATE.md
b933c8f 
Require LICENSE.txt in the repository root, recommend MIT and Apache.
@lassoan
Add TotalSegmentator extension
f9f606c 
Allows running TotalSegmentator AI segmenter from Slicer.
PyTorch and TotalSegmentator are installed in Slicer's Python environment and run natively, without docker.
@kyliekeijzer
Add MUST-segmenter extension (Slicer#1895)
bebbaa2 
* Add MUST-segmenter extension

* Update MUST-segmenter

- repository url
- icon url
- description
- add more screenshot urls
- dependencies

* Update MUST-segmenter.s4ext
@ChenXiang96 @jcfr
Update the description in ColocZStats.s4ext
c00f7bd 
Update the description in ColocZStats.s4ext
@MarinaSandonis
Update SlicerTissueSegmentation extension
dfb9d6e 
Update icon URL and screenshot URLs
@chir-set @lassoan
Propose ExtraMarkups extension.
fea13cd
@chir-set @lassoan
Update repository name.
99058b5 
ExtraMarkups -> SlicerExtraMarkups.
@chir-set @lassoan
Propose ExtraMarkups extension as SlicerExtraMarkups.
c7810c1
@chir-set @lassoan
Update screenshoturls and description fields.
267c997
@chir-set @lassoan
Remove StenosisMeasurement3D module.
a71a9cd 
It will be proposed in SlicerVMTK with a soft dependency on SlicerExtraMarkups.
@RafaelPalomar @jamesobutler
BUG: Fix double space between urls in SlicerLiver
ac6c461 
This commit replaces the double space between screenshot urls for the
SlicerLiver extension by single space. This was causing issues with the
extension slideshow.

Co-authored-by: James Butler <[email protected]>
@smrolfe
Add MEMOS extension (Slicer#1908)
8432c81
@smrolfe
Fix SlicerMEMOS repo branch name (Slicer#1909)
02deded
@smrolfe @jcfr
Add PyTorch extension as a dependency
abab8ff
@lassoan
Rename SlicerExtraMarkups to ExtraMarkups to match the extension name
c79027b 
Repository name is SlicerExtraMarkups, extension name is ExtraMarkups.
@lassoan @pieper
Add SlicerNeuro extension
6ea8e46 
While translating Slicer to different languagues we noticed that a very specialized brain coordinate system transformation module (ACPCTransform) is still in Slicer core. This is an outlier, because all other domain-specific modules are now in extensions. To make translation and maintenance of Slicer core easier it makes sense to move ACPCTransform to an extension.

Since there was no existing extension for generic neuroimaging modules, a new SlicerNeuro extension has been added.

Since the extension only contains one module, it would not be that useful, so some other neuroimaging related extensions are added as dependencies, so the extension can serve as a starting point for users in this field (they need to install only one extension to get all). If more modules will be added to the extension then this may be revisited (extensions that are not actually required can be removed from the extension dependency list).

Co-authored-by: Steve Pieper <[email protected]>
@lassoan
Added disabling unused github features to pull request checklist
a851a82
@chir-set @lassoan
Update SlicerVMTK.
37cf597 
In the process of adding 'StenosisMeasurement3D' module to SlicerVMTK, a
dependency on 'ExtraMarkups' extension is introduced. The s4ext file is hereby
updated.
@NicerNewerCar @jcfr
Add SlicerAutoscoperM extension
367cc3c 
See https://autoscoperm.slicer.org/

Co-authored-by: Jean-Christophe Fillion-Robin <[email protected]>
@simonoxen @lassoan
SlicerNetstim update screenshot path
0396cfb
@jcfr
DOC: Update obsolete comments describing the source code manager
c80243d 
This is a follow-up of Slicer/Slicer@7f533d3d0
@jamesobutler
ENH: Update SlicerPyTorch to use main branch
5e54b30
@jamesobutler
ENH: Update TorchIO to use main branch
96a7d50 
The master branch was renamed to main.
@zapaishchykova @sjh26
Add SlicerLikertDLrating extension
1aacbe9 
SlicerLikertDLrating extension for fast clinician review of Deep-learning-generated masks using Likert-type score (4 Scale, 1: Acceptable, no changes; 2: Acceptable, minor changes; 3: Unacceptable, major changes; 4: Unacceptable, not visible/wrong location), with segment editor functionality. The dataset loads in one batch with no need to load masks and volumes separately. The results are saved in a CSV file, which can be used for further analysis.
@zapaishchykova @sjh26
Update SlicerLikertDLrating.s4ext
91d0b8c
@zapaishchykova @sjh26
Rename SlicerLikertDLrating.s4ext to SlicerSegReview.s4ext
a140b7d
@zapaishchykova @sjh26
Update SlicerSegReview.s4ext
9999e8c
@ZhyBrian
Add new extension AI Assisted BUS Diagnosis for 3D Slicer (Slicer#1920)
227db4b 
* Add new extension AI Assisted BUS Diagnosis

* change the new extension name to SlicerAIBreastUSDiagnosis

* remove old

* change the new extension name to BreastUltrasoundAnalysis

* update: depend on PyTorch
@zapaishchykova @jcfr
Rename SlicerSegReview to SegmentationReview
fe6dd1f 
The underlying GitHub project was renamed

Co-authored-by: Jean-Christophe Fillion-Robin <[email protected]>
@seanchoi0519
Add files via upload
890097e
@seanchoi0519
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Am not sure how to resolve this conflict, could anyone please help, thanks!

@jamesobutler
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You will need to create a new branch off of https://github.com/Slicer/ExtensionsIndex/tree/5.2 and then add the same type changes that you made in the commit for #1941. Consult general git instructions on the web for additional help and relevant for your developer tools of choice.

@seanchoi0519
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seanchoi0519 commented Jun 1, 2023 •
edited
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Sorry I'm quite new to github, not sure what this means..
Can I un-do my pull requests and try again?
I've just made a change to my file so I'm afraid it might affect the rest of it, would like to start fresh

@jcfr jcfr changed the title QuickAlign Extension Pull Request [5.2] Add QuickAlign extension Aug 15, 2023
@jcfr jcfr changed the title [5.2] Add QuickAlign extension [5.2] Add QuickModelAlign extension Aug 16, 2023
@jcfr
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jcfr commented Aug 16, 2023

I am closing this pull request, we will revisit once the extension has been integrated into the main branch through this pull request:

@jcfr jcfr closed this Aug 16, 2023
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