[REVIEW]: ParticleTracking: A GUI and library for particle tracking on stereo camera images

[editorialbot]

Submitting author: @a-niem (Adrian Niemann)
Repository: https://github.com/ANP-Granular/ParticleTracking
Branch with paper.md (empty if default branch): joss_paper
Version: v0.6.0
Editor: @jgostick
Reviewers: @mhubii, @aquilesC, @merrygoat
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/41caf0076b48061c1efcc2810b85543f/status.svg)](https://joss.theoj.org/papers/41caf0076b48061c1efcc2810b85543f)

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

@mhubii, 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 @jgostick 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 @mhubii

📝 Checklist for @aquilesC

📝 Checklist for @merrygoat

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.21 s (739.1 files/s, 133487.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          76           3005           7317          12987
Qt                               1              0              0           2348
Markdown                        19            296              0           1091
JSON                             7              0              0            508
TeX                              1             10              0            193
TOML                             2             13              0            155
reStructuredText                45             66            245             94
YAML                             3              8             14             69
DOS Batch                        2             14              1             49
Bourne Shell                     1              3              6             24
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                           158           3419           7590          17527
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1030

[editorialbot]

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

OK DOIs

- 10.1038/s41592-019-0686-2 is OK
- 10.1038/s41586-020-2649-2 is OK
- 10.5281/zenodo.7344967 is OK
- 10.1103/physrevlett.83.440 is OK
- 10.1209/epl/i2005-10589-8 is OK
- 10.1209/0295-5075/123/14003 is OK
- 10.1103/PhysRevLett.110.144102 is OK
- 10.1103/PhysRevLett.120.214301 is OK
- 10.1103/PhysRevLett.124.208007 is OK
- 10.1038/s41526-022-00196-6 is OK
- 10.1007/s12217-020-09800-4 is OK
- 10.1051/epjconf/202124904003 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[jgostick]

@editorialbot add @aquilesC as reviewer

[editorialbot]

@aquilesC added to the reviewers list!

[jgostick]

Hi @mhubii and @aquilesC, the review is now underway. Thanks to you both for donating your time and expertise to this endeavor. (I often wonder how much the peer review system would cost if journals actually paid reviewers as consultants...)

The JOSS review process, if you're not familiar, is based around filling out a checklist (the instructions for generating your own are given at the top of this thread). If you have changes to ask of the author(s) you can use the issue tracker on their repo, which is on github and is public.

Hopefully you can complete your reviewers in 2-3 week time frame, as this this submission has been sitting for a while already.

Happy coding!

[mhubii]

Review checklist for @mhubii

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/ANP-Granular/ParticleTracking?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@a-niem) 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?

[aquilesC]

Review checklist for @aquilesC

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/ANP-Granular/ParticleTracking?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@a-niem) 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?

[aquilesC]

Some issues along the way:

• The install misses some dependencies (link)
• Missing trained model to analyze example data (link)

[jgostick]

Hi @mhubii, how are things progressing with your review? You created the checklist, so I assume you're trying out the package still?

[mhubii]

hi @jgostick , I am in the process of writing up a Phd and will likely have time for a proper review beginning of January. Would that be too late?

I can begin with an initial review earlier.

[jgostick]

Hmmm, one one had it's a bit late since the authors have been waiting a while already. But on the other hand the authors have not responded to @aquilesC comments yet, so they may not be in a hurry?

@a-niem, do have any specific timeline in mind?

[aquilesC]

@jgostick, there was a comment on one of the issues I opened, with some proposed timeline, which also made me drop a bit my focus. I'm aiming to wrapping up my review by the end of this week, or mid-next week. Especially considering the end-of-year break, I will try not to delay it much, but not sure whether the authors have time to invest on the manuscript before the end of the year.

[jgostick]

Shutting down for the northern hemisphere winter solstice to hibernate with friends and family is my favorite time of the year, I don't blame them. Let's see if they drop in here with a response to my question about timeline.

[a-niem]

@jgostick, @aquilesC Unfortunately, I've been on vacation which continues until the end of the year. Therefore, I'm not able to properly respond to any reviews that are done right now and will only continue working on it thoroughly from the beginning of next year.

[jgostick]

Then that is perfect, as one of our reviewers is only able to get started on it in the new year as well.
@mhubii, you have your extension :-) Thanks all for the quick response.

[jgostick]

Hi Everyone...things are very quiet here, and I am at least partly to blame. @a-niem, I was waiting for you to respond to the comments of @aquilesC which I why I let things drag on so long. @mhubii, I hope you had a good vacation and are still able to review this package?

[mhubii]

hi, yes I'll start working on this @jgostick. Sorry, busy times!

[aquilesC]

I think @a-niem addressed the comments on the code repository. My bad for not checking earlier. I'll re-start the review process early next week.

[dmitrypuzyrev]

Dear @merrygoat,

I fully agree with the issue and your comment, and you are right about the displacement curve - it would roughly indicate the evolution of kinetic energy of the system which is one of the biggest research points.

Of cause, we were/are constantly using the package and observe the people using it)
The problem is that the sample data came from early development time, when the program was only intended to correct the 2D particle positions, and 3D matching and tracking was performed entirely outside of the GUI. In reality, we always worked with much longer image sequences from other experiments with smaller frame-to-frame displacements.

This is indeed a glaring problem and will be fixed ASAP.

[jgostick]

I think @merrygoat has precisely identified the problem I had when using the software. The software just did not seem to behave as described even though I was using sample data and doing a basic analysis. Anyway, this is why we do JOSS reviews. So, I will await word from the authors when they have tightened up the workflows and we can revisit.

I would also like to apologize for my other comments. I guess I was feeling a bit agitated that day.

[mhubii]

no worries, been just caught up with life, like everybody else. I'll run through a functional review now

[mhubii]

okay so what leaves me a little confused is the following: You've got stereo images (right?) and very well separable rods (even by means of color). I am reviewing software, not the methodology, but how come such a sophisticated approach fails to autodetect (following https://particletracking.readthedocs.io/en/latest/RodTracker/RodTracker.html#automated-detection-of-particles). Installation-wise, I am now happy with the adjustments made.

[dmitrypuzyrev]

Dear @mhubii,
thank you for resuming the review process!)
I have replied to you in the issue thread (ANP-Granular/ParticleTracking#104)
I think there might be some confusion between 2D detection (which sees almost all of the rods but reassigns their numbers quasi-randomly between frames) and 3D tracking process.

[mhubii]

well sure, I was doing 2D detection following the demo, but it didn't detect. Please fix. I think a good start for you would be to get ANP-Granular/ParticleTracking#102 sorted

[dmitrypuzyrev]

well sure, I was doing 2D detection following the demo, but it didn't detect. Please fix. I think a good start for you would be to get ANP-Granular/ParticleTracking#102 sorted

Agreed, we first fix the technical/documentation issues and update the JOSS branch. We can then discuss the detection/tracking question.

[dmitrypuzyrev]

Dear @jgostick, dear @mhubii, dear @merrygoat,
I was notified on Sunday that the main developer, @a-niem, will not be able to actively work on the project and can only provide some consultation, at least for a while. This is totally understandable, since this year he did a lot of work after his contract with the university ended.
I am focusing my time on fixing the remaining issues but it will take me some time to fully take over all the development. It's is a little complicated by the fact that we expect a baby next month with my wife) Still, the delay should not be substantial. I hope for your understanding.

[jgostick]

Hmmm. The following statement gives me pause:

"...we expect a baby next month with my wife) Still, the delay should not be substantial."

These seems like contradictory facts.

Are you sure that pursuing the JOSS paper at this time is the right approach? The software still exists and can be used and cited by end-users. The only advantage of a JOSS paper is to appear as an official publication on your CV, but spending time with your family is definitely a higher priority.

[dmitrypuzyrev]

Dear @jgostick,

you are partly right, for sure, the CV of me and even more so of my colleague is an important factor. It cannot be the only advantage of JOSS paper though, since JOSS publication dramatically improves the quality of scientific software - this we learned first-hand - and overall dissemination of research methods and results.

As to delay, I don't plan to take any more than few days holiday at the moment and still working my working hours, which I will now focus more on finishing this review process. Just needed to inform you of the current situation.

Anyway, I suggest that I try to deal with open issues in the next 10 working days (until 04.10) and inform you on the progress done. If it is not satisfactory, we can put the review process to rest.

If it is OK for all of you, I would also kindly ask @merrygoat to update the review checklist, if not done yet - I think it is not fully updated, or some issues have not been submitted. The checklist of @mhubii seems to be up-to-date, there are only three unchecked marks related to functionality.

[mhubii]

no problem on my end @dmitrypuzyrev

[dmitrypuzyrev]

Dear @jgostick, dear @mhubii, dear @merrygoat,
The new release of the package has been prepared:
https://github.com/ANP-Granular/ParticleTracking/releases/tag/v0.6.4

The existing issues are adressed, I also commented on all of them sepately.
Please check out the results.

I also kindly ask @merrygoat to resume the review and update the checklist, there was no feedback from him recently.
Thank you in advance!

[jgostick]

Hey all, I have been waiting for either @merrygoat or @mhubii to make some updates about their reviews, but neither have. So I"m here to prod this process along a bit. Any progress?

[mhubii]

hi all, been a dense month. Apologies for the delay. I'll try to squeeze in a reviewing day on the weekend

[dmitrypuzyrev]

Dear @jgostick, @mhubii, @merrygoat,

I did not have (almost) no feedback from the reviewers.
Please, if possible, try to check the remaining issues. I will have some extra time in January to work on it if needed. Also, we have students currently who work on and can test the program.

Regards, and all the best in the holiday times!

[jgostick]

Hi All, happy new year to everyone. It's just a day on the calendar, but somehow feels like a new start.

I will start by apologizing for my lack of engagement on this submission over the last couple of months. I was absolutely slammed by my teaching load this fall, and simply could not find the time/energy to move this submission along. Anyway, new year, new teaching schedule, and renewed energy.

So, firstly, @mhubii, did you manage to find the time to play around with this package again over the break?

@merrygoat, how about you? The authors have been busy working on this over the fall, so hopefully you can take a quick look to see if it meets all your standards?

I know this submission is probably the longest running in JOSSs history, but I am feeling hopeful that it's almost over.

PS - If either @mhubii or @merrygoat are no longer able to commit their time to this review, please let me know so I can search for replacements.

Thanks,
Jeff

[mhubii]

really sorry for the delay. Genuinely don't mean any harm. Reviewing now.

So some issues were fixed, which is nice! However, I am still struggling with 3D reconstruction. Please advise. I will respond frequently moving forward.

These are the currently remaining issues (most of which seem easy fixes):

• JOSS: Documentation ANP-Granular/ParticleTracking#103
• JOSS: Automated detection of particles ANP-Granular/ParticleTracking#104
• JOSS: Version? ANP-Granular/ParticleTracking#106
• JOSS: No valid image data ANP-Granular/ParticleTracking#107
• JOSS: Batched detection ANP-Granular/ParticleTracking#108
• JOSS: 3D reconstruction ANP-Granular/ParticleTracking#109
• JOSS: Fail to load rod data ANP-Granular/ParticleTracking#110
• JOSS: No more than 2 digits ANP-Granular/ParticleTracking#111

[dmitrypuzyrev]

Dear @jgostick, dear @mhubii,
happy new year and thank you for the feedback! I will work on remaining issues and reply soon.

[jgostick]

@dmitrypuzyrev It has bee 28 days since you posted this reply. Glancing at the issues above it seems you have only addressed a few of them. The pace of this review has been glacial...I would be willing to bet it is the slowest/longest review in JOSS history. I am going to impose a deadline, which is standard for most journals. Please have all of the above issues addressed by February 24th (2 weeks from today). Otherwise I will close this review.