GETRUNDATA
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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: 17:58:04 GMT, February 20, 2019
Copyright © G. R. Detillieux,
Spinal Cord Research Centre,
The University of Manitoba.