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

whedon commented 5 years ago

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

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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:

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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

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

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: v1.0.0
[x] 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

[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 function of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

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

Review checklist for @thejanzimmermann

Conflict of interest

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

Code of Conduct

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

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Version: v1.0.0
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

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

whedon commented 5 years ago

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 :tada:.

:star: Important :star:

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whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

whedon commented 5 years ago

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

cMadan commented 5 years ago

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

thejanzimmermann commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

@conradsnicta, how are things progressing?

mailchand commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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

conradsnicta commented 5 years ago

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

cMadan commented 5 years ago

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

conradsnicta commented 5 years ago

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

conradsnicta commented 5 years ago

@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 commented 5 years ago

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 commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

chand-lab commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

chand-lab commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

chand-lab commented 5 years ago

Hi @cMadan and @conradsnicta -- Any chance we can wrap this up soon :)! Happy to be as responsive as needed if there are issues that need fixing.

conradsnicta commented 5 years ago

@chand-lab - I'm still going through this, with the aim of getting the review done by friday or saturday. Unfortunately I currently have a work project which takes precedence, and it's taking up all of my time.

chand-lab commented 5 years ago

@conradsnicta --- I totally understand. No worries at all! Just thought I could check if I was being a rate limiter.

conradsnicta commented 5 years ago

@chand-lab - Problems with the references:

The updated citation to Bradsky & Kaehler has several issues:
- The given URL (https://www.academia.edu/download/32167394/OReilly_Learning_OpenCV.pdf) ends up with Error 404.
- The publisher's name has unnecessary quotes around it.
- OpenCV is printed as lowercase opencv, twice. In paper.bib, use curly braces around the word to force Bibtex to respect the upper case letters: {OpenCV}
Clicking on the DOI link for Zimmerann et al (2016) leads to an error. The DOI listed in paper.bib should only have the DOI number, not the URL.

conradsnicta commented 5 years ago

@chand-lab - Grammar suggestions in the Algorithm section:

It's not clear what is meant by "processed" in the sentence "as frames transition between the captured, processed and display processes". What do "captured process" and "processed process" mean ? Perhaps the sentence would be clearer like so: "as frames transition between capture, processing and display stages". The "processing stage" should clarified or renamed, as it's too generic -- everything is "processing" in the end.
Change "enable the different processes" to "enable the separate stages".
Change "and stores in a queue" to "and stored in a queue".

conradsnicta commented 5 years ago

@chand-lab

In the Statement of Need section, there is a superfluous (or effectively circular) citation to Casas & Chandrasekaran (2019). This paper is about the very software being cited, so the citation is not necessary or needed. You already have a link to GitHub page in the paragraph right after the list of limitations.
Grammar suggestions in the Limitations section. In the numbered list, there is no point in stating "first", "second", etc. The number already gives that information.
In the paragraph right after the list of limitations:
- Spelling issue: "nueral dynamics". Maybe a spell check of the entire paper would be useful.
- Not sure what is the point of stating "We also anticipate using it in the Zimmerman Lab at the University of Minnesota", or even the sentence starting with "Currently, there are plans to incorporate ...". The use cases should already be explained in the Statement of Need section, so there is no point in detailing where the software is used / might be used.

mailchand commented 5 years ago

@conradsnicta - Thank you for a thorough read. I will attempt to address these issues and improve the manuscript ASAP. These are all excellent suggestions and will make the manuscript significantly better.

jpaolocasas commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

jpaolocasas commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

jpaolocasas commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

jpaolocasas commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

jpaolocasas commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

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

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