GETRUNDATA

Section: User Commands (1)
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NAME

getrundata - get data for experiment database from run files  

SYNOPSIS

getrundata [-t] [directory ...] > output.csv  

DESCRIPTION

Getrundata runs lsrun(1) and dumprun(1) to get run names, lengths, descriptions, and summaries of trace and waveform names. It outputs all of these data as comma-separated ASCII values, one line per run file, suitable for importing into a database. One or more directory arguments may be specified. Getrundata will recursively descend these directories, or the current directory if none is specified, looking for any run files to be catalogued. The output goes to the standard output, which should be redirected to a file. A file name suffix of .csv is recommended for this output file.  

Output Format

The following fields (or columns) will appear in the output, as double-quoted, comma-separated ASCII text:
Experiment Name
The name of the directory containing the run file, which is assumed to be named after the experiment in which a set of runs is captured.
Run Name
The name of a specific run of captured data, without the .frm suffix.
Path
The whole directory pathname up to and including the experiment directory name.
Seconds
The run length in seconds.
Description
The run description from first line of the run's .txt file.
Trace Names
The names of all traces in the run, separated by spaces.
Waveform Names
The names of all waveforms in the run, separated by spaces.

If available, these additional fields will appear after the waveform names. These are generally extracted from additional lines in the run description file, for runs converted from ABF files by axon2run(1).

Series
The name of the experiment series, extracted from a Series= string in the run description file.
Experimenter
Initials of the person running the experiment, extracted from a E= string.
Age
Age of preperation, extracted from a Age=RDn string.
Level
Highest level of lesion at start of experiment, from a level= string.
Recording Type
Type of recordings used (e.g. VR, EMB, ENG, IC), from a Rec= string. Multiple entries are separated by ASCII GS control characters (hex 1D value).
Stimulation
Stimulation method, from a Stim= string. Multiple entries are separated by ASCII GS control characters (hex 1D value).
Purpose
Brief description of experiment objective, from a Purp= string.
No. of Barriers
Number of barriers.
Barrier Levels
Both this and the number above are from a nb= string in the description. Multiple entries are separated by ASCII GS control characters (hex 1D value).
Time Tags
List of times and descriptions from time tags extracted from ABF file during conversion. Multiple entries are separated by ASCII GS control characters (hex 1D value).
Date
If the date can be obtained from an ABF file of the same name as the run, via the axon2run(1) utility's -d option, if the run has a recorded start time in its header, or if the date is obviously part of the experiment name, this field will appear after all the others above.
Start Time
If the -t option is specified, getrundata will display, as the last field on each line, the run's start time as recorded in the run header (if available), or an estimate of the start time based on the modification time of the least-recently modified file associated with a run, minus the run length. In the case where the time must be estimated, it is shown followed by a "~" (tilde) character. If the run has an associated ABF file, it will show the start time from that, rather than an estimated run start time which would likely be inaccurate for an old run converted from an ABF file.
 

SEE ALSO

lsrun(1), dumprun(1), axon2run(1)
http://www.scrc.umanitoba.ca/doc/tutorial/tutorial_10.html and
http://www.scrc.umanitoba.ca/doc/tutorial/tutorial_15.html
for more examples using getrundata.

 

Index

NAME
SYNOPSIS
DESCRIPTION
Output Format
SEE ALSO

This document was created by man2html, using the manual pages.
Time: 20:21:27 GMT, November 21, 2017
Copyright © G. R. Detillieux, Spinal Cord Research Centre, The University of Manitoba.