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<title>Scripts — Fityk 1.3.0 manual</title>
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<h3><a href="fityk-manual.html">Table Of Contents</a></h3>
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="intro.html">Introduction</a></li>
<li class="toctree-l1"><a class="reference internal" href="getstarted.html">Getting Started</a></li>
<li class="toctree-l1"><a class="reference internal" href="lang.html">Mini-Language</a></li>
<li class="toctree-l1"><a class="reference internal" href="data.html">Data</a></li>
<li class="toctree-l1"><a class="reference internal" href="model.html">Models</a></li>
<li class="toctree-l1"><a class="reference internal" href="fit.html">Curve Fitting</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Scripts</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#working-with-scripts">Working with Scripts</a></li>
<li class="toctree-l2"><a class="reference internal" href="#fityk-library-api">Fityk library API</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#input-output">Input / output</a></li>
<li class="toctree-l3"><a class="reference internal" href="#settings">Settings</a></li>
<li class="toctree-l3"><a class="reference internal" href="#data">Data</a></li>
<li class="toctree-l3"><a class="reference internal" href="#general-info">General Info</a></li>
<li class="toctree-l3"><a class="reference internal" href="#model-info">Model info</a></li>
<li class="toctree-l3"><a class="reference internal" href="#fit-statistics">Fit statistics</a></li>
</ul>
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<li class="toctree-l2"><a class="reference internal" href="#examples">Examples</a></li>
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<li class="toctree-l1"><a class="reference internal" href="ref.html">All the Rest</a></li>
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<div class="section" id="scripts">
<h1>Scripts<a class="headerlink" href="#scripts" title="Permalink to this headline">¶</a></h1>
<div class="section" id="working-with-scripts">
<h2>Working with Scripts<a class="headerlink" href="#working-with-scripts" title="Permalink to this headline">¶</a></h2>
<p>Scripts can be executed using the command:</p>
<div class="highlight-fityk"><div class="highlight"><pre><span></span>exec filename
</pre></div>
</div>
<p>The file can be either a fityk script (usually with extension <code class="docutils literal"><span class="pre">fit</span></code>),
or a Lua script (extension <code class="docutils literal"><span class="pre">lua</span></code>).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Fityk can save its state to a script (<code class="docutils literal"><span class="pre">info</span> <span class="pre">state</span> <span class="pre">></span> <span class="pre">file.fit</span></code>).
It can also save all commands executed (directly or via GUI) in the session
to a script (<code class="docutils literal"><span class="pre">info</span> <span class="pre">history</span> <span class="pre">></span> <span class="pre">file.fit</span></code>).</p>
</div>
<p>Since a Fityk script with all the data inside can be a large file,
the files may be stored compressed and it is possible to directly read
gzip-compressed fityk script (<code class="docutils literal"><span class="pre">.fit.gz</span></code>).</p>
<p>Embedded Lua interpreter can execute any program in Lua 5.1.
One-liners can be run with command <code class="docutils literal"><span class="pre">lua</span></code>:</p>
<div class="highlight-fityk"><div class="highlight"><pre><span></span><span class="gp">=-> </span>lua print(_VERSION)
Lua 5.1
<span class="gp">=-> </span>lua print(os.date("Today is %A."))
Today is Thursday.
<span class="gp">=-> </span>lua for n,f in F:all_functions() do print(n, f, f:get_template_name()) end
0 %_1 Constant
1 %_2 Cycle
</pre></div>
</div>
<p>(The Lua <code class="docutils literal"><span class="pre">print</span></code> function in fityk is redefined to show the output
in the GUI instead of writing to <code class="docutils literal"><span class="pre">stdout</span></code>).</p>
<p>Like in the Lua interpreter, <code class="docutils literal"><span class="pre">=</span></code> at the beginning of line can be used
to save some typing:</p>
<div class="highlight-fityk"><div class="highlight"><pre><span></span><span class="gp">=-> </span>= os.date("Today is %A.")
Today is Thursday.
</pre></div>
</div>
<p>Similarly, <code class="docutils literal"><span class="pre">exec=</span></code> also interprets the rest of line
as Lua expressions, but this time the resulting string is executed
as a fityk command:</p>
<div class="highlight-fityk"><div class="highlight"><pre><span></span><span class="gp">=-> </span>= string.format("fit @%d", math.random(0,5))
fit 17
<span class="gp">=-> </span>exec= string.format("fit @%d", math.random(0,5))
<span class="c"># fitting random dataset (useless example)</span>
</pre></div>
</div>
<p>The Lua interpreter in Fityk has defined global object <code class="docutils literal"><span class="pre">F</span></code> which
enables interaction with the program:</p>
<div class="highlight-fityk"><div class="highlight"><pre><span></span><span class="gp">=-> </span>= F:get_info("version")
Fityk 1.2.1
</pre></div>
</div>
<p>Now the first example that can be useful. For each dataset write output
of the <code class="docutils literal"><span class="pre">info</span> <span class="pre">peaks</span></code> command to a file named after the data file,
with appended ”.out”:</p>
<div class="highlight-fityk"><div class="highlight"><pre><span></span><span class="gp">=-> </span>@*: lua F:execute("info peaks ><span class="s1">'%s.out'</span>" % F:get_info("filename"))
</pre></div>
</div>
<p>This and other methods of <code class="docutils literal"><span class="pre">F</span></code> are documented in the next section.</p>
<p>Here is an example of Lua-Fityk interactions:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="c1">-- load data from files file01.dat, file02.dat, ... file13.dat</span>
<span class="k">for</span> <span class="n">i</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span><span class="mi">13</span> <span class="k">do</span>
<span class="n">F</span><span class="p">:</span><span class="n">execute</span><span class="p">(</span><span class="s2">"</span><span class="s">@+ < file%02d.dat:0:1::"</span> <span class="o">%</span> <span class="n">i</span><span class="p">)</span>
<span class="k">end</span>
<span class="c1">-- print some statistics about the loaded data</span>
<span class="n">n</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">get_dataset_count</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="n">n</span> <span class="o">..</span> <span class="s2">"</span><span class="s"> datasets loaded."</span><span class="p">)</span>
<span class="n">total_max_y</span> <span class="o">=</span> <span class="mi">0</span>
<span class="k">for</span> <span class="n">i</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">n</span><span class="o">-</span><span class="mi">1</span> <span class="k">do</span>
<span class="n">max_y</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">calculate_expr</span><span class="p">(</span><span class="s2">"</span><span class="s">max(y)"</span><span class="p">,</span> <span class="n">i</span><span class="p">)</span>
<span class="k">if</span> <span class="n">max_y</span> <span class="o">></span> <span class="n">total_max_y</span> <span class="k">then</span>
<span class="n">total_max_y</span> <span class="o">=</span> <span class="n">max_y</span>
<span class="k">end</span>
<span class="k">end</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="s">The largest y: "</span> <span class="o">..</span> <span class="n">total_max_y</span><span class="p">)</span>
</pre></div>
</div>
<p>If a fityk command executed from Lua script fails, the whole script is
stopped, unless you catch the error:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="c1">-- wrap F:execute() in pcall to handle possible errors</span>
<span class="n">status</span><span class="p">,</span> <span class="n">err</span> <span class="o">=</span> <span class="nb">pcall</span><span class="p">(</span><span class="k">function</span><span class="p">()</span> <span class="n">F</span><span class="p">:</span><span class="n">execute</span><span class="p">(</span><span class="s2">"</span><span class="s">fit"</span><span class="p">)</span> <span class="k">end</span><span class="p">)</span>
<span class="k">if</span> <span class="n">status</span> <span class="o">==</span> <span class="kc">false</span> <span class="k">then</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="s">Error: "</span> <span class="o">..</span> <span class="n">err</span><span class="p">)</span>
<span class="k">end</span>
</pre></div>
</div>
<p>The Lua interpreter was added in ver. 1.0.3. If you have any questions
about it, feel free to ask.</p>
<p>Older, but still supported way to automate Fityk is to prepare
a stand-alone program that writes a valid fityk script to the standard output.
To run such program and execute the output use command:</p>
<div class="highlight-fityk"><div class="highlight"><pre><span></span>exec ! program [args...]
</pre></div>
</div>
</div>
<div class="section" id="fityk-library-api">
<h2>Fityk library API<a class="headerlink" href="#fityk-library-api" title="Permalink to this headline">¶</a></h2>
<p>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 <code class="docutils literal"><span class="pre">F</span></code> of type <code class="docutils literal"><span class="pre">Fityk</span></code>.
To call the methods listed below use <code class="docutils literal"><span class="pre">F:method()</span></code>, for example
<code class="docutils literal"><span class="pre">F:get_dof()</span></code> (not <code class="docutils literal"><span class="pre">Fityk.get_dof()</span></code>).</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p>Other supported languages include C++, C, Python, Perl, Ruby and Java.
Except for C, all APIs are similar.</p>
<p>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 <code class="docutils literal"><span class="pre">F</span></code> is used below.</p>
<p>The <a class="reference external" href="https://github.com/wojdyr/fityk/blob/master/src/fityk.h">fityk.h</a> header file is the best reference.
Additionally, C++ and Python have access to functions from
the <a class="reference external" href="https://github.com/wojdyr/fityk/blob/master/src/ui_api.h">ui_api.h</a> header. These functions are used in command line
versions of fityk (<code class="docutils literal"><span class="pre">cfityk</span></code> or its equivalent – <code class="docutils literal"><span class="pre">samples/cfityk.py</span></code>).</p>
<p class="last">Examples of scripts in all the listed languages and in the <a class="reference external" href="https://github.com/wojdyr/fityk/blob/master/samples/">samples</a>
directory.</p>
</div>
<p>Here is the most general function:</p>
<dl class="method">
<dt id="Fityk.execute">
<code class="descclassname">Fityk.</code><code class="descname">execute</code><span class="sig-paren">(</span><em>cmd</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.execute" title="Permalink to this definition">¶</a></dt>
<dd><p>Executes a fityk command. Example: <code class="docutils literal"><span class="pre">F:execute("fit")</span></code>.</p>
</dd></dl>
<p>The <code class="docutils literal"><span class="pre">%</span></code> operator for the string type is pre-set to support Python-like
formatting:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="o">=</span> <span class="s2">"</span><span class="s">%d pigs"</span> <span class="o">%</span> <span class="mi">3</span>
<span class="o">=</span> <span class="s2">"</span><span class="s">%d %s"</span> <span class="o">%</span> <span class="p">{</span><span class="mi">3</span><span class="p">,</span> <span class="s2">"</span><span class="s">pigs"</span><span class="p">}</span>
</pre></div>
</div>
<div class="section" id="input-output">
<h3>Input / output<a class="headerlink" href="#input-output" title="Permalink to this headline">¶</a></h3>
<dl class="method">
<dt id="Fityk.input">
<code class="descclassname">Fityk.</code><code class="descname">input</code><span class="sig-paren">(</span><em>prompt</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.input" title="Permalink to this definition">¶</a></dt>
<dd><p>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.</p>
<p>Example: TODO</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.out">
<code class="descclassname">Fityk.</code><code class="descname">out</code><span class="sig-paren">(</span><em>s</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.out" title="Permalink to this definition">¶</a></dt>
<dd><p>Print string in the output area. The <code class="docutils literal"><span class="pre">print()</span></code> function in built-in Lua
is redefined to do the same.</p>
</dd></dl>
</div>
<div class="section" id="settings">
<h3>Settings<a class="headerlink" href="#settings" title="Permalink to this headline">¶</a></h3>
<dl class="method">
<dt id="Fityk.set_option_as_string">
<code class="descclassname">Fityk.</code><code class="descname">set_option_as_string</code><span class="sig-paren">(</span><em>opt</em>, <em>val</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.set_option_as_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Set option <em>opt</em> to value <em>val</em>.
Equivalent of fityk command <code class="docutils literal"><span class="pre">set</span> <span class="pre">opt=val</span></code>.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.set_option_as_number">
<code class="descclassname">Fityk.</code><code class="descname">set_option_as_number</code><span class="sig-paren">(</span><em>opt</em>, <em>val</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.set_option_as_number" title="Permalink to this definition">¶</a></dt>
<dd><p>Set option <em>opt</em> to numeric value <em>val</em>.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_option_as_string">
<code class="descclassname">Fityk.</code><code class="descname">get_option_as_string</code><span class="sig-paren">(</span><em>opt</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_option_as_string" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns value of <em>opt</em> (string).</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_option_as_number">
<code class="descclassname">Fityk.</code><code class="descname">get_option_as_number</code><span class="sig-paren">(</span><em>opt</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_option_as_number" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns value of <em>opt</em> (real number).</p>
</dd></dl>
</div>
<div class="section" id="data">
<h3>Data<a class="headerlink" href="#data" title="Permalink to this headline">¶</a></h3>
<dl class="method">
<dt id="Fityk.load">
<code class="descclassname">Fityk.</code><code class="descname">load</code><span class="sig-paren">(</span><em>spec</em><span class="optional">[</span>, <em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.load" title="Permalink to this definition">¶</a></dt>
<dd><p>Load data to @*d* slot. The first argument is either a string with path
or LoadSpec struct that apart from the <code class="docutils literal"><span class="pre">path</span></code> has also the following
optional members: <code class="docutils literal"><span class="pre">x_col</span></code>, <code class="docutils literal"><span class="pre">y_col</span></code>, <code class="docutils literal"><span class="pre">sig_col</span></code>, <code class="docutils literal"><span class="pre">blocks</span></code>,
<code class="docutils literal"><span class="pre">format</span></code>, <code class="docutils literal"><span class="pre">options</span></code>. The meaning of these parameters is the same
as described in <a class="reference internal" href="data.html#dataload"><span class="std std-ref">Loading Data</span></a>.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.load_data">
<code class="descclassname">Fityk.</code><code class="descname">load_data</code><span class="sig-paren">(</span><em>d</em>, <em>xx</em>, <em>yy</em>, <em>sigmas</em><span class="optional">[</span>, <em>title</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.load_data" title="Permalink to this definition">¶</a></dt>
<dd><p>Load data to @*d* slot. <em>xx</em> and <em>yy</em> must be numeric arrays
of the same size, <em>sigmas</em> must either be empty or have the same size.
<em>title</em> is an optional data title (string).</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.add_point">
<code class="descclassname">Fityk.</code><code class="descname">add_point</code><span class="sig-paren">(</span><em>x</em>, <em>y</em>, <em>sigma</em><span class="optional">[</span>, <em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.add_point" title="Permalink to this definition">¶</a></dt>
<dd><p>Add one data point ((<em>x</em>, <em>y</em>) with std. dev. set to <em>sigma</em>)
to an existing dataset <em>d</em>.
If <em>d</em> is not specified, the default dataset is used.</p>
<p>Example: <code class="docutils literal"><span class="pre">F:add_point(30,</span> <span class="pre">7.5,</span> <span class="pre">1)</span></code>.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_dataset_count">
<code class="descclassname">Fityk.</code><code class="descname">get_dataset_count</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_dataset_count" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns number of datasets (n >= 1).</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_default_dataset">
<code class="descclassname">Fityk.</code><code class="descname">get_default_dataset</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_default_dataset" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns default dataset. Default dataset is set by the “use @n” command.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_data">
<code class="descclassname">Fityk.</code><code class="descname">get_data</code><span class="sig-paren">(</span><span class="optional">[</span><em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_data" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns points for dataset <em>d</em>.</p>
<ul class="simple">
<li>in C++ – returns vector<Point></li>
<li>in Lua – userdata with array-like methods, indexed from 0.</li>
</ul>
<p>Each point has 4 properties:
<code class="docutils literal"><span class="pre">x</span></code>, <code class="docutils literal"><span class="pre">y</span></code>, <code class="docutils literal"><span class="pre">sigma</span></code> (real numbers) and <code class="docutils literal"><span class="pre">is_active</span></code> (bool).</p>
<p>Example:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="n">points</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">get_data</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="o">#</span><span class="n">points</span><span class="o">-</span><span class="mi">1</span> <span class="k">do</span>
<span class="n">p</span> <span class="o">=</span> <span class="n">points</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="k">if</span> <span class="n">p</span><span class="p">.</span><span class="n">is_active</span> <span class="k">then</span>
<span class="nb">print</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">p</span><span class="p">.</span><span class="n">x</span><span class="p">,</span> <span class="n">p</span><span class="p">.</span><span class="n">y</span><span class="p">,</span> <span class="n">p</span><span class="p">.</span><span class="n">sigma</span><span class="p">)</span>
<span class="k">end</span>
<span class="k">end</span>
<span class="mi">1</span> <span class="mf">4.24</span> <span class="mf">1.06</span> <span class="mi">1</span>
<span class="mi">2</span> <span class="mf">6.73</span> <span class="mf">1.39</span> <span class="mi">1</span>
<span class="mi">3</span> <span class="mf">8.8</span> <span class="mf">1.61</span> <span class="mi">1</span>
<span class="o">...</span>
</pre></div>
</div>
</dd></dl>
</div>
<div class="section" id="general-info">
<h3>General Info<a class="headerlink" href="#general-info" title="Permalink to this headline">¶</a></h3>
<dl class="method">
<dt id="Fityk.get_info">
<code class="descclassname">Fityk.</code><code class="descname">get_info</code><span class="sig-paren">(</span><em>s</em><span class="optional">[</span>, <em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_info" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns output of the fityk <code class="docutils literal"><span class="pre">info</span></code> command as a string.
If <em>d</em> is not specified, the default dataset is used (the dataset
is relevant for few arguments of the <code class="docutils literal"><span class="pre">info</span></code> command).</p>
<p>Example: <code class="docutils literal"><span class="pre">F:get_info("history")</span></code> – returns a multiline string
containing all fityk commands issued in this session.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.calculate_expr">
<code class="descclassname">Fityk.</code><code class="descname">calculate_expr</code><span class="sig-paren">(</span><em>s</em><span class="optional">[</span>, <em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.calculate_expr" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns output of the fityk <code class="docutils literal"><span class="pre">print</span></code> command as a number.
If <em>d</em> is not specified, the default dataset is used.</p>
<p>Example: <code class="docutils literal"><span class="pre">F:calculate_expr("argmax(y)",</span> <span class="pre">0)</span></code>.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_view_boundary">
<code class="descclassname">Fityk.</code><code class="descname">get_view_boundary</code><span class="sig-paren">(</span><em>side</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_view_boundary" title="Permalink to this definition">¶</a></dt>
<dd><p>Get coordinates of the plotted rectangle,
which is set by the <code class="docutils literal"><span class="pre">plot</span></code> command.
Return numeric value corresponding to given <em>side</em>, which should be
a letter <code class="docutils literal"><span class="pre">L</span></code>(eft), <code class="docutils literal"><span class="pre">R</span></code>(ight), <code class="docutils literal"><span class="pre">T</span></code>(op) or <code class="docutils literal"><span class="pre">B</span></code>(ottom).</p>
</dd></dl>
</div>
<div class="section" id="model-info">
<h3>Model info<a class="headerlink" href="#model-info" title="Permalink to this headline">¶</a></h3>
<dl class="method">
<dt id="Fityk.get_parameter_count">
<code class="descclassname">Fityk.</code><code class="descname">get_parameter_count</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_parameter_count" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns number of simple-variables (parameters that can be fitted)</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.all_parameters">
<code class="descclassname">Fityk.</code><code class="descname">all_parameters</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.all_parameters" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns array of simple-variables.</p>
<ul class="simple">
<li>in C++ – vector<double></li>
<li>in Lua – userdata with array-like methods, indexed from 0.</li>
</ul>
</dd></dl>
<dl class="method">
<dt id="Fityk.all_variables">
<code class="descclassname">Fityk.</code><code class="descname">all_variables</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.all_variables" title="Permalink to this definition">¶</a></dt>
<dd><blockquote>
<div><p>Returns array of all defined variables.</p>
<ul class="simple">
<li>in C++ – vector<Var*></li>
<li>in Lua – userdata with array-like methods, indexed from 0.</li>
</ul>
</div></blockquote>
<p>Example:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="n">variables</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">all_variables</span><span class="p">()</span>
<span class="k">for</span> <span class="n">i</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="o">#</span><span class="n">variables</span><span class="o">-</span><span class="mi">1</span> <span class="k">do</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">variables</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
<span class="nb">print</span><span class="p">(</span><span class="n">i</span><span class="p">,</span> <span class="n">v</span><span class="p">.</span><span class="n">name</span><span class="p">,</span> <span class="n">v</span><span class="p">:</span><span class="n">value</span><span class="p">(),</span> <span class="n">v</span><span class="p">.</span><span class="n">domain</span><span class="p">.</span><span class="n">lo</span><span class="p">,</span> <span class="n">v</span><span class="p">.</span><span class="n">domain</span><span class="p">.</span><span class="n">hi</span><span class="p">,</span>
<span class="n">v</span><span class="p">:</span><span class="n">gpos</span><span class="p">(),</span> <span class="n">v</span><span class="p">:</span><span class="n">is_simple</span><span class="p">())</span>
<span class="k">end</span>
</pre></div>
</div>
<p><code class="docutils literal"><span class="pre">Var.is_simple()</span></code> returns true for simple-variables.</p>
<p><code class="docutils literal"><span class="pre">Var.gpos()</span></code> returns position of the variable in the global array
of parameters (Fityk.all_parameters()), or -1 for compound variables.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_variable">
<code class="descclassname">Fityk.</code><code class="descname">get_variable</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_variable" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns variable <em>$name</em>.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.all_functions">
<code class="descclassname">Fityk.</code><code class="descname">all_functions</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.all_functions" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns array of functions.</p>
<ul class="simple">
<li>in C++ – vector<Func*></li>
<li>in Lua – userdata with array-like methods, indexed from 0.</li>
</ul>
<p>Example:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="n">f</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">all_functions</span><span class="p">()[</span><span class="mi">0</span><span class="p">]</span> <span class="c1">-- first functions</span>
<span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="p">.</span><span class="n">name</span><span class="p">,</span> <span class="n">f</span><span class="p">:</span><span class="n">get_template_name</span><span class="p">())</span> <span class="c1">-- _1 Gaussian</span>
<span class="nb">print</span><span class="p">(</span><span class="n">f</span><span class="p">:</span><span class="n">get_param</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">f</span><span class="p">:</span><span class="n">get_param</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span> <span class="c1">-- height center</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="s">$"</span> <span class="o">..</span> <span class="n">f</span><span class="p">:</span><span class="n">var_name</span><span class="p">(</span><span class="s2">"</span><span class="s">height"</span><span class="p">))</span> <span class="c1">-- $_4</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="s">center:"</span><span class="p">,</span> <span class="n">f</span><span class="p">:</span><span class="n">get_param_value</span><span class="p">(</span><span class="s2">"</span><span class="s">center"</span><span class="p">))</span> <span class="c1">-- center: 24.72235945525</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="s">f(25)="</span><span class="p">,</span> <span class="n">f</span><span class="p">:</span><span class="n">value_at</span><span class="p">(</span><span class="mi">25</span><span class="p">))</span> <span class="c1">-- f(25)= 4386.95533969</span>
</pre></div>
</div>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_function">
<code class="descclassname">Fityk.</code><code class="descname">get_function</code><span class="sig-paren">(</span><em>name</em><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_function" title="Permalink to this definition">¶</a></dt>
<dd><p>Return the function with given <em>name</em>, or NULL if there is no such
function.</p>
<p>Example:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="n">f</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">get_function</span><span class="p">(</span><span class="s2">"</span><span class="s">_1"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">"</span><span class="s">f(25)="</span><span class="p">,</span> <span class="n">f</span><span class="p">:</span><span class="n">value_at</span><span class="p">(</span><span class="mi">25</span><span class="p">))</span> <span class="c1">-- f(25)= 4386.95533969</span>
</pre></div>
</div>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_components">
<code class="descclassname">Fityk.</code><code class="descname">get_components</code><span class="sig-paren">(</span><em>d</em><span class="optional">[</span>, <em>fz</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_components" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns %functions used in dataset <em>d</em>. If <em>fz</em> is <code class="docutils literal"><span class="pre">Z</span></code>, returns
zero-shift functions.</p>
<p>Example:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="n">func</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">get_components</span><span class="p">(</span><span class="mi">1</span><span class="p">)[</span><span class="mi">3</span><span class="p">]</span> <span class="c1">-- get 4th (index 3) function in @1</span>
<span class="nb">print</span><span class="p">(</span><span class="n">func</span><span class="p">)</span> <span class="c1">-- <Func %_6></span>
<span class="n">vname</span> <span class="o">=</span> <span class="n">func</span><span class="p">:</span><span class="n">var_name</span><span class="p">(</span><span class="s2">"</span><span class="s">hwhm"</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">vname</span><span class="p">)</span> <span class="c1">-- _21</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">get_variable</span><span class="p">(</span><span class="n">vname</span><span class="p">)</span>
<span class="nb">print</span><span class="p">(</span><span class="n">v</span><span class="p">,</span> <span class="n">v</span><span class="p">:</span><span class="n">value</span><span class="p">())</span> <span class="c1">-- <Var $_21> 0.1406587</span>
</pre></div>
</div>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_model_value">
<code class="descclassname">Fityk.</code><code class="descname">get_model_value</code><span class="sig-paren">(</span><em>x</em><span class="optional">[</span>, <em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_model_value" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the value of the model for dataset <code class="docutils literal"><span class="pre">@</span></code><em>d</em> at <em>x</em>.</p>
</dd></dl>
</div>
<div class="section" id="fit-statistics">
<h3>Fit statistics<a class="headerlink" href="#fit-statistics" title="Permalink to this headline">¶</a></h3>
<dl class="method">
<dt id="Fityk.get_wssr">
<code class="descclassname">Fityk.</code><code class="descname">get_wssr</code><span class="sig-paren">(</span><span class="optional">[</span><em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_wssr" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns WSSR (weighted sum of squared residuals).</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_ssr">
<code class="descclassname">Fityk.</code><code class="descname">get_ssr</code><span class="sig-paren">(</span><span class="optional">[</span><em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_ssr" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns SSR (sum of squared residuals).</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_rsquared">
<code class="descclassname">Fityk.</code><code class="descname">get_rsquared</code><span class="sig-paren">(</span><span class="optional">[</span><em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_rsquared" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns R-squared.</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_dof">
<code class="descclassname">Fityk.</code><code class="descname">get_dof</code><span class="sig-paren">(</span><span class="optional">[</span><em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_dof" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns the number of degrees of freedom (#points - #parameters).</p>
</dd></dl>
<dl class="method">
<dt id="Fityk.get_covariance_matrix">
<code class="descclassname">Fityk.</code><code class="descname">get_covariance_matrix</code><span class="sig-paren">(</span><span class="optional">[</span><em>d</em><span class="optional">]</span><span class="sig-paren">)</span><a class="headerlink" href="#Fityk.get_covariance_matrix" title="Permalink to this definition">¶</a></dt>
<dd><p>Returns covariance matrix.</p>
</dd></dl>
</div>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<p>List peak center of series of data:</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="c1">-- file list-max.lua</span>
<span class="n">prev_x</span> <span class="o">=</span> <span class="kc">nil</span>
<span class="k">for</span> <span class="n">n</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="n">F</span><span class="p">:</span><span class="n">get_dataset_count</span><span class="p">()</span><span class="o">-</span><span class="mi">1</span> <span class="k">do</span>
<span class="kd">local</span> <span class="n">path</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">get_info</span><span class="p">(</span><span class="s2">"</span><span class="s">filename"</span><span class="p">,</span> <span class="n">n</span><span class="p">)</span>
<span class="kd">local</span> <span class="n">filename</span> <span class="o">=</span> <span class="nb">string.match</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s2">"</span><span class="s">[^/</span><span class="se">\\</span><span class="s">]+$"</span><span class="p">)</span> <span class="ow">or</span> <span class="s2">"</span><span class="s">"</span>
<span class="c1">-- local x = F:calculate_expr("argmax(y)", n)</span>
<span class="kd">local</span> <span class="n">x</span> <span class="o">=</span> <span class="n">F</span><span class="p">:</span><span class="n">calculate_expr</span><span class="p">(</span><span class="s2">"</span><span class="s">F[0].center"</span><span class="p">,</span> <span class="n">n</span><span class="p">)</span>
<span class="n">s</span> <span class="o">=</span> <span class="nb">string.format</span><span class="p">(</span><span class="s2">"</span><span class="s">%s: max at x=%.4f"</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">x</span><span class="p">)</span>
<span class="k">if</span> <span class="n">prev_x</span> <span class="o">~=</span> <span class="kc">nil</span> <span class="k">then</span>
<span class="n">s</span> <span class="o">=</span> <span class="n">s</span> <span class="o">..</span> <span class="nb">string.format</span><span class="p">(</span><span class="s2">"</span><span class="s"> (%+.4f)"</span><span class="p">,</span> <span class="n">x</span><span class="o">-</span><span class="n">prev_x</span><span class="p">)</span>
<span class="k">end</span>
<span class="n">prev_x</span> <span class="o">=</span> <span class="n">x</span>
<span class="nb">print</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
<span class="k">end</span>
</pre></div>
</div>
<div class="highlight-fityk"><div class="highlight"><pre><span></span><span class="gp">=-> </span>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)
</pre></div>
</div>
<p>Write to file values of the model F(x) at chosen x’s
(in this example x = 0, 1.5, 3, ... 150):</p>
<div class="highlight-lua"><div class="highlight"><pre><span></span><span class="c1">-- file tabular-f.lua</span>
<span class="n">file</span> <span class="o">=</span> <span class="nb">io.open</span><span class="p">(</span><span class="s2">"</span><span class="s">output.dat"</span><span class="p">,</span> <span class="s2">"</span><span class="s">w"</span><span class="p">)</span>
<span class="k">for</span> <span class="n">x</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">150</span><span class="p">,</span> <span class="mf">1.5</span> <span class="k">do</span>
<span class="n">file</span><span class="p">:</span><span class="n">write</span><span class="p">(</span><span class="nb">string.format</span><span class="p">(</span><span class="s2">"</span><span class="s">%g</span><span class="se">\t</span><span class="s">%g</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span> <span class="n">x</span><span class="p">,</span> <span class="n">F</span><span class="p">:</span><span class="n">get_model_value</span><span class="p">(</span><span class="n">x</span><span class="p">)))</span>
<span class="k">end</span>
<span class="n">file</span><span class="p">:</span><span class="n">close</span><span class="p">()</span>
</pre></div>
</div>
<div class="highlight-fityk"><div class="highlight"><pre><span></span><span class="gp">=-> </span>exec tabular-f.lua
<span class="gp">=-> </span>!head -5 output.dat
0 12.1761
1.5 12.3004
3 10.9096
4.5 9.12635
6 8.27044
</pre></div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="clearer"></div>
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