edf2asc: Call SRR "edf2asc" command line utility to do some work.

In PennStateDEPENdLab/experiment_pipeline: Generates data markdown for NeuroMap Task

Call SRR "edf2asc" command line utility to do some work.

Description

A convenience wrapper around the SR Research edf2asc file conversion utility. Adapted by Michael Hallquist to handle options as an argument, support gzip compression, and support an output directory

Usage

edf2asc(
  edf_files,
  edf2asc_opts = "-y",
  asc_output_dir = NULL,
  gzip_asc = TRUE,
  running = "mac"
)

Arguments

edf_files	Character vector of *edf file names to be converted. File names should include paths relative to the current working directory, or fully qualified paths.
edf2asc_opts	Options passed to edf2asc command

Details

Call SR Research "edf2asc" command line utility to convert *edf files to *asc files. Each *asc file is placed in the same directory as the *edf file that it is derived from. Existing *asc files will NOT be over-written by default, because that is the default for the SRR edf2asc utility.

To prepare edf2asc() to work with the edf2asc command line utility provided by SR Research, follow these steps:

• Mac OS X

  1. Download and install the Eyelink Developers Kit from SR Research: https://www.sr-support.com/forum/downloads/eyelink-display-software/45-eyelink-developers-kit-for-mac-os-x-mac-os-x-display-software?15-EyeLink-Developers-Kit-for-Mac-OS-X=

     Documentation for using edf2asc utility is in the EyeLink 1000 User Manual, section 4.8 "Using ASC files".

  2. Identify the path to the edf2asc utility; something like "/Applications/Eyelink/EDF_Access_API/Example"

  3. In R, check if the path to the edf2asc utility is in the R environment by running Sys.getenv("PATH"). If yes, you may skip the following steps. If not, do the following.

  4. Open (or create) a file called ".Renviron" in the home directory (applied system-wise) or current directory (applied project-wise)

  5. Add the path to the edf2asc utility to PATH in ".Renviron", followed by the output from Sys.getenv("PATH"); for example, PATH="/Applications/Eyelink/EDF_Access_API/Example:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin"

  6. You may need to restart R for the changes to apply.

• Windows

  1. Download and install the Eyelink Developers Kit from SR Research: https://www.sr-support.com/forum/downloads/eyelink-display-software/39-eyelink-developers-kit-for-windows-windows-display-software?6-EyeLink-Developers-Kit-for-Windows-=

     Documentation for using edf2asc utility is in the EyeLink 1000 User Manual, section 4.8 "Using ASC files".

  2. Identify the path to the edf2asc utility; something like "C:/Program Files (x86)/SR Research/Eyelink/EDF_Access_API/Example"

  3. Make sure "edfapi.dll" and "edfapi.lib" are somewhere on the path, for example "C:\Windows\System32" (see /path/to/EDF_Access_API/readme.txt for more detail)

  4. In R, check if the path to the edf2asc utility is in the R environment by running Sys.getenv("PATH"). If yes, you may skip the following steps. If not, do the following.

  5. Go to Control Panel > System and Security > Advanced System Settings > Environmental Variables...

  6. Under System Variables, choose Path, click Edit..., add the path to the edf2asc utility to the list, and click OK (For more detail, see https://www.howtogeek.com/118594/how-to-edit-your-system-path-for-easy-command-line-access/)

  7. You may need to restart R for the changes to apply.

Before calling the utility, this function will check to see that the specified file exists and is executable. However, if the selected version of the edf2asc executable is in some way incompatible with your platform, then this function will fail with a cryptic error. The best way to guard against this is to check that your edf2asc executable file works as expected from the command line before attempting to use it from within FDBeye.

The function edf2asc() also checks getOption("FDBeye_edf2asc_opts"). If this option exists, it should be a valid string of command line options to pass to the SRR edf2asc utility (e.g., "-y -ns"). See the SRR documentation for details. We recommend to use the "-y" option to overwrite existing *asc files; otherwise, edf2asc() may not work properly.

In addition to creating the requested *asc files, this function will write a log file ('edf2asc.log') of messages captured from the stdout of SRR edf2asc utility and place it in the current working directory.

Value

Called for the side effect of converting SRR *edf files to *asc files. Returns a character vector listing output files (*asc files).

Author(s)

Dave Braze [e-mail]

Monica Li [e-mail]

Examples

## Not run: 
fin <- list.files(".", pattern="edf$", recursive=TRUE)
fout <- edf2asc(fin)
fout

## End(Not run)

PennStateDEPENdLab/experiment_pipeline documentation built on Nov. 27, 2024, 4:56 a.m.