GazeR and edfR functions exceed my working space limit: how to downsample

[juthzi]

Hello everyone,

I have trouble processing my pupil data with some of the GazeR and edfR functions. I run into working space limit problems.

Therefore, I wanted to downsample the files (they have been created with 1000 Hz) to 250 Hz for a start. In the GazeR manual they describe a way to downsample using "downsample_gaze", but for me, this step occurs too late in the script, so that I run into problems beforehand. Do you know, if there is a way to downsample the edf files when they are initially parsed/imported into R? Or can I simply use the "downsample_gaze" at an earlier point in the script without messing other things up?

Thank you for your advice, Juliane

[tmalsburg]

To my knowledge, it's not possible to downsample during reading of the data from .edf. Do you run into memory issues even if you read a single .edf file? Otherwise, I'd recommend to read one file, downsample, then read the next, and so on.

[juthzi]

Thanks for getting back to me! The problem is not so much the reading in of the files, but running the functions following after that, so far: behave_pupil() and baseline_correction_pupil_msg().

I guess I could run these functions on individual files or on only a couple of files. However, I am reluctant to do this, because this means, that I have to run the whole pipeline for an individual file and afterwards concatenate the files, which always creates new sources of errors (I am not that firm with R yet, or the packages). But I guess I have no other choice, unless somebody has a different idea?

[tmalsburg]

I see. In this case I would contact the authors of GazeR since the bottle neck seems to arise in their package. Perhaps they ran already into this issue themselves and have solutions.

[juthzi]

Thank you for the advice, I will do that.

Best wishes, Juliane