Joss-reviews: [REVIEW]: idvf: Iterative Inversion of Deformation Vector Field with Adaptive Bi-residual Feedback Control

[whedon]

Submitting author: @ailiop (Alexandros-Stavros Iliopoulos)
Repository: https://github.com/ailiop/idvf
Version: v1.0.3b
Editor: @arokem
Reviewer: @Kevin-Mattheus-Moerman
Archive: 10.5281/zenodo.2610844

Status

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Reviewers and authors:

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Reviewer instructions & questions

@Kevin-Mattheus-Moerman, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ Please try and complete your review in the next two weeks ✨

Review checklist for @Kevin-Mattheus-Moerman

Conflict of interest

• [x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: v1.0.3b
• [x] Authorship: Has the submitting author (@ailiop) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

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

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Kevin-Mattheus-Moerman it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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 😿

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@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[ailiop]

Hi @Kevin-Mattheus-Moerman : did you run into any difficulties with the code that I could help with by any chance? I do not mean to press, just seeing if there is anything I can do.

[Kevin-Mattheus-Moerman]

Hi @ailiop apologies for the delay. I'm starting review today. I'll let you know if there are any issues.

[Kevin-Mattheus-Moerman]

@wouterpotters would you be interested in helping with this review? Flow inversion sounds like your :tea: ?

[ailiop]

@Kevin-Mattheus-Moerman : That sounds great, thank you.

[wouterpotters]

unfortunately my knowledge on this topic is (too) limited to facilitate a
proper review. Maybe one of the CFD experts can help you out?

Best,
Wouter

Op wo 5 dec. 2018 om 09:32 schreef Kevin Mattheus Moerman <
[email protected]>

@wouterpotters https://github.com/wouterpotters would you be interested
in helping with this review? Flow inversion sounds like your 🍵 ?

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[Kevin-Mattheus-Moerman]

This is a well written and well documented submission. Below are my questions/comments and links to issues so far.

__Questions__

• [x] Can you explain why simple interpolation is not sufficient? (see issue https://github.com/ailiop/idvf/issues/2)

__General comments__

• [x] Please add community guidelines (see issue: https://github.com/ailiop/idvf/issues/1)
• [x] Can you please add a more complex spatially varying 3D demo? (see issue: https://github.com/ailiop/idvf/issues/3)
• [x] Can you explain the artifacts occurring in the demos? (see issue: https://github.com/ailiop/idvf/issues/5)

__Recommendations__

• [x] Consider using a larger default figure size (see issue: https://github.com/ailiop/idvf/issues/4)
• [x] Can you include visualization of errors in the reconstructed image domain e.g. the reference image subtracted from the reconstructed reference image (e.g. like presented in https://github.com/ailiop/idvf/issues/5)? And perhaps also plotting of errors of the coordinates (e.g. after using inverse mapping on the coordinates in the deformed configuration). These errors visualize nicely and are easy to interpret.

[arokem]

@Kevin-Mattheus-Moerman : I just saw the exchange above. Do you want me to find one more reviewer for this? Looks like you have this under control 😄

[ailiop]

@Kevin-Mattheus-Moerman : Thank you very much for your detailed comments! I am sorry for not replying earlier; I will work on addressing all of your comments this week.

[labarba]

👋 @ailiop — It's been a month and we've not heard from you. What's your status?

[arokem]

Hey @ailiop : have you had a chance to work through these comments?

[arokem]

Hey @ailiop -- just making sure that you are still there? We had a brief email exchange a couple of weeks ago, and you told me that you are coming back to this. Have you had a chance to take another look and address the comments?

[ailiop]

Dear @arokem and @Kevin-Mattheus-Moerman -- I am really sorry for my unacceptably long absence from this thread. I cannot apologize enough, but I want to sincerely thank @arokem for his patience and @Kevin-Mattheus-Moerman for his thorough and very helpful review.

I have updated the idvf repository to release v1.0.2 and posted responses to the issues opened by @Kevin-Mattheus-Moerman.

[labarba]

👋 @Kevin-Mattheus-Moerman — It looks like we're now waiting for you to have a look at the revisions and responses posted by the author. Can you give us a status update?

[Kevin-Mattheus-Moerman]

Thanks for the reminder @labarba I'll resume work on this on Wednesday.

[Kevin-Mattheus-Moerman]

@ailiop thanks for implementing lots of my suggestions.

When I try to run demo_inversion_3d_z0.m I get this error:

Error using reshape
To RESHAPE the number of elements must not change.

Error in util.imageGridSmooth (line 84)
    width     = reshape( width    , [1, nDim] );

Error in demo_inversion_3d_z0 (line 118)
IRef = util.imageGridSmooth( [szDom zdim], [15 15 5] );

It points to:

IRef = util.imageGridSmooth( [szDom zdim], [15 15 5] );

Can you check what is going on?

[ailiop]

@Kevin-Mattheus-Moerman : Thank you for pointing this out---and for all of your suggestions, which were very helpful!

I have fixed the offending line in the repository (removing zdim). The demo should run without issue now. I do apologize for the error, it should not have slipped through.

[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[Kevin-Mattheus-Moerman]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1002/mp.12962 is OK
• 10.5281/zenodo.1476602 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[Kevin-Mattheus-Moerman]

@ailiop one box above remains unticked i.e. the one relating to automated testing. If the demos test the full functionality perhaps you can create a single script called test_idvf.mwhich simply calls all demos and runs them consecutively.

[ailiop]

@Kevin-Mattheus-Moerman : Thank you for all your help! I have committed such a testing script exactly per your suggestion.

[Kevin-Mattheus-Moerman]

@arokem I've just ticked all the boxes and recommend this work is accepted in JOSS. Thanks for the opportunity to review this interesting work.

[arokem]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[arokem]

@Kevin-Mattheus-Moerman : thanks for reviewing!

@ailiop : your paper is ready to be accepted. Could you please make an archive of the accepted version of the software (e.g., using zenodo) and post the DOI here? Once I register the archive for your software we will be able to do the final checks with the EIC to accept your paper.

[ailiop]

@arokem : I have just made a new release (v1.0.3). The version-specific Zenodo archive DOI is 10.5281/zenodo.2605532. (In case you need it, the version-less DOI which always points to the latest version is 10.5281/zenodo.1476601.) Thank you for all your help!

@Kevin-Mattheus-Moerman : Thank you once again for your effort in reviewing this work!

[ailiop]

@arokem : I just realized that I had forgotten to update the release version tag to v1.0.3 in the codemeta.json metadata. I am sorry I did not notice that yesterday before archiving the release. Should I delete and re-create the release to make sure the JSON metadata are consistent with it before you run through the final checks you mentioned?

[arokem]

@ailiop : If it's not too much to ask, please do update the codemeta file and make a new release, so that everything's consistent and then create a new archive with this version. Thanks!

[ailiop]

@arokem : No problem at all, I figured it might be an issue. I just created a new release (v1.0.3b) with a corrected codemeta.json file. The Zenodo DOI for v1.0.3b is 10.5281/zenodo.2610844.

[arokem]

@whedon set 10.5281/zenodo.2610844 as archive

[whedon]

OK. 10.5281/zenodo.2610844 is the archive.

[arokem]

@whedon set v1.0.3b as version

[whedon]

OK. v1.0.3b is the version.

[arokem]

OK. This is ready to be accepted.

One of the EIC will come by, make comments if they have any, and finish the process.

[danielskatz]

thanks to @arokem for editing and @Kevin-Mattheus-Moerman for reviewing!!

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/589

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/589, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[whedon]

```Reference check summary:

OK DOIs

• 10.1002/mp.12962 is OK
• 10.5281/zenodo.1476602 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[danielskatz]

@whedon accept deposit=true

[whedon]

Doing it live! Attempting automated processing of paper acceptance...

[whedon]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/590
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01076
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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[ailiop]

Thank you all very much!