toelis 2.1.3

toelis

Toelis stands for Time Of Event LISt and refers to a type of data consisting of a series of events occurring at discrete times. Each event is associated with a specific channel (i.e. source), and trial (i.e. presentation of a stimulus or set of experimental conditions), and is defined by a positive or negative temporal from a defined reference time. This project (1) defines a file format for storing toelis data in plain text files (original developed by Amish Dave), and (2) contains a Python module with data structures for storing toelis data and functions for reading and writing files in the toelis format.

toelis files

Toelis files must be ISO-8859-1 or UTF-8 text encoding, and must have the format specified by the following ABNF grammar:

toelis-file   = num-channels NL num-trials NL *channel-index *channel
num-channels  = 1*DIGIT
num-reps      = 1*DIGIT
channel-index = 1*DIGIT NL           ; starting line for each channel
                                     ; number of channel-index items must equal num-channels
channel       = event-counts events
event-counts  = *(1*DIGIT NL)        ; number of events in each repetition
                                     ; number of event-count lines must equal num-reps
events        = *(time NL)
time          = [%x1D] 1*DIGIT [%x1E *DIGIT] ; floating point number
NL            = CR / CRLF / LF       ; all file encodings accepted

The time elements indicate a positive or temporal interval from an externally defined reference time (e.g., the onset of a stimulus), and should be in units of milliseconds.

Informally, the file consists of a series of integers and floating point numbers on separate lines. The first two lines give the number of channels and trials in the file. For each channel, there is a line giving the offset of the channel in the file. These offsets indicate the start of a block which begins with a series of integers giving the number of events in each trial, followed by a series of floating point numbers giving the time of the events. All channels must have the same number of trials.

python module

The toelis module requires Python 2.6+ or 3.2+ and numpy 1.3+. To install:

pip install toelis

Or to install from source:

python setup.py install

The module contains functions for reading and writing toelis files, as well as for manipulating toelis data, which are represented as lists of numpy arrays. The functions are well-documented within Python.

An example of loading two files, concatenating the trials, restricting the trials to a time window, and writing a new file. The functional programming style allows for compact, expressive syntax:

import toelis as tl

files = ('file1.toe_lis', 'file2.toe_lis')
t_merged = tl.merge(tl.read(open(fname, 'rU'))[0] for fname in files)
with open('merged.toe_lis', 'wt') as fp:
    tl.write(fp, tl.subrange(t_merge, 0, 1000))

acknowledgments and license

The toelis format was originally developed by Amish Dave (http://amishdave.net) for Dan Margoliash’s lab at the University of Chicago (http://margoliashlab.uchicago.edu). The formalized ABNF grammar and python implementation were written by Dan Meliza (http://meliza.org).

Copyright (c) 2006-2012 C Daniel Meliza. See COPYING for license information.

This Specification and Implementation are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, see http://www.gnu.org/licenses.