[REVIEW]: openEyeTrack - A high speed multi-threaded eye tracker for head-fixed applications

[whedon]

Submitting author: @chand-lab (Chandramouli Chandrasekaran)
Repository: https://github.com/chand-lab/openEyeTrack
Version: v1.0.0
Editor: @cMadan
Reviewer: @conradsnicta, @thejanzimmermann
Archive: 10.5281/zenodo.3515534

Status

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Markdown: [![status](http://joss.theoj.org/papers/31079ebca9523ee9a2306631a8585a89/status.svg)](http://joss.theoj.org/papers/31079ebca9523ee9a2306631a8585a89)

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

@conradsnicta & @thejanzimmermann, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @cMadan know.

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

Review checklist for @conradsnicta

Conflict of interest

• 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

• 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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: v1.0.0
• Authorship: Has the submitting author (@chand-lab) 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 @thejanzimmermann

Conflict of interest

• 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

• 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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Version: v1.0.0
• Authorship: Has the submitting author (@chand-lab) 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)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @conradsnicta, @thejanzimmermann it looks like you're currently assigned to review 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:

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

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

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[whedon]

I'm sorry @thejanzimmermann, I'm afraid I can't do that. That's something only editors are allowed to do.

[cMadan]

@thejanzimmermann, it looks like you finished your review, can you provide some comments on your assessment?

[thejanzimmermann]

The authors provide a logical and necessary extension of previously published work on high speed eye tracking. This is especially important since most human applications or other open source initiatives provide low tracking speeds not acceptable to research applications.

The software is easy to compile, very well documented and understandable and provides a great place to start for researchers.

One thing that should be noted is that the system does not handle ocular occlusions very well because it computes the pupil based on a circular fit rather than a center of mass of an arbitrarily shaped object. This is non problematic in healthy human subjects but can become problematic in animal models.

Overall a great piece of software, well documented.

[chand-lab]

Dear @thejanzimmermann,

Thank you for the kind comments on the manuscript. As far as we understand it, the opencv blob detector which is what is used for detecting the pupil should function even with partially occluded pupils.

The circle is drawn as a visual aid to denote to the experimenter that a position was identified. We found that when windowing the image to only detect images within a particular region of interest, we could not find a reliable way to take the keypoints detected by the blob detector and show what was detected. Instead, we used the center and the "size" of the blob to draw a red circle.

In tests with artificial stimuli, our blob detector is even able to detect small black crescents drawn on a piece of paper. Of course, if this issue persists in animal models, we will consider other approaches for detecting the pupil. We believe the multithreaded approach allows for a little bit more leeway in implementing more computationally expensive algorithms.

best,

Chand

[thejanzimmermann]

Dear @chand-lab , I could not agree more with you ! and it's not a dealbreaker at all.

I can forward you experimental code on adjusted center of mass approaches that I have written that might at least mitigate this a little.

Best

Jan

[cMadan]

@conradsnicta, how are things progressing?

[mailchand]

Hi @thejanzimmermann,

Thanks! I think this would be a great addition to v2.0 of the Eye Tracker. It might also make sense to incorporate corneal reflections from the Purkinje image in future versions.

best,

Chand

[mailchand]

Hi @cMadan -- Just gently wondering if we could help in any way to wrap up the code review or any changes we need.

best,

Chand

[cMadan]

@conradsnicta, are you still able to review this submission? Thank you!

[conradsnicta]

@cMadan - apologies, been away sick. will take a look at this later on this week.

[cMadan]

@conradsnicta, thanks for letting me know. I hope you feel better soon!

[conradsnicta]

@cMadan - in progress; I'll add comments as I go along

[conradsnicta]

@chand-lab @mailchand There seems to be a problem with the reference to OpenCV, which is listed as "Bradski, G. (2000). The OpenCV Library. Dr. Dobb’s Journal of Software Tools". I can't seem to find the actual article.

• There is an apparent link listed at http://ftp.math.utah.edu/pub/tex/bib/dr-dobbs-2000.html#Bradski:2000:OL but following the link results in error 404.
• Searching https://www.drdobbs.com and http://www.ddj.com for OpenCV (directly and indirectly via Google) seems to yield nothing.
• Bradski's Google Scholar profile (https://scholar.google.com/citations?user=yeDFJgoAAAAJ&hl=en) has an entry for the article, but there is no link to the actual text / pdf.

So the cited article doesn't exist or has effectively ceased to exist. I suggest changing the reference to an article that is currently accessible.

[mailchand]

Thanks @conradsnicta ! I was trying to find a way to cite openCV and chose what has been recommended online :). We used all the online resources when we were programming with openCV. Instead, what we will do is to use this reference

Open CV book

[chand-lab]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[chand-lab]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[chand-lab]

@chand-lab, it looks like two of your references didn't resolve correctly in the PDF. See the second line of the "Software and Hardware components" section.

@cMadan - This has been fixed. I think the issue was you need to separate by ; for multiple references instead of a ,.

[chand-lab]

@chand-lab, it looks like two of your references didn't resolve correctly in the PDF. See the second line of the "Software and Hardware components" section.

This has been fixed. I think the issue was you need to separate by ; for multiple references instead of a ,. Apologies for the error!

[cMadan]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1111/j.1469-8986.2007.00606.x is OK
- 10.1016/j.jneumeth.2016.06.016 is OK
- 10.3389/fnbeh.2012.00049 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[cMadan]

@chand-lab, everything looks good to me!

To move forward with accepting your submission, there are a few last things to take care of:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo
• Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• List the Zenodo DOI of the archived version here.

You may find this helpful: https://guides.github.com/activities/citable-code/

[chand-lab]

Hi @cMadan,

Terrific. Please see mixed in below. I believe all the steps are done!

@chand-lab, everything looks good to me!

To move forward with accepting your submission, there are a few last things to take care of:

• Make a tagged release of your software, and list the version tag of the archived version here.

v1.0.0 - Available here
https://github.com/chand-lab/openEyeTrack/tree/v1.0.0

• Archive the reviewed software in Zenodo

Done!

• Check the Zenodo deposit has the correct metadata, this includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it); you may also add the authors' ORCID.
• Authors
• Paper title is correct
• Added ORCID

• List the Zenodo DOI of the archived version here.

You may find this helpful: https://guides.github.com/activities/citable-code/

Please let me know if I missed something :).

Warm Regards,

Chand

[cMadan]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[cMadan]

@whedon set 10.5281/zenodo.3515534 as archive

[whedon]

OK. 10.5281/zenodo.3515534 is the archive.

[cMadan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1111/j.1469-8986.2007.00606.x is OK
- 10.1016/j.jneumeth.2016.06.016 is OK
- 10.3389/fnbeh.2012.00049 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1040

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1040, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[cMadan]

@openjournals/joss-eics, I think we're all set to accept here!

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01631 joss-papers#1045
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01631
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[kthyng]

Congratulations @chand-lab on your JOSS submission!! 🎉 🎉

Thank you to @conradsnicta and @thejanzimmermann for your time and expertise reviewing this submission. Thanks also to @cMadan for editing.

[whedon]

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

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