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<div class="section" id="configuration-files">
<h1>Configuration files<a class="headerlink" href="#configuration-files" title="Permalink to this headline">¶</a></h1>
<div class="section" id="preliminaries">
<h2>Preliminaries<a class="headerlink" href="#preliminaries" title="Permalink to this headline">¶</a></h2>
<p>The configuration files used by the PyroPython command line tools are <a class="reference external" href="http://yaml.org/">yaml</a> files.
They are plain text files that consists of key - value pairs. Below is an example
of a valid <em>yaml</em> input (_not_ a valid PyroPython input!)</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">key</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">value</span>
<span class="l l-Scalar l-Scalar-Plain">person</span><span class="p p-Indicator">:</span>
<span class="l l-Scalar l-Scalar-Plain">age</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">100</span>
<span class="l l-Scalar l-Scalar-Plain">name</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">NA</span>
</pre></div>
</div>
<p>In the above example, the keyword “age” is tied to a single value (100) while the
keyword person is tied to a <em>dictionary</em>. The dicitonary of a person can also
be written</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">person</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">{</span><span class="nv">age</span><span class="p p-Indicator">:</span> <span class="nv">100</span><span class="p p-Indicator">,</span> <span class="nv">name</span><span class="p p-Indicator">:</span> <span class="nv">NA</span><span class="p p-Indicator">}</span>
</pre></div>
</div>
<p>This should look familiar to everyone familiar with the Python programming language.</p>
</div>
<div class="section" id="configuration-file-structure">
<h2>Configuration file structure<a class="headerlink" href="#configuration-file-structure" title="Permalink to this headline">¶</a></h2>
<p>PyroPython configuration file consists of a number of keywords some of which are
optional. A minimal configuration file looks like this:</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">num_jobs</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">1</span> <span class="c1"># number of parallel jobs</span>
<span class="l l-Scalar l-Scalar-Plain">max_iter</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">10</span> <span class="c1"># maximum number of iterations</span>
<span class="l l-Scalar l-Scalar-Plain">num_points</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">1</span> <span class="c1"># How many points explored per iteration</span>
<span class="l l-Scalar l-Scalar-Plain">num_initial</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">10</span> <span class="c1"># Number of points in initial design (here 100*ndim)</span>
<span class="l l-Scalar l-Scalar-Plain">fds_command</span><span class="p p-Indicator">:</span>
<span class="l l-Scalar l-Scalar-Plain">variables</span><span class="p p-Indicator">:</span> <span class="c1"># VAR_NAME: [LOWER,UPPER]</span>
<span class="l l-Scalar l-Scalar-Plain">var1</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">[</span><span class="nv">0</span><span class="p p-Indicator">,</span> <span class="nv">1</span><span class="p p-Indicator">]</span>
<span class="l l-Scalar l-Scalar-Plain">var2</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">[</span><span class="nv">0</span><span class="p p-Indicator">,</span> <span class="nv">2</span><span class="p p-Indicator">]</span>
<span class="l l-Scalar l-Scalar-Plain">simulation</span><span class="p p-Indicator">:</span>
<span class="l l-Scalar l-Scalar-Plain">MASS2</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">{</span><span class="nv">fname</span><span class="p p-Indicator">:</span> <span class="s">'birch_tga_gronli_2_tga.csv'</span><span class="p p-Indicator">,</span><span class="nv">dep_col_name</span><span class="p p-Indicator">:</span> <span class="s">'Mass'</span><span class="p p-Indicator">,</span><span class="nv">ind_col_name</span><span class="p p-Indicator">:</span> <span class="s">'Temp'</span><span class="p p-Indicator">}</span>
<span class="l l-Scalar l-Scalar-Plain">GMASS2</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">{</span><span class="nv">fname</span><span class="p p-Indicator">:</span> <span class="s">'birch_tga_gronli_2_tga.csv'</span><span class="p p-Indicator">,</span><span class="nv">dep_col_name</span><span class="p p-Indicator">:</span> <span class="s">'MLR'</span><span class="p p-Indicator">,</span><span class="nv">ind_col_name</span><span class="p p-Indicator">:</span> <span class="s">'Temp'</span><span class="p p-Indicator">}</span>
<span class="l l-Scalar l-Scalar-Plain">experiment</span><span class="p p-Indicator">:</span>
<span class="l l-Scalar l-Scalar-Plain">MASS2</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">{</span><span class="nv">fname</span><span class="p p-Indicator">:</span> <span class="s">'birch_tga_2_exp.csv'</span><span class="p p-Indicator">,</span><span class="nv">dep_col_name</span><span class="p p-Indicator">:</span> <span class="s">'Mass'</span><span class="p p-Indicator">,</span><span class="nv">ind_col_name</span><span class="p p-Indicator">:</span> <span class="s">'Temp'</span><span class="p p-Indicator">,</span><span class="nv">normalize</span><span class="p p-Indicator">:</span> <span class="nv">True</span><span class="p p-Indicator">}</span>
<span class="l l-Scalar l-Scalar-Plain">GMASS2</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">{</span><span class="nv">fname</span><span class="p p-Indicator">:</span> <span class="s">'birch_tga_2_exp.csv'</span><span class="p p-Indicator">,</span><span class="nv">dep_col_name</span><span class="p p-Indicator">:</span> <span class="s">'Mass'</span><span class="p p-Indicator">,</span><span class="nv">ind_col_name</span><span class="p p-Indicator">:</span> <span class="s">'Temp'</span><span class="p p-Indicator">,</span><span class="nv">conversion_factor</span><span class="p p-Indicator">:</span> <span class="nv">0.0333</span><span class="p p-Indicator">,</span><span class="nv">normalize</span><span class="p p-Indicator">:</span> <span class="nv">True</span><span class="p p-Indicator">,</span><span class="nv">gradient</span><span class="p p-Indicator">:</span> <span class="nv">True</span><span class="p p-Indicator">}</span>
<span class="l l-Scalar l-Scalar-Plain">templates</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">[</span><span class="s">"birch_tga_gronli_2.fds"</span><span class="p p-Indicator">]</span>
</pre></div>
</div>
<p>This configuration file instructs PyroPython to match the variables MASS2 and GMASS2
by changing the variables var1 and var2. The optimization is done using a single process
and optimization continues for 10 iterations.</p>
</div>
<div class="section" id="configuration-file-keywords">
<h2>Configuration file keywords<a class="headerlink" href="#configuration-file-keywords" title="Permalink to this headline">¶</a></h2>
<dl class="data">
<dt id="num_jobs">
<code class="descname">num_jobs</code><a class="headerlink" href="#num_jobs" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of parallel jobs used. (default: 1)</p>
</dd></dl>
<dl class="data">
<dt id="max_iter">
<code class="descname">max_iter</code><a class="headerlink" href="#max_iter" title="Permalink to this definition">¶</a></dt>
<dd><p>Maximum number of iterations. Meaning of this parameter depends on the
algorithm used</p>
</dd></dl>
<dl class="data">
<dt id="num_points">
<code class="descname">num_points</code><a class="headerlink" href="#num_points" title="Permalink to this definition">¶</a></dt>
<dd><p>Maximum number of points explored per iteration. BEhaviour depends on the
optimization algortihm. Default (num_point = num_jobs)</p>
</dd></dl>
<dl class="data">
<dt id="num_initial">
<code class="descname">num_initial</code><a class="headerlink" href="#num_initial" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of points chosen randomly in the beginning. Also known as initial design.</p>
</dd></dl>
<dl class="data">
<dt id="initial_design">
<code class="descname">initial_design</code><span class="sig-paren">(</span><em>optional</em>, <em>default: lhs</em><span class="sig-paren">)</span><a class="headerlink" href="#initial_design" title="Permalink to this definition">¶</a></dt>
<dd><p>Type of initial design. Choices are “rand” and “lhs” for uniform random and
latin hypercube sampling</p>
</dd></dl>
<dl class="data">
<dt id="initial_design_file">
<code class="descname">initial_design_file</code><span class="sig-paren">(</span><em>optional</em><span class="sig-paren">)</span><a class="headerlink" href="#initial_design_file" title="Permalink to this definition">¶</a></dt>
<dd><p>A comma separated text file containing a initial design. The file should
contain one header line and a column for each variable being optimized and
optionally objective value. Overrides <em>initial_design</em> and <em>num_initial</em>
options.</p>
</dd></dl>
<dl class="data">
<dt id="casename">
<code class="descname">casename</code><span class="sig-paren">(</span><em>optional</em><span class="sig-paren">)</span><a class="headerlink" href="#casename" title="Permalink to this definition">¶</a></dt>
<dd><p>Casename used for naming log file and output directories. By default
Pyropython creates the following files and directories:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Work</span><span class="o">/</span>
<span class="n">Best</span><span class="o">/</span>
<span class="n">Figs</span><span class="o">/</span>
<span class="n">log</span><span class="o">.</span><span class="n">csv</span>
</pre></div>
</div>
<p>If the casename is set to ‘CASE’, the followin g files and directories
will be created:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Work</span><span class="o">/</span>
<span class="n">CASE_Best</span><span class="o">/</span>
<span class="n">CASE_Figs</span><span class="o">/</span>
<span class="n">CASE</span><span class="o">.</span><span class="n">csv</span>
</pre></div>
</div>
<p>This is useful if you want to several cases in the same folder.</p>
</dd></dl>
<dl class="data">
<dt id="fds_command">
<code class="descname">fds_command</code><a class="headerlink" href="#fds_command" title="Permalink to this definition">¶</a></dt>
<dd><p>Full path to the executable, including the executable. For example, if you
installed FDS from the official distribution on Windows, this line would most
likely read:</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">fds_command</span><span class="p p-Indicator">:</span> <span class="l l-Scalar l-Scalar-Plain">C:\Program Files\firemodels\FDS6\bin\fds.exe</span>
</pre></div>
</div>
</dd></dl>
<dl class="data">
<dt id="variables">
<code class="descname">variables</code><a class="headerlink" href="#variables" title="Permalink to this definition">¶</a></dt>
<dd><p>A list of variables and corresponding bounds in format:</p>
<p>For example:</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">variables</span><span class="p p-Indicator">:</span>
<span class="l l-Scalar l-Scalar-Plain">var1</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">[</span><span class="nv">0</span><span class="p p-Indicator">,</span><span class="nv">1</span><span class="p p-Indicator">]</span>
<span class="l l-Scalar l-Scalar-Plain">var2</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">[</span><span class="nv">-1</span><span class="p p-Indicator">,</span><span class="nv">1</span><span class="p p-Indicator">]</span>
</pre></div>
</div>
<p>The above block defines two variables named “var1” and “var2”. Variable “var1”
has lower bound 0 and upper bound 1.</p>
</dd></dl>
<dl class="data">
<dt id="simulation">
<code class="descname">simulation</code><a class="headerlink" href="#simulation" title="Permalink to this definition">¶</a></dt>
<dd><p>A list of variables to be read from the simulation output. Each variable is
given in format:</p>
<div class="highlight-yaml notranslate"><div class="highlight"><pre><span></span><span class="l l-Scalar l-Scalar-Plain">varname</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">{</span><span class="nv">fname</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">,</span> <span class="nv">dep_col_name</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">,</span> <span class="nv">ind_col_name</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">,</span> <span class="nv">header</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">,</span> <span class="nv">normalize</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">,</span> <span class="nv">gradient</span><span class="p p-Indicator">:</span> <span class="p p-Indicator">,</span> <span class="nv">filter</span><span class="p p-Indicator">:}</span>
</pre></div>
</div>
<dl class="attribute">
<dt id="varname">
<code class="descname">varname</code><a class="headerlink" href="#varname" title="Permalink to this definition">¶</a></dt>
<dd><p>Variable name. Used to mach variables from “simulation” with variables
from “experiment”</p>
</dd></dl>
<dl class="attribute">
<dt id="fname">
<code class="descname">fname</code><a class="headerlink" href="#fname" title="Permalink to this definition">¶</a></dt>
<dd><p>A csv filename, where the simulator output can be read.</p>
</dd></dl>
<dl class="attribute">
<dt id="dep_col_name">
<code class="descname">dep_col_name</code><a class="headerlink" href="#dep_col_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of the column containing the <em>dependent</em> variable data.</p>
</dd></dl>
<dl class="attribute">
<dt id="ind_col_name">
<code class="descname">ind_col_name</code><a class="headerlink" href="#ind_col_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of the column containing the <em>independent</em> variable data.</p>
</dd></dl>
<p>The following keywords are <em>optional</em></p>
<dl class="attribute">
<dt id="header">
<code class="descname">header</code><span class="sig-paren">(</span><em>optional</em>, <em>default = 1</em><span class="sig-paren">)</span><a class="headerlink" href="#header" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of header lines to skip. Default value is 1 and implies that
the variable names are given on the <em>second</em> row of the .csv file.
The default value is chosen with FDS output files in mind, where
the first row contains unit info.</p>
</dd></dl>
<dl class="attribute">
<dt id="normalize">
<code class="descname">normalize</code><span class="sig-paren">(</span><em>optional</em>, <em>default = False</em><span class="sig-paren">)</span><a class="headerlink" href="#normalize" title="Permalink to this definition">¶</a></dt>
<dd><p>Should TGA normalization be applied to data? Default: False. If set
to True, the data is normalized as</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">y</span> <span class="o">=</span> <span class="n">y</span> <span class="o">/</span> <span class="n">y</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span>
</pre></div>
</div>
</dd></dl>
<dl class="attribute">
<dt>
<code class="descname">normalize</code><span class="sig-paren">(</span><em>optional</em>, <em>default = False</em><span class="sig-paren">)</span></dt>
<dd><p>Should gradient be calculated from the data? If set to True, gradient
is calculated using numpy.</p>
</dd></dl>
<dl class="attribute">
<dt id="filter">
<code class="descname">filter</code><span class="sig-paren">(</span><em>optional</em>, <em>default = None</em><span class="sig-paren">)</span><a class="headerlink" href="#filter" title="Permalink to this definition">¶</a></dt>
<dd><p>Filter to be appleid to the data. Choices are:</p>
<blockquote>
<div><ol class="arabic simple">
<li><dl class="first docutils">
<dt>“gp”, for Gaussian process. This fits a GaussianProcessRegressor</dt>
<dd>from scikit-learn to the data and uses the predicted mean of the
fitted process as the smoothed data</dd>
</dl>
</li>
<li>“ma”, for moving average.</li>
<li>“median”, for median filter.</li>
</ol>
</div></blockquote>
</dd></dl>
</dd></dl>
<dl class="data">
<dt id="experiment">
<code class="descname">experiment</code><a class="headerlink" href="#experiment" title="Permalink to this definition">¶</a></dt>
<dd><p>A list of variables that form the experimental data. Each entry in
<em>simulation</em> should have a corresponding entry in <em>experiment</em>.
The format is exactly the same as in <em>simulation</em>, with one exception:
The default value of <em>header</em> keyword is 0, implying that the variable
names should be given in the first row of the .csv - file.</p>
</dd></dl>
<dl class="data">
<dt id="objective">
<code class="descname">objective</code><span class="sig-paren">(</span><em>optional</em>, <em>Default: mse</em><span class="sig-paren">)</span><a class="headerlink" href="#objective" title="Permalink to this definition">¶</a></dt>
<dd><p>Type of objective function</p>
</dd></dl>
<dl class="data">
<dt id="plots">
<code class="descname">plots</code><span class="sig-paren">(</span><em>optional</em><span class="sig-paren">)</span><a class="headerlink" href="#plots" title="Permalink to this definition">¶</a></dt>
<dd><p>List of plots to be drawn. See the section <a class="reference internal" href="plots.html#plotting"><span class="std std-ref">Plotting</span></a> for more information.
:noindex:</p>
</dd></dl>
<dl class="data">
<dt id="optimizer_name">
<code class="descname">optimizer_name</code><span class="sig-paren">(</span><em>default: 'skopt'</em><span class="sig-paren">)</span><a class="headerlink" href="#optimizer_name" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of the optimizer. See <a class="reference internal" href="optimizers.html#optimizers"><span class="std std-ref">Optimizers</span></a> for more information.</p>
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<dt id="optimizer">
<code class="descname">optimizer</code><span class="sig-paren">(</span><em>optional</em><span class="sig-paren">)</span><a class="headerlink" href="#optimizer" title="Permalink to this definition">¶</a></dt>
<dd><p>Optimizer options. Curretly only supported for scikit-optimize. This is
a dictionary of options passed to the <a class="reference external" href="https://scikit-optimize.github.io/optimizer/index.html">skopt.optimizer</a> module.</p>
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