All the Rest

Settings

The syntax is simple:

  • set option = value changes the option,
  • info set option shows the current value,
  • info set lists all available options.

In the GUI

the options can be set in a dialog (Session ‣ Settings).

The GUI configuration (colors, fonts, etc.) is changed in a different way (GUI ‣ …) and is not covered here.

It is possible to change the value of the option temporarily:

with option1=value1 [,option2=value2]  command args...

For example:

info set fitting_method  # show the current fitting method
set fitting_method = nelder_mead_simplex # change the method
# change the method only for this one fit command
with fitting_method = levenberg_marquardt fit
# and now the default method is back Nelder-Mead

# multiple comma-separated options can be given
with fitting_method=levenberg_marquardt, verbosity=quiet fit

The list of available options:

autoplot
See autoplot.
cwd
Current working directory or empty string if it was not set explicitely. Affects relative paths.
default_sigma
Default y standard deviation. See Standard Deviation (or Weight). Possible values: sqrt max(y1/2, 1) and one (1).
domain_percent
See the section about variables.
epsilon
The ε value used to test floating-point numbers a and b for equality (it is well known that due to rounding errors the equality test for two numbers should have some tolerance, and the tolerance should be tailored to the application): |a−b| < ε. Default value: 10-12. You may need to decrease it when working with very small numbers.
fit_replot
Refresh the plot when fitting (0/1).
fitting_method
See Fitting Related Commands.
function_cutoff
See description in the chapter about model.
height_correction
See Guessing Initial Parameters.
lm_*
Setting to tune the Levenberg-Marquardt fitting method.
logfile
String. File where the commands are logged. Empty – no logging.
log_output
When logfile is set, log output together with input (0/1).
max_fitting_time
Stop fitting when this number of seconds of processor time is exceeded. See Fitting Related Commands.
max_wssr_evaluations
See Fitting Related Commands.
nm_*
Setting to tune the Nelder-Mead downhill simplex fitting method.
numeric_format
Format of numbers printed by the info command. It takes as a value a format string, the same as sprintf() in the C language. For example set numeric_format='%.3f' changes the precision of numbers to 3 digits after the decimal point. Default value: %g.
on_error
Action performed on error. If the option is set to stop (default) and the error happens in script, the script is stopped. Other possible values are nothing (do nothing) and exit (finish program – ensures that no error can be overlooked).
pseudo_random_seed
Some fitting methods and functions, such as randnormal in data expressions use a pseudo-random number generator. In some situations one may want to have repeatable and predictable results of the fitting, e.g. to make a presentation. Seed for a new sequence of pseudo-random numbers can be set using the option pseudo_random_seed. If it is set to 0, the seed is based on the current time and a sequence of pseudo-random numbers is different each time.
refresh_period
During time-consuming computations (like fitting) user interface can remain not changed for this time (in seconds). This option was introduced, because on one hand frequent refreshing of the program’s window notably slows down fitting, and on the other hand irresponsive program is a frustrating experience.
verbosity
Possible values: -1 (silent), 0 (normal), 1 (verbose), 2 (very verbose).
width_correction
See Guessing Initial Parameters.

Data View

The command plot controls the region of the graph that is displayed:

plot [[xrange] yrange] [@n, ...]

xrange and yrange has syntax [min:max]. If the boundaries are skipped, they are automatically determined using the given datasets.

In the GUI

there is hardly ever a need to use this command directly.

The CLI version on Unix systems visualizes the data using the gnuplot program, which has similar syntax for the plot range.

Examples:

plot [20.4:50] [10:20] # show x from 20.4 to 50 and y from 10 to 20
plot [20.4:] # x from 20.4 to the end,
             # y range will be adjusted to encompass all data
plot         # all data will be shown

The values of the options autoplot and fit_replot change the automatic plotting behaviour. By default, the plot is refreshed automatically after changing the data or the model (autoplot=1). It is also possible to replot the model when fitting, to show the progress (see the options fit_replot and refresh_period).

Redirecting the plot command to a file saves a plot as an image:

plot [20.4:50] [10:20] > myplot.png

For now, it works only in fityk (not cfityk) and is less flexible than Session ‣ Save as Image.

Information Display

First, there is an option verbosity which sets the amount of messages displayed when executing commands.

There are three commands that print explicitely requested information:

  • info – used to show preformatted information
  • print – mainly used to output numbers (expression values)
  • debug – used for testing the program itself

The output of info and print can be redirected to a file:

info args > filename    # truncate the file
info args >> filename   # append to the file
info args > 'filename'  # the filename can (and sometimes must) be in quotes

The redirection can create a file, so there is also a command to delete it:

delete file filename

info

The following info arguments are recognized:

  • TypeName – definition
  • $variable_name – formula and value
  • %function_name – formula
  • F – the list of functions in F
  • Z – the list of functions in Z
  • compiler – options used when compiling the program
  • confidence level @n – confidence limits for given confidence level
  • cov @n – covariance matrix
  • data – number of points, data filename and title
  • dataset_count – number of datasets
  • errors @n – estimated uncertainties of parameters
  • filename – dataset filename
  • fit – goodness of fit
  • fit_history – info about recorded parameter sets
  • formula – full formula of the model
  • functions – the list of %functions
  • gnuplot_formula – full formula of the model, gnuplot style
  • guess – peak-detection and linear regression info
  • guess [from:to] – the same, but in the given range
  • history – the list of all the command issued in this session
  • history [m:n] – selected commands from the history
  • history_summary – the summary of command history
  • models – script that re-constructs all variables, functions and models
  • peaks – formatted list of parameters of functions in F.
  • peaks_err – the same as peaks + uncertainties
  • prop %function_name – parameters of the function
  • refs $variable_name – references to the variable
  • set – the list of settings
  • set option – the current value of the option
  • simplified_formula – simplified formula
  • simplified_gnuplot_formula – simplified formula, gnuplot style
  • state – generates a script that can reproduce the current state of the program. The scripts embeds all datasets.
  • title – dataset title
  • types – the list of function types
  • variables – the list of variables
  • version – version number
  • view – boundaries of the visualized rectangle

Both info state and info history can be used to restore the current session.

In the GUI

Session ‣ Save State and Session ‣ Save History.

print

The print command is followed by a comma-separated list of expressions and/or strings:

=-> p pi, pi^2, pi^3
3.14159 9.8696 31.0063
=-> with numeric_format='%.15f' print pi
3.141592653589793
=-> p '2+3 =', 2+3
2+3 = 5

The other valid arguments are filename and title. They are useful for listing the same values for multiple datasets, e.g.:

=-> @*: print filename, F[0].area, F[0].area.error

print can also print a list where each line corresponds to one data point, as described in the section Exporting Data.

As an exception, print expression > filename does not work if the filename is not enclosed in single quotes. That is because the parser interprets > as a part of the expression. Just use quotes (print 2+3 > 'tmp.dat').

debug

Only a few debug sub-commands are documented here:

  • der mathematic-function – shows derivatives:

    =-> debug der sin(a) + 3*exp(b/a)
f(a, b) = sin(a)+3*exp(b/a)
df / d a = cos(a)-3*exp(b/a)*b/a^2
df / d b = 3*exp(b/a)/a

  • df x – compares the symbolic and numerical derivatives of F in x.

  • lex command – the list of tokens from the Fityk lexer

  • parse command – show the command as stored after parsing

  • expr expression – VM code from the expression

  • rd – derivatives for all variables

  • %function – bytecode, if available

  • $variable – derivatives

Other Commands

  • reset – reset the session
  • sleep sec – makes the program wait sec seconds.
  • quit – works as expected; if it is found in a script it quits the program, not only the script.
  • ! – commands that start with ! are passed (without the !) to the system() call (i.e. to the operating system).

Starting fityk and cfityk

On startup, the program runs a script from the $HOME/.fityk/init file (on MS Windows XP: C:\Documents and Settings\USERNAME\.fityk\init). Following this, the program executes command passed with the --cmd option, if given, and processes command line arguments:

  • if the argument starts with =->, the string following =-> is regarded as a command and executed (otherwise, it is regarded as a filename),
  • if the filename has extension “.fit” or the file begins with a “# Fityk” string, it is assumed to be a script and is executed,
  • otherwise, it is assumed to be a data file; columns and data blocks can be specified in the normal way, see Loading Data.

There are also other parameters to the CLI and GUI versions of the program. Option “-h” (“/h” on MS Windows) gives the full listing:

$ fityk -h
Usage: fityk [-h] [-V] [--full-version] [-c <str>] [-g <str>] [-I] [-r] [script or data file...]
  -h, --help        	show this help message
  -V, --version     	output version information and exit
  --full-version    	print version with additional info and exit
  -c, --cmd=<str>   	script passed in as string
  -g, --config=<str>	choose GUI configuration
  -I, --no-init     	don't process $HOME/.fityk/init file
  -r, --reorder     	reorder data (50.xy before 100.xy)

$ cfityk -h
Usage: cfityk [-h] [-V] [-c <str>] [script or data file...]
  -h, --help            show this help message
  -V, --version         output version information and exit
  -c, --cmd=<str>       script passed in as string
  -I, --no-init         don't process $HOME/.fityk/init file
  -n, --no-plot         disable plotting (gnuplot)
  -q, --quit            don't enter interactive shell

The example of non-interactive using CLI version on Linux:

wojdyr@ubu:~/foo$ ls *.rdf
dat_a.rdf  dat_r.rdf  out.rdf
wojdyr@ubu:~/foo$ cfityk -q -I "=-> set verbosity=-1, autoplot=0" \
> *.rdf "=-> @*: print min(x if y > 0)"
in @0 dat_a: 1.8875
in @1 dat_r: 1.5105
in @2 out: 1.8305