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--- manual:auryn_binary_extract [2016/06/16 16:45] – Adds short cli example to aube page zenke
+++ manual:auryn_binary_extract [2016/06/16 17:01] (current) – deleted zenke
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-====== Auryn Binary Extract (aube) ======
-This command line tool extracts spike information from [[spk|binary spike raster files]] and converts them in the more digestible [[ras]] format. Binary files provide a significant simulation speed advantage over the old [[ras]] file format and allow random access to spike information. ''aube'' is capable of efficiently merging multiple [[spk]] files and export select temporal ranges from it to the more digestible [[ras]] format. It can be efficiently incorporated into Linux command-line and pipe based work flow and works flawlessly with [[gnuplot]]. The tool included with Auryn releases (ver. >0.6.1) and can be found in the ''tools'' directory.
-===== Compiling/Installing aube =====
-''aube'' is [[manual:compileauryn|compiled]] automatically with the rest of Auryn and located in the tools directory. It can be installed to your systems default install location (e.g. ''/usr/local/bin'') with the help of ''make install''. Otherwise you will have to ensure yourself that ''aube'' is in the PATH for the following examples to work.
-===== Usage examples =====
-Suppose you have the spk file ''/tmp/coba.0.e.spk'' and want to extract all spikes from it and write them to stdout. All you need to do is to call:
-<code>
-aube --input /tmp/coba.0.e.spk
-</code>
-Note, you find an example program generating binary spike output at ''examples/sim_coba_binmon.cpp''.
-Suppose you ran your simulation in parallel (you end up with multiple files /tmp/coba.*.e.spk) and you would like to merge these files and then write spikes from 7s to 10s to a file ''output.ras''. The aube call for you is:
-<code>
-aube --inputs /tmp/coba.*.e.spk --from 7 --to 10 --output output.ras
-</code>
-Alternatively you can use a shorter notation which achieves the same:
-<code>
-aube -i /tmp/coba.*.e.spk -f 7 -t 10 > output.ras
-</code>
-You can use ''aube'' in pipes which for instance allows you calling it from without [[gnuplot]]. To plot the last 1s of spikes from a simulation from within gnuplot run:
-<code>
-plot '< aube --inputs /tmp/coba.*.e.spk --last 1' with dots
-</code>