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<!DOCTYPE html>
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<li class="toctree-l1"><a class="reference internal" href="installation.html">Installing brutifus</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Running brutifus</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#setting-parameters-with-params-brutifus-yaml">Setting parameters with <code class="docutils literal notranslate"><span class="pre">params_brutifus.yaml</span></code></a></li>
<li class="toctree-l2"><a class="reference internal" href="#setting-the-processing-steps-with-procsteps-brutifus-yaml">Setting the processing steps with <code class="docutils literal notranslate"><span class="pre">procsteps_brutifus.yaml</span></code></a></li>
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<div class="section" id="running-brutifus">
<h1>Running brutifus<a class="headerlink" href="#running-brutifus" title="Permalink to this headline">¶</a></h1>
<p>The spirit of brutifus is that each user can choose, depending on the object at hand & the
quality of the data, what processing steps are warranted. These are governed by the
<code class="docutils literal notranslate"><span class="pre">procsteps_brutifus.yaml</span></code> file. In parallel, the user can define all relevant parameters using
the <code class="docutils literal notranslate"><span class="pre">params_brutifus.yaml</span></code> file. The two files (that rely on YAML syntax) are <a class="reference external" href="https://github.com/fpavogt/brutifus/blob/master/brutifus/exec_scripts/">shipped as
supplementary files with the code</a>.
The following high-level entry point will create local copies in your current location (assumed to be your
favorite processing area). In a terminal:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="o">~/</span><span class="n">where</span><span class="o">/</span><span class="n">ever</span><span class="o">/</span><span class="n">you</span><span class="o">/</span><span class="n">want</span>
<span class="n">brutifus</span> <span class="o">--</span><span class="n">setup</span>
</pre></div>
</div>
<p>Doing so will create a local copy of both files in the current directory, together with generic
working directories.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>I very much suggest to run a <code class="docutils literal notranslate"><span class="pre">brutifus</span> <span class="pre">--setup</span></code> for each project, rather than using
a single processing area for all projects.</p>
</div>
<div class="section" id="setting-parameters-with-params-brutifus-yaml">
<h2>Setting parameters with <code class="docutils literal notranslate"><span class="pre">params_brutifus.yaml</span></code><a class="headerlink" href="#setting-parameters-with-params-brutifus-yaml" title="Permalink to this headline">¶</a></h2>
<p>All the brutifus parameters with a <cite>scientific impact</cite> can be specified inside this file.</p>
<div class="highlight-yaml notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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34</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="c1"># === Very-high-level parameters ===</span>
<span class="nt">systemtex</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span> <span class="c1"># Use the system LaTeX instead of the Python one ?</span>
<span class="c1"># === High-level parameters ===</span>
<span class="nt">target</span><span class="p">:</span> <span class="s">'SNR123'</span> <span class="c1"># Short and sweet string, for the filenames</span>
<span class="nt">z_target</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">0.0</span> <span class="c1"># Redshift of the target</span>
<span class="nt">inst</span><span class="p">:</span> <span class="s">'MUSE'</span> <span class="c1"># Instrument name</span>
<span class="nt">multiprocessing</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span> <span class="c1"># Use multi-cpus ? integer for upper limit, or True for all</span>
<span class="nt">verbose</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span> <span class="c1"># Print stuff that may be of interest ?</span>
<span class="c1"># === Data location ===</span>
<span class="nt">data_loc</span><span class="p">:</span> <span class="s">'./some/relative/path'</span> <span class="c1"># Where is the data ?</span>
<span class="nt">data_fn</span><span class="p">:</span> <span class="s">'some_cube.fits'</span> <span class="c1"># What is the name of the datacube ?</span>
<span class="c1"># === Processing parameters ===</span>
<span class="c1"># --- Constructing SNR maps ---</span>
<span class="nt">snr_ranges</span><span class="p">:</span> <span class="c1"># lam_min, lam_max, 'c'ontinuum, or 'e'mission</span>
<span class="c1"># - [7400., 8500., 'c']</span>
<span class="c1"># - [6560., 6570., 'e']</span>
<span class="c1"># --- Manual sky subtraction ---</span>
<span class="nt">sky_regions</span><span class="p">:</span> <span class="c1"># x0,y0, radius, or x0,y0,dx,dy</span>
<span class="c1"># - [265, 88, 3]</span>
<span class="c1"># - [254, 51, 2]</span>
<span class="c1"># --- Correcting for the Galactic extinction ---</span>
<span class="nt">gal_curve</span><span class="p">:</span> <span class="s">'f99'</span> <span class="c1"># Set to 'f99' to follow NED.</span>
<span class="nt">gal_rv</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">3.1</span> <span class="c1"># Set to 3.1 to follow NED.</span>
<span class="nt">Ab</span><span class="p">:</span> <span class="c1"># Ab (Landolt) from NED.</span>
<span class="nt">Av</span><span class="p">:</span> <span class="c1"># Av (Landolt) from NED.</span>
<span class="c1"># --- LOWESS Continuum fitting --- </span>
<span class="nt">lowess_it</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">10</span> <span class="c1"># Number of iteration for sigma-clipping to get rid of outliers</span>
<span class="nt">lowess_frac</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">0.05</span> <span class="c1"># % of the array used for deriving each point. 0.05 = sweet spot?</span>
</pre></div>
</td></tr></table></div>
<div class="admonition-todo admonition" id="id1">
<p class="admonition-title">Todo</p>
<p>A detailed list of what everything is/does would be nice. Until then, look at the
comments inside the file for a clarification of what everything does.</p>
</div>
</div>
<div class="section" id="setting-the-processing-steps-with-procsteps-brutifus-yaml">
<h2>Setting the processing steps with <code class="docutils literal notranslate"><span class="pre">procsteps_brutifus.yaml</span></code><a class="headerlink" href="#setting-the-processing-steps-with-procsteps-brutifus-yaml" title="Permalink to this headline">¶</a></h2>
<p>brutifus is designed to batch process all the individual spectra inside a given IFU datacube
individually, exploiting multiple cpus (when available) to gain speed.</p>
<p>The different steps to be executed, in sequential order, are defined in <code class="docutils literal notranslate"><span class="pre">procsteps_brutifus.py</span></code>.
Each step can be re-arranged as needed by the user. In practice, it is mostly the plotting steps
that will be most duplicated to visualize the different intermediate products.</p>
<p>Each step contains a handful of common parameters, including a step name, whether to run it (True) or
not (False), and the suffix added to the associated product file. Arguments (such as cut levels for
images) are passed via the <code class="docutils literal notranslate"><span class="pre">args</span></code> container. Of note are the <code class="docutils literal notranslate"><span class="pre">name_in</span></code> and <code class="docutils literal notranslate"><span class="pre">name_out</span></code> values:
these allow the user to give <cite>short reference tags</cite> to specific intermediate products, in order to
easily feed them to subsequent steps.</p>
<div class="highlight-yaml notranslate"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre> 1
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96</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="c1"># Each step below will be execute in order. Users should feel free to re-arrange/skip/</span>
<span class="c1"># delete/duplicate steps as needed. Note: step names are not optional !!!</span>
<span class="c1"># --------------------------------------------------------------------------------------------------</span>
<span class="c1"># The first two functions are used for plotting ... use them as often as needed to visualize</span>
<span class="c1"># the different data products !</span>
<span class="c1"># --- Make some RGB plots from the datacube ... ---</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'plot_RGB'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'rgb1'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'wcs-corr_cube'</span> <span class="c1"># What cube do I want to plot ?</span>
<span class="nt">bands</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">6560</span><span class="p p-Indicator">,</span><span class="nv">6570</span><span class="p p-Indicator">,</span><span class="nv">7500</span><span class="p p-Indicator">,</span><span class="nv">8750</span><span class="p p-Indicator">,</span><span class="nv">4750</span><span class="p p-Indicator">,</span><span class="nv">5500</span><span class="p p-Indicator">]]</span>
<span class="nt">stretches</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="s">'arcsinh'</span><span class="p p-Indicator">,</span><span class="s">'arcsinh'</span><span class="p p-Indicator">,</span><span class="s">'arcsinh'</span><span class="p p-Indicator">]]</span> <span class="c1"># arcsinh, linear</span>
<span class="nt">plims</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">1.</span><span class="p p-Indicator">,</span><span class="nv">98.</span><span class="p p-Indicator">,</span><span class="nv">1.</span><span class="p p-Indicator">,</span><span class="nv">98.</span><span class="p p-Indicator">,</span><span class="nv">1.</span><span class="p p-Indicator">,</span><span class="nv">98.</span><span class="p p-Indicator">]]</span>
<span class="nt">vlims</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">]]</span>
<span class="nt">gauss_blurs</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">]]</span>
<span class="nt">conts</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">]]</span>
<span class="c1"># --- Make some BW plots ... ---</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'plot_BW'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'bw1'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'wcs-corr_cube'</span> <span class="c1"># What cube do I want to plot ?</span>
<span class="nt">bands</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">6556</span><span class="p p-Indicator">,</span> <span class="nv">6579</span><span class="p p-Indicator">]]</span> <span class="c1"># lam min and max ... add more pairs to plot more plots !</span>
<span class="nt">stretches</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="s">'linear'</span><span class="p p-Indicator">]</span> <span class="c1"># Image stretch ... add more to tweak different plots.</span>
<span class="nt">plims</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">10</span><span class="p p-Indicator">,</span> <span class="nv">99</span><span class="p p-Indicator">]]</span>
<span class="nt">vlims</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">]]</span>
<span class="nt">gauss_blurs</span><span class="p">:</span> <span class="p p-Indicator">[</span><span class="nv">null</span><span class="p p-Indicator">]</span>
<span class="nt">conts</span><span class="p">:</span> <span class="p p-Indicator">[[</span><span class="nv">null</span><span class="p p-Indicator">,</span> <span class="nv">null</span><span class="p p-Indicator">]]</span>
<span class="c1"># --------------------------------------------------------------------------------------------------</span>
<span class="c1"># === Correct the WCS values to check with Gaia. ===</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'adjust_WCS'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'s00'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'raw_cube'</span>
<span class="nt">name_out</span><span class="p">:</span> <span class="s">'wcs-corr_cube'</span>
<span class="c1"># === First, compute some S/N maps for the continuum and emission lines of interest ... ===</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'crude_snr_maps'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'s01'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'raw_cube'</span> <span class="c1"># What cube do I want to process ?</span>
<span class="nt">do_plot</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span> <span class="c1"># Do I want to save some pretty pictures ?</span>
<span class="nt">zcorr_lams</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span> <span class="c1"># True = correct wavelength ranges for redshift</span>
<span class="c1"># === Perform some sky subtraction, if needed ===</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'sky_sub'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'s03'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'raw_cube'</span>
<span class="nt">name_out</span><span class="p">:</span> <span class="s">'skysub_cube'</span>
<span class="c1"># === Correct for galactic reddening via the values given on NED ===</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'gal_dered'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'s04'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'skysub_cube'</span>
<span class="nt">name_out</span><span class="p">:</span> <span class="s">'galdered_cube'</span>
<span class="nt">do_plot</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">True</span>
<span class="c1"># === Continuum fitting ===</span>
<span class="c1"># First, fit the continuum using a LOWESS filter. Much more elegant than a polynomial!</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">fit_continuum</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'s05'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'galdered_cube'</span>
<span class="nt">start_row</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">0</span> <span class="c1"># Where to start the fitting ? None = 0</span>
<span class="nt">end_row</span><span class="p">:</span> <span class="c1"># Where to end the fitting ? None = max</span>
<span class="nt">method</span><span class="p">:</span> <span class="s">'lowess'</span> <span class="c1"># What kind of fitting is this ?</span>
<span class="c1"># Gather the output in a single datacube</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'make_continuum_cube'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'s06'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="l l-Scalar l-Scalar-Plain">method:'lowess'</span>
<span class="c1"># Subtract the sky continuum</span>
<span class="p p-Indicator">-</span> <span class="nt">step</span><span class="p">:</span> <span class="s">'subtract_continuum'</span>
<span class="nt">run</span><span class="p">:</span> <span class="l l-Scalar l-Scalar-Plain">False</span>
<span class="nt">suffix</span><span class="p">:</span> <span class="s">'s07'</span>
<span class="nt">args</span><span class="p">:</span>
<span class="nt">name_in</span><span class="p">:</span> <span class="s">'galdered_cube'</span>
<span class="nt">name_out</span><span class="p">:</span> <span class="s">'consub_cube'</span>
<span class="nt">method</span><span class="p">:</span> <span class="s">'lowess'</span>
</pre></div>
</td></tr></table></div>
<div class="admonition-todo admonition" id="id2">
<p class="admonition-title">Todo</p>
<p>A detailed list of what everything is/does would be nice. Until then, look at the
comments inside the file for a clarification of what everything does.</p>
</div>
</div>
<div class="section" id="launching-the-post-processing">
<h2>Launching the post-processing<a class="headerlink" href="#launching-the-post-processing" title="Permalink to this headline">¶</a></h2>
<p>Having prepared both <code class="docutils literal notranslate"><span class="pre">params_brutifus.yaml</span></code> and <code class="docutils literal notranslate"><span class="pre">procsteps_brutifus.yaml</span></code>, you are ready to launch
brutifus. This is done via the following high-level entry point:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="n">brutifus</span> <span class="o">-</span><span class="n">e</span> <span class="n">procsteps_brutifus</span><span class="o">.</span><span class="n">yaml</span> <span class="n">params_brutifus</span><span class="o">.</span><span class="n">yaml</span>
</pre></div>
</div>
<p>If all goes according to plan, brutifus will start processing your data, one step after the
other, printing some info along the way. <strong>Some steps can take time (up to several hours) !</strong>
Just be patient - progress indicators will help you monitor each task, if you set <code class="docutils literal notranslate"><span class="pre">'verbose':</span> <span class="pre">True</span></code>
inside <code class="docutils literal notranslate"><span class="pre">params_brutifus.yaml</span></code>.</p>
</div>
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