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[REVIEW]: The Vascular Modeling Toolkit: A Python Library for the Analysis of Tubular Structures in Medical Images #745

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whedon opened this Issue May 21, 2018 · 33 comments

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whedon commented May 21, 2018

Submitting author: @rlizzo (Richard Izzo)
Repository: https://github.com/vmtk/vmtk
Version: v1.4.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @wouterpotters, @brainstorm
Archive: 10.5281/zenodo.1253598

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/238cc3a9c1c4105b616cc3a0f2414ecb"><img src="http://joss.theoj.org/papers/238cc3a9c1c4105b616cc3a0f2414ecb/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/238cc3a9c1c4105b616cc3a0f2414ecb/status.svg)](http://joss.theoj.org/papers/238cc3a9c1c4105b616cc3a0f2414ecb)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@wouterpotters & @brainstorm, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

Review checklist for @wouterpotters

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v1.4.0)?
  • Authorship: Has the submitting author (@rlizzo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @brainstorm

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v1.4.0)?
  • Authorship: Has the submitting author (@rlizzo) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
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whedon commented May 21, 2018

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @wouterpotters, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐️ Important ⭐️

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands
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whedon commented May 21, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented May 21, 2018

@Kevin-Mattheus-Moerman

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Kevin-Mattheus-Moerman commented May 21, 2018

@rlizzo, @wouterpotters, @brainstorm this is where the review process takes place. There are sets of tickboxes for both reviewers at the top of this issue (let me know if you are unable to tick them). If you have questions please let me know. You may also want to check out the JOSS reviewer guidelines.

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Kevin-Mattheus-Moerman commented May 21, 2018

@osmsc @sshadden @jmerkow @alexkaiser @updega2 @gmaher @fkong7 this is a JOSS review issue for The Vascular Modeling Toolkit . Please let me know if you are interested in reviewing this submission.

The review process is focused largely on the software and a short paper, see the reviewer guidelines.

--> Check article proof 📄 <--

--> Check software repository 💾 <--

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wouterpotters commented May 21, 2018

minor issue: license in LICENSE file vmtk/vmtk#283

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wouterpotters commented May 21, 2018

Extensive testing system; all explained in the CONTRIBUTING.md file, test folder and on https://github.com/vmtk/vmtk-test-data.

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wouterpotters commented May 21, 2018

already fixed; new user instructions: vmtk/vmtk#286

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wouterpotters commented May 21, 2018

Despite the fact that there already is a lot of useful documentation for both users and developers: issue with (incomplete) documentation: http://github.com/vmtk/vmtk/issues/288

Improving this point would improve the open source aspect of vmtk

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wouterpotters commented May 21, 2018

Some small issues with the submitted manuscript: vmtk/vmtk#289

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wouterpotters commented May 21, 2018

Overall opinion on the submitted paper:
The VMTK software package is a scientifically relevant open source software package that is relevant specifically to the field of vascular imaging and simulation.

The package is useful for users at different levels. Clinicians and non-technical users can use their precompiled version, more advanced developers can use either the python or the C++ libraries.

As the package is largely based on the common VTK and ITK packages, the software is easily used within other VTK / ITK based packages and the other way around. VTK / ITK features are easily implemented in vmtk.

Key features besides VTK / ITK are the pypes pipeline, which enables users to manually or automatically process all types of files into custom pipelines with custom output files.
Another key feature is the unique and robust way to detect and process the centrelines of tubular structures. Together with several surface processing and mesh generating functions, this software package can quantify basic vascular/tubular properties and perform the required preparations for (open source) CFD simulations.
The extensive manuals and (almost complete) documentation pages guide new user through these features.

The previous release of this software (2008) has been cited and used a lot by many users. In the past years the software package went through some significant and important changes (test system, user interface improvements, new features).

Overall I would advise to accept the publication of this excellent open source software package, provided that the authors improve the C++ classes documentation and the paper.md.

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rlizzo commented May 22, 2018

@whedon generate pdf

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whedon commented May 22, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented May 22, 2018

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rlizzo commented May 22, 2018

@whedon generate pdf

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whedon commented May 22, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented May 22, 2018

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wouterpotters commented May 24, 2018

Already looking good now with the latest additions. As soon as the C++ docs are (more) complete, I vote to accept the package. What do you think @brainstorm?

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brainstorm commented May 25, 2018

Yeah, likewise @wouterpotters, the functional docs are the only area where a bit more text/work would be great to have to pass this review, imho.

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rlizzo commented May 25, 2018

@brainstorm and @wouterpotters: Just letting you know that we have merged the improvements to the C++ class level documentation you requested. You can review the the changes in the Merged PR vmtk/vmtk#295, or view the additions online: http://www.vmtk.org/doc/html/annotated.html. The majority of effort went into documenting the code which has to do with data structures or processing methods which are more specialized to the field of computational vascular analysis. For your reference, the centerline analysis scripts primarily exist within the vtkVmtk/ComputationalGeometry subdirectory of the repository.

I hope this addresses your concern on the low level library documentation.Please let me know your thoughts. Thank you!

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brainstorm commented May 25, 2018

There seems to be a few function description gaps still left to fill on the http://www.vmtk.org/doc/html/annotated.html link, but overall looks good, what do you think @wouterpotters?

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wouterpotters commented May 25, 2018

@brainstorm Looks like a great addition to the docs. I vote to accept this manuscript & code for publication.

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Kevin-Mattheus-Moerman commented May 25, 2018

Thanks @wouterpotters and @brainstorm for this excellent and smooth review process! @wouterpotters if you feel we are good to go please tick all the boxes at the top of this issue.
@rlizzo can you reply to @brainstorm 's issue with respect to gaps in function description?

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wouterpotters commented May 25, 2018

@Kevin-Mattheus-Moerman unfortunately I can’t due to technical limitations. I don’t have acces to a physical computer in the next few days and both my iPhone and my Android phone are not allowed (by github) to check that box. Maybe @brainstorm or you could check it?

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rlizzo commented May 25, 2018

@Kevin-Mattheus-Moerman thank you, I will have some time in a few hours to update the last few functions @brainstorm mentioned. I appreciate the feedback!

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Kevin-Mattheus-Moerman commented May 25, 2018

@wouterpotters I ticked it for you now thanks again for your help with this review! 🎉

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rlizzo commented May 26, 2018

@brainstorm and @Kevin-Mattheus-Moerman, I have updated the documentation at your request. See changes in http://www.vmtk.org/doc/html/annotated.html.

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brainstorm commented May 26, 2018

Fantastic, thanks! All thumbs up from my side, I just ticked the last box, thanks everyone.

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rlizzo commented May 26, 2018

Thanks everyone! Archived the version with all the boxes checked on zendoo:

DOI

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arfon commented May 26, 2018

@whedon set 10.5281/zenodo.1253598 as archive

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whedon commented May 26, 2018

OK. 10.5281/zenodo.1253598 is the archive.

@arfon arfon added the accepted label May 26, 2018

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arfon commented May 26, 2018

@wouterpotters, @brainstorm - many thanks for your reviews here and to @Kevin-Mattheus-Moerman for editing this submission

@rlizzo - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00745 ⚡️ 🚀 💥

@arfon arfon closed this May 26, 2018

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whedon commented May 26, 2018

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00745/status.svg)](https://doi.org/10.21105/joss.00745)

This is how it will look in your documentation:

DOI

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