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A library to parse SR research EDF files into python.
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setup.py

Readme.md

pyedfread

A utility that parses SR research EDF data files into pandas DataFrames.

Requirements

  • python 3.6 recommended. Not tested with 2.7 anymore, but probably works.
  • EyeLink Developers Kit. Download from SR-Research support forum (forum registration required).
  • cython. Use conda/pip etc. to install
  • pandas + h5py. Required to run command line scripts. You can still parse edfs into numpy array and list of dicts without pandas.

I do not include the SR Research EDF Access API header files and libraries. These are needed to compile pyedfread with cython. If you use a mac you can download a package from the SR-Research support forum. If you use Ubuntu you can install them via apt-get. The setup.py might not run properly on a linux box, because I don't have one around for testing.

If you use any other linux distribution, download the API files and place libedfapi.so in lib/ and *.h files in include. Setup.py should be able to work with this.

Windows Support

As of this writing (July 2019), the EyeLink Developers Kit for Windows requires small modifications before it will work with this project. Administrator access is required to edit the files in their default directory: C:\Program Files (x86)\SR Research\EyeLink\EDF_Access_API\Example

Edit edftypes.h. Replace the chunk of typedefs (lines 16-25) with the following:

#ifndef BYTEDEF
	#define BYTEDEF 1
	typedef unsigned char  byte;
	#ifndef _BASETSD_H_ /* windows header */
		typedef short          INT16;
		typedef int            INT32;
		typedef unsigned short UINT16;
		typedef unsigned int   UINT32;
	#endif
#endif

One of the DLLs from SR Research (zlibwapi.dll) depends on MSVCP90.dll. This should come with MS Visual Studio C++ 2008 SP1 redistributable, but its installer didn't seem to put the file on the PATH. Instead, I had already installed Mercurial for Windows which comes with the correct version of that file and puts it on the PATH by default.

Follow this sr-support forum post for updates.

Setup

Run 'python setup.py install' to compile and install. This will install the python library and a command line script to parse edfs.

Usage

pyedfread can be used on the command line (read_edf) or called from within python.

From python

After compilation run the following lines for a quick test.

>>> from pyedfread import edf
>>> samples, events, messages = edf.pread('SUB001.EDF')

This opens SUB001.EDF and parses it three two DataFrames:

  • samples contain individual samples.
  • events contains fixation and saccade definitions
  • messages contains meta data associated with each trial.

To add the trial meta data into the eye tracking data run:

>>> events = edf.trials2events(events, messages)

pyedfread allows to select which meta data you want to read from your edf file. This happens through the 'filter' argument of edf.pread / edfread.fread. It can contain a list of 'message' identifiers. A message identifier in the EDF is trial metadata injected into the data stream during eye tracking. If for example after the start of a trial you send the message "condition 1", you can add 'condition' to the filter list and edfread will automagically add a field condition with value 1 for each trial to the messages structure. Of course, if the value varies across trials this will be reflected in the messages structure. This is what it looks like in python code:

>>> samples, events, messages = edf.pread('SUB001.EDF', ignore_samples=True, filter=['condition'])

If filter='all', pyedfread saves all messages it can parse.

In earlier versions of pyedfread one could also specify which sample properties to pull out from the data stream. This has been deprecated.

The column names map almost directly to C structure names in the EDF C API. To understand column content check the edf acces api documentation (2.1.1 FSAMPLE Structure + 2.1.2 FEVENT Struct.) and see the examples listed below. Column names for each eye are suffixed by 'left' or 'right' respectively.

Some examples for samples:

  • time: time stamp of sample
  • flags: flags to indicate contents
  • px: pupil x, y
  • py
  • hx: headref x, y
  • hy
  • pa: pupil size / area
  • gx: screen gaze x, y
  • gy
  • rx: screen pixels per degree
  • ry
  • status: status flags
  • input: extra input word
  • buttons: button state & change
  • htype: head-tracker data
  • hdata: Not included
  • errors: process error flags
  • gxvel: gaze x,y velocity
  • gyvel
  • hxvel: headref x,y velocity
  • hyvel
  • rxvel: raw x, y velocity
  • ryvel
  • fgxvel: fast gaze x, y velocity
  • fgyvel
  • fhxvel: fast headref x, y velocity
  • fhyvel
  • frxvel: fast raw x, y velocity
  • fryvel

Some examples for events:

  • time - time point where event occured
  • type - event type
  • eye - eye: 0=left, 1=right
  • start - start time
  • end - end time
  • gavx, gavy - average gaze location

Command line

If you have an EDF file with "standard" meta data (e.g. key and value are seperated by a blank) you can call

$> read_edf SUB001.EDF sub001.hdf

The .hdf file is a valid hdf5 file that can be read into matlab. The default is to simplify the HDF file by replacing strings with numbers. The original strings are saved as attributes in the HDF file. Fields that contain python objects (e.g. arrays, lists etc.) are skipped.

Run 'read_edf -h' for some help.

Matlab

To read a datamat into matlab do this:

>> info = h5info('SUB001.hdf');
>> info.Groups.Datasets
>> field = h5read('SUB001.hdf', '/events/gavx');

License

BSD License, see LICENSE file

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