Setup all node arrays to be passed to the brainsimulation. More...

#include "definitions.h"

Include dependency graph for brainsetup.h:

Macros
#define	FLAG_TICKS "--ticks"
	Command line flag for number of ticks (single integer paramter). More...

#define	FLAG_X_OBSERVATIONNODES "--xobs"
	Command line flag for x indices of observation nodes (multiple integer paramters). More...

#define	FLAG_Y_OBSERVATIONNODES "--yobs"
	Command line flag for y indices of observation nodes (multiple integer paramters). More...

#define	FLAG_X_NODES "-x"
	Command line flag for node grid size on the x axis (single integer paramter). More...

#define	FLAG_Y_NODES "-y"
	Command line flag for node grid size on the y axis (single integer paramter). More...

#define	FLAG_START_LEVELS "--startlevels"
	Command line flag for starting energy levels of start nodes (multiple double paramters). More...

#define	FLAG_START_NODES_X "--startx"
	Command line flag for x indices of start nodes (multiple integer paramters). More...

#define	FLAG_START_NODES_Y "--starty"
	Command line flag for y indices of start nodes (multiple integer paramters). More...

#define	FLAG_FREQUENCIES "--freqs"
	Command line flag for frequencies of frequency generating nodes (multiple intger paramters). More...

#define	FLAG_FREQ_NODES_X "--freqx"
	Command line flag for x indices of frequency generating nodes (multiple integer paramters). More...

#define	FLAG_FREQ_NODES_Y "--freqy"
	Command line flag for y indices of frequency generating nodes (multiple integer paramters). More...

#define	FLAG_FREQ_BITMAPS "--freqbitmaps"
	Command line flag for bitmap image paths, interpreted as frequencies (multiple string paramters). More...

#define	FLAG_MIN_BITMAP_FREQ "--minbitmapfreq"
	Command line flag for the frequency to be used for the min non-0 bitmap value (1) (single integer paramter). More...

#define	FLAG_MAX_BITMAP_FREQ "--maxbitmapfreq"
	Command line flag for the frequency to be used for the max bitmap value (assumes 24-bit: 765) (single integer paramter). More...

#define	FLAG_BITMAP_DURATION "--bitmapduration"
	Command line flag for the duration (in ticks) a bitmap is to be used for input before it is followed by the next bitmap (single integer paramter).

Functions
unsigned int	contains_flag (const int argc, const char argv[], const char flag)
	Checks if the command line contains a flag. More...

int	parse_int_arg (const int argc, const char argv[], const char flag)
	Parses an integer argument from the command line for a specified flag. More...

nodetimeseries_t *	init_observation_timeseries_from_sh (const int argc, const char argv[], int num_observationnodes)
	Initializes num_oberservationnodes timeseries structs and returns them in an array using settings from the command line. More...

nodetimeseries_t *	init_observation_timeseries_default (int *num_observationnodes, int num_ticks)
	Initializes num_oberservationnodes timeseries structs with default values and returns them in an array. More...

nodetimeseries_t *	init_observation_timeseries (const int num_oberservationnodes, const int x_indices, const int y_indices, const int num_timeseries_elements)
	Initializes num_oberservationnodes timeseries structs and returns them in an array. More...

void	init_start_time_state_from_sh (const int argc, const char argv[], const int number_nodes_x, const int number_nodes_y, nodeval_t *nodes)
	Sets a start time energy state for the node field. More...

nodeval_t **	init_nodegrid_default (int number_nodes_x, int number_nodes_y)
	Initializes a nodegrid with a default size and initializes it with zero. More...

void	init_start_time_state (const int number_nodes_x, const int number_nodes_y, nodeval_t *nodes, const int num_start_levels, const nodeval_t start_levels, const int start_nodes_x, const int start_nodes_y)
	Sets a start time energy state for the node field. More...

nodeinputseries_t *	read_input_behavior (const int number_of_inputnodes, const int x_indices, const int y_indices, const char *inputnodefilenames, const int number_of_elements)
	Reads and parses the inputs defined as csv files to be added to the given nodes during the simulation. More...

double *	generate_sin_time_series (int hz, const double tick_ms, int number_of_samples)
	Generates a specified number of samples of a discretized sinoidal timeseries with the specified frequency and returns it. More...

double *	generate_sin_frequency (int hz, const double tick_ms)
	Generates a discretized sinoidal timeseries with the specified frequency and returns it. More...

int	calculate_period_length (int hz, const double tick_ms)
	Calcuated the period length of the given frequency at the specified resolution, i.e., the number of samples to generate, until the period is reached. More...

nodeinputseries_t *	generate_input_frequencies_from_sh (const int argc, const char argv[], int num_inputnodes, const double tick_ms)
	Generates input timeseries for the given nodes with the specified frequency. More...

nodeinputseries_t *	generate_input_frequencies_default (int *num_inputnodes, const double tick_ms)
	Generates input timeseries for a set of default given nodes with default frequencies. More...

nodeinputseries_t *	generate_input_frequencies (const int number_of_inputnodes, const int x_indices, const int y_indices, const int *frequencies, const double tick_ms)
	Generates input timeseries for the given nodes with the specified frequency. More...

unsigned int *	read_bitmap_contents (const char bitmap_path, unsigned int bitmap_size_x, unsigned int *bitmap_size_y)
	Reads a bitmap image file and returns the sum color values for each pixel in a array. More...

nodeinputseries_t *	generate_input_frequencies_from_bitmap (const char filenames[], const unsigned int num_filenames, const int min_freq, const int max_freq, const int bitmap_duration_ticks, int num_inputnodes, const double tick_ms)
	Generates input timeseries for all non-zero (non-black) nodes from the specified 24-bit bitmap images. More...

nodeinputseries_t *	generate_input_frequencies_from_sh_bitmap (const int argc, const char argv[], int num_inputnodes, const double tick_ms)
	Generates input timeseries for all non-zero (non-black) nodes from the specified 24-bit bitmap images. More...

Detailed Description

Setup all node arrays to be passed to the brainsimulation.

Macro Definition Documentation

#define FLAG_FREQ_BITMAPS "--freqbitmaps"

Command line flag for bitmap image paths, interpreted as frequencies (multiple string paramters).

#define FLAG_FREQ_NODES_X "--freqx"

Command line flag for x indices of frequency generating nodes (multiple integer paramters).

#define FLAG_FREQ_NODES_Y "--freqy"

Command line flag for y indices of frequency generating nodes (multiple integer paramters).

#define FLAG_FREQUENCIES "--freqs"

Command line flag for frequencies of frequency generating nodes (multiple intger paramters).

#define FLAG_MAX_BITMAP_FREQ "--maxbitmapfreq"

Command line flag for the frequency to be used for the max bitmap value (assumes 24-bit: 765) (single integer paramter).

#define FLAG_MIN_BITMAP_FREQ "--minbitmapfreq"

Command line flag for the frequency to be used for the min non-0 bitmap value (1) (single integer paramter).

#define FLAG_START_LEVELS "--startlevels"

Command line flag for starting energy levels of start nodes (multiple double paramters).

#define FLAG_START_NODES_X "--startx"

Command line flag for x indices of start nodes (multiple integer paramters).

#define FLAG_START_NODES_Y "--starty"

Command line flag for y indices of start nodes (multiple integer paramters).

#define FLAG_TICKS "--ticks"

Command line flag for number of ticks (single integer paramter).

#define FLAG_X_NODES "-x"

Command line flag for node grid size on the x axis (single integer paramter).

#define FLAG_X_OBSERVATIONNODES "--xobs"

Command line flag for x indices of observation nodes (multiple integer paramters).

#define FLAG_Y_NODES "-y"

Command line flag for node grid size on the y axis (single integer paramter).

#define FLAG_Y_OBSERVATIONNODES "--yobs"

Command line flag for y indices of observation nodes (multiple integer paramters).

Function Documentation

int calculate_period_length	(	int	hz,
		const double	tick_ms
	)

Calcuated the period length of the given frequency at the specified resolution, i.e., the number of samples to generate, until the period is reached.

Parameters

hz	The desired frequency in Hz.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds.

Returns: The number of samples required for one period.

unsigned int contains_flag	(	const int	argc,
		const char *	argv[],
		const char *	flag
	)

Checks if the command line contains a flag.

Parameters

argc	Number of command line arguments.
argv	Command line arguments.
flag	The command line flag.

Returns: 1 if it contains, 0 if not.

nodeinputseries_t* generate_input_frequencies	(	const int	number_of_inputnodes,
		const int *	x_indices,
		const int *	y_indices,
		const int *	frequencies,
		const double	tick_ms
	)

Generates input timeseries for the given nodes with the specified frequency.

The different time-series may vary as the minimal period length is detected.

Parameters

number_of_inputnodes	The number of input nodes and frequencies to generate.
x_indices	An array of x-coordinates of the nodes. Defines which node will be modified with the defined frequency. Length: number_of_inputnodes.
y_indices	An array of y-coordinates of the nodes. Defines which node will be modified with the defined frequency. Length: number_of_inputnodes.
frequencies	An array describing the desired frequencies in periods/second (Hz) to generate for each node. Length: number_of_inputnodes.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds. This parameter influences the number of generated samples, as frequency is defined in periods/second (Hz).

Returns: The array of input nodes initialized with the specified frequencies. Length: number_of_inputnodes.

nodeinputseries_t* generate_input_frequencies_default	(	int *	num_inputnodes,
		const double	tick_ms
	)

Generates input timeseries for a set of default given nodes with default frequencies.

The different time-series may vary as the minimal period length is different.

Parameters

num_inputnodes	The number of frequency generating nodes is written to this pointer.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds. This parameter influences the number of generated samples, as frequency is defined in periods/second (Hz).

Returns: The array of input nodes initialized with the frequencies. Length: num_inputnodes.

nodeinputseries_t* generate_input_frequencies_from_bitmap	(	const char *	filenames[],
		const unsigned int	num_filenames,
		const int	min_freq,
		const int	max_freq,
		const int	bitmap_duration_ticks,
		int *	num_inputnodes,
		const double	tick_ms
	)

Generates input timeseries for all non-zero (non-black) nodes from the specified 24-bit bitmap images.

Bitmaps must have the same dimensions and be encoded using uncompressed, 24-bit bitmap files. Bitmap color values are summed (R+G+B) and translated to frequencies. The minimum non-0 color (1) is mapped to min_freq and the maximum color (765) is mapped to max_freq. Other frequencies are determined using linear interpolation.

Parameters

filenames	File names of the .bmp files to read.
num_filenames	The number of .bmp files to read.
min_freq	The minimum frequency to generate. The minimum non-0 color (1) is mapped to min_freq.
max_freq	The maximum frequency to generate. The maximum color (765) is mapped to max_freq.
bitmap_duration_ticks	The number of ticks for which to generate a signal for a bitmap before moving on to the next bitmap (analogous to a frame's duration in a movie).
num_inputnodes	The number of frequency generating nodes is written to this pointer.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds. This parameter influences the number of generated samples, as frequency is defined in periods/second (Hz).

Returns: The array of input nodes initialized with the specified frequencies. Length: num_inputnodes.

nodeinputseries_t* generate_input_frequencies_from_sh	(	const int	argc,
		const char *	argv[],
		int *	num_inputnodes,
		const double	tick_ms
	)

Generates input timeseries for the given nodes with the specified frequency.

The different time-series may vary as the minimal period length is detected. Uses command line arguments.

Parameters

argc	Number of command line arguments.
argv	Command line arguments.
num_inputnodes	The number of frequency generating nodes is written to this pointer.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds. This parameter influences the number of generated samples, as frequency is defined in periods/second (Hz).

Returns: The array of input nodes initialized with the specified frequencies. Length: num_inputnodes.

nodeinputseries_t* generate_input_frequencies_from_sh_bitmap	(	const int	argc,
		const char *	argv[],
		int *	num_inputnodes,
		const double	tick_ms
	)

Generates input timeseries for all non-zero (non-black) nodes from the specified 24-bit bitmap images.

Bitmaps must have the same dimensions and be encoded using uncompressed, 24-bit bitmap files. Uses command line arguments.

Parameters

argc	Number of command line arguments.
argv	Command line arguments.
num_inputnodes	The number of frequency generating nodes is written to this pointer.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds. This parameter influences the number of generated samples, as frequency is defined in periods/second (Hz).

Returns: The array of input nodes initialized with the specified frequencies. Length: num_inputnodes.

double* generate_sin_frequency	(	int	hz,
		const double	tick_ms
	)

Generates a discretized sinoidal timeseries with the specified frequency and returns it.

Automatically detects the period, and returns exactly only period. Should be preferred way to generate the time-series.

Parameters

hz	The desired frequency in Hz.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds.

Returns: A series of doubles. Length: Period of the frequency.

double* generate_sin_time_series	(	int	hz,
		const double	tick_ms,
		int	number_of_samples
	)

Generates a specified number of samples of a discretized sinoidal timeseries with the specified frequency and returns it.

Parameters

hz	The desired frequency in Hz.
tick_ms	The milliseconds in between each simulation tick, i.e., the required resolution in milliseconds.
number_of_samples	The number of samples to generate.

Returns: A series of doubles. Length: number_of_samples.

nodeval_t** init_nodegrid_default	(	int *	number_nodes_x,
		int *	number_nodes_y
	)

Initializes a nodegrid with a default size and initializes it with zero.

Parameters

number_nodes_x	Writes the number of nodes in the x-axis to this pointer.
number_nodes_y	Writes the number of nodes in the y-axis to this pointer.

Returns: The initialized 2D node field. Size: number_nodes_x * number_nodes_y.

nodetimeseries_t* init_observation_timeseries	(	const int	num_oberservationnodes,
		const int *	x_indices,
		const int *	y_indices,
		const int	num_timeseries_elements
	)

Initializes num_oberservationnodes timeseries structs and returns them in an array.

Parameters

num_oberservationnodes	The number of timeseries to create.
x_indices	The x indices of the nodes to observe. Must have num_obervationnodes as length.
y_indices	The y indices of the nodes to observe. Must have num_obervationnodes as length.
num_timeseries_elements	The number of elements for the timeseries to hold. Timeseries memory is allocated as part of initialization.

Returns: Array of newly initialized timeseries structs. Array has num_oberservationnodes as length.

nodetimeseries_t* init_observation_timeseries_default	(	int *	num_observationnodes,
		int	num_ticks
	)

Initializes num_oberservationnodes timeseries structs with default values and returns them in an array.

Parameters

num_observationnodes	Writes the number of timeseries to this pointer.
num_ticks	The number of ticks to simulate, as memory is reserved beforehand.

Returns: Array of newly initialized timeseries structs. Array has num_oberservationnodes as length.

nodetimeseries_t* init_observation_timeseries_from_sh	(	const int	argc,
		const char *	argv[],
		int *	num_observationnodes
	)

Initializes num_oberservationnodes timeseries structs and returns them in an array using settings from the command line.

Parameters

argc	Number of command line arguments.
argv	Command line arguments.
num_observationnodes	Writes the number of timeseries to this pointer.

Returns: Array of newly initialized timeseries structs. Array has num_oberservationnodes as length.

void init_start_time_state	(	const int	number_nodes_x,
		const int	number_nodes_y,
		nodeval_t **	nodes,
		const int	num_start_levels,
		const nodeval_t *	start_levels,
		const int *	start_nodes_x,
		const int *	start_nodes_y
	)

Sets a start time energy state for the node field.

All unspecified nodes start with 0.

Parameters

number_nodes_x	The x dimension of the node field.
number_nodes_y	The y dimension of the node field.
nodes	The 2D node field to initialize.
num_start_levels	The number of nodes in the field to initialize with non-zero values.
start_levels	The energy levels of the starting non-zero nodes. Must have num_start_levels length.
start_nodes_x	The x indices of the starting non-zero nodes. Must have num_start_levels length.
start_nodes_y	The y indices of the starting non-zero nodes. Must have num_start_levels length.

void init_start_time_state_from_sh	(	const int	argc,
		const char *	argv[],
		const int	number_nodes_x,
		const int	number_nodes_y,
		nodeval_t **	nodes
	)

Sets a start time energy state for the node field.

All unspecified nodes start with 0 using settings from the command line.

Parameters

argc	Number of command line arguments.
argv	Command line arguments.
number_nodes_x	The x dimension of the node field.
number_nodes_y	The y dimension of the node field.
nodes	The 2D node field to initialize.

int parse_int_arg	(	const int	argc,
		const char *	argv[],
		const char *	flag
	)

Parses an integer argument from the command line for a specified flag.

Parameters

argc	Number of command line arguments.
argv	Command line arguments.
flag	The command line flag.

Returns: The parsed integer argument for the flag.

unsigned int* read_bitmap_contents	(	const char *	bitmap_path,
		unsigned int *	bitmap_size_x,
		unsigned int *	bitmap_size_y
	)

Reads a bitmap image file and returns the sum color values for each pixel in a array.

Array length is width * height. Get pixel using array[y * width + x]. Allocates the new array on the heap (do not forget to free it after use).

Parameters

bitmap_path	Path of the bitmap file to read.
bitmap_size_x	The x dimension of the read bitmap is written to this pointer.
bitmap_size_y	The y dimension of the read bitmap is written to this pointer.

Returns: The array of the sum of the bitmap's color values.

nodeinputseries_t* read_input_behavior	(	const int	number_of_inputnodes,
		const int *	x_indices,
		const int *	y_indices,
		const char **	inputnodefilenames,
		const int *	number_of_elements
	)

Reads and parses the inputs defined as csv files to be added to the given nodes during the simulation.

Parameters

number_of_inputnodes	The number of input nodes and files.
x_indices	An array of x-coordinates of the nodes. Defines, which node will be added the values written in the corresponding csv file. Length: number_of_inputnodes.
y_indices	An array of y-coordinates of the nodes. Defines, which node will be added the values written in the corresponding csv file. Length: number_of_inputnodes.
inputnodefilenames	The .csv filenames to read. Order must match the order of x_coordinates and y_coordinates. Length: number_of_inputnodes.
number_of_elements	Elements assigning each node the number of input elements in the corresponding file. Length: number_of_inputnodes.

Returns: The array of input nodes as read from the given filepaths. Length: number_of_inputnodes.

Macros

Functions

Detailed Description

Macro Definition Documentation

Function Documentation