unable to use edfR

[ufangYang]

I wonder is there anyone having a similar problem as me that edfR does not work (had reported an issue in edfR: jashubbard/edfR#12). Is there any other alternative approach to parse the edf file when package edfR doesn't work? thanks a lot!

[jgeller112]

Hello,

Yeah this is common issue with edfR. Luckily I have gazeR in a container on Code Ocean that also includes edfR. Here is a link showing how to use the gazeR package with Code Ocean: https://www.youtube.com/watch?v=5IQmP9Yrh1k.

[jgeller112]

Can you please post the code you used when you got the error?

[ufangYang]

Hi, here is the error message for parsing the data on Code Ocean

Error: Can't subset columns that don't exist. x The column blinkdoesn't exist. Runrlang::last_error()to see where the error occurred.

any suggestion to add this column before parsing? Thanks a lot

[jgeller112]

Please see my comment above. I need the code chunks you ran to diagnose the problem.

[ufangYang]

Hi, I use this line of code to load *.edf file,
gazer:: parse_edf(file.choose(), output_dir = '/root/capsule/code')

[jgeller112]

Can you share your EDF file with me? I cant replicate this problem, so it might be due to the file you are using.

[jgeller112]

Also, are you using this for pupil or gaze experiment?

[ufangYang]

Also, are you using this for pupil or gaze experiment?

it was a gaze experiment, I can share the data with you via email/private message since it is unpublished data, thank you. I wonder how heavy the dependency of using gazer::parse_edf() on Code Ocean. Because I ran out of the quote already on CO for further testing (1hr per month).

[jgeller112]

gazer:: parse_edf(file.choose(), output_dir = '/root/capsule/code', type="gaze")

The default is pupil.

I would check out this: https://psyarxiv.com/gvcxb/. You should be able to use Data Viewer and extract the data.

[jgeller112]

If you sign-up you should get 10 hours a month.

[ufangYang]

hi @jgeller112 I tried parsing the edf files with new eye-tracking data; this time it seemed to have parsed the data, but the process did not complete due to one file. I'm not sure why I got a different error because all of the files had the same structure. Below is the error (I masked the name of the file). Here I shared the codeocean with you, it might be easier to debug, let me know if you cannot access it. thanks a bunch!

Done processing all files! Error in samps_all[[1]] : subscript out of bounds In addition: Warning message: Problem with file XXX.edf #(specific file name)

https://codeocean.com/capsule/9187727/tree

[jgeller112]

Can you send me the EDF that is causing the issue?

[ufangYang]

sure, which email should I send to you?

[jgeller112]

drjasongeller@gmail.com