Collection of usefull Utilities not directly related to spiking networks. More...

#include <utilities.hpp>

Static Public Member Functions
static std::vector< std::string > &	split (const std::string &s, char delim, std::vector< std::string > &elems)
	Splits a string s into parts devided by delim and stores the result in elems and returns it. More...

static std::vector< std::string >	split (const std::string &s, char delim)
	The same as Utilities::split, but only returning the vector. More...

static void	progress_callback (double p)
	Funtion for generating a progress bar on terminal. More...

template<typename T >
static void	calculate_statistics (const std::vector< T > &data, T &min, T &max, double &avg, double &std_dev)
	Calculating statistics of a vector, using an estimator for std_dev (sample covariance) More...

template<typename T >
static void	write_vector_to_csv (T &data, std::string file_name)
	Writes a vector to a csv. More...

template<typename T >
static void	write_vector2_to_csv (T &data, std::string file_name, std::string first_line="")
	Writes a 2D vector to a csv. More...

static Json	merge_json (const Json &a, const Json &b)
	Merge two json objects. Note: Values already included in a will be overwritten! See github for source. More...

static Json	manipulate_backend_string (std::string &backend, Json &json)
	Merge the backend strings with a provided json object. Note: options already included in backend will not be overwritten! More...

static void	plot_spikes (std::string filename, std::string simulator)
	Given a filename of a csv with list of spikes this will produce a raster plot. More...

static void	plot_histogram (std::string filename, std::string simulator, bool normalized, int n_bins, std::string title)
	Plotting a histogram a one dimensional data in a csv. More...

static void	plot_voltages_spikes (std::string filename, std::string simulator, size_t mem_col=1, size_t t_col=0, std::string spikes_file="", size_t spikes_col=0)
	Plotting membrane voltage and (optional) plotting vertical lines for spikes on top. More...

static void	plot_1d_curve (std::string filename, std::string simulator, size_t x_col, size_t y_col, int std_dev_vol=-1)
	Plotting a curve with optional standard deviation. More...

Detailed Description

Collection of usefull Utilities not directly related to spiking networks.

Definition at line 43 of file utilities.hpp.

Member Function Documentation

template<typename T >

static void SNAB::Utilities::calculate_statistics	(	const std::vector< T > &	data,
		T &	min,
		T &	max,
		double &	avg,
		double &	std_dev
	)

inlinestatic

Calculating statistics of a vector, using an estimator for std_dev (sample covariance)

Parameters

data	contains sample data
min	object for minimal value
max	object for maximal value
avg	object for sample average
std_dev	object for smaple covariance

Definition at line 82 of file utilities.hpp.

     {
         if (data.size() > 1) {
             // Calculate statistics
             max = *std::max_element(data.begin(), data.end());
             min = *std::min_element(data.begin(), data.end());
             avg = double(std::accumulate(data.begin(), data.end(), 0.0)) /
                   double(data.size());
             std_dev = 0.0;
             std::for_each(data.begin(), data.end(), [&](const T val) {
                 std_dev += (val - avg) * (val - avg);
             });
             std_dev = std::sqrt(double(std_dev) / double(data.size() - 1));
         }
         else if (data.size() == 1) {
             min = data[0];
             max = data[0];
             avg = data[0];
             std_dev = 0;
         }
         else {
             min = 0;
             max = 0;
             avg = 0;
             std_dev = 0;
         }
     }

static Json SNAB::Utilities::manipulate_backend_string	(	std::string &	backend,
		Json &	json
	)

static

Merge the backend strings with a provided json object. Note: options already included in backend will not be overwritten!

Parameters

backend	string containig "[backend]" (+ "={setup options}"), will contain combined setup after execution
json	Object containig additional options for backend

Returns: : Combined json object

static Json SNAB::Utilities::merge_json	(	const Json &	a,
		const Json &	b
	)

static

Merge two json objects. Note: Values already included in a will be overwritten! See github for source.

Parameters

a	target json, keys will b overwritten
b	source json, will be copied into a

Returns: combined json object

static void SNAB::Utilities::plot_1d_curve	(	std::string	filename,
		std::string	simulator,
		size_t	x_col,
		size_t	y_col,
		int	std_dev_vol = `-1`
	)

static

Plotting a curve with optional standard deviation.

Parameters

filename	file containing data
simulator	the (unshortened) backend/simulator string
x_col	column of x values
y_col	column of y values
std_dev_vol	column of standard deviation values

static void SNAB::Utilities::plot_histogram	(	std::string	filename,
		std::string	simulator,
		bool	normalized,
		int	n_bins,
		std::string	title
	)

static

Plotting a histogram a one dimensional data in a csv.

Parameters

filename	File and path to the csv
simulator	simulator string, options will be stripped insider
normalized	flag whether histogram should be normalized
n_bins	number of bins for the histogram, negative values use 'auto' in pyplot
title	title to be plotted on top of histogram

static void SNAB::Utilities::plot_spikes	(	std::string	filename,
		std::string	simulator
	)

static

Given a filename of a csv with list of spikes this will produce a raster plot.

Parameters

filename	name and path to a csv
simulator	simulator string, simulator options will be stripped inside

static void SNAB::Utilities::plot_voltages_spikes	(	std::string	filename,
		std::string	simulator,
		size_t	mem_col = `1`,
		size_t	t_col = `0`,
		std::string	spikes_file = `""`,
		size_t	spikes_col = `0`
	)

static

Plotting membrane voltage and (optional) plotting vertical lines for spikes on top.

Parameters

filename	name of the file containing membrane voltage, csv style
simulator	the (unshortened) backend/simulator string
mem_col	column containing the membrane potential (default = 1)
t_col	column containing the time values (default = 0)
spikes_file	(optional) file containing spikes of the same neuron
spikes_col	column of spike data in spikes_file

static void SNAB::Utilities::progress_callback ( double p )

static

Funtion for generating a progress bar on terminal.

Parameters

p	value between 0 and 1 representing current progress

static std::vector<std::string>& SNAB::Utilities::split	(	const std::string &	s,
		char	delim,
		std::vector< std::string > &	elems
	)

static

Splits a string s into parts devided by delim and stores the result in elems and returns it.

Parameters

s	string to be splitted
delim	char which seperated the strings
elems	container in which result is appended at the end

Returns: the new elems

static std::vector<std::string> SNAB::Utilities::split	(	const std::string &	s,
		char	delim
	)

static

The same as Utilities::split, but only returning the vector.

Parameters

s	string to be splitted
delim	char which seperated the strings

template<typename T >

static void SNAB::Utilities::write_vector2_to_csv	(	T &	data,
		std::string	file_name,
		std::string	first_line = `""`
	)

inlinestatic

Writes a 2D vector to a csv.

Parameters

T	Type of data e.g. vector of a vector of ints, iterator musst support '<<' for output
data	Reference to the data
file_name	string containing filename, make sure folders already exists

Definition at line 147 of file utilities.hpp.

     {
         std::ofstream file;
         file.open(file_name, std::ofstream::out);
         if (file.good()) {
             if (first_line != "") {
                 file << first_line << std::endl;
             }
             for (auto i : data) {
                 for (auto j : i) {
                     file << j << ", ";
                 }
                 file << std::endl;
             }
         }
         else {
             std::cerr << "Could not open file " << file_name
                       << "for writing csv!" << std::endl;
         }
     }

template<typename T >

static void SNAB::Utilities::write_vector_to_csv	(	T &	data,
		std::string	file_name
	)

inlinestatic

Writes a vector to a csv.

Parameters

T	Type of data e.g. vector of ints, iterator musst support '<<' for output
data	Reference to the data
file_name	string containing filename, make sure folders already exists

Definition at line 121 of file utilities.hpp.

     {
         std::ofstream file;
         file.open(file_name, std::ofstream::out);
         if (file.good()) {
             for (auto i : data) {
                 file << i << std::endl;
             }
             // file << std::endl;
         }
         else {
             std::cerr << "Could not open file " << file_name
                       << "for writing csv!" << std::endl;
         }
     }

The documentation for this class was generated from the following file:

source/util/utilities.hpp

Static Public Member Functions

Detailed Description

Member Function Documentation