All the Rest¶
The syntax is simple:
set option = valuechanges the option,
info set optionshows the current value,
info setlists all available options.
In the GUI
the options can be set in a dialog ().
The GUI configuration (colors, fonts, etc.) is changed in a different way () and is not covered here.
It is possible to change the value of the option temporarily:
with option1=value1 [,option2=value2] command args...
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:
- See autoplot.
- Current working directory or empty string if it was not set explicitely. Affects relative paths.
- Default y standard deviation. See Standard Deviation (or Weight).
sqrtmax(y1/2, 1) and
- See the section about variables.
- 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.
- Refresh the plot when fitting (0/1).
- See Fitting Related Commands.
- See description in the chapter about model.
- See Guessing Initial Parameters.
- Setting to tune the Levenberg-Marquardt fitting method.
- String. File where the commands are logged. Empty – no logging.
- When logfile is set, log output together with input (0/1).
- Stop fitting when this number of seconds of processor time is exceeded. See Fitting Related Commands.
- See Fitting Related Commands.
- Setting to tune the Nelder-Mead downhill simplex fitting method.
- Format of numbers printed by the
infocommand. 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:
- 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).
- Some fitting methods and functions, such as
randnormalin 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.
- 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.
- Possible values: -1 (silent), 0 (normal), 1 (verbose), 2 (very verbose).
- See Guessing Initial Parameters.
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
program, which has similar syntax for the plot range.
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
change the automatic plotting behaviour. By default, the plot is
refreshed automatically after changing the data or the model (
It is also possible to replot the model when fitting, to show the progress
(see the options
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.
First, there is an option
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
debug– used for testing the program itself
The output of
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 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
setoption – 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
info state and
info history can be used to restore the current
In the GUI
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
They are useful for listing the same values for multiple datasets, e.g.:
=-> @*: print filename, F.area, F.area.error
As an exception,
print expression > filename does not work
if the filename is not enclosed in single quotes. That is because the parser
> as a part of the expression.
Just use quotes (
print 2+3 > 'tmp.dat').
Only a few
debug sub-commands are documented here:
dermathematic-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
dfx – compares the symbolic and numerical derivatives of F in x.
lexcommand – the list of tokens from the Fityk lexer
parsecommand – show the command as stored after parsing
exprexpression – VM code from the expression
rd– derivatives for all variables
%function– bytecode, if available
reset– reset the session
sleepsec – 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
$HOME/.fityk/init file (on MS Windows XP:
C:\Documents and Settings\USERNAME\.fityk\init).
Following this, the program executes command passed with the
option, if given, and processes command line arguments:
- if the argument starts with
=->, the string following
=->is regarded as a command and executed (otherwise, it is regarded as a filename),
- if the filename has extension ”.fit” or the file begins with a “# Fityk” string, it is assumed to be a script and is executed,
- otherwise, it is assumed to be a data file; columns and data blocks can be specified in the normal way, see Loading Data.
There are also other parameters to the CLI and GUI versions of the program. Option “-h” (“/h” on MS Windows) gives the full listing:
wojdyr@ubu:~/fityk/src$ ./fityk -h Usage: fityk \[-h] \[-V] \[-c <str>] \[-I] \[-r] \[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 -g, --config=<str> choose GUI configuration -I, --no-init don't process $HOME/.fityk/init file -r, --reorder reorder data (50.xy before 100.xy) wojdyr@ubu:~/foo$ 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