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<li><a class="reference internal" href="#">The xsh_mbias recipe</a><ul>
<li><a class="reference internal" href="#synopsis">Synopsis</a></li>
<li><a class="reference internal" href="#description">Description</a></li>
<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-xsh-mbias-recipe">
<h1>The xsh_mbias recipe<a class="headerlink" href="#the-xsh-mbias-recipe" title="Permalink to this headline">¶</a></h1>
<dl class="data">
<dt id="xsh_mbias">
<code class="descname">xsh_mbias</code><a class="headerlink" href="#xsh_mbias" 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>Create the master bias frame</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>This recipe creates a master bias frame by computing the median of all input bias frames.</p>
<dl class="docutils">
<dt>Input Frames :</dt>
<dd><ul class="first last simple">
<li>A set of n RAW frames (Format=RAW, n >=3, Tag = BIAS_arm)</li>
<li>[OPTIONAL] A map of non linear bad pixels (Format=QUP, Tag = BP_MAP_NL_arm)</li>
<li>[OPTIONAL] A map of reference bad pixels (Format = QUP,RAW, Tag = BP_MAP_RP_arm)</li>
</ul>
</dd>
<dt>Products :</dt>
<dd><ul class="first last simple">
<li>A master bias frame (Format=PRE, PRO.CATG = MASTER_BIAS_arm)</li>
</ul>
</dd>
</dl>
</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>"xsh_mbias"</em><span class="sig-paren">)</span></dt>
<dd><p>Create an object for the recipe xsh_mbias.</p>
</dd></dl>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cpl</span>
<span class="n">xsh_mbias</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="s2">"xsh_mbias"</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="xsh_mbias.param.keep_temp">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">keep_temp</code><a class="headerlink" href="#xsh_mbias.param.keep_temp" title="Permalink to this definition">¶</a></dt>
<dd><p>If ‘no’, temporary files are deleted. (str; default: ‘no’) [default=”no”].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.debug_level">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">debug_level</code><a class="headerlink" href="#xsh_mbias.param.debug_level" title="Permalink to this definition">¶</a></dt>
<dd><p>Additional xshooter debug level. One of ‘none’, ‘low’, ‘medium’, ‘high’ (str; default: ‘none’) [default=”none”].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.time_stamp">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">time_stamp</code><a class="headerlink" href="#xsh_mbias.param.time_stamp" title="Permalink to this definition">¶</a></dt>
<dd><p>Add timestamp to product file name. (bool; default: False) [default=False].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.decode_bp">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">decode_bp</code><a class="headerlink" href="#xsh_mbias.param.decode_bp" title="Permalink to this definition">¶</a></dt>
<dd><p>Integer representation of the bits to be considered bad when decoding the bad pixel mask pixel values. Most frequent codes relevant for the user: 0: good pixel, 8: pick-up noise, 16: cosmic-ray removed, 32: cosmic-ray unremoved, 128: calibration file defect, 256: hot pixel, 512: dark pixel, 4096: A/D converted saturation, 32768: non linear pixel, 1048576: extrapolated flux in NIR, 4194304: Interpolated flux during extraction. (long; default: 2144337919) [default=2144337919].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.stack_method">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">stack_method</code><a class="headerlink" href="#xsh_mbias.param.stack_method" title="Permalink to this definition">¶</a></dt>
<dd><p>Method used to build master frame. (str; default: ‘median’) [default=”median”].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.klow">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">klow</code><a class="headerlink" href="#xsh_mbias.param.klow" title="Permalink to this definition">¶</a></dt>
<dd><p>Kappa used to clip low level values, when method is set to ‘mean’ (float; default: 5.0) [default=5.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.khigh">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">khigh</code><a class="headerlink" href="#xsh_mbias.param.khigh" title="Permalink to this definition">¶</a></dt>
<dd><p>Kappa used to clip high level values, when method is set to ‘mean’ (float; default: 5.0) [default=5.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.fpn_llx">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">fpn_llx</code><a class="headerlink" href="#xsh_mbias.param.fpn_llx" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower left reference area X coordinate for Fixed Pattern Noise computation (long; default: 10) [default=10].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.fpn_lly">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">fpn_lly</code><a class="headerlink" href="#xsh_mbias.param.fpn_lly" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower left reference area Y coordinate for Fixed Pattern Noise computation (long; default: 10) [default=10].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.fpn_urx">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">fpn_urx</code><a class="headerlink" href="#xsh_mbias.param.fpn_urx" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper right reference area X coordinate for Fixed Pattern Noise computation (long; default: 1024) [default=1024].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.fpn_ury">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">fpn_ury</code><a class="headerlink" href="#xsh_mbias.param.fpn_ury" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper right reference area Y coordinate for Fixed Pattern Noise computation (long; default: 1024) [default=1024].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.fpn_hsize">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">fpn_hsize</code><a class="headerlink" href="#xsh_mbias.param.fpn_hsize" title="Permalink to this definition">¶</a></dt>
<dd><p>Sample size for Fixed Pattern Noise computation (long; default: 10) [default=10].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.fpn_nsamples">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">fpn_nsamples</code><a class="headerlink" href="#xsh_mbias.param.fpn_nsamples" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of sampling points for Fixed Pattern Noise computation (long; default: 100) [default=100].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ron_method">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ron_method</code><a class="headerlink" href="#xsh_mbias.param.ron_method" title="Permalink to this definition">¶</a></dt>
<dd><p>RON computation method (str; default: ‘ALL’) [default=”ALL”].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.random_sizex">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">random_sizex</code><a class="headerlink" href="#xsh_mbias.param.random_sizex" title="Permalink to this definition">¶</a></dt>
<dd><p>Region X size for random computation (long; default: 10) [default=10].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.random_nsamples">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">random_nsamples</code><a class="headerlink" href="#xsh_mbias.param.random_nsamples" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of random samples (long; default: 100) [default=100].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref1_llx">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref1_llx</code><a class="headerlink" href="#xsh_mbias.param.ref1_llx" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower left X of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref1_lly">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref1_lly</code><a class="headerlink" href="#xsh_mbias.param.ref1_lly" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower left Y of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref1_urx">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref1_urx</code><a class="headerlink" href="#xsh_mbias.param.ref1_urx" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper right X of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref1_ury">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref1_ury</code><a class="headerlink" href="#xsh_mbias.param.ref1_ury" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper right Y of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref2_llx">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref2_llx</code><a class="headerlink" href="#xsh_mbias.param.ref2_llx" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower left X of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref2_lly">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref2_lly</code><a class="headerlink" href="#xsh_mbias.param.ref2_lly" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower left Y of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref2_urx">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref2_urx</code><a class="headerlink" href="#xsh_mbias.param.ref2_urx" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper right X of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.ref2_ury">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">ref2_ury</code><a class="headerlink" href="#xsh_mbias.param.ref2_ury" title="Permalink to this definition">¶</a></dt>
<dd><p>Upper right Y of reference region (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.stacking_ks_low">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">stacking_ks_low</code><a class="headerlink" href="#xsh_mbias.param.stacking_ks_low" title="Permalink to this definition">¶</a></dt>
<dd><p>Lower value of kappa-sigma clip in stacking (long; default: 3) [default=3].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.stacking_ks_iter">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">stacking_ks_iter</code><a class="headerlink" href="#xsh_mbias.param.stacking_ks_iter" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of iterations in kappa-sigma clip in stacking (long; default: 25) [default=25].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.struct_refx">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">struct_refx</code><a class="headerlink" href="#xsh_mbias.param.struct_refx" title="Permalink to this definition">¶</a></dt>
<dd><p>Reference X value to compute structure (long; default: -1) [default=-1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_mbias.param.struct_refy">
<code class="descclassname">xsh_mbias.param.</code><code class="descname">struct_refy</code><a class="headerlink" href="#xsh_mbias.param.struct_refy" title="Permalink to this definition">¶</a></dt>
<dd><p>Reference Y value to compute structure (long; default: -1) [default=-1].</p>
</dd></dl>
<p>The following code snippet shows the default settings for the available
parameters.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cpl</span>
<span class="n">xsh_mbias</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="s2">"xsh_mbias"</span><span class="p">)</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">keep_temp</span> <span class="o">=</span> <span class="s2">"no"</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">debug_level</span> <span class="o">=</span> <span class="s2">"none"</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">time_stamp</span> <span class="o">=</span> <span class="kc">False</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">decode_bp</span> <span class="o">=</span> <span class="mi">2144337919</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">stack_method</span> <span class="o">=</span> <span class="s2">"median"</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">klow</span> <span class="o">=</span> <span class="mf">5.0</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">khigh</span> <span class="o">=</span> <span class="mf">5.0</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">fpn_llx</span> <span class="o">=</span> <span class="mi">10</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">fpn_lly</span> <span class="o">=</span> <span class="mi">10</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">fpn_urx</span> <span class="o">=</span> <span class="mi">1024</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">fpn_ury</span> <span class="o">=</span> <span class="mi">1024</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">fpn_hsize</span> <span class="o">=</span> <span class="mi">10</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">fpn_nsamples</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ron_method</span> <span class="o">=</span> <span class="s2">"ALL"</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">random_sizex</span> <span class="o">=</span> <span class="mi">10</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">random_nsamples</span> <span class="o">=</span> <span class="mi">100</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref1_llx</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref1_lly</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref1_urx</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref1_ury</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref2_llx</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref2_lly</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref2_urx</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">ref2_ury</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">stacking_ks_low</span> <span class="o">=</span> <span class="mi">3</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">stacking_ks_iter</span> <span class="o">=</span> <span class="mi">25</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">struct_refx</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">xsh_mbias</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">struct_refy</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</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-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">cpl</span>
<span class="n">xsh_mbias</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="s2">"xsh_mbias"</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">xsh_mbias</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="s2">"keep_temp"</span><span class="p">:</span><span class="s2">"no"</span><span class="p">,</span> <span class="s2">"debug_level"</span><span class="p">:</span><span class="s2">"none"</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:amodigli%40eso.org">P<span>.</span>Goldoni, L<span>.</span>Guglielmi, R<span>.</span> Haigron, F<span>.</span> Royer, D<span>.</span> Bramich, A<span>.</span> Modigliani</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 part of the X-shooter Instrument Pipeline
Copyright (C) 2006 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., 59 Temple Place, Suite 330, Boston,
MA 02111-1307 USA</p>
<p><em>Code author: P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <<a class="reference external" href="mailto:amodigli%40eso.org">amodigli<span>@</span>eso<span>.</span>org</a>></em></p>
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