utilities.cpp File Reference

Library functions useful in all the package. More...

#include <errno.h>
#include <sys/sysctl.h>
#include <stdio.h>
#include "utilities.h"
#include <iostream>

Macros
#define	MAX_GET_LEN   32

Functions
int	verbose (0)
int	thread_limit (1000000)
ostream &	tab (ostream &out)
int	cmd_line (int argc, char **argv)
	Reconstructs the command line as a global string. More...
Bstring	command_line ()
	Returns the command line. More...
Bstring	command_line_time ()
	Returns the command line and time in a string. More...
string	command_line_time2 ()
string	get_user_name ()
	Returns the user name. More...
void	usage (const char **use, int all)
	Prints usage information. More...
SysType	systype (int show)
	Finds the system type - mostly just for byte order. More...
size_t	system_processors ()
	Returns the number of processors. More...
long	system_memory ()
	Returns system memory size. More...
int	memory_check (long mem_required)
	Checking if there is enough memory, abort if not. More...
int	bexit (int value)
	Exit function for cleanup and debugging. More...
DataType	getdatatype (char letter)
	Get the data type indicated by a single letter code. More...
CompoundType	getcompoundtype (int ch, string sct)
	Get the compound type indicated by a single letter code. More...
int	select_numbers (Bstring &string, int n, int *numsel)
	Converts a string with a selection specification into an integer array. More...
vector< int >	select_numbers (Bstring &string, int n)
int	findNextPowerOf (int startNumber, int powerOf)
	Finds the next greatest number that is a power of a given number. More...
int	get_integer (char *ptr, int len)
	Converts a defined length string into an integer. More...
float	get_float (char *ptr, int len)
	Converts a defined length string into a floating point number. More...
void	swapbytes (unsigned char *v, size_t n)
	Swaps bytes. More...
void	swapbytes (size_t size, unsigned char *v, size_t n)
	Swaps bytes. More...
void	vax2ieee (unsigned char *v, int sb)
	Converts VAX floating point format to IEEE floating point format. More...
double	angle_set_negPI_to_PI (double angle)
	Returns an angle between -PI and PI. More...
double	angle_set_0_to_TWOPI (double angle)
	Returns an angle between 0 and 2*PI. More...
float	remove_negative_zeros (float value0, float threshold)
	Prevent a negative sign from being placed in front of zero value in a text file. More...
size_t	get_chunk_size (size_t datasize)
	Returns the chunk size per thread. More...
size_t	get_chunk_size (size_t datasize, size_t c)
	Returns the chunk size per thread. More...
int	error_show (const char *message, const char *file, int line)
	Displays the error with file and line reference. More...
int	error_show (string message, string file, int line)
	Displays the error with file and line reference. More...

Variables
string	command

Detailed Description

Library functions useful in all the package.

Author

Bernard Heymann

Date

Created: 19990722

Modified: 20220722

Macro Definition Documentation

MAX_GET_LEN

#define MAX_GET_LEN   32

Function Documentation

angle_set_0_to_TWOPI()

double angle_set_0_to_TWOPI

(

double

angle

)

Returns an angle between 0 and 2*PI.

Parameters

angle

input angle.

Returns

double angle between 0 and 2*PI.

angle_set_negPI_to_PI()

double angle_set_negPI_to_PI

(

double

angle

)

Returns an angle between -PI and PI.

Parameters

angle

input angle.

Returns

double angle between -PI and PI.

bexit()

int bexit

(

int

value

)

Exit function for cleanup and debugging.

Parameters

value

exit value.

Returns

int given value.

cmd_line()

int cmd_line	(	int	argc,
		char **	argv
	)

Reconstructs the command line as a global string.

Parameters

argc	the number of command line arguments.
**argv	the command line arguments.

Returns

int 0.

Concatenates the command line arguments into one string.

command_line()

Bstring command_line

(

)

Returns the command line.

Returns

Bstring new string.

This is designed to pack the command line into a string.

command_line_time()

Bstring command_line_time

(

)

Returns the command line and time in a string.

Returns

Bstring new string.

This is designed to pack the command line into a string followed by
a second string for the time.

command_line_time2()

string command_line_time2

(

)

error_show() [1/2]

int error_show	(	const char *	message,
		const char *	file,
		int	line
	)

Displays the error with file and line reference.

Parameters

*message	a string to be included.
*file	the file name (should be FILE).
line	the line number (should be LINE).

Returns

int error number.

The function uses perror() to display a message containing the source
file and line number where it originated.

Reference: Derived from CCP4 code

error_show() [2/2]

int error_show	(	string	message,
		string	file,
		int	line
	)

Displays the error with file and line reference.

Parameters

*message	a string to be included.
*file	the file name (should be FILE).
line	the line number (should be LINE).

Returns

int error number.

The function uses perror() to display a message containing the source
file and line number where it originated.

Reference: Derived from CCP4 code

findNextPowerOf()

int findNextPowerOf	(	int	startNumber,
		int	powerOf
	)

Finds the next greatest number that is a power of a given number.

Author

Dan Krainak

Parameters

startNumber	number to begin from.
powerOf	power of this number is the number returned.

Returns

int the next greatest power (i.e. 128) or 0 on error.

Loop through the powerOf variable, multiplying it each successive
iteration until it is greater than the starting number.
Eg., the next greatest power of 2 starting at 100 is 128.

get_chunk_size() [1/2]

size_t get_chunk_size

(

size_t

datasize

)

Returns the chunk size per thread.

Parameters

datasize

size of data to be divided into chunks.

Returns

long chunk size.

If multiple processors are used, the chunk size is set to the data size
divided by the number of processors.
Otherwise, the chunk size is equal to the data size.

Reference: Derived from CCP4 code

get_chunk_size() [2/2]

size_t get_chunk_size	(	size_t	datasize,
		size_t	c
	)

Returns the chunk size per thread.

Parameters

datasize	size of data to be divided into chunks.
c	channel size to align chunk to.

Returns

long chunk size.

If multiple processors are used, the chunk size is set to the data size
divided by the number of processors.
Otherwise, the chunk size is equal to the data size.

Reference: Derived from CCP4 code

get_float()

float get_float	(	char *	ptr,
		int	len
	)

Converts a defined length string into a floating point number.

Parameters

*ptr	pointer to the string.
len	length to be scanned.

Returns

float the floating point number.

The string is copied, 0-terminated, and scanned for a floating point number.

get_integer()

int get_integer	(	char *	ptr,
		int	len
	)

Converts a defined length string into an integer.

Parameters

*ptr	pointer to the string.
len	length to be scanned.

Returns

int the integer.

The string is copied, 0-terminated, and scanned for an integer.

get_user_name()

string get_user_name

(

)

Returns the user name.

Returns

string user name.

It uses getpwuid_r (thread safe) to find the user in the password file.

getcompoundtype()

CompoundType getcompoundtype	(	int	ch,
		string	sct
	)

Get the compound type indicated by a single letter code.

Parameters

ch	number of channels.
sct	string indicating compound type.

Returns

CompoundType compound type.

This function is used in optional command-line arguments to indicate
a new compound type for an image.

getdatatype()

DataType getdatatype

(

char

letter

)

Get the data type indicated by a single letter code.

Parameters

letter

letter indicating data type.

Returns

DataType data type.

This function is used in optional command-line arguments to indicate 
a new data type for an image.

memory_check()

int memory_check

(

long

mem_required

)

Checking if there is enough memory, abort if not.

Parameters

mem_required

memory required.

Returns

int 1 if enough.

remove_negative_zeros()

float remove_negative_zeros	(	float	value0,
		float	threshold
	)

Prevent a negative sign from being placed in front of zero value in a text file.

Author

David Belnap

Parameters

value0	input value to be tested
threshold	a small negative number

Returns

float "Corrected" or input value

This function is intended to be used when obvious zero values are set
to a very small negative number.  Input value is set to zero if
              value0 > threshold  and  value0 < 0
If so, the value is reset to zero.  Otherwise, the input value is 
returned.

Reference: Derived from CCP4 code

select_numbers() [1/2]

vector< int > select_numbers	(	Bstring &	string,
		int	n
	)

select_numbers() [2/2]

int select_numbers	(	Bstring &	string,
		int	n,
		int *	numsel
	)

Converts a string with a selection specification into an integer array.

Parameters

&string	string.
n	length of integer array.
*numsel	pre-allocated integer array.

Returns

int number of levels.

The integer array must be allocated to a length that would accommodate
the highest number in the selection.
If the string length is zero, all elements are selected.
Multiple subsets are separated by colons

swapbytes() [1/2]

void swapbytes	(	size_t	size,
		unsigned char *	v,
		size_t	n
	)

Swaps bytes.

Parameters

size	size of the block to be swapped.
*v	a pointer to the bytes.
n	number of bytes to swap. Byte swapping is done in place.

swapbytes() [2/2]

void swapbytes	(	unsigned char *	v,
		size_t	n
	)

Swaps bytes.

Parameters

*v	a pointer to the bytes.
n	number of bytes to swap. Byte swapping is done in place.

system_memory()

long system_memory

(

)

Returns system memory size.

Returns

long memory size.

system_processors()

size_t system_processors

(

)

Returns the number of processors.

Returns

long number of processors.

systype()

SysType systype

(

int

show

)

Finds the system type - mostly just for byte order.

Parameters

show	a flag to indicate if the result should be shown.

Returns

SysType an enumerated type.

Test the byte order of an arbitrary byte sequence by interpreting it as
an integer or a floating point number.

tab()

ostream & tab

(

ostream &

out

)

thread_limit()

int thread_limit

(

1000000

)

usage()

void usage	(	const char **	use,
		int	all
	)

Prints usage information.

Parameters

**use

the string array.

all

flag to output all usage information. The usage information must be written into an array of srings, with each string a line and following a specific convention for the Bsoft package. The first line with non-space characters must start with "Usage:" followed by the command-line syntax. The next lines should describe the program. The options are indicated by lines strating with "-". The options are categorized as "Actions", "Parameters", "Input", and "Output". This constitutes the brief form. An additional section can be added as "Examples", that is shown only when the "all" argument is set.

vax2ieee()

void vax2ieee	(	unsigned char *	v,
		int	sb
	)

Converts VAX floating point format to IEEE floating point format.

Parameters

*v	four-byte array holding the floating point value
sb	flag to swap bytes before conversion Swap bytes prior to conversion if the swap flag is set. Handle special cases of zero, infinity, NaN or normalized values Otherwise assign the new byte values Reference: Derived from CCP4 code

verbose()

int verbose

(

0

)

Variable Documentation

command

string command