[REVIEW]: Sports2D: Compute 2D joint and segment angles from your smartphone

editorialbot commented 2 months ago

Submitting author: !--author-handle-->@DavidPagnon@Kevin-Mattheus-Moerman<!--end-editor-- Reviewers: @tuliofalmeida, @nicos1993, @johnjdavisiv Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/1d525bbb2695c88c6ebbf2297bd35897/status.svg)](https://joss.theoj.org/papers/1d525bbb2695c88c6ebbf2297bd35897)

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) by leaving comments 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

@tuliofalmeida & @nicos1993 & @johnjdavisiv, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Kevin-Mattheus-Moerman know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @nicos1993

📝 Checklist for @johnjdavisiv

📝 Checklist for @tuliofalmeida

editorialbot commented 2 months ago

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editorialbot commented 2 months ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.48550/arXiv.2006.10204 is OK
- 10.1007/978-1-4842-4470-8 is OK
- 10.1038/s41746-023-00775-1 is OK
- 10.7326/0003-4819-157-1-201207030-00450 is OK
- 10.1109/TPAMI.2019.2929257 is OK
- 10.2307/2683591 is OK
- 10.1186/s40798-018-0139-y is OK
- 10.1007/s00167-021-06709-2 is OK
- 10.1038/s41467-020-17807-z is OK
- 10.1038/s41593-018-0209-y is OK
- 10.2139/ssrn.3413035 is OK
- 10.1080/24748668.2008.11868456 is OK
- 10.21105/joss.04362 is OK
- 10.1080/00140139.2015.1057238 is OK
- 10.1101/2022.07.07.499061 is OK
- 10.2307/41410412 is OK
- 10.7717/peerj.12995 is OK
- 10.1152/japplphysiol.00772.2007 is OK
- 10.1145/3603618 is OK

MISSING DOIs

- No DOI given, and none found for title: The OpenCV Library
- No DOI given, and none found for title: On the theory of filter amplifiers
- No DOI given, and none found for title: Kinovea - A microscope for your videos
- No DOI given, and none found for title: A 3D markerless protocol with action cameras – Key...
- No DOI given, and none found for title: Gait analysis: an introduction

INVALID DOIs

- None

editorialbot commented 2 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (572.0 files/s, 243661.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0            931           1911
Python                          11            424            690           1380
Jupyter Notebook                 1              0           2816            298
Markdown                         2            112              0            245
TeX                              1             23              0            241
TOML                             3             38             39             96
YAML                             3             17             14             96
-------------------------------------------------------------------------------
SUM:                            22            614           4490           4267
-------------------------------------------------------------------------------

Commit count by author:

   114  David PAGNON
    79  davidpagnon

editorialbot commented 2 months ago

Paper file info:

📄 Wordcount for paper.md is 1281

✅ The paper includes a Statement of need section

editorialbot commented 2 months ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

johnjdavisiv commented 2 months ago

Review checklist for @johnjdavisiv

Conflict of interest

[ ] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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

General checks

[ ] Repository: Is the source code for this software available at the https://github.com/davidpagnon/Sports2D?
[ ] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@DavidPagnon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[ ] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[ ] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[ ] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[ ] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Kevin-Mattheus-Moerman commented 2 months ago

@tuliofalmeida, @nicos1993, @johnjdavisiv This is where the review takes place. To get started, like @johnjdavisiv did just now, you can call @editorialbot generate my checklist. Thanks again for your help!!! Let me know if you have any questions.

nicos1993 commented 2 months ago

Review checklist for @nicos1993

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/davidpagnon/Sports2D?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@DavidPagnon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] 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

[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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

tuliofalmeida commented 2 months ago

Review checklist for @tuliofalmeida

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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 https://github.com/davidpagnon/Sports2D?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@DavidPagnon) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

nicos1993 commented 1 month ago

Apologies for the delay in this review. I will complete by the end of this week if that is okay?

Nicos

davidpagnon commented 1 month ago

Hi, thank you Nicos and the other reviewers.

To @Kevin-Mattheus-Moerman: @hunminkim98 and I are currently working to make it run in real time, I wonder if it's worth completing the review with the library the way it is, or if it's better to wait?

Note that it could be a couple months because it's not the hottest priority right now.

https://github.com/user-attachments/assets/ffc549b4-f76f-4fa5-a7d8-6bfae7e702ba

Kevin-Mattheus-Moerman commented 1 month ago

@davidpagnon I suggest we continue with the current state of things as submitted. If you've implemented the features before this review is over we can revisit this. In any case I recommend you implement it with a clear example for instance, so that testing this new functionality is quick and simple, and would not take a lot of additional time.

Kevin-Mattheus-Moerman commented 1 month ago

@tuliofalmeida, @nicos1993, @johnjdavisiv thanks again for your help with this review. Would you be able to provide a quick update on where things stand? Are there some key points the authors should work on? Thanks!

tuliofalmeida commented 1 month ago

Hey @Kevin-Mattheus-Moerman I'm planning to finish this week!

nicos1993 commented 1 month ago

Hello @Kevin-Mattheus-Moerman,

I have tested the software using installation option 2 and followed the example, I can confirm the instructions are very clear and the demonstration ran smoothly with no issues. I believe this software will be very useful for coaches or practitioners wishing to perform a 2D automated kinematic analysis.

I do have a couple of suggestions that the author may wish to consider.

The demo video in the online repository and Figure 1 in the accompanying paper. Whilst the author acknowledges the limitation of using the software to analyze non-sagittal/frontal videos, the demo video/figure is very much non-planar and I would recommend using a demo video/figure which is specifically from either the sagittal plane or the frontal plane. In the software examples perhaps it would be nice to have both examples.
Segment and joint angle conventions. The author provides a citation for the convention of the angles used, but I would recommend using a more common and intuitive convention (e.g., from Winter 2009, Biomechanics and motor control of human movement). I believe this would also be more beneficial to coaches/practitioners. Lastly, in the figure I would consider including the definitions of the segment angles together with the joint angles.

Best wishes,

Nicos Haralabidis

davidpagnon commented 1 month ago

Hi Nicos,

Thank you for your review!

I fully agree with your statement that the Demo video was probably not the best, given that it does not lie in the plane. I will replace it with a video of someone doing jumping jacks (frontal plane) and another person doing tuck jumps (sagittal plane).
I believe the joint angle convention is the same as the one from Winter 2009, but I agree that the way it is represented makes it confusing. I will add this figure to the article and the tutorial.

I will ping you once the fixes have been made.

Kevin-Mattheus-Moerman commented 3 weeks ago

@nicos1993 thanks for your review and comments. Could you respond to the authors reply :point_up: ? Let me know if you are now happy (some of your boxes are not ticked) with this submission or if there are any other points that the authors should work on. Thanks!

Kevin-Mattheus-Moerman commented 3 weeks ago

@johnjdavisiv thanks for your help with this review. Would you be able to finalise your review shortly? We do have two nearly completed reviews, but if you are able to complete yours that would be great. Thanks!

Kevin-Mattheus-Moerman commented 3 weeks ago

@tuliofalmeida it looks like you've ticked all boxes. Are you happy to recommend acceptance of this work for JOSS? Thanks for your help!

johnjdavisiv commented 3 weeks ago

@Kevin-Mattheus-Moerman Will be a bit of a stretch to finish it this week, but I can get it done by the end of next!

Kevin-Mattheus-Moerman commented 1 week ago

@johnjdavisiv thanks. Let me know if you have any questions or if you are good to proceed.

Kevin-Mattheus-Moerman commented 1 week ago

@tuliofalmeida it looks like you've ticked all boxes. Are you happy to recommend acceptance of this work for JOSS? Thanks for your help!

davidpagnon commented 1 week ago

Hi @Kevin-Mattheus-Moerman, Thank you for following up. Can we wait about a week before acceptance? We made it work in real-time, and we would like to add one or two lines in the paper to mention it. Also, there is still one point that @nicos1993 brought up that has not been taken into account.

tuliofalmeida commented 1 week ago

@tuliofalmeida it looks like you've ticked all boxes. Are you happy to recommend acceptance of this work for JOSS? Thanks for your help!

I'm sorry, I thought I had already answered you. And yes, I recommend it for publication. It's working well, I reported him a small bug that I found and I also agree with the suggestion that Nico made.

Kevin-Mattheus-Moerman commented 1 week ago

@davidpagnon That is fine. I was not suggesting moving to acceptance yet. I was just trying to get reviewers that are done to complete all the boxes. Once all reviews are finished, and recommendations are in order, we are ready to proceed.

Kevin-Mattheus-Moerman commented 1 week ago

@nicos1993 thanks again for reviewing here. Are you also able to finalize the checklist or are there any remaining issues that need to be addressed?

nicos1993 commented 1 week ago

Hi Nicos,

Thank you for your review!

I fully agree with your statement that the Demo video was probably not the best, given that it does not lie in the plane. I will replace it with a video of someone doing jumping jacks (frontal plane) and another person doing tuck jumps (sagittal plane).

I believe the joint angle convention is the same as the one from Winter 2009, but I agree that the way it is represented makes it confusing. I will add this figure to the article and the tutorial.

I will ping you once the fixes have been made.

Hello @Kevin-Mattheus-Moerman ,

I believe the changes I suggested regarding the examples in the article and paper have not been made/updated yet (please correct me if I am wrong. I also believe the updated joint angle convention figure has not been included in the article.

Best wishes,

Nicos

davidpagnon commented 1 week ago

You are right, there is more cleaning up to do in the new code than I expected so it takes a bit of time. I'm in a rushed period so it's hard to prioritize it but I'll try to get it done by next week, sorry about it!

Kevin-Mattheus-Moerman commented 4 days ago

@davidpagnon although we are flexible in principle, I do recommend that you make the changes as soon as possible to avoid loosing track of the reviewers. Can you provide an indication as to when the changes will be finished?

Kevin-Mattheus-Moerman commented 4 days ago

@johnjdavisiv can you resume your review please? Thanks!

davidpagnon commented 16 hours ago

The new version has been released!

Used RTMPose rather than OpenPose or BlazePose (faster, more accurate, more flexible)
Single process for both pose and angle estimation
Webcam analysis available
Body angle visualization
Used entry points by default for clarity and simplicity
Saved as OpenSim files: TRC for pose, MOT for angles
Clearer documentation
Better demo video
Improved tracking IDs across frames
Added some segment angles: Pelvis, Shoulders, Head

I am now working on editing the paper and fixing the Colab version.

openjournals / joss-reviews