examples:sim_poisson
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examples:sim_poisson [2013/12/09 15:18] – [The full script] zenke | examples:sim_poisson [2016/02/04 17:39] (current) – typo zenke | ||
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- | ====== | + | ====== |
- | Running the example program '' | + | Simulates an array of Poisson processes to illustrate the use of [[manual: |
+ | |||
+ | Full source code: [[https:// | ||
+ | |||
+ | |||
+ | ===== Running code ===== | ||
+ | |||
+ | Running the example program '' | ||
<code shell> | <code shell> | ||
- | bash-4.1$ ./ | + | zenke@foobar: |
- | seed set to 1231231. | + | [=========================] 100% t=1.0s f=5.1 Hz |
- | [=========================] 100% t=10.0 s f=21.3 Hz | + | |
( 0) Freeing ... | ( 0) Freeing ... | ||
</ | </ | ||
In addition the script will create a [[manual: | In addition the script will create a [[manual: | ||
- | Let's look at the code inside. | + | |
+ | ===== Visualizing the output ===== | ||
+ | |||
+ | Our simulation has written its output (1 second of Poisson spiking from 1000 Poisson neurons firing at 5Hz) to '' | ||
+ | If you have gnuplot installed you can take a quick peek using the command line | ||
+ | < | ||
+ | echo "plot ' | ||
+ | </ | ||
+ | from within gnuplot | ||
+ | <code gnuplot> | ||
+ | plot ' | ||
+ | </ | ||
+ | Either way the output will look similar to this: | ||
+ | {{ : | ||
+ | |||
+ | |||
+ | ===== Randomness and seeding the random number generator ===== | ||
+ | |||
+ | If you run the code again, you will notice that Auryn will generate the same spikes. This is due to the fact that it uses pseudo random numbers which is good for debugging. If you want to generate a different Poisson spike trains try running the code with a random seed. In this simulation this can be done with a command line parameter, but typically this will be done automatically somewhere in your code. | ||
+ | |||
+ | <code shell> | ||
+ | zenke@foobar: | ||
+ | [=========================] 100% t=1.0s | ||
+ | ( 0) Freeing ... | ||
+ | </ | ||
+ | |||
+ | |||
+ | ===== Some more options ===== | ||
+ | |||
+ | This simple simulation has some more parameters. To see which ones they are, you can call the script with | ||
+ | <code shell> | ||
+ | zenke@foobar: | ||
+ | Allowed options: | ||
+ | --help | ||
+ | --simtime arg | ||
+ | --kappa arg | ||
+ | --size arg poisson group size | ||
+ | --seed arg random seed | ||
+ | </ | ||
+ | As you can see you can easily change a few key parameters of the simulation such as runtime, or the Poisson firing rate. It's always a good idea to export some paramters of your code through command line arguments. How this is done will become clearer in the examples. Things that require less flexibility, | ||
+ | |||
+ | ====== The code behind all this ====== | ||
+ | |||
+ | Let's look at the code inside. | ||
+ | You find the source for simulations in the directory '' | ||
<code cpp> | <code cpp> | ||
Line 23: | Line 73: | ||
SpikeMonitor * smon_e = new SpikeMonitor( poisson, strbuf, size); | SpikeMonitor * smon_e = new SpikeMonitor( poisson, strbuf, size); | ||
</ | </ | ||
- | which creates a [[SpikeMonitor]]. The '' | + | which creates a [[manual:SpikeMonitor]]. The '' |
<code cpp> | <code cpp> | ||
Line 42: | Line 92: | ||
</ | </ | ||
here '' | here '' | ||
- | ====== The full program ====== | ||
- | |||
- | |||
- | <code cpp> | ||
- | #include < | ||
- | #include < | ||
- | #include < | ||
- | #include < | ||
- | |||
- | #include < | ||
- | #include < | ||
- | #include < | ||
- | #include < | ||
- | |||
- | #include " | ||
- | #include " | ||
- | #include " | ||
- | #include " | ||
- | #include " | ||
- | #include " | ||
- | #include " | ||
- | #include " | ||
- | |||
- | using namespace std; | ||
- | |||
- | namespace po = boost:: | ||
- | namespace mpi = boost::mpi; | ||
- | |||
- | int main(int ac, char* av[]) | ||
- | { | ||
- | |||
- | string dir = " | ||
- | string file_prefix = " | ||
- | |||
- | char strbuf [255]; | ||
- | string msg; | ||
- | |||
- | NeuronID size = 1000; | ||
- | NeuronID seed = 1; | ||
- | double kappa = 5.; | ||
- | double simtime = 10.; | ||
- | |||
- | int errcode = 0; | ||
- | |||
- | try { | ||
- | |||
- | po:: | ||
- | desc.add_options() | ||
- | (" | ||
- | (" | ||
- | (" | ||
- | (" | ||
- | (" | ||
- | ; | ||
- | |||
- | po:: | ||
- | po:: | ||
- | po:: | ||
- | |||
- | if (vm.count(" | ||
- | cout << desc << " | ||
- | return 1; | ||
- | } | ||
- | |||
- | |||
- | if (vm.count(" | ||
- | cout << "kappa set to " | ||
- | << | ||
- | kappa = vm[" | ||
- | } | ||
- | |||
- | if (vm.count(" | ||
- | cout << " | ||
- | << | ||
- | simtime = vm[" | ||
- | } | ||
- | |||
- | if (vm.count(" | ||
- | cout << "size set to " | ||
- | << | ||
- | size = vm[" | ||
- | } | ||
- | |||
- | if (vm.count(" | ||
- | cout << "seed set to " | ||
- | << | ||
- | seed = vm[" | ||
- | } | ||
- | } | ||
- | catch(exception& | ||
- | cerr << " | ||
- | return 1; | ||
- | } | ||
- | catch(...) { | ||
- | cerr << " | ||
- | } | ||
- | |||
- | // BEGIN Global stuff | ||
- | mpi:: | ||
- | mpi:: | ||
- | communicator = &world; | ||
- | |||
- | sprintf(strbuf, | ||
- | string logfile = strbuf; | ||
- | logger = new Logger(logfile, | ||
- | |||
- | sys = new System(& | ||
- | // END Global stuff | ||
- | |||
- | PoissonGroup * poisson = new PoissonGroup(size, | ||
- | poisson-> | ||
- | |||
- | sprintf(strbuf, | ||
- | SpikeMonitor * smon_e = new SpikeMonitor( poisson, strbuf, size); | ||
- | |||
- | sprintf(strbuf, | ||
- | PopulationRateMonitor * pmon_e = new PopulationRateMonitor( poisson, strbuf, 1.0 ); | ||
- | |||
- | RateChecker * chk = new RateChecker( poisson , -1 , 20.*kappa , 10); | ||
- | if (!sys-> | ||
- | errcode = 1; | ||
- | |||
- | logger-> | ||
- | delete sys; | ||
- | |||
- | if (errcode) | ||
- | env.abort(errcode); | ||
- | return errcode; | ||
- | } | ||
- | </ | ||
- | |||
+ | The full source code can be found here [[https:// | ||
examples/sim_poisson.1386602336.txt.gz · Last modified: 2013/12/09 15:18 by zenke