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--- examples:sim_poisson [2014/10/07 11:28] – Fixes links to manual zenke
+++ examples:sim_poisson [2016/02/04 17:39] (current) – typo zenke
@@ Line 1: / Line 1: @@
 ====== sim_poisson example ======
-Running the example program ''sim_poisson'' will usually yield an output like this one
+Simulates an array of Poisson processes to illustrate the use of [[manual:PoissonGroup]]. The output is written to a [[manual:ras]] file in the same directory.
+Full source code: [[https://github.com/fzenke/auryn/blob/master/examples/sim_poisson.cpp]]
+===== Running code =====
+Running the example program ''sim_poisson'' yields an output like this one
 <code shell>
--bash-4.1$ ./sim_poisson --seed 1231231
+zenke@foobar:~/auryn/build/examples$ ./sim_poisson
-seed set to 1231231.
+[=========================] 100%      t=1.0s  f=5.1 Hz
-[=========================] 100%      t=1.0 s  f=45.3 Hz
 ( 0) Freeing ...
 </code>
 In addition the script will create a [[manual:ras]] and a [[manual:prate]] output file (''poisson.0.ras'', ''poisson.0.prate'') as well as a log file ''poisson.0.log''.
-===== The important bits =====
-Let's look at the code inside. you find the source for simulations in the directory ''./sim/sim_poisson.cpp''. Since Auryn simulations are executable C++ programs there is quite some overhead (see below). However since the header logic is usually the same let's focus first on the interesting bits, where the interesting stuff happens. The interesting stuff starts here:
+===== Visualizing the output =====
+Our simulation has written its output (1 second of Poisson spiking from 1000 Poisson neurons firing at 5Hz) to ''poisson.0.ras'', a human-readable [[manual:ras]] file which contains the Poisson spikes. You can peek into the file using a text editor. However, to visualize the  data you need a plotter. I generally like using [[gnuplot]], but any other plotting software which allows reading time series data from columnar ASCII files will do (e.g. [[matplotlib]] in conjunction with [[numpy]]).
+If you have gnuplot installed you can take a quick peek using the command line
+<code>
+echo "plot 'poisson.0.ras' with dots lc rgb 'black'" | gnuplot -p
+</code>
+from within gnuplot
+<code gnuplot>
+plot 'poisson.0.ras' with dots lc rgb 'black'
+</code>
+Either way the output will look similar to this:
+{{ :examples:poisson_output.png |}}
+===== 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:~/auryn/build/examples$ ./sim_poisson --seed 182319
+[=========================] 100%      t=1.0s  f=5.1 Hz
+( 0) Freeing ...
+</code>
+===== 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:~/auryn/build/examples$ ./sim_poisson --help
+Allowed options:
+  --help                produce help message
+  --simtime arg         simulation time
+  --kappa arg           poisson group rate
+  --size arg            poisson group size
+  --seed arg            random seed
+</code>
+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, such as the structure of your simulation itself will be fixed in the simulation file, which is a file with C++ code. Let's have a look at this code in the present example now.
+====== The code behind all this ======
+Let's look at the code inside.
+You find the source for simulations in the directory ''examples/sim_poisson.cpp''. Since Auryn simulations are executable C++ programs there is quite some overhead (see below). However since the header logic is usually the same let's focus first on the interesting bits, where the interesting stuff happens. The interesting stuff starts here:
 <code cpp>
@@ Line 44: / Line 92: @@
 </code>
 here ''run'' takes at least one parameter which is the simulation time ''simtime''. That is one second in this example. The second parameter is optional. The ''false'' in the example tells run to ignore the RateChecker that we painfully added in the last step. This does not make much sense here, but neither did the Checker in the first place. We will see that the switch is useful in other examples such as [[sim_background]], where one can avoid checking during a transient priming period.
-===== The full program =====
-<code cpp>
-#include <iostream>
-#include <iomanip>
-#include <stdlib.h>
-#include <string>
-#include <boost/program_options.hpp>
-#include <boost/mpi/environment.hpp>
-#include <boost/mpi/communicator.hpp>
-#include <boost/mpi.hpp>
-#include "auryn_global.h"
-#include "auryn_definitions.h"
-#include "System.h"
-#include "Logger.h"
-#include "PoissonGroup.h"
-#include "SpikeMonitor.h"
-#include "PopulationRateMonitor.h"
-#include "RateChecker.h"
-using namespace std;
-namespace po = boost::program_options;
-namespace mpi = boost::mpi;
-int main(int ac, char* av[])
-{
-	string dir = "./";
-	string file_prefix = "poisson";
-	char strbuf [255];
-	string msg;
-	NeuronID size = 1000;
-	NeuronID seed = 1;
-	double kappa = 5.;
-	double simtime = 10.;
-	int errcode = 0;
-    try {
-        po::options_description desc("Allowed options");
-        desc.add_options()
-            ("help", "produce help message")
-            ("simtime", po::value<double>(), "simulation time")
-            ("kappa", po::value<double>(), "poisson group rate")
-            ("size", po::value<int>(), "poisson group size")
-            ("seed", po::value<int>(), "random seed")
-        ;
-        po::variables_map vm;
-        po::store(po::parse_command_line(ac, av, desc), vm);
-        po::notify(vm);
-        if (vm.count("help")) {
-            cout << desc << "\n";
-            return 1;
-        }
-        if (vm.count("kappa")) {
-            cout << "kappa set to "
-                 << vm["kappa"].as<double>() << ".\n";
-			kappa = vm["kappa"].as<double>();
-        }
-        if (vm.count("simtime")) {
-            cout << "simtime set to "
-                 << vm["simtime"].as<double>() << ".\n";
-			simtime = vm["simtime"].as<double>();
-        }
-        if (vm.count("size")) {
-            cout << "size set to "
-                 << vm["size"].as<int>() << ".\n";
-			size = vm["size"].as<int>();
-        }
-        if (vm.count("seed")) {
-            cout << "seed set to "
-                 << vm["seed"].as<int>() << ".\n";
-			seed = vm["seed"].as<int>();
-        }
-    }
-    catch(exception& e) {
-        cerr << "error: " << e.what() << "\n";
-        return 1;
-    }
-    catch(...) {
-        cerr << "Exception of unknown type!\n";
-    }
-	// BEGIN Global stuff
-	mpi::environment env(ac, av);
-	mpi::communicator world;
-	communicator = &world;
-	sprintf(strbuf, "%s/%s.%d.log", dir.c_str(), file_prefix.c_str(), world.rank());
-	string logfile = strbuf;
-	logger = new Logger(logfile,world.rank(),PROGRESS,EVERYTHING);
-	sys = new System(&world);
-	// END Global stuff
-	PoissonGroup * poisson = new PoissonGroup(size,kappa);
-	poisson->seed(seed);
-	sprintf(strbuf, "%s/%s.%d.ras", dir.c_str(), file_prefix.c_str(), world.rank() );
-	SpikeMonitor * smon_e = new SpikeMonitor( poisson, strbuf, size);
-	sprintf(strbuf, "%s/%s.%d.prate", dir.c_str(), file_prefix.c_str(), world.rank() );
-	PopulationRateMonitor * pmon_e = new PopulationRateMonitor( poisson, strbuf, 1.0 );
-	RateChecker * chk = new RateChecker( poisson , -1 , 20.*kappa , 10);
-	if (!sys->run(simtime,false))
-			errcode = 1;
-	logger->msg("Freeing ...",PROGRESS,true);
-	delete sys;
-	if (errcode)
-		env.abort(errcode);
-	return errcode;
-}
-</code>
+The full source code can be found here [[https://github.com/fzenke/auryn/blob/master/examples/sim_poisson.cpp]]