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--- for_developers/SphinxDoc/_build/html/code.html	(revision 25b14bea5de21f28364c210382513c1c9b792d61)
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@@ -0,0 +1,415 @@
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Auto Generated Documentation &#8212; flex_extract_test 7.1 documentation</title>
+    <link rel="stylesheet" href="_static/classic.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript">
+      var DOCUMENTATION_OPTIONS = {
+        URL_ROOT:    './',
+        VERSION:     '7.1',
+        COLLAPSE_INDEX: false,
+        FILE_SUFFIX: '.html',
+        HAS_SOURCE:  true,
+        SOURCELINK_SUFFIX: '.txt'
+      };
+    </script>
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+    <script type="text/javascript" src="_static/underscore.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="prev" title="Welcome to flex_extract_test’s documentation!" href="index.html" /> 
+  </head>
+  <body>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             accesskey="I">index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="Welcome to flex_extract_test’s documentation!"
+             accesskey="P">previous</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">flex_extract_test 7.1 documentation</a> &#187;</li> 
+      </ul>
+    </div>  
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+          <div class="body" role="main">
+            
+  <div class="section" id="module-Tools">
+<span id="auto-generated-documentation"></span><h1>Auto Generated Documentation<a class="headerlink" href="#module-Tools" title="Permalink to this headline">¶</a></h1>
+<dl class="function">
+<dt id="Tools.cleanup">
+<code class="descclassname">Tools.</code><code class="descname">cleanup</code><span class="sig-paren">(</span><em>c</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#cleanup"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.cleanup" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Remove all files from intermediate directory
+(inputdir from control file).</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt>c: instance of class Control</dt>
+<dd><p class="first">Contains all the parameters of control files, which are e.g.:
+DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
+STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
+LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
+OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
+ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
+MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
+DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS</p>
+<p class="last">For more information about format and content of the parameter
+see documentation.</p>
+</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd>&lt;nothing&gt;</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.getListAsString">
+<code class="descclassname">Tools.</code><code class="descname">getListAsString</code><span class="sig-paren">(</span><em>listobj</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#getListAsString"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.getListAsString" title="Permalink to this definition">¶</a></dt>
+<dd><p>&#64;Description:</p>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.init128">
+<code class="descclassname">Tools.</code><code class="descname">init128</code><span class="sig-paren">(</span><em>fn</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#init128"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.init128" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Opens and reads the grib file with table 128 information.</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt>fn: string</dt>
+<dd>Path to file of ECMWF grib table number 128.</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd><dl class="first last docutils">
+<dt>table128: dictionary</dt>
+<dd>Contains the ECMWF grib table 128 information.
+The key is the parameter number and the value is the
+short name of the parameter.</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.interpret_args_and_control">
+<code class="descclassname">Tools.</code><code class="descname">interpret_args_and_control</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#interpret_args_and_control"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.interpret_args_and_control" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Assigns the command line arguments and reads control file
+content. Apply default values for non mentioned arguments.</dd>
+<dt>&#64;Input:</dt>
+<dd>&lt;nothing&gt;</dd>
+<dt>&#64;Return:</dt>
+<dd><dl class="first last docutils">
+<dt>args: instance of ArgumentParser</dt>
+<dd>Contains the commandline arguments from script/program call.</dd>
+<dt>c: instance of class Control</dt>
+<dd>Contains all necessary information of a control file. The parameters
+are: DAY1, DAY2, DTIME, MAXSTEP, TYPE, TIME, STEP, CLASS, STREAM,
+NUMBER, EXPVER, GRID, LEFT, LOWER, UPPER, RIGHT, LEVEL, LEVELIST,
+RESOL, GAUSS, ACCURACY, OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA,
+SMOOTH, FORMAT, ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS,
+ECFSDIR, MAILOPS, MAILFAIL, GRIB2FLEXPART, DEBUG, INPUTDIR,
+OUTPUTDIR, FLEXPART_ROOT_SCRIPTS
+For more information about format and content of the parameter see
+documentation.</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.myerror">
+<code class="descclassname">Tools.</code><code class="descname">myerror</code><span class="sig-paren">(</span><em>c</em>, <em>message='ERROR'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#myerror"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.myerror" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Prints a specified error message which can be passed to the function
+before exiting the program.</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt>c: instance of class Control</dt>
+<dd><p class="first">Contains all the parameters of control files, which are e.g.:
+DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
+STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
+LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
+OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
+ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
+MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
+DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS</p>
+<p class="last">For more information about format and content of the parameter
+see documentation.</p>
+</dd>
+<dt>message: string, optional</dt>
+<dd>Error message. Default value is “ERROR”.</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd>&lt;nothing&gt;</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.normalexit">
+<code class="descclassname">Tools.</code><code class="descname">normalexit</code><span class="sig-paren">(</span><em>c</em>, <em>message='Done!'</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#normalexit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.normalexit" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Prints a specific exit message which can be passed to the function.</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt>c: instance of class Control</dt>
+<dd><p class="first">Contains all the parameters of control files, which are e.g.:
+DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
+STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
+LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
+OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
+ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
+MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR, BASETIME
+DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS</p>
+<p class="last">For more information about format and content of the parameter
+see documentation.</p>
+</dd>
+<dt>message: string, optional</dt>
+<dd>Message for exiting program. Default value is “Done!”.</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd>&lt;nothing&gt;</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.product">
+<code class="descclassname">Tools.</code><code class="descname">product</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwds</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#product"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.product" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd><p class="first">This method is taken from an example at the ECMWF wiki website.
+<a class="reference external" href="https://software.ecmwf.int/wiki/display/GRIB/index.py">https://software.ecmwf.int/wiki/display/GRIB/index.py</a>; 2018-03-16</p>
+<p>This method combines the single characters of the passed arguments
+with each other. So that each character of each argument value
+will be combined with each character of the other arguments as a tuple.</p>
+<p class="last">Example:
+product(‘ABCD’, ‘xy’) –&gt; Ax Ay Bx By Cx Cy Dx Dy
+product(range(2), repeat = 3) –&gt; 000 001 010 011 100 101 110 111</p>
+</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt><a href="#id1"><span class="problematic" id="id2">*</span></a>args: tuple</dt>
+<dd>Positional arguments (arbitrary number).</dd>
+<dt><a href="#id3"><span class="problematic" id="id4">**</span></a>kwds: dictionary</dt>
+<dd>Contains all the keyword arguments from <a href="#id5"><span class="problematic" id="id6">*</span></a>args.</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd><dl class="first last docutils">
+<dt>prod: tuple</dt>
+<dd>Return will be done with “yield”. A tuple of combined arguments.
+See example in description above.</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.silentremove">
+<code class="descclassname">Tools.</code><code class="descname">silentremove</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#silentremove"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.silentremove" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Removes the file which name is passed to the function if
+it exists. The function does not fail if the file does not
+exist.</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt>filename: string</dt>
+<dd>The name of the file to be removed without notification.</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd>&lt;nothing&gt;</dd>
+</dl>
+</dd></dl>
+
+<dl class="function">
+<dt id="Tools.toparamId">
+<code class="descclassname">Tools.</code><code class="descname">toparamId</code><span class="sig-paren">(</span><em>pars</em>, <em>table</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/Tools.html#toparamId"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#Tools.toparamId" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Transform parameter names to parameter ids
+with ECMWF grib table 128.</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt>pars: string</dt>
+<dd>Addpar argument from control file in the format of
+parameter names instead of ids. The parameter short
+names are sepearted with “/” and they are passed as
+one single string.</dd>
+<dt>table: dictionary</dt>
+<dd>Contains the ECMWF grib table 128 information.
+The key is the parameter number and the value is the
+short name of the parameter.</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd><dl class="first last docutils">
+<dt>ipar: list of integer</dt>
+<dd>List of addpar parameters from control file transformed to
+parameter ids in the format of integer.</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="class">
+<dt id="Tools.Control">
+<em class="property">class </em><code class="descclassname">Tools.</code><code class="descname">Control</code><a class="headerlink" href="#Tools.Control" title="Permalink to this definition">¶</a></dt>
+<dd><p>&#64;Author: Leopold Haimberger (University of Vienna)</p>
+<p>&#64;Date: November 2015</p>
+<dl class="docutils">
+<dt>&#64;ChangeHistory:</dt>
+<dd><dl class="first last docutils">
+<dt>February 2018 - Anne Philipp (University of Vienna):</dt>
+<dd><ul class="first last simple">
+<li>applied PEP8 style guide</li>
+<li>added documentation</li>
+<li>applied some minor modifications in programming style/structure</li>
+<li>moved Control class in a file for its own</li>
+</ul>
+</dd>
+</dl>
+</dd>
+<dt>&#64;License:</dt>
+<dd><ol class="first upperalpha simple" start="3">
+<li>Copyright 2015-2018.</li>
+</ol>
+<p class="last">This software is licensed under the terms of the Apache Licence Version 2.0
+which can be obtained at <a class="reference external" href="http://www.apache.org/licenses/LICENSE-2.0">http://www.apache.org/licenses/LICENSE-2.0</a>.</p>
+</dd>
+<dt>&#64;Requirements:</dt>
+<dd>A standard python 2.6 or 2.7 installation</dd>
+<dt>&#64;Description:</dt>
+<dd>The Control files are the steering part of the FLEXPART extraction
+software. All necessary parameters needed to retrieve the data fields
+from the MARS archive for driving FLEXPART are set in a Control file.
+Some specific parameters like the start and end dates can be overwritten
+by the command line parameters, but in generel all parameters needed
+for a complete set of fields for FLEXPART can be set in the Control files.</dd>
+</dl>
+<dl class="class">
+<dt id="Tools.Control.Control">
+<em class="property">class </em><code class="descname">Control</code><span class="sig-paren">(</span><em>filename</em><span class="sig-paren">)</span><a class="headerlink" href="#Tools.Control.Control" title="Permalink to this definition">¶</a></dt>
+<dd><p>Class containing the information of the ECMWFDATA control file.</p>
+<p>Contains all the parameters of control files, which are e.g.:
+DAY1(start_date), DAY2(end_date), DTIME, MAXSTEP, TYPE, TIME,
+STEP, CLASS(marsclass), STREAM, NUMBER, EXPVER, GRID, LEFT,
+LOWER, UPPER, RIGHT, LEVEL, LEVELIST, RESOL, GAUSS, ACCURACY,
+OMEGA, OMEGADIFF, ETA, ETADIFF, DPDETA, SMOOTH, FORMAT,
+ADDPAR, WRF, CWC, PREFIX, ECSTORAGE, ECTRANS, ECFSDIR,
+MAILOPS, MAILFAIL, GRIB2FLEXPART, FLEXPARTDIR,
+BASETIME, DATE_CHUNK, DEBUG, INPUTDIR, OUTPUTDIR, FLEXPART_ROOT_SCRIPTS</p>
+<p>For more information about format and content of the parameter
+see documentation.</p>
+<dl class="method">
+<dt id="Tools.Control.Control.tolist">
+<code class="descname">tolist</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#Tools.Control.Control.tolist" title="Permalink to this definition">¶</a></dt>
+<dd><dl class="docutils">
+<dt>&#64;Description:</dt>
+<dd>Just generates a list of strings containing the attributes and
+assigned values except the attributes “_expanded”, “exedir”,
+“ecmwfdatadir” and “flexpart_root_scripts”.</dd>
+<dt>&#64;Input:</dt>
+<dd><dl class="first last docutils">
+<dt>self: instance of Control class</dt>
+<dd>Description see class documentation.</dd>
+</dl>
+</dd>
+<dt>&#64;Return:</dt>
+<dd><dl class="first last docutils">
+<dt>l: list</dt>
+<dd>A sorted list of the all Control class attributes with
+their values except the attributes “_expanded”, “exedir”,
+“ecmwfdatadir” and “flexpart_root_scripts”.</dd>
+</dl>
+</dd>
+</dl>
+</dd></dl>
+
+</dd></dl>
+
+<dl class="attribute">
+<dt id="Tools.Control.Tools">
+<code class="descname">Tools</code><em class="property"> = &lt;module 'Tools' from '/nas16/tmc/Anne/Interpolation/flexextract/flexextract/python/Tools.pyc'&gt;</em><a class="headerlink" href="#Tools.Control.Tools" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="Tools.Control.inspect">
+<code class="descname">inspect</code><em class="property"> = &lt;module 'inspect' from '/opt/anaconda/lib/python2.7/inspect.pyc'&gt;</em><a class="headerlink" href="#Tools.Control.inspect" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+<dl class="attribute">
+<dt id="Tools.Control.os">
+<code class="descname">os</code><em class="property"> = &lt;module 'os' from '/opt/anaconda/lib/python2.7/os.pyc'&gt;</em><a class="headerlink" href="#Tools.Control.os" title="Permalink to this definition">¶</a></dt>
+<dd></dd></dl>
+
+</dd></dl>
+
+</div>
+
+
+          </div>
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+  <h4>Previous topic</h4>
+  <p class="topless"><a href="index.html"
+                        title="previous chapter">Welcome to flex_extract_test’s documentation!</a></p>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <form class="search" action="search.html" method="get">
+      <div><input type="text" name="q" /></div>
+      <div><input type="submit" value="Go" /></div>
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="related" role="navigation" aria-label="related navigation">
+      <h3>Navigation</h3>
+      <ul>
+        <li class="right" style="margin-right: 10px">
+          <a href="genindex.html" title="General Index"
+             >index</a></li>
+        <li class="right" >
+          <a href="py-modindex.html" title="Python Module Index"
+             >modules</a> |</li>
+        <li class="right" >
+          <a href="index.html" title="Welcome to flex_extract_test’s documentation!"
+             >previous</a> |</li>
+        <li class="nav-item nav-item-0"><a href="index.html">flex_extract_test 7.1 documentation</a> &#187;</li> 
+      </ul>
+    </div>
+    <div class="footer" role="contentinfo">
+        &#169; Copyright 2018, AP.
+      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.6.6.
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+</html>
