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<li><a class="reference internal" href="#">The xsh_flexcomp 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-flexcomp-recipe">
<h1>The xsh_flexcomp recipe<a class="headerlink" href="#the-xsh-flexcomp-recipe" title="Permalink to this headline">¶</a></h1>
<dl class="data">
<dt id="xsh_flexcomp">
<code class="descname">xsh_flexcomp</code><a class="headerlink" href="#xsh_flexcomp" 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>Compute the flexure of the instrument</p>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>This recipe computes the flexure of the instrument and correct CAL files.</p>
<blockquote>
<div><dl class="docutils">
<dt>Input Frames :</dt>
<dd><ul class="first last simple">
<li>[UVB, VIS] One RAW frame (Format = RAW, Tag = AFF_ATT_arm)</li>
<li>[NIR] Two RAW frames ((Format = RAW, Tag = AFC_ATT_arm_ON,AFC_ATT_arm_OFF)</li>
<li>An arc line list (Format = TABLE, Tag = ARC_LINE_LIST_AFC_arm)</li>
<li>A spectral format table frame (Format = TABLE, Tag = SPECTRAL_FORMAT_TAB_arm)</li>
<li>[UVB,VIS] A master bias (Format = PRE, Tag = MASTER_BIAS_arm)</li>
<li>[UVB,VIS] A master dark (Format = PRE, Tag = MASTER_DARK_arm)</li>
<li>An order table frame (Format = TABLE, Tag = ORDER_TAB_EDGES_IFU_arm)</li>
</ul>
</dd>
</dl>
<ul class="simple">
<li>[OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)</li>
<li>[OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm)
- [poly mode] A wave solution frame (Format = TABLE, Tag = WAVE_TAB_2D_arm)
- [physical model mode] A model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_OPT_2D_arm)</li>
</ul>
<dl class="docutils">
<dt>Products :</dt>
<dd><ul class="first last simple">
<li>[poly mode] An updated wave solution frame (Format = TABLE, Tag = WAVE_TAB_AFC_arm)</li>
<li>[physical model mode] An updated model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_OPT_AFC_arm)</li>
<li>An updated order table frame (Format = TABLE, Tag = ORDER_TAB_AFC_IFU_arm)</li>
<li>[poly mode] A dispersion table frame (Format = TABLE, Tag = DISP_TAB_AFC_arm)</li>
</ul>
</dd>
</dl>
</div></blockquote>
</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_flexcomp"</em><span class="sig-paren">)</span></dt>
<dd><p>Create an object for the recipe xsh_flexcomp.</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_flexcomp</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_flexcomp"</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_flexcomp.param.keep_temp">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">keep_temp</code><a class="headerlink" href="#xsh_flexcomp.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_flexcomp.param.debug_level">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">debug_level</code><a class="headerlink" href="#xsh_flexcomp.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_flexcomp.param.time_stamp">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">time_stamp</code><a class="headerlink" href="#xsh_flexcomp.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_flexcomp.param.decode_bp">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">decode_bp</code><a class="headerlink" href="#xsh_flexcomp.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_flexcomp.param.pre_overscan_corr">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">pre_overscan_corr</code><a class="headerlink" href="#xsh_flexcomp.param.pre_overscan_corr" title="Permalink to this definition">¶</a></dt>
<dd><p>pre-overscan correction.0: no correction1: mean overscan correction2: mean prescan correction3: (mean pre+mean overscan)/2 correction (long; default: 1) [default=1].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_fit_win_hsize">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_fit_win_hsize</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_fit_win_hsize" title="Permalink to this definition">¶</a></dt>
<dd><p>Half window size (HWS) in pixels for the line 2D fitting window (total window size = 2*HWS+1) (long; default: 6) [default=6].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_search_win_hsize">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_search_win_hsize</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_search_win_hsize" title="Permalink to this definition">¶</a></dt>
<dd><p>Half window size (HWS) in pixels for the line search box around the expected position (total window size = 2*HWS+1) [bin units] (long; default: 3) [default=3].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_running_median_hsize">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_running_median_hsize</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_running_median_hsize" title="Permalink to this definition">¶</a></dt>
<dd><p>Half window size in pixels (HWS) for the running median box (long; default: 0) [default=0].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_wavesol_deg_lambda">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_wavesol_deg_lambda</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_wavesol_deg_lambda" title="Permalink to this definition">¶</a></dt>
<dd><p>Degree in lambda in the polynomial solution X=f(lambda,order,slit) and Y=f(lambda,order,slit) (POLY mode) (long; default: 5) [default=5].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_wavesol_deg_order">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_wavesol_deg_order</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_wavesol_deg_order" title="Permalink to this definition">¶</a></dt>
<dd><p>Degree in order in the polynomial solution X=f(lambda,order,slit) and Y=f(lambda,order,slit) (POLY mode) (long; default: 5) [default=5].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_min_sn">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_min_sn</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_min_sn" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimum signal-to-noise ratio to filter lines [xsh_predict: UVB,VIS=5,NIR=4; xsh_2dmap: UVB=3, VIS=6, NIR=10] (float; default: 5.0) [default=5.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_find_lines_center">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_find_lines_center</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_find_lines_center" title="Permalink to this definition">¶</a></dt>
<dd><p>Method used to find the center of the lines: gaussian, barycenter. Gaussian method applies a Gaussian fit to the line. Barycenter method computes the line centroid. (str; default: ‘gaussian’) [default=”gaussian”].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_clip_sigma">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_clip_sigma</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_clip_sigma" title="Permalink to this definition">¶</a></dt>
<dd><p>Kappa value in sigma clipping during the polynomial solution fit (POLY mode) (float; default: 2.0) [default=2.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_clip_niter">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_clip_niter</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_clip_niter" title="Permalink to this definition">¶</a></dt>
<dd><p>Number of iterations in sigma clipping during the polynomial solution fit (POLY mode) (long; default: 10) [default=10].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.detectarclines_clip_frac">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">detectarclines_clip_frac</code><a class="headerlink" href="#xsh_flexcomp.param.detectarclines_clip_frac" title="Permalink to this definition">¶</a></dt>
<dd><p>Minimal fractions of bad pixel allowed in sigma clipping duringthe polynomial solution fit (POLY mode) (float; default: 0.7) [default=0.7].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.dispersol_deg_x">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">dispersol_deg_x</code><a class="headerlink" href="#xsh_flexcomp.param.dispersol_deg_x" title="Permalink to this definition">¶</a></dt>
<dd><p>Degree in X in the polynomial dispersion solution lambda=f(X,Y) and slit=f(X,Y) (long; default: 4) [default=4].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.dispersol_deg_y">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">dispersol_deg_y</code><a class="headerlink" href="#xsh_flexcomp.param.dispersol_deg_y" title="Permalink to this definition">¶</a></dt>
<dd><p>Degree in Y in the polynomial dispersion solution lambda=f(X,Y) and slit=f(X,Y) (long; default: 5) [default=5].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.model_maxit">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">model_maxit</code><a class="headerlink" href="#xsh_flexcomp.param.model_maxit" title="Permalink to this definition">¶</a></dt>
<dd><p>Number/10 of annealing iterations if in physical model mode. (long; default: 1000) [default=1000].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.model_anneal_factor">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">model_anneal_factor</code><a class="headerlink" href="#xsh_flexcomp.param.model_anneal_factor" title="Permalink to this definition">¶</a></dt>
<dd><p>Multiplier applied to the automatic parameter ranges (i.e. when scenario!=0). For routine operations should be 1.0. (physical model mode). (float; default: 1.0) [default=1.0].</p>
</dd></dl>
<dl class="attribute">
<dt id="xsh_flexcomp.param.model_scenario">
<code class="descclassname">xsh_flexcomp.param.</code><code class="descname">model_scenario</code><a class="headerlink" href="#xsh_flexcomp.param.model_scenario" title="Permalink to this definition">¶</a></dt>
<dd><p>selects preset flag and range combinations appropriate to common scenarios: -1 - Only the position across the slit and camera focal length are open 0 - No scenario, input cfg flags and limits used. 1 - scenario appropriate for the startup recipe (large ranges for parameters affecting single ph exposures, dist coeff fixed) 2 - Like 1, but includes parameters affecting all ph positions 3 - Scenario for use in fine tuning cfg to match routine wavecal exposures. All parameters affecting 1ph exposures except dist coeffs are included and parameter ranges are small. (For use by flexcomp in 1ph case). 4 - Like 3 but includes parameters affecting all ph positions (Standard for use by flexcomp in 9ph case and 2dmap). 5 - Like 4 but includes also dist coeffs 6 - Just dist coeffs (and chipx, chipy) (long; default: 3) [default=3].</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_flexcomp</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_flexcomp"</span><span class="p">)</span>
<span class="n">xsh_flexcomp</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_flexcomp</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_flexcomp</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_flexcomp</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_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">pre_overscan_corr</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_fit_win_hsize</span> <span class="o">=</span> <span class="mi">6</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_search_win_hsize</span> <span class="o">=</span> <span class="mi">3</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_running_median_hsize</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_wavesol_deg_lambda</span> <span class="o">=</span> <span class="mi">5</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_wavesol_deg_order</span> <span class="o">=</span> <span class="mi">5</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_min_sn</span> <span class="o">=</span> <span class="mf">5.0</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_find_lines_center</span> <span class="o">=</span> <span class="s2">"gaussian"</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_clip_sigma</span> <span class="o">=</span> <span class="mf">2.0</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_clip_niter</span> <span class="o">=</span> <span class="mi">10</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">detectarclines_clip_frac</span> <span class="o">=</span> <span class="mf">0.7</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">dispersol_deg_x</span> <span class="o">=</span> <span class="mi">4</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">dispersol_deg_y</span> <span class="o">=</span> <span class="mi">5</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">model_maxit</span> <span class="o">=</span> <span class="mi">1000</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">model_anneal_factor</span> <span class="o">=</span> <span class="mf">1.0</span>
<span class="n">xsh_flexcomp</span><span class="o">.</span><span class="n">param</span><span class="o">.</span><span class="n">model_scenario</span> <span class="o">=</span> <span class="mi">3</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_flexcomp</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_flexcomp"</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_flexcomp</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</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 <<a class="reference external" href="mailto:amodigli%40eso.org">amodigli<span>@</span>eso<span>.</span>org</a>></em></p>
</div>
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