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An extensible parser for EyeLink data files (EDF)

Project description

Python EyeLinkParser

Sebastiaan Mathôt
Copyright 2016-2022
http://www.cogsci.nl/smathot

About

The python-eyelinkparser module provides a framework to parse EyeLink data files in .asc format, that is, the format that you get after converting an .edf file with edf2asc. This module is mostly for personal use, and is not very well documented.

Installation

pip install python-eyelinkparser

Expected format

The parser assumes monocular recording.

Expected messages

By default, the parser assumes that particular messages are sent to the logfile. If you use different messages, you need to override functions in _eyelinkparser.EyeLinkParser. This is not explained here, but you can look in the source code to see how it works.

Trial start:

start_trial [trialid]

Trial end:

end_trial
stop_trial

Variables:

var [name] [value]

Start of a period of continuous data:

start_phase [name]
phase [name]

End of a period of continuous data:

end_phase [name]
stop_phase [name]

Function reference

eyelinkparser.EyeLinkParser(folder='data', ext=('.asc', '.edf', '.tar.xz'), downsample=None, maxtracelen=None, traceprocessor=None, phasefilter=None, phasemap={}, trialphase=None, edf2asc_binary='edf2asc', multiprocess=False, asc_encoding=None, pupil_size=True, gaze_pos=True, time_trace=True)

The main parser class. This is generally not created directly, but through the eyelinkparser.parse() function, which takes the same keywords as the EyeLinkParser constructor (i.e. the keywords below).

Parameters

  • folder: str, optional : The folder that contains .edf or .asc data files, or files compressed as .tar.xz archives.

  • ext: str or tuple, optional : Allowed file extensions, or a tuple of extensions, for data files.

  • downsample: int or None, optional : Indicates whether traces (if any) should be downsampled. For example, a value of 10 means that the signal becomes 10 times shorter. Downsample creates a simple traceprocessor, and can therefore not be used in combination with the traceprocessor argument.

  • maxtracelen: int or None, optional : A maximum length for traces. Longer traces are truncated and a UserWarning is emitted. This length refers to the trace after downsampling/ processing.

  • traceprocessor: callable or None, optional : A function that is applied to each trace before the trace is written to the SeriesColumn. This can be used to apply a series of operations that are best done on the raw signal, such as first correcting blinks and then downsampling the signal.

    The function must accept two arguments: first a label for the trace, which is 'pupil', 'xcoor', 'ycoor', or 'time'. This allows the function to distinguish the different kinds of singals; second, the trace itself.

    See eyelinkparser.defaulttraceprocessor for a convenience function that applies blink correction and downsampling.

  • trialphase: str or None, optional : Indicates the name of a phase that should be automatically started when the trial starts, or None when no trial should be automatically started. This is mostly convenient for processing trials that consist of a single long epoch, or when no start_phase messages were written to the log file.

  • phasefilter: callable or None, optional : A function that receives a phase name as argument, and returns a bool indicating whether that phase should be retained.

  • phasemap: dict, optional : A dict in which keys are phase names that are renamed to the associated values. This is mostly useful to merge subsequent traces, in which case the key is the first trace and the value is the second trace.

  • edf2asc_binary: str, optional : The name of the edf2asc executable, which if available can be used to automatically convert .edf files to .asc. If not available, the parser can only parse .asc files.

  • multiprocess: bool or int or None, optional : Indicates whether each file should be processed in a different process. This can speed up parsing considerably. If not False, this should be an int to indicate the number of processes, or None to indicate that the number of processes should be the same as the number of cores.

  • asc_encoding: str or None, optional : Indicates the character encoding of the .asc files, or None to use system default.

  • pupil_size: bool, optional : Indicates whether pupil-size traces should be stored. If enabled, pupil size is stored as ptrace_[phase] columns.

  • gaze_pos: bool, optional : Indicates whether horizontal and vertical gaze-position traces should be stored. If enabled, gaze position is stored as xtrace_[phase] and ytrace_[phase] columns.

  • time_trace: bool, optional : Indicates whether timestamp traces should be stored, which indicate the timestamps of the corresponding pupil and gaze-position traces. If enabled, timestamps are stored as ptrace_[phase] columns.

Examples

import eyelinkparser as ep
dm = ep.parse(defaulttraceprocessor=ep.defaulttraceprocessor(
    blinkreconstruct=True, downsample=True, mode='advanced'))

Tutorial

For a tutorial about using EyeLinkParser, see:

License

python-eyelinkparser is licensed under the GNU General Public License v3.

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