Auryn simulator

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====== stim file type ======

Stimfiles are IO files in Auryn with extension *.stim or *.stimtimes that contain a timeseries of stimulus activation time points. In Auryn a stimulus is characterized by the cells that are stimulated, i.e. a [[pattern]] of cells which is generally stored in a [[pat]] file.

Stimfiles are generated as an output of [[StimulusGroup]] which serves to keep track of the stimulation history, when this is generated randomly by [[StimulusGroup]]. However, they can also serve as an input to StimulusGroup.


===== Format =====

The format of the file follows again a text standard which is directly interpretable by [[Gnuplot]]. It event based and features three columns. The first column denotes the time of the event, the second column contains either a 0 or a 1 depending on whether or not a stimulus is inactive or active. The third column contains the stimulus ID which has been loaded into the [[StimulusGroup]] and refers usually to a set (pattern) of cells.

===== Example =====

A simple example of a stimfile could look as follows:
<code>
50.000000 0 0
50.000100 1 2
50.581800 1 2
50.581900 0 2
51.557600 0 2
51.557700 1 3
52.598500 1 3
52.598600 0 3
53.925900 0 3
53.926000 1 1
54.938600 1 1
54.938700 0 1
</code>

It is easiest to understand what is happening by looking at the gnuplot output of the following script
<code gnuplot>
set border 3
set xtics nomirror
set ytics nomirror
unset key
set xlabel 'Time [s]'
set ylabel 'Active [0/1]'
plot 'test.stim' with lines lw 4 palette
</code>
which yields the following plot:

{{:manual:stimfile_example.png?300|}}

We can see that at t=50s stimulus 2 (brown) is activated and deactivated after about half a second. Shortly after that stimulus 3 (yellow) comes on etc ...