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<li><a class="reference internal" href="#">The fors_extract recipe</a><ul>
<li><a class="reference internal" href="#synopsis">Synopsis</a></li>
<li><a class="reference internal" href="#description">Description</a><ul>
<li><a class="reference internal" href="#input-files">Input files</a></li>
<li><a class="reference internal" href="#output-files">Output files</a></li>
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<li><a class="reference internal" href="#constructor">Constructor</a></li>
<li><a class="reference internal" href="#parameters">Parameters</a></li>
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<div class="section" id="the-fors-extract-recipe">
<h1>The fors_extract recipe<a class="headerlink" href="#the-fors-extract-recipe" title="Permalink to this headline">¶</a></h1>
<dl class="data">
<dt id="fors_extract">
<tt class="descname">fors_extract</tt><a class="headerlink" href="#fors_extract" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<div class="section" id="synopsis">
<h2>Synopsis<a class="headerlink" href="#synopsis" title="Permalink to this headline">¶</a></h2>
<p>Extraction of scientific spectra</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>This recipe is used to reduce scientific spectra using the global
distortion table created by the recipe fors_calib. The spectra are
bias subtracted, flat fielded (if a normalised flat field is specified)
and remapped eliminating the optical distortions. The wavelength calibration
can be optionally upgraded using a number of sky lines: if no sky lines
catalog of wavelengths is specified, an internal one is used instead.</p>
<p>If the alignment to the sky lines is performed, the applied dispersion
coefficient table is upgraded and saved to disk, and a new CCD wavelengths
map is created.</p>
<p>This recipe accepts both FORS1 and FORS2 frames. A grism table (typically
depending on the instrument mode, and in particular on the grism used)
may also be specified: this table contains a default recipe parameter
setting to control the way spectra are extracted for a specific instrument
mode, as it is used for automatic run of the pipeline on Paranal and in
Garching. If this table is specified, it will modify the default recipe
parameter setting, with the exception of those parameters which have been
explicitly modifyed on the command line. If a grism table is not specified,
the input recipe parameters values will always be read from the command
line, or from an esorex configuration file if present, or from their
generic default values (that are rarely meaningful).</p>
<p>In the table below the MXU acronym can be read alternatively as MOS
and LSS, depending on the instrument mode of the input data. Either a
scientific or a standard star exposure can be specified in input (not
both).</p>
<div class="section" id="input-files">
<h3>Input files<a class="headerlink" href="#input-files" title="Permalink to this headline">¶</a></h3>
<div class="highlight-python"><pre>DO category: Type: Explanation: Required:
SCIENCE_MXU Raw Scientific exposure Y
or STANDARD_MXU Raw Standard star exposure Y
MASTER_BIAS Calib Master bias Y
GRISM_TABLE Calib Grism table .
MASTER_SKYLINECAT Calib Sky lines catalog .
MASTER_NORM_FLAT_MXU Calib Normalised flat field .
MASTER_DISTORTION_TABLE Calib Global distortion model .
or, in case of LSS-like MOS/MXU data,
MASTER_NORM_FLAT_LONG_MXU Calib Normalised flat field .</pre>
</div>
</div>
<div class="section" id="output-files">
<h3>Output files<a class="headerlink" href="#output-files" title="Permalink to this headline">¶</a></h3>
<div class="highlight-python"><pre>DO category: Data type: Explanation:
REDUCED_SCI_MXU FITS image Extracted scientific spectra
REDUCED_SKY_SCI_MXU FITS image Extracted sky spectra
REDUCED_ERROR_SCI_MXU FITS image Errors on extracted spectra
UNMAPPED_SCI_MXU FITS image Sky subtracted scientific spectra
MAPPED_SCI_MXU FITS image Rectified scientific spectra
MAPPED_ALL_SCI_MXU FITS image Rectified science spectra with sky
MAPPED_SKY_SCI_MXU FITS image Rectified sky spectra
UNMAPPED_SKY_SCI_MXU FITS image Sky on CCD
GLOBAL_SKY_SPECTRUM_MXU FITS table Global sky spectrum
OBJECT_TABLE_SCI_MXU FITS table Positions of detected objects
Only if the sky-alignment of the wavelength solution is requested:
SKY_SHIFTS_LONG_SCI_MXU FITS table Sky lines offsets (LSS-like data)
or SKY_SHIFTS_SLIT_SCI_MXU FITS table Sky lines offsets (MOS-like data)
DISP_COEFF_SCI_MXU FITS table Upgraded dispersion coefficients
WAVELENGTH_MAP_SCI_MXU FITS image Upgraded wavelength map</pre>
</div>
</div>
</div>
<div class="section" id="constructor">
<h2>Constructor<a class="headerlink" href="#constructor" title="Permalink to this headline">¶</a></h2>
<dl class="method">
<dt>
<tt class="descclassname">cpl.</tt><tt class="descname">Recipe</tt><big>(</big><em>"fors_extract"</em><big>)</big></dt>
<dd><p>Create an object for the recipe fors_extract.</p>
</dd></dl>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cpl</span>
<span class="n">fors_extract</span> <span class="o">=</span> <span class="n">cpl</span><span class="o">.</span><span class="n">Recipe</span><span class="p">(</span><span class="s">"fors_extract"</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="parameters">
<h2>Parameters<a class="headerlink" href="#parameters" title="Permalink to this headline">¶</a></h2>
<dl class="attribute">
<dt id="fors_extract.param.dispersion">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">dispersion</tt><a class="headerlink" href="#fors_extract.param.dispersion" title="Permalink to this definition">¶</a></dt>
<dd><p>Resampling step (Angstrom/pixel) (float; default: 0.0) [default=0.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.skyalign">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">skyalign</tt><a class="headerlink" href="#fors_extract.param.skyalign" title="Permalink to this definition">¶</a></dt>
<dd><p>Polynomial order for sky lines alignment, or -1 to avoid alignment (long; default: 0) [default=0].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.wcolumn">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">wcolumn</tt><a class="headerlink" href="#fors_extract.param.wcolumn" title="Permalink to this definition">¶</a></dt>
<dd><p>Name of sky line catalog table column with wavelengths (str; default: ‘WLEN’) [default=”WLEN”].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.startwavelength">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">startwavelength</tt><a class="headerlink" href="#fors_extract.param.startwavelength" title="Permalink to this definition">¶</a></dt>
<dd><p>Start wavelength in spectral extraction (float; default: 0.0) [default=0.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.endwavelength">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">endwavelength</tt><a class="headerlink" href="#fors_extract.param.endwavelength" title="Permalink to this definition">¶</a></dt>
<dd><p>End wavelength in spectral extraction (float; default: 0.0) [default=0.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.flux">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">flux</tt><a class="headerlink" href="#fors_extract.param.flux" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply flux conservation (bool; default: True) [default=True].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.flatfield">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">flatfield</tt><a class="headerlink" href="#fors_extract.param.flatfield" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply flat field (bool; default: False) [default=False].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.skyglobal">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">skyglobal</tt><a class="headerlink" href="#fors_extract.param.skyglobal" title="Permalink to this definition">¶</a></dt>
<dd><p>Subtract global sky spectrum from CCD (bool; default: False) [default=False].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.skymedian">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">skymedian</tt><a class="headerlink" href="#fors_extract.param.skymedian" title="Permalink to this definition">¶</a></dt>
<dd><p>Sky subtraction from extracted slit spectra (bool; default: False) [default=False].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.skylocal">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">skylocal</tt><a class="headerlink" href="#fors_extract.param.skylocal" title="Permalink to this definition">¶</a></dt>
<dd><p>Sky subtraction from CCD slit spectra (bool; default: True) [default=True].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.cosmics">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">cosmics</tt><a class="headerlink" href="#fors_extract.param.cosmics" title="Permalink to this definition">¶</a></dt>
<dd><p>Eliminate cosmic rays hits (only if global sky subtraction is also requested) (bool; default: False) [default=False].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.slit_margin">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">slit_margin</tt><a class="headerlink" href="#fors_extract.param.slit_margin" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of pixels to exclude at each slit in object detection and extraction (long; default: 3) [default=3].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.ext_radius">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">ext_radius</tt><a class="headerlink" href="#fors_extract.param.ext_radius" title="Permalink to this definition">¶</a></dt>
<dd><p>Maximum extraction radius for detected objects (pixel) (long; default: 6) [default=6].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.cont_radius">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">cont_radius</tt><a class="headerlink" href="#fors_extract.param.cont_radius" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimum distance at which two objects of equal luminosity do not contaminate each other (pixel) (long; default: 0) [default=0].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.ext_mode">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">ext_mode</tt><a class="headerlink" href="#fors_extract.param.ext_mode" title="Permalink to this definition">¶</a></dt>
<dd><p>Object extraction method: 0 = aperture, 1 = Horne optimal extraction (long; default: 1) [default=1].</p>
</dd></dl>
<dl class="attribute">
<dt id="fors_extract.param.time_normalise">
<tt class="descclassname">fors_extract.param.</tt><tt class="descname">time_normalise</tt><a class="headerlink" href="#fors_extract.param.time_normalise" title="Permalink to this definition">¶</a></dt>
<dd><p>Normalise output spectra by the exposure time (bool; default: True) [default=True].</p>
</dd></dl>
<p>The following code snippet shows the default settings for the available
parameters.</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cpl</span>
<span class="n">fors_extract</span> <span class="o">=</span> <span class="n">cpl</span><span class="o">.</span><span class="n">Recipe</span><span class="p">(</span><span class="s">"fors_extract"</span><span class="p">)</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">dispersion</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">skyalign</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">wcolumn</span> <span class="o">=</span> <span class="s">"WLEN"</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">startwavelength</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">endwavelength</span> <span class="o">=</span> <span class="mf">0.0</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">flux</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">flatfield</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">skyglobal</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">skymedian</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">skylocal</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">cosmics</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">slit_margin</span> <span class="o">=</span> <span class="mi">3</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ext_radius</span> <span class="o">=</span> <span class="mi">6</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">cont_radius</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ext_mode</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">fors_extract</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">time_normalise</span> <span class="o">=</span> <span class="bp">True</span>
</pre></div>
</div>
<p>You may also set or overwrite some or all parameters by the recipe
parameter <cite>param</cite>, as shown in the following example:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cpl</span>
<span class="n">fors_extract</span> <span class="o">=</span> <span class="n">cpl</span><span class="o">.</span><span class="n">Recipe</span><span class="p">(</span><span class="s">"fors_extract"</span><span class="p">)</span>
<span class="p">[</span><span class="o">...</span><span class="p">]</span>
<span class="n">res</span> <span class="o">=</span> <span class="n">fors_extract</span><span class="p">(</span> <span class="o">...</span><span class="p">,</span> <span class="n">param</span> <span class="o">=</span> <span class="p">{</span><span class="s">"dispersion"</span><span class="p">:</span><span class="mf">0.0</span><span class="p">,</span> <span class="s">"skyalign"</span><span class="p">:</span><span class="mi">0</span><span class="p">})</span>
</pre></div>
</div>
<div class="admonition seealso">
<p class="first admonition-title">See also</p>
<p class="last"><a class="reference external" href="http://packages.python.org/python-cpl/recipe.html">cpl.Recipe</a>
for more information about the recipe object.</p>
</div>
</div>
<div class="section" id="bug-reports">
<h2>Bug reports<a class="headerlink" href="#bug-reports" title="Permalink to this headline">¶</a></h2>
<p>Please report any problems to <a class="reference external" href="mailto:usd-help%40eso.org">Carlo Izzo</a>. Alternatively, you may
send a report to the <a class="reference external" href="mailto:usd-help%40eso.org">ESO User Support Department</a>.</p>
</div>
<div class="section" id="copyright">
<h2>Copyright<a class="headerlink" href="#copyright" title="Permalink to this headline">¶</a></h2>
<p>This file is currently part of the FORS Instrument Pipeline
Copyright (C) 2002-2010 European Southern Observatory</p>
<p>This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.</p>
<p>This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.</p>
<p>You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software Foundation,
Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA</p>
<p><em>Code author: Carlo Izzo <<a class="reference external" href="mailto:usd-help%40eso.org">usd-help<span>@</span>eso<span>.</span>org</a>></em></p>
</div>
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