Using the software

Using the software

Summary of commands

A summary of commands is listed in the tables below, where {argument} denotes a mandatory argument, {arguments} denotes a list of mandatory arguments, [argument] denotes an optional argument, [arguments] denotes a list of optional arguments, and [...] denotes an optional part of the command line.

Table 1: Commands

Program name and usage	Purpose
azafran {parameters} < {model file} [> {result file}]	Perform a many-multiplet inversion
curcuma {parameters} < {model file} [> {result file}]	Perform a Doppler profile inversion
oregano {parameters} < {model file} [> {result file}]	Perform a Voigt profile inversion (pseudo-Voigt approximation)
mascada {parameters} < {model file} [> {result file}]	Perform a Voigt profile inversion (extended pseudo-Voigt approximation)
ecom < {result file} [> {target file}]	Extract the command included with a result file
edat < {result file} [> {target file}]	Extract the section data included with a result file
elog < {result file} [> {target file}]	Extract the log data included with a result file
emes < {result file} [> {target file}]	Extract the status messages included with a result file
emod < {result file} [> {target file}]	Extract the model definition included with a result file
erun {result file} {target file} [values]	Run the command included with a result file
ezip {flux file} {uncertainty file} [lines to skip] [> {target file}]	Merge separate flux and uncertainty data files

Table 2: Argument lists

Argument list	Arguments
{parameters}	{random seed} {parent number} {population size} {initial step size} {accuracy goal} {stop generation} {trace modulus}
[values]	[value of cost function] [value of cost function] ...

Note that the population size must be twice the parent number or greater. No error message is given, if it is not, however.

Table 3: Arguments

Argument	Type	Description
{random seed}	Positive integer (up to 64 bits)	The seed of the random number generator
{parent number}	Positive integer	The number of parents of the evolution strategy
{population size}	Positive integer	The population size of the evolution strategy (must be twice the parent number or greater)
{initial step size}	Positive real	The initial global step size of the evolution strategy
{accuracy goal}	Positive real	The accuracy goal of the evolution strategy
{stop generation}	Positive integer	The stop generation of the evolution strategy
{trace modulus}	Positive integer	The trace modulus m (every mth generation is logged)
{model file}	Pathname	The pathname of the model definition file
{result file}	Pathname	The pathname of the HTML result file
{target file}	Pathname	The pathname of the target file
[value of cost function]	Positive real	The expected value of the cost function for a section of spectroscopic data. Used for testing only
{flux file}	Pathname	The pathname of the flux data file
{uncertainty file}	Pathname	The pathname of the uncertainty data file
[lines to skip]	Positive integer	The number of lines to skip at the beginning of a source file

For further detail, refer to the source code and the example model definition and result HTML files included with Especia.

Concatenation of commands

Commands sending > output to and receiving < input from standard streams may be concatenated | on the command line. For example

emod < {result file} | $(ecom < {result file}) | tee {target file} | elog

extracts the model definition (emod) and command (ecom) from a result HTML file, sends the model definition to the extracted command, which sends its output to the tee command, which echoes its input into a target file and to the standard output stream, which is filtered (elog) to display log messages of the extracted command.