Scripts — Fityk 1.3.2 manual

# Scripts

## Working with Scripts

Fityk can run two kinds of scripts:

- Fityk scripts composed of the commands described in previous sections,

- and Lua scripts (extension `.lua`), in the Lua language.

Scripts are executed using the exec command:

    exec file1.fit
    exec file2.lua
    exec file3.fit.gz  # read script compressed with gzip

Note

Fityk can save its state to a script (`info state > file.fit`). It can also save all commands executed (directly or via GUI) in the session to a script (`info history > file.fit`).

Embedded Lua interpreter can execute any program in Lua 5.2. One-liners can be run with command `lua`:

    =-> lua print(_VERSION)
    Lua 5.1
    =-> lua print(os.date("Today is %A."))
    Today is Thursday.
    =-> lua for n,f in F:all_functions() do print(n, f, f:get_template_name()) end
    0       %_1     Constant
    1       %_2     Cycle

(The Lua `print` function in fityk is redefined to show the output in the GUI instead of writing to `stdout`).

Like in the Lua interpreter, `=` at the beginning of line can be used to save some typing:

    =-> = os.date("Today is %A.")
    Today is Thursday.

Similarly, `exec=` also interprets the rest of line as Lua expressions, but this time the resulting string is executed as a fityk command:

    =-> = string.format("fit @%d", math.random(0,5))
    fit @4
    =-> exec= string.format("fit @%d", math.random(0,5))
    # fitting random dataset (useless example)

The embedded Lua interpreter interacts with the rest of the program through the global object `F`:

    =-> = F:get_info("version")
    Fityk 1.2.1

All methods of `F` are documented in the section Fityk library API.

A few more examples.

Let’s say that we work with a number of datasets, and for each of them we want to save output of the `info peaks` command to a file named original-data-filename.out. This can be done in one line:

    =-> @*: lua F:execute("info peaks >'%s.out'" % F:get_info("filename"))

Now a more complex script that would need to be put into a file (with extension `.lua`) and run with `exec`. :

    -- load data from files file01.dat, file02.dat, ... file13.dat
    for i=1,13 do
        F:execute("@+ < file%02d.dat:0:1::" % i)
    end

    -- print some statistics about the loaded data
    n = F:get_dataset_count()
    print(n .. " datasets loaded.")

    total_max_y = 0
    for i=0, n-1 do
        max_y = F:calculate_expr("max(y)", i)
        if max_y > total_max_y then
            total_max_y = max_y
        end
    end
    print("The largest y: " .. total_max_y)

If a fityk command executed from Lua script fails, the whole script is stopped, unless you catch the error:

    -- wrap F:execute() in pcall to handle possible errors
    status, err = pcall(function() F:execute("fit") end)
    if status == false then
        print("Error: " .. err)
    end

The Lua interpreter was added in ver. 1.0.3. If you need help with writing Lua scripts - feel free to ask. Usage scenarios give us a better idea what functions should be available from the Lua interface.

Fityk also has a simple mechanism to interact with external programs. It is useful mostly on Unix systems. `!` runs a program, `exec!` runs a program, reads its standard output and executes it as a Fityk script. Here is an example of using Unix utilties `echo`, `ls` and `head` to load the newest CIF file from the current directory:

    =-> ! pwd
    /home/wojdyr/fityk/data
    =-> ! ls -t *.cif | head -1
    lab6_3-2610-q.cif
    =-> exec! echo "@+ < $(ls -t *.cif | head -1)"
    > @+ < lab6_3-2610-q.cif
    2300 points. No explicit std. dev. Set as sqrt(y)

## Fityk DSL

As was described in Command Line, each line has a syntax:

> [[@…:] [with …] command [“;” command]…] [#comment]

The datasets listed before the colon (`:`) make a foreach loop. Here is a silly example:

    =-> $a=0
    =-> @0 @0 @0: $a={$a+1}; print $a
    1
    2
    3

Command that follows the colon is run for each specified dataset in the context of that dataset. This is to say that:

    =-> @2 @4: guess Voigt

is equivalent to:

    =-> use @2
    =-> guess Voigt
    =-> use @4
    =-> guess Voigt

(except that the latter sets permenently default dataset to `@4`.

`@*` stands for all datasets, from `@0` to the last one.

Usually, when working with multiple datasets, one executes a command either for a single dataset or for all of them:

    =-> @3: guess Voigt  # just for @3
    =-> @*: guess Voigt  # for all datasets

The whole line is parsed and partly validated before the execution. This may lead to unexpected errors when the line has multiple semicolon-separated commands:

    =-> $a=4; print $a  # print gives unexpected error
    Error: undefined variable: $a

    =-> $b=2
    =-> $b=4; print $b  # $b is already defined at the check time
    4

Therefore, it is recommended to have one command in one line.

### Grammar

The grammar is expressed in EBNF-like notation:

- `(*this is a comment*)`

- `A*` means 0 or more occurrences of A.

- `A+` means 1 or more occurrences of A.

- `A % B` means `A (B A)*` and the `%` operator has the highest precedence. For example: `term % "+" comment` is the same as `term ("+" term)* comment`.

- The colon `:` in quoted string means that the string can be shortened, e.g. `"del:ete"` means that any of `del`, `dele`, `delet` and `delete` can be used.

The functions that can be used in `p_expr` and `v_expr` are available here and here, respectively. `v_expr` contains only a subset of functions from `p_expr` (partly, because we need to calculate symbolical derivatives of `v_expr`)

Line structure

    line      ::=  [statement] [comment]
    statement ::=  [Dataset+ ":"] [with_opts] command % ";"
    with_opts ::=  "w:ith" (Lname "=" value) % ","
    comment   ::=  "#" AllChars*

Commands

The kCmd* names in the comments correspond to constants in the code.

    command ::=  (
                 "deb:ug" RestOfLine              | (*kCmdDebug*)
                 "def:ine" define                 | (*kCmdDefine*)
                 "del:ete" delete                 | (*kCmdDelete*)
                 "del:ete" delete_points          | (*kCmdDeleteP*)
                 "e:xecute" exec                  | (*kCmdExec*)
                 "f:it" fit                       | (*kCmdFit*)
                 "g:uess" guess                   | (*kCmdGuess*)
                 "i:nfo" info_arg % "," [redir]   | (*kCmdInfo*)
                 "l:ua" RestOfLine                | (*kCmdLua*)
                 "=" RestOfLine                   | (*kCmdLua*)
                 "pl:ot" [range] [range] Dataset* [redir] | (*kCmdPlot*)
                 "p:rint" print_args [redir]      | (*kCmdPrint*)
                 "quit"                           | (*kCmdQuit*)
                 "reset"                          | (*kCmdReset*)
                 "s:et" (Lname "=" value) % ","   | (*kCmdSet*)
                 "sleep" expr                     | (*kCmdSleep*)
                 "title" "=" filename             | (*kCmdTitle*)
                 "undef:ine" Uname % ","          | (*kCmdUndef*)
                 "use" Dataset                    | (*kCmdUse*)
                 "!" RestOfLine                   | (*kCmdShell*)
                 Dataset "<" load_arg             | (*kCmdLoad*)
                 Dataset "=" dataset_expr         | (*kCmdDatasetTr*)
                 Funcname "=" func_rhs            | (*kCmdNameFunc*)
                 param_lhs "=" v_expr             | (*kCmdAssignParam*)
                 Varname "=" v_expr               | (*kCmdNameVar*)
                 Varname "=" "copy" "(" var_id ")" | (*kCmdNameVar*)
                 model_id ("="|"+=") model_rhs    | (*kCmdChangeModel*)
                 (p_attr "[" expr "]" "=" p_expr) % "," | (*kCmdPointTr*)
                 (p_attr "=" p_expr) % ","        | (*kCmdAllPointsTr*)
                 "M" "=" expr                     ) (*kCmdResizeP*)

Other rules

    define         ::=  Uname "(" (Lname [ "=" v_expr]) % "," ")" "="
                           ( v_expr |
                             component_func % "+" |
                             "x" "<" v_expr "?" component_func ":" component_func
                           )
    component_func ::=  Uname "(" v_expr % "," ")"
    delete         ::=  (Varname | func_id | Dataset | "file" filename) % ","
    delete_points  ::=  "(" p_expr ")"
    exec           ::=  filename |
                        "!" RestOfLine |
                        "=" RestOfLine
    fit            ::=  [Number] [Dataset*] |
                        "undo" |
                        "redo" |
                        "history" Number |
                        "clear_history"
    guess          ::=  [Funcname "="] Uname ["(" (Lname "=" v_expr) % "," ")"] [range]
    info_arg       ::=  ...TODO
    print_args     ::=  [("all" | ("if" p_expr ":")]
                        (p_expr | QuotedString | "title" | "filename") % ","
    redir          ::=  (">"|">>") filename
    value          ::=  (Lname | QuotedString | expr) (*value type depends on the option*)
    model_rhs      ::=  "0" |
                        func_id |
                        func_rhs |
                        model_id |
                        "copy" "(" model_id ")"
    func_rhs       ::=  Uname "(" ([Lname "="] v_expr) % "," ")" |
                        "copy" "(" func_id ")"
    load_arg       ::=  filename Lname* |
                        "."
    p_attr         ::=  ("X" | "Y" | "S" | "A")
    model_id       ::=  [Dataset "."] ("F"|"Z")
    func_id        ::=  Funcname |
                        model_id "[" Number "]"
    param_lhs      ::=  Funcname "." Lname |
                        model_id "[" (Number | "*") "]" "." Lname
    var_id         ::=  Varname |
                        func_id "." Lname
    range          ::=  "[" [expr] ":" [expr] "]"
    filename       ::=  QuotedString | NonblankString

Mathematical expressions

    expr        ::=  expr_or ? expr_or : expr_or
    expr_or     ::=  expr_and % "or"
    expr_and    ::=  expr_not % "and"
    expr_not    ::=  "not" expr_not | comparison
    comparison  ::=  arith % ("<"|">"|"=="|">="|"<="|"!=")
    arith       ::=  term % ("+"|"-")
    term        ::=  factor % ("*"|"/")
    factor      ::=  ('+'|'-') factor | power
    power       ::=  atom ['**' factor]
    atom        ::=  Number | "true" | "false" | "pi" |
                     math_func | braced_expr | ?others?
    math_func   ::=  "sqrt" "(" expr ")" |
                     "gamma" "(" expr ")" |
                      ...
    braced_expr ::=  "{" [Dataset+ ":"] p_expr "}"

The `atom` rule also accepts some fityk expressions, such as $variable, %function.parameter, %function(expr), etc.

`p_expr` and `v_expr` are similar to `expr`, but they use additional variables in the `atom` rule.

`p_expr` recognizes `n`, `M`, `x`, `y`, `s`, `a`, `X`, `Y`, `S` and `A`. All of them but `n` and `M` can be indexed (e.g. `x[4]`). Example: `(x+x[n-1])/2`.

`v_expr` uses all unknown names (`Lname`) as variables (example: `a+b*x^2`). Only a subset of functions (`math_func`) from `expr` is supported. The tilde (`~`) can be used to create simple-variables (`~5`), optionally with a domain in square brackets (`~5[1:6]`).

Since `v_expr` is used to define variables and user-defined functions, the program calculates symbolically derivatives of `v_expr`. That is why not all the function from `expr` are supported (they may be added in the future).

`dataset_expr` supports very limited set of operators and a few functions that take Dataset token as argument (example: `@0 - shirley_bg(@0)`).

Lexer

Below, some of the tokens produced by the fityk lexer are defined.

The lexer is context-dependend: `NonblankString` and `RestOfLine` are produced only when they are expected in the grammar.

`Uname` is used only for function types (Gaussian) and pseudo-parameters (%f.Area).

    Dataset        ::=  "@"(Digit+|"+"|"*")
    Varname        ::=  "$" Lname
    Funcname       ::=  "%" Lname
    QuotedString   ::=  "'" (AllChars - "'")* "'"
    Lname          ::=  (LowerCase | "_") (LowerCase | Digit | "_")*
    Uname          ::=  UpperCase AlphaNum+
    Number         ::=  ?number read by strtod()?
    NonblankString ::=  (AllChars - (WhiteSpace | ";" | "#" ))*
    RestOfLine     ::=  AllChars*

## Fityk library API

Fityk comes with embedded Lua interpreter and this language is used in this section. The API for other supported languages is similar. Lua communicates with Fityk using object `F` of type `Fityk`. To call the methods listed below use `F:method()`, for example `F:get_dof()` (not `Fityk.get_dof()`).

Note

Other supported languages include C++, C, Python, Perl, Ruby and Java. Except for C, all APIs are similar.

Unlike in built-in Lua, in other cases it is necessary to create an instance of the Fityk class first. Then you use this object in the same way as `F` is used below.

The fityk.h header file is the best reference. Additionally, C++ and Python have access to functions from the ui_api.h header. These functions are used in command line versions of fityk (`cfityk` or its equivalent – `samples/cfityk.py`).

Examples of scripts in all the listed languages and in the samples directory.

Here is the most general function:

Fityk.execute(cmd)

  Executes a fityk command. Example: `F:execute("fit")`.

The `%` operator for the string type is pre-set to support Python-like formatting:

    = "%d pigs" % 3
    = "%d %s" % {3, "pigs"}

### Input / output

Fityk.input(prompt)

  Query user. In the CLI user is asked for input in the command line, and in the GUI in a pop-up box. As a special case, if the prompt contains string “[y/n]” the GUI shows Yes/No buttons instead of text entry.

  Example: TODO

Fityk.out(s)

  Print string in the output area. The `print()` function in built-in Lua is redefined to do the same.

### Settings

Fityk.set_option_as_string(opt, val)

  Set option opt to value val. Equivalent of fityk command `set opt=val`.

Fityk.set_option_as_number(opt, val)

  Set option opt to numeric value val.

Fityk.get_option_as_string(opt)

  Returns value of opt (string).

Fityk.get_option_as_number(opt)

  Returns value of opt (real number).

### Data

Fityk.load(spec[, d])

  Load data to @*d* slot. The first argument is either a string with path or LoadSpec struct that apart from the `path` has also the following optional members: `x_col`, `y_col`, `sig_col`, `blocks`, `format`, `options`. The meaning of these parameters is the same as described in Loading Data.

  For example, due to limitations of the Fityk DSL a file with the `'` character in the path must be loaded through Lua:

      lua F:load([[Kat's file.dat]])

  LoadSpec is used to specify also format of the file, columns, etc:

      spec = fityk.LoadSpec('my.csv')
      spec.x_col = 1
      spec.y_col = 3
      spec.format = 'csv'
      spec.options = 'decimal_comma'
      F:load(spec)

Fityk.load_data(d, xx, yy, sigmas[, title])

  Load data to @*d* slot. xx and yy must be numeric arrays of the same size, sigmas must either be empty or have the same size. title is an optional data title (string).

Fityk.add_point(x, y, sigma[, d])

  Add one data point ((x, y) with std. dev. set to sigma) to an existing dataset d. If d is not specified, the default dataset is used.

  Example: `F:add_point(30, 7.5, 1)`.

Fityk.get_dataset_count()

  Returns number of datasets (n >= 1).

Fityk.get_default_dataset()

  Returns default dataset. Default dataset is set by the “use @n” command.

Fityk.get_data([d])

  Returns points for dataset d.

  - in C++ – returns vector<Point>

  - in Lua – userdata with array-like methods, indexed from 0.

  Each point has 4 properties: `x`, `y`, `sigma` (real numbers) and `is_active` (bool).

  Example:

      points = F:get_data()
      for i = 0, #points-1 do
          p = points[i]
          if p.is_active then
              print(i, p.x, p.y, p.sigma)
          end
      end

      1       4.24    1.06    1
      2       6.73    1.39    1
      3       8.8     1.61    1
      ...

### General Info

Fityk.get_info(s[, d])

  Returns output of the fityk `info` command as a string. If d is not specified, the default dataset is used (the dataset is relevant for few arguments of the `info` command).

  Example: `F:get_info("history")` – returns a multiline string containing all fityk commands issued in this session.

Fityk.calculate_expr(s[, d])

  Returns output of the fityk `print` command as a number. If d is not specified, the default dataset is used.

  Example: `F:calculate_expr("argmax(y)", 0)`.

Fityk.get_view_boundary(side)

  Get coordinates of the plotted rectangle, which is set by the `plot` command. Return numeric value corresponding to given side, which should be a letter `L`(eft), `R`(ight), `T`(op) or `B`(ottom).

### Model info

Fityk.get_parameter_count()

  Returns number of simple-variables (parameters that can be fitted)

Fityk.all_parameters()

  Returns array of simple-variables.

  - in C++ – vector<double>

  - in Lua – userdata with array-like methods, indexed from 0.

Fityk.all_variables()

  > Returns array of all defined variables.

  > - in C++ – vector<Var*>

  > - in Lua – userdata with array-like methods, indexed from 0.

  Example:

      variables = F:all_variables()
      for i = 0, #variables-1 do
          v = variables[i]
          print(i, v.name, v:value(), v.domain.lo, v.domain.hi,
                v:gpos(), v:is_simple())
      end

  `Var.is_simple()` returns true for simple-variables.

  `Var.gpos()` returns position of the variable in the global array of parameters (Fityk.all_parameters()), or -1 for compound variables.

Fityk.get_variable(name)

  Returns variable $name.

Fityk.all_functions()

  Returns array of functions.

  - in C++ – vector<Func*>

  - in Lua – userdata with array-like methods, indexed from 0.

  Example:

      f = F:all_functions()[0] -- first functions
      print(f.name, f:get_template_name())          -- _1        Gaussian
      print(f:get_param(0), f:get_param(1))         -- height  center
      print("$" .. f:var_name("height"))            -- $_4
      print("center:", f:get_param_value("center")) -- center: 24.72235945525
      print("f(25)=", f:value_at(25))               -- f(25)=  4386.95533969

Fityk.get_function(name)

  Return the function with given name, or NULL if there is no such function.

  Example:

      f = F:get_function("_1")
      print("f(25)=", f:value_at(25))               -- f(25)=  4386.95533969

Fityk.get_components(d[, fz])

  Returns %functions used in dataset d. If fz is `Z`, returns zero-shift functions.

  Example:

      func = F:get_components(1)[3] -- get 4th (index 3) function in @1
      print(func)                   -- <Func %_6>
      vname = func:var_name("hwhm")
      print(vname)                  -- _21
      v = get_variable(vname)
      print(v, v:value())           -- <Var $_21>       0.1406587

Fityk.get_model_value(x[, d])

  Returns the value of the model for dataset `@`d at x.

### Fit statistics

Fityk.get_wssr([d])

  Returns WSSR (weighted sum of squared residuals).

Fityk.get_ssr([d])

  Returns SSR (sum of squared residuals).

Fityk.get_rsquared([d])

  Returns R-squared.

Fityk.get_dof([d])

  Returns the number of degrees of freedom (#points - #parameters).

Fityk.get_covariance_matrix([d])

  Returns covariance matrix.

## Examples in Lua

Show how the peak center moves between datasets:

    -- file list-max.lua
    prev_x = nil
    for n = 0, F:get_dataset_count()-1 do
        local path = F:get_info("filename", n)
        local filename = string.match(path, "[^/\\]+$") or ""
        -- local x = F:calculate_expr("argmax(y)", n)
        local x = F:calculate_expr("F[0].center", n)
        s = string.format("%s: max at x=%.4f", filename, x)
        if prev_x ~= nil then
            s = s .. string.format("  (%+.4f)", x-prev_x)
        end
        prev_x = x
        print(s)
    end

    =-> exec list-max.lua
    frame-000.dat: max at x=-0.0197
    frame-001.dat: max at x=-0.0209  (-0.0012)
    frame-002.dat: max at x=-0.0216  (-0.0007)
    frame-003.dat: max at x=-0.0224  (-0.0008)

Write to file values of the model F(x) at chosen x’s (in this example x = 0, 1.5, 3, … 150):

    -- file tabular-f.lua
    file = io.open("output.dat", "w")
    for x = 0, 150, 1.5 do
        file:write(string.format("%g\t%g\n", x, F:get_model_value(x)))
    end
    file:close()

    =-> exec tabular-f.lua
    =-> !head -5 output.dat
    0       12.1761
    1.5     12.3004
    3       10.9096
    4.5     9.12635
    6       8.27044