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dmirman / gazer

Functions for reading and pre-processing eye tracking data.
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Loading edfs on Code Ocean #19

Open Iman-Idrees opened 2 years ago

Iman-Idrees commented 2 years ago

Hi,

I would like to use gazeR to analyse my pupil data. I tried to load in an edf on Code Ocean but I received the following error message:

Error: Can't subset columns that don't exist.
x The column `blink` doesn't exist.

I've also tried to load in a few different edfs but I receive the same error message each time. Any advice on what the issue might be here would be greatly appreciated!

Many thanks, Iman

jgeller112 commented 2 years ago

Try suggestions reported here: https://github.com/dmirman/gazer/issues/3

Iman-Idrees commented 2 years ago

Hi again,

I was able to load in the edfs following your guidance on the previous posts. Thank you! However, I am now having an issue with the find_messages_edf function where I get the following error:

find_messages_edf(file_list=file_list_edf, varnames=c("TRIALID", "RT", "ACCURACY", "RESPONSE"), patterns=c("TRIALID", "RT", "ACCURACY", "RESPONSE"), output_dir)
Reading Messages from 011.edf ...Success! (52785 messages)
Error: Argument 2 must be length 150, not 300

Any advice on how to fix this?

Thanks in advance, Iman

jgeller112 commented 2 years ago

I have no clue what you named your variables. Can you send me one of your EDF files?

Iman-Idrees commented 2 years ago

012.edf.zip

Sure, I've attached one here.

jgeller112 commented 2 years ago

This should do the trick: 

find_messages_edf(file.choose(), varnames=c("TRIALID", "!V TRIAL_VAR RT","!V TRIAL_VAR ACCURACY", "!V TRIAL_VAR RESPONSE"), patterns=c("TRIALID", "!V TRIAL_VAR RT", "!V TRIAL_VAR ACCURACY", "!V TRIAL_VAR RESPONSE"), output_dir=output)

You have a lot of messages so the patterns need to be pretty specific or you end up picking up more rows than you want.

Iman-Idrees commented 2 years ago

Thanks, I tried the code suggested and it returned the following error message:

Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :

 Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
jgeller112 commented 2 years ago

file.choose() should be replaced with an object that has each of your EDF files.

jgeller112 commented 2 years ago

Can you also show me your code?

Iman-Idrees commented 2 years ago

Sure...

directory_edf= "/root/capsule/code/R/raw_data"

directory_csv_from_edf_conversion ="/root/capsule/code/R/raw_data"

file_list_edf <- list.files(path=directory_edf, pattern= ".edf")

parse_edf(file_list = file_list_edf, directory_csv_from_edf_conversion, type = "pupil")

file_list_pupil_samp <- list.files(path=directory_csv_from_edf_conversion, pattern = ".csv")

pd <- merge_gazer_files(file_list_pupil_samp, filetype = "edf")

find_messages_edf(file_list =file_list_edf, varnames=c("TRIALID", "!V TRIAL_VAR RT","!V TRIAL_VAR ACCURACY", "!V TRIAL_VAR RESPONSE"), patterns=c("TRIALID", "!V TRIAL_VAR RT", "!V TRIAL_VAR ACCURACY", "!V TRIAL_VAR RESPONSE"), output_dir= "/root/capsule/code/R/raw_data")

This seems to work but I receive the following error as before: Error: Argument 2 must be length 150, not 149

Having a look at the output it seems that the trials start from 0 instead of 1 which I think might be the issue here? Is there a way to change this to begin at 1?

jgeller112 commented 2 years ago

SR records the first trial as 0–you can easily change that by adding 1 to the trial id. That is not the issue. Your issue seems to be a wonky edf file. One of your files is missing a row of data. I would go through each of your edf files and see which one only has 149 rows of data.

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From: Iman-Idrees @.> Sent: Wednesday, August 18, 2021 4:43:46 PM To: dmirman/gazer @.> Cc: Geller, Jason @.>; Comment @.> Subject: [External] Re: [dmirman/gazer] Loading edfs on Code Ocean (#19)

Sure...

directory_edf= "/root/capsule/code/R/raw_data"

directory_csv_from_edf_conversion ="/root/capsule/code/R/raw_data"

file_list_edf <- list.files(path=directory_edf, pattern= ".edf")

parse_edf(file_list = file_list_edf, directory_csv_from_edf_conversion, type = "pupil")

file_list_pupil_samp <- list.files(path=directory_csv_from_edf_conversion, pattern = ".csv")

pd <- merge_gazer_files(file_list_pupil_samp, filetype = "edf")

find_messages_edf(file_list =file_list_edf, varnames=c("TRIALID", "!V TRIAL_VAR RT","!V TRIAL_VAR ACCURACY", "!V TRIAL_VAR RESPONSE"), patterns=c("TRIALID", "!V TRIAL_VAR RT", "!V TRIAL_VAR ACCURACY", "!V TRIAL_VAR RESPONSE"), output_dir= "/root/capsule/code/R/raw_data")

This seems to work but I receive the following error as before: Error: Argument 2 must be length 150, not 149

Having a look at the output it seems that the trials start from 0 instead of 1 which I think might be the issue here? Is there a way to change this to begin at 1?

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skalhan14 commented 2 years ago

Hi, I'm having an issue with uploading my EDF file through Code Ocean, when using parse_edf. I get the following error: Error in names(output$header) <- c("eyetrial", "starttime", "endtime", : 'names' attribute [4] must be the same length as the vector [1]

Here is my EDF file: https://drive.google.com/file/d/1yx-35FRNdNQ5SPUKBoJLgDnc6qU-VAD9/view?usp=sharing

Please let me know if there is a way to resolve this issue.

With thanks,

jgeller112 commented 2 years ago

Hi, I'm having an issue with uploading my EDF file through Code Ocean, when using parse_edf. I get the following error: Error in names(output$header) <- c("eyetrial", "starttime", "endtime", : 'names' attribute [4] must be the same length as the vector [1]

Here is my EDF file: https://drive.google.com/file/d/1yx-35FRNdNQ5SPUKBoJLgDnc6qU-VAD9/view?usp=sharing

Please let me know if there is a way to resolve this issue.

With thanks,

Hi. There appears to be something wrong with the EDF file you are trying to use. With the edfR function contained within parse_edf it is trying to find a column name for trial and it cannot (which is why the error is being thrown). How did you collect this collect data?

sarahakhras commented 1 year ago

Hello,

I am getting the same error as @skalhan14. Any updates on how it was resolved?

I collected my data using SR EyeLink 1000 Plus using PsychoPy experimental design. My design was based on one long continuous trial. So when I export the sample report using DataViewer, I get a column for trial ID that says '1' for all data.

Any help is appreciated. Thanks!

jgeller112 commented 1 year ago

Hi @skalhan14,

edfR (which is not no longer being maintained) is trying to parse trial information through edf.trials.

If you have access to DataViewer, just export the files as csvs or txt files and use gazeR package to process those.

sarahakhras commented 1 year ago

Thanks @jgeller112!

Are there any specific columns that have to be in the sample report? Or can it include any variables I need? I am trying to analyze pupil size timestamped to specific messages only.

jgeller112 commented 1 year ago

[image0.jpeg] Min these Jason Geller, Ph.D.(he/him/his) Lecturer Princeton University Website: www.drjasongeller.com

On Feb 22, 2023, at 6:00 PM, sarahakhras @.***> wrote:



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Are there any specific columns that have to be in the sample report? Or can it include any variables I need? I am trying to analyze pupil size timestamped to specific messages only.

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jgeller112 commented 1 year ago

As long as you have messages it should work!

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On Feb 22, 2023, at 6:00 PM, sarahakhras @.***> wrote:



Thanks @jgeller112https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjgeller112&data=05%7C01%7Cjg9120%40princeton.edu%7C20a6019d8b854d42139c08db1528a12d%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638127036481019921%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IOrSnSMd7CzTnLc0oF5F9eug%2BcJT8zwSP9VQTvb7rx8%3D&reserved=0!

Are there any specific columns that have to be in the sample report? Or can it include any variables I need? I am trying to analyze pupil size timestamped to specific messages only.

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sarahakhras commented 1 year ago

Thanks!

I am trying to read the .csv file now, but I'm getting the following error:

Error in data.table::fread(pupil_path) : Input is empty or only contains BOM or terminal control characters

Here's my file: test.csv

I'm not sure what the problem is. I appreciate your help!

jgeller112 commented 1 year ago

There must be something weird going on with your csv files

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From: sarahakhras @.> Sent: Wednesday, February 22, 2023 6:38:13 PM To: dmirman/gazer @.> Cc: Jason Geller @.>; Mention @.> Subject: Re: [dmirman/gazer] Loading edfs on Code Ocean (#19)

Thanks!

I am trying to read the .csv file now, but I'm getting the following error:

Error in data.table::fread(pupil_path) : Input is empty or only contains BOM or terminal control characters

Here's my file: test.csvhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdmirman%2Fgazer%2Ffiles%2F10809157%2Ftest.csv&data=05%7C01%7Cjg9120%40princeton.edu%7C069d3c5ad91949876b9608db152dddb6%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638127058960394569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=uDeUym0u9OGlO7p%2BnULBo%2BI7uyXac3M7yUT6zC6HBIE%3D&reserved=0

I'm not sure what the problem is. I appreciate your help!

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jgeller112 commented 1 year ago

Can you just send me one of your files?

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From: Jason Geller @.> Sent: Wednesday, February 22, 2023 6:39:25 PM To: dmirman/gazer @.>; dmirman/gazer @.> Cc: Mention @.> Subject: Re: [dmirman/gazer] Loading edfs on Code Ocean (#19)

There must be something weird going on with your csv files

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From: sarahakhras @.> Sent: Wednesday, February 22, 2023 6:38:13 PM To: dmirman/gazer @.> Cc: Jason Geller @.>; Mention @.> Subject: Re: [dmirman/gazer] Loading edfs on Code Ocean (#19)

Thanks!

I am trying to read the .csv file now, but I'm getting the following error:

Error in data.table::fread(pupil_path) : Input is empty or only contains BOM or terminal control characters

Here's my file: test.csvhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fdmirman%2Fgazer%2Ffiles%2F10809157%2Ftest.csv&data=05%7C01%7Cjg9120%40princeton.edu%7C069d3c5ad91949876b9608db152dddb6%7C2ff601167431425db5af077d7791bda4%7C0%7C0%7C638127058960394569%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=uDeUym0u9OGlO7p%2BnULBo%2BI7uyXac3M7yUT6zC6HBIE%3D&reserved=0

I'm not sure what the problem is. I appreciate your help!

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sarahakhras commented 1 year ago

Thanks for your help!

Here's the edf file: https://drive.google.com/file/d/1Y81OzAibkLARiYyJffJWssukiy9cP89j/view?usp=sharing.

jgeller112 commented 1 year ago

The link is not to a csv file. Can you send that?

sarahakhras commented 1 year ago

Here's the csv file: test.csv

jgeller112 commented 1 year ago

Okay. The csv file does not contain the columns needed to use gazeR.

you need at the min these columns from DataViewer: 

RECORDING_SESSION_LABEL
TRIAL_INDEX
AVERAGE_IN_BLINK RIGHT_IN_BLINK or LEFT_IN_BLINK
AVERAGE_PUPIL_SIZE  RIGHT_PUPIL_SIZE LEFT_PUPIL_SIZE
IP_START_TIME
SAMPLE_MESSAGE
sarahakhras commented 1 year ago

I'm still getting the same error even after including all the required columns. Here's my updated csv file if you'd like to take a look at it: testest.csv

jgeller112 commented 1 year ago

If you are using merge_gazer_files It is expecting an xslx file. You can change the csv to xslx or copy the below code.

#' Merge eye files from a ufolder
#' if filetype is from sr renames column variables and makes them lower case
#' Places time in ms
#' if edf files just reads them in
#'@import tidyverse
#'@import vroom
#' @param file_list path to .xls files
#' @param blink_colname name of your blink colname:AVERAGE_IN_BLINK, LEFT_, #RIGHT
#' @param pupil_colname name of your pupil colname:AVERAGE_IN_Pupil, LEFT_, #RIGHT
#' @param filetype if reading raw edf file use 'edf' if using sr files use type 'sr'
#' @export
#' @return data frame containing pupil data
merge_gazer_files <- function (file_list, blink_colname="blink", pupil_colname="pupil", filetype="sr") {  
  #file list is path to .xls files
  #vroom is faster
  library(data.table)

  if (filetype=="sr") {

    dataset <- do.call("rbind", lapply(file_list, FUN=function(files){

      for (i in 1:length(files)){ 
        if(file.exists(files[i])){
          message( "now processing:", files[i])
        }
      }

      fread(files, header=TRUE,  na.strings = ".", fill=TRUE)})) #vroom makes reading in files quick

    change_name <- dataset %>% 
      dplyr::select(!!quo_name("subject"):= RECORDING_SESSION_LABEL,
                    !!quo_name("blink"):= blink_colname,
                    !!quo_name("pupil"):= pupil_colname,
                    !!quo_name("trial"):= TRIAL_INDEX,
                    !!quo_name("message"):= SAMPLE_MESSAGE,
                    everything())

    names(change_name) <- tolower(names(change_name))

    change_name$time <- change_name$timestamp-change_name$ip_start_time

    return(as_tibble(change_name))
  }

  if (filetype=="edf") { 

    dataset <- do.call("rbind", lapply(file_list, FUN=function(files){

      for (i in 1:length(files)){ 
        if(file.exists(files[i])){
          message( "now processing:", files[i])
        }
      }

      fread(files, header=TRUE, na.strings = "NA", fill=TRUE)})) #vroom makes reading in files quicke

    return(as_tibble(dataset))
  }

}

x=merge_gazer_files(file, blink_colname = "RIGHT_IN_BLINK", pupil_colname = "RIGHT_PUPIL_SIZE")
sarahakhras commented 1 year ago

Thanks for your reply!

I am not using merger function. I'm only trying to see if it can read my data. Here's my code:

setwd(here())
csv.directory=here()
file_list <- list.files(path=edf.directory, pattern=".csv")

pupil_path <- system.file("extdata", "testest.csv", package = "gazer")
pupil_raw <- data.table::fread(pupil_path)

pupil_data <- as_tibble(pupil_raw)

head(pupil_data)

I thought I don't need merger function since I'm not using edf files. Is there anything missing from my code?

jgeller112 commented 1 year ago

Are you doing this in Code Ocean. If so, just run it from local machine.

Also the system file thing is not needed (not sure what that does as that’s specific to the gazeR stuff). You can Run this:

Fread(file.choose()) # input the file

Jason Geller, Ph.D.(he/him/his) Lecturer Princeton University Website: www.drjasongeller.com

On Feb 23, 2023, at 5:16 PM, sarahakhras @.***> wrote:



Thanks for your reply!

I am not using merger function. I'm only trying to see if it can read my data. Here's my code:

setwd(here()) csv.directory=here() file_list <- list.files(path=edf.directory, pattern=".csv")

pupil_path <- system.file("extdata", "testest.csv", package = "gazer") pupil_raw <- data.table::fread(pupil_path)

pupil_data <- as_tibble(pupil_raw)

head(pupil_data)

I thought I don't need merger function since I'm not using edf files. Is there anything missing from my code?

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