[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

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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.

[merrygoat]

Review checklist for @merrygoat

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 or COPYING 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?

[merrygoat]

@editorialbot generate pdf

[editorialbot]

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

[dmitrypuzyrev]

Dear @jgostick, thank you for contacting and appointment of the second reviewer.
@merrygoat and @mhubii, thank you a lot for your time, we are starting to work on the open issues.

[jgostick]

Hi @dmitrypuzyrev
This submission is called ParticleTracking, yet the github repo has a downloadable GUI called RodTracker, while the ParticleTracker seems to be a python package that is not a gui. Can we find a way to unify these names?

[jgostick]

Also, I am trying to use this GUI with the default images and example files, but keep getting error messages. I think @merrygoat is having the same issue. I'm on windows installed the exe from the github releases page.

[dmitrypuzyrev]

Dear @jgostick ,
I've just made a fresh install from .exe on Windows 11 (release 0.6.2 from releases page) and have no problems with example data.
I think we require more information, @merrygoat seemed to have a different problem with installation with pip.
Could you please submit an issue with the log file?

Also, we have a discussion with @a-niem today about the naming and other issues and then will get back to fixing it.

[a-niem]

Hi @jgostick

Hi @dmitrypuzyrev This submission is called ParticleTracking, yet the github repo has a downloadable GUI called RodTracker, while the ParticleTracker seems to be a python package that is not a gui. Can we find a way to unify these names?

I've just talked with @dmitrypuzyrev, and we were not 100% sure what you want us to rename. The simplest thing we thought of was to just rename the RodTracker GUI. The resulting names would be as shown below:

Repo-Name: ParticleTracking
Submission-Name: ParticleTracking
GUI-Name: RodTracker → ParticleTracker or 3D-ParticleTracker
Library-Name: ParticleDetection

On the other hand, we thought that you might want us to clear up any naming conflicts with the ParticleTracker software published in JOSS in 2021.

Please let me know if the proposed name changes are sufficient.

---

Also, I am trying to use this GUI with the default images and example files, but keep getting error messages. I think @merrygoat is having the same issue. I'm on windows installed the exe from the github releases page.

It looks like the errors you are experiencing have been posted as bugs by @merrygoat already (see #91 and #92). I am currently resolving them.

[a-niem]

Hi everyone.
All bugs and enhancements posted by @merrygoat have been fixed/implemented. This is now available in the joss_paper branch, as well as a new release including updated installers for the RodTracker.

I did not change any names in this version yet, because there was no further feedback to my previous comment here. @jgostick, @merrygoat, and @mhubii could you let me know about your opinion on my suggestion there, such that I can change the naming, if necessary.

[mhubii]

really need to get this review rolling again

[jgostick]

Hi Everyone. Thanks to @a-niem for addressing the comments of @merrygoat (and myself). I'm sorry I didn't reply with more input about the name change...I didn't feel right forcing you to change the name so I just kept quiet on that and left it up to you.

Anyway, to echo @mhubii's comments, we REALLY need to get the review moving. The review process at JOSS is pretty simple: the authors need to convince the reviewers to 'tick all the checkboxes'. As it stands now, all three reviewers have a lot of 'unticked' boxes. I have played with the software myself and also had problems. I got the impression that perhaps it is trying to do too much, and thus failing to deliver on it's core purpose (which TBH isn't really clear). On the other hand, the software is obviously very sophisticated and has many/most of the ingredients of a professional package in place.

So, based on the above, I am currently feeling like this submission might not ever get across the finish line. It's already dragged on so long that we've lost one reviewer, and I'm guessing we're getting perilously close to losing others. Committing to do a peer-review is not supposed to be a months-long process after all. So, I wonder if @mhubii and @merrygoat could please let me know how they feel about the prospects of this package being publication-ready within a 1-2 week span, either on this thread or via email if they feel more comfortable.

[dmitrypuzyrev]

Dear @jgostick,
did you get the feedback from @mhubii and @merrygoat?
In any case, I went through the JOSS guidelines once again and I do not see objective reasons why the submission should be dropped. The Journal aims at ~3 months of the review cycle, but there should be some outliers in this case, given the sophisticated/narrowly focused nature of the software, as you mentioned. Moreover, while it does not directly adress the case of longer submissions, this paragraph (https://joss.readthedocs.io/en/latest/review_criteria.html#what-happens-if-the-software-i-m-reviewing-doesn-t-meet-the-joss-criteria) indicates that:

Unlike some journals we do not reject outright submissions requiring major revisions - we’re more than happy to give the author as long as they need to make these modifications/improvements.

I am once again sorry for one longer period when we did not fix the issues timely due to the heath reasons.
At the same time, while in a way we need to "convince" the reviewers to finish the review (although it is never put like this in the guidelines), as authors we have very limited power and authority to push the reviewers in this direction except for replying to their raised issues and fixing them. (Please don't take it at as criticizing the reviewers, I just indicate that the review process might not be as smooth as expected).
The current checklists of the reviewers do not seem to indicate critical problems, and it seems that at parts they were not updated with the fixes which were already provided.

I also strongly object your point that software is failing to deliver on its core purpose, since it is actively used to produce acknowledged scientific results and is currently irreplaceable for study of real 3D granular matter in microgravity.
I can understand the critique that "it is trying to do too much", since it includes some additional features which are more experimental, but this is indicated in documentation. If it is a major issue that prevents the publication, it should be indicated and can be fixed.

I would kindly request to re-evaluate and finish the review of this submission. From the next week (Aug 12), @a-niem will be available as well and we can immediately discuss and fix any issues.

[merrygoat]

Apologies, I have been away for a couple of weeks.

My basic expectation for the package, is that I would be able to take the sample data, follow the documentation and produce some sort of simple physics - (I guess some sort of smooth curve of displacement). I would have expected it to be at this state at the time of submission. I think a lot of the issues that have been highlighted by the reviewers could have been fixed prior to submission by giving the software to some people locally who had not used it before and watching them try to use it.

I have come to look at it again this afternoon and it has improved a lot based on your recent changes. However, I have not yet been able to complete an analysis with the sample data.

I do not doubt that you have used the package to create good science, but for JOSS, the criteria are not just about science but about accessibility and usability. It is getting there, but there is still some way to go.

I have added another issue to the project repo and will add a pull request for suggested improvements to the documentation.

[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!