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[PRE REVIEW]: openEyeTrack - A high speed multi-threaded eye tracker for head-fixed applications #1598

Closed whedon closed 5 years ago

whedon commented 5 years ago

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

Author instructions

Thanks for submitting your paper to JOSS @chand-lab. Currently, there isn't an JOSS editor assigned to your paper.

@chand-lab if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands
whedon commented 5 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

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

What happens now?

This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

You can help the editor by looking at this list of potential reviewers to identify individuals who might be able to review your submission (please start at the bottom of the list). Also, feel free to suggest individuals who are not on this list by mentioning their GitHub handles here.

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1598 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:115:in check_fields': Paper YAML header is missing expected fields: tags, authors, affiliations (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:80:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

kyleniemeyer commented 5 years ago

Hi @chand-lab, thanks for your submission to JOSS. Please merge the PR I just submitted to your paper, which makes some necessary fixes to the authors and affiliation fields: https://github.com/chand-lab/openEyeTrack/pull/1

Also, please add ORCIDs for both authors; even after merging my PR, the paper will still not build correctly without those. (If you don't have ORCIDs, you can register for them here: https://orcid.org/register). Thanks!

kyleniemeyer commented 5 years ago

@cMadan can you edit this submission?

chand-lab commented 5 years ago

Hi Kyle,

Yes. Adding orcids. I need to get my undergraduate to get one as well.

best,

Chand

On Fri, Jul 26, 2019 at 12:33 PM Kyle Niemeyer notifications@github.com wrote:

Hi @chand-lab https://github.com/chand-lab, thanks for your submission to JOSS. Please merge the PR I just submitted to your paper, which makes some necessary fixes to the authors and affiliation fields: chand-lab/openEyeTrack#1 https://github.com/chand-lab/openEyeTrack/pull/1

Also, please add ORCIDs for both authors; even after merging my PR, the paper will still not build correctly without those. (If you don't have ORCIDs, you can register for them here: https://orcid.org/register). Thanks!

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1598?email_source=notifications&email_token=AMM4DRP2JOIRB5PWNSE64WDQBMRMFA5CNFSM4IHFL6K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD25DETI#issuecomment-515519053, or mute the thread https://github.com/notifications/unsubscribe-auth/AMM4DRL4DHJ5PNKC6PKNC43QBMRMFANCNFSM4IHFL6KQ .

-- Chandramouli Chandrasekaran Assistant Professor of Anatomy and Neurobiology Assistant Professor of Psychological and Brain Sciences Boston University Boston, MA, USA http://www.chandlab.org Ph: 617 358 8359 (MED)

chand-lab commented 5 years ago

@whedon commands

whedon commented 5 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references
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

PDF failed to compile for issue #1598 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:115:in check_fields': Paper YAML header is missing expected fields: tags (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:80:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

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

PDF failed to compile for issue #1598 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:115:in check_fields': Paper YAML header is missing expected fields: tags (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:80:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

kyleniemeyer commented 5 years ago

@chand-lab my new PR should fix the issue: https://github.com/chand-lab/openEyeTrack/pull/2

kyleniemeyer commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

PDF failed to compile for issue #1598 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:123:in block in check_orcids': Problem with ORCID (0000-0000-0000-0000) for Jorge (Paolo) Casas (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:121:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:121:in check_orcids' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon.rb:81:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/lib/whedon/processor.rb:36:inset_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:55:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-5a9319b684e6/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

chand-lab commented 5 years ago

Yep - let me get a proper orcid for Paolo. I have emailed him :)!

kyleniemeyer commented 5 years ago

@chand-lab ah, the issue now is that we need an actual ORCID for your coauthor; using zeros will not work. Thanks!

chand-lab commented 5 years ago

No problem :)! Just making sure the rest is working. Paolo is traveling I believe and we can resolve this shortly. Sorry!

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 commands

whedon commented 5 years ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references
chand-lab commented 5 years ago

@whedon list reviewers

whedon commented 5 years ago

Here's the current list of reviewers: https://bit.ly/joss-reviewers

cMadan commented 5 years ago

@whedon assign @cMadan as editor

whedon commented 5 years ago

OK, the editor is @cMadan

cMadan commented 5 years ago

@kyleniemeyer, sure, I can edit this one.

chand-lab commented 5 years ago

@cMadan - Can we suggest reviewers outside the list of reviewers with expertise in eye tracking?

kyleniemeyer commented 5 years ago

@chand-lab yes, feel free to suggest any domain experts, with contact information if possible.

cMadan commented 5 years ago

@chand-lab, can you clarify for me, what specialised hardware is needed for a reviewer to be able to evaluate this submission? How much of the submission can be evaluated without any specialised hardware?

chand-lab commented 5 years ago

@cmadan, this is code for an open source eye tracker which can be used for research settings. It unfortunately needs a high speed camera from Teledyne DALSA and an infrared emitter for getting purkinje images of the eye. Teledyne DALSA has an open source linux API. Our contribution comes from developing a multithreaded C++ client that can leverage their API and then use opencv to detect the pupil and send this data to other downstream applications through UDP. I recognize now that the need for hardware may make it unsuitable for JOSS :).

chand-lab commented 5 years ago

Reviewer suggestion: Jan Zimmerman (janz@umn.edu). Jan built the original open source non threaded video eye tracker. Our project builds on top of it.

cMadan commented 5 years ago

@thejanzimmermann, would you be available and interested in reviewing this submission?

thejanzimmermann commented 5 years ago

Sure !

From: Christopher Madan notifications@github.com Sent: Wednesday, July 31, 2019 12:18 AM To: openjournals/joss-reviews Cc: Jan Zimmermann; Mention Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: openEyeTrack - A high speed multi-threaded eye tracker for head-fixed applications (#1598)

@thejanzimmermannhttps://github.com/thejanzimmermann, would you be available and interested in reviewing this submission?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/1598?email_source=notifications&email_token=ACCBIISZGKHG3FG4RLZNY5DQCEODTA5CNFSM4IHFL6K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3GDL3A#issuecomment-516699628, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ACCBIIRXRLZQOSVSGCCYIDDQCEODTANCNFSM4IHFL6KQ.

cMadan commented 5 years ago

@thejanzimmermann, great, I assume you have access to the requisite hardware? I'll try and also get someone who's previously reviewed for JOSS on-board as well to help review the code, but likely wouldn't have the requiste hardware to do a full review of the functionality.

@adswa, would you be available and interested in reviewing this submission?

thejanzimmermann commented 5 years ago

I have all the necessary hardware in the lab. Let me know the steps involved since this is the first time I am doing a review like this.

Let me look at the other repo and give you a heads up in a bit

From: Christopher Madan notifications@github.com Sent: Wednesday, July 31, 2019 3:46 AM To: openjournals/joss-reviews Cc: Jan Zimmermann; Mention Subject: Re: [openjournals/joss-reviews] [PRE REVIEW]: openEyeTrack - A high speed multi-threaded eye tracker for head-fixed applications (#1598)

@thejanzimmermannhttps://github.com/thejanzimmermann, great, I assume you have access to the requisite hardware? I'll try and also get someone who's previously reviewed for JOSS on-board as well to help review the code, but likely wouldn't have the requiste hardware to do a full review of the functionality.

@adswahttps://github.com/adswa, would you be available and interested in reviewing this submission?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/openjournals/joss-reviews/issues/1598?email_source=notifications&email_token=ACCBIIXHJGZMXE2RNQAXG5DQCFGODA5CNFSM4IHFL6K2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD3GRQSY#issuecomment-516757579, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ACCBIIXHWRANALKFMYC6UXLQCFGODANCNFSM4IHFL6KQ.

adswa commented 5 years ago

Hey @cMadan, thanks for thinking of me! I don't think I'm able to provide the necessary prerequisites for this submission, though. I don't have access to the required hardware, and work with Python instead of c++. I'm happy to review submissions that are in the area of my expertise in the future, though :slightly_smiling_face:

mailchand commented 5 years ago

Hi @cMadan. My other reviewer suggestions after looking through your list of reviewers is

1) @rougier who seems to be a computational neuroscientist with C++ experience. 2) @casteer who is a physicist interested in research instrumentation.

Just thoughts off the top of my head.

cMadan commented 5 years ago

@rougier @casteer, if you are available to do a code review of this submission, it would be much appreciated! I figure you probably don't have access to the hardware to test the functionality of the submission, but we do have another reviewer that has that part covered.

rougier commented 5 years ago

I'm currently involved in two reviews for JOSS (and I'm on vacation) so it might be better to ask someone else, sorry.

mailchand commented 5 years ago

@cMadan I would perhaps suggest @conradsnicta as a potential reviewer as well. He has C++ experience and also appears to be involved in computer vision and might actually be an ideal reviewer for this small package.

conradsnicta commented 5 years ago

@cMadan @mailchand - I'll take a look, though it may take a little while (~2 weeks) as I'm juggling a few projects. I do not have the requisite hardware to do proper testing, so any review will necessarily not cover all the aspects of the software.

cMadan commented 5 years ago

@conradsnicta, thank you for agreeing, that's fine with me. We do have another reviewer with access to the hardware, so just be as thorough as you can.