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<li><a class="reference internal" href="#">The vmifucalib 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>
</ul>
</li>
<li><a class="reference internal" href="#constructor">Constructor</a></li>
<li><a class="reference internal" href="#parameters">Parameters</a></li>
<li><a class="reference internal" href="#bug-reports">Bug reports</a></li>
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<div class="section" id="the-vmifucalib-recipe">
<h1>The vmifucalib recipe<a class="headerlink" href="#the-vmifucalib-recipe" title="Permalink to this headline">¶</a></h1>
<dl class="data">
<dt id="vmifucalib">
<code class="descname">vmifucalib</code><a class="headerlink" href="#vmifucalib" 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>Generate IFU calibrations from a set of flat and arc lamp exposures.</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>This recipe produces the extraction mask, the wavelength calibration,
and the relative transmission correction, from a set of flat field
and one arc lamp exposures (IFU mode).</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"><div class="highlight"><pre>DO category: Type: Explanation: Required:
IFU_SCREEN_FLAT Raw Flat field Y
IFU_ARC_SPECTRUM Raw Arc spectrum .
LINE_CATALOG Calib Arc line catalog .
MASTER_BIAS Calib Master bias Y
IFU_IDENT Calib Fiber identification .
CCD_TABLE Calib Bad pixel table .
</pre></div>
</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"><div class="highlight"><pre>DO category: Data type: Explanation:
IFU_MASTER_SCREEN_FLAT FITS image Stack of all raw flat fields
IFU_ARC_SPECTRUM_EXTRACTED FITS image Extracted arc spectra
IFU_FLAT_SPECTRUM_EXTRACTED FITS image Extracted flat field spectra
IFU_TRACE FITS table Extraction mask
IFU_IDS FITS table Wavelength calibration
IFU_TRANSMISSION FITS table Transmission correction
</pre></div>
</div>
<p>An arc spectrum exposure may not be specified in input, but in that
case no wavelength calibration nor fiber relative transmission
correction will be computed, and further reduction of associated
scientific data will not be possible; the only products in this
case will be the stack of all the input raw flat field exposures,
and the extraction mask. If the arc spectrum exposure is specified
in input, then also a line catalog must be given. The fiber
identification table, if given, ensures that all spectra will be
safely identified and assigned to the correct spatial position,
but in most cases it will be possible to reduce the data even
without specifying this table in the input SOF. A CCD table
must be specified only if a bad pixel cleaning is requested.</p>
<p>For more details, please refer to the VIMOS Pipeline User’s Guide.</p>
</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>
<code class="descclassname">cpl.</code><code class="descname">Recipe</code><span class="sig-paren">(</span><em>"vmifucalib"</em><span class="sig-paren">)</span></dt>
<dd><p>Create an object for the recipe vmifucalib.</p>
</dd></dl>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">cpl</span>
<span class="n">vmifucalib</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">"vmifucalib"</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="vmifucalib.param.AllowSingleFrames">
<code class="descclassname">vmifucalib.param.</code><code class="descname">AllowSingleFrames</code><a class="headerlink" href="#vmifucalib.param.AllowSingleFrames" title="Permalink to this definition">¶</a></dt>
<dd><p>Flat fields combination method is ignored. (bool; default: True) [default=True].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.StackMethod">
<code class="descclassname">vmifucalib.param.</code><code class="descname">StackMethod</code><a class="headerlink" href="#vmifucalib.param.StackMethod" title="Permalink to this definition">¶</a></dt>
<dd><p>Flat fields combination method. (str; default: ‘MinMax’) [default=”MinMax”].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.KSigmaLow">
<code class="descclassname">vmifucalib.param.</code><code class="descname">KSigmaLow</code><a class="headerlink" href="#vmifucalib.param.KSigmaLow" title="Permalink to this definition">¶</a></dt>
<dd><p>Low threshold for K-sigma clipping method. (float; default: 5.0) [default=5.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.KSigmaHigh">
<code class="descclassname">vmifucalib.param.</code><code class="descname">KSigmaHigh</code><a class="headerlink" href="#vmifucalib.param.KSigmaHigh" title="Permalink to this definition">¶</a></dt>
<dd><p>High threshold for K-sigma clipping method. (float; default: 5.0) [default=5.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.MinRejection">
<code class="descclassname">vmifucalib.param.</code><code class="descname">MinRejection</code><a class="headerlink" href="#vmifucalib.param.MinRejection" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of lowest rejected values for rejection method. (long; default: 0) [default=0].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.MaxRejection">
<code class="descclassname">vmifucalib.param.</code><code class="descname">MaxRejection</code><a class="headerlink" href="#vmifucalib.param.MaxRejection" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of highest rejected values for rejection method. (long; default: 1) [default=1].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.BiasMethod">
<code class="descclassname">vmifucalib.param.</code><code class="descname">BiasMethod</code><a class="headerlink" href="#vmifucalib.param.BiasMethod" title="Permalink to this definition">¶</a></dt>
<dd><p>Bias removal method. (str; default: ‘Zmaster’) [default=”Zmaster”].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.CleanBadPixel">
<code class="descclassname">vmifucalib.param.</code><code class="descname">CleanBadPixel</code><a class="headerlink" href="#vmifucalib.param.CleanBadPixel" title="Permalink to this definition">¶</a></dt>
<dd><p>Bad pixel correction on master flat field. (bool; default: False) [default=False].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.ApplyTransmission">
<code class="descclassname">vmifucalib.param.</code><code class="descname">ApplyTransmission</code><a class="headerlink" href="#vmifucalib.param.ApplyTransmission" title="Permalink to this definition">¶</a></dt>
<dd><p>Apply transmission correction to extracted arc lamp spectra (bool; default: True) [default=True].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.MaxIdsRms">
<code class="descclassname">vmifucalib.param.</code><code class="descname">MaxIdsRms</code><a class="headerlink" href="#vmifucalib.param.MaxIdsRms" title="Permalink to this definition">¶</a></dt>
<dd><p>Maximum tolerated RMS of residuals in IDS fit (float; default: 2.0) [default=2.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.LineIdent">
<code class="descclassname">vmifucalib.param.</code><code class="descname">LineIdent</code><a class="headerlink" href="#vmifucalib.param.LineIdent" title="Permalink to this definition">¶</a></dt>
<dd><p>Arc line identification method. (str; default: ‘Blind’) [default=”Blind”].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.MaxTraceRejection">
<code class="descclassname">vmifucalib.param.</code><code class="descname">MaxTraceRejection</code><a class="headerlink" href="#vmifucalib.param.MaxTraceRejection" title="Permalink to this definition">¶</a></dt>
<dd><p>Maximum percentage of rejected positions in fiber spectra tracing (long; default: 33) [default=33].</p>
</dd></dl>
<dl class="attribute">
<dt id="vmifucalib.param.ComputeQC">
<code class="descclassname">vmifucalib.param.</code><code class="descname">ComputeQC</code><a class="headerlink" href="#vmifucalib.param.ComputeQC" title="Permalink to this definition">¶</a></dt>
<dd><p>Compute QC1 parameters (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">vmifucalib</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">"vmifucalib"</span><span class="p">)</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">AllowSingleFrames</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">StackMethod</span> <span class="o">=</span> <span class="s">"MinMax"</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">KSigmaLow</span> <span class="o">=</span> <span class="mf">5.0</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">KSigmaHigh</span> <span class="o">=</span> <span class="mf">5.0</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">MinRejection</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">MaxRejection</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">BiasMethod</span> <span class="o">=</span> <span class="s">"Zmaster"</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">CleanBadPixel</span> <span class="o">=</span> <span class="bp">False</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ApplyTransmission</span> <span class="o">=</span> <span class="bp">True</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">MaxIdsRms</span> <span class="o">=</span> <span class="mf">2.0</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">LineIdent</span> <span class="o">=</span> <span class="s">"Blind"</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">MaxTraceRejection</span> <span class="o">=</span> <span class="mi">33</span>
<span class="n">vmifucalib</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ComputeQC</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">vmifucalib</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">"vmifucalib"</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">vmifucalib</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">"AllowSingleFrames"</span><span class="p">:</span><span class="bp">True</span><span class="p">,</span> <span class="s">"StackMethod"</span><span class="p">:</span><span class="s">"MinMax"</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">ESO VIMOS Pipeline Team and VIMOS Consortium</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 VIMOS Instrument Pipeline
Copyright (C) 2002-2011 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: ESO VIMOS Pipeline Team and VIMOS Consortium <<a class="reference external" href="mailto:usd-help%40eso.org">usd-help<span>@</span>eso<span>.</span>org</a>></em></p>
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