source: flex_extract.git/Documentation/html/_modules/prepare_flexpart.html @ eca358d

ctbtodev
Last change on this file since eca358d was eca358d, checked in by Anne Philipp <anne.philipp@…>, 4 years ago

updated online documentation with links on index page
  • Property mode set to 100644
File size: 23.0 KB
Line 
1
2
3<!DOCTYPE html>
4<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
5<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
6<head>
7  <meta charset="utf-8">
8 
9  <meta name="viewport" content="width=device-width, initial-scale=1.0">
10 
11  <title>prepare_flexpart &mdash; flex_extract 7.1 alpha documentation</title>
12 
13
14 
15 
16 
17 
18
19 
20  <script type="text/javascript" src="../_static/js/modernizr.min.js"></script>
21 
22   
23      <script type="text/javascript" id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
24        <script type="text/javascript" src="../_static/jquery.js"></script>
25        <script type="text/javascript" src="../_static/underscore.js"></script>
26        <script type="text/javascript" src="../_static/doctools.js"></script>
27        <script type="text/javascript" src="../_static/language_data.js"></script>
28        <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
29   
30    <script type="text/javascript" src="../_static/js/theme.js"></script>
31
32   
33
34 
35  <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
36  <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
37  <link rel="stylesheet" href="../_static/css/custom.css" type="text/css" />
38  <link rel="stylesheet" href="../_static/css/theme_overrides.css" type="text/css" />
39    <link rel="index" title="Index" href="../genindex.html" />
40    <link rel="search" title="Search" href="../search.html" /> 
41</head>
42
43<body class="wy-body-for-nav">
44
45   
46  <div class="wy-grid-for-nav">
47   
48    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
49      <div class="wy-side-scroll">
50        <div class="wy-side-nav-search" >
51         
52
53         
54            <a href="../index.html" class="icon icon-home"> flex_extract
55         
56
57         
58          </a>
59
60         
61           
62           
63              <div class="version">
64                7.1
65              </div>
66           
67         
68
69         
70<div role="search">
71  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
72    <input type="text" name="q" placeholder="Search docs" />
73    <input type="hidden" name="check_keywords" value="yes" />
74    <input type="hidden" name="area" value="default" />
75  </form>
76</div>
77
78         
79        </div>
80
81        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
82         
83           
84           
85             
86           
87           
88              <p class="caption"><span class="caption-text">Table of Contents:</span></p>
89<ul>
90<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
91<li class="toctree-l1"><a class="reference internal" href="../quick_start.html">Quick Start</a></li>
92<li class="toctree-l1"><a class="reference internal" href="../ecmwf_data.html">ECMWF Data</a></li>
93<li class="toctree-l1"><a class="reference internal" href="../documentation.html">Documentation</a></li>
94<li class="toctree-l1"><a class="reference internal" href="../evaluation.html">Evaluation</a></li>
95<li class="toctree-l1"><a class="reference internal" href="../dev_guide.html">Developer Guide</a></li>
96<li class="toctree-l1"><a class="reference internal" href="../changelog.html">Changelog</a></li>
97<li class="toctree-l1"><a class="reference internal" href="../support.html">Support</a></li>
98<li class="toctree-l1"><a class="reference internal" href="../Support/faq.html">FAQ - Frequently asked questions</a></li>
99<li class="toctree-l1"><a class="reference internal" href="../authors.html">Developer Team</a></li>
100</ul>
101
102           
103         
104        </div>
105      </div>
106    </nav>
107
108    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
109
110     
111      <nav class="wy-nav-top" aria-label="top navigation">
112       
113          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
114          <a href="../index.html">flex_extract</a>
115       
116      </nav>
117
118
119      <div class="wy-nav-content">
120       
121        <div class="rst-content">
122       
123         
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139<div role="navigation" aria-label="breadcrumbs navigation">
140
141  <ul class="wy-breadcrumbs">
142   
143      <li><a href="../index.html">Docs</a> &raquo;</li>
144       
145          <li><a href="index.html">Module code</a> &raquo;</li>
146       
147      <li>prepare_flexpart</li>
148   
149   
150      <li class="wy-breadcrumbs-aside">
151       
152      </li>
153   
154  </ul>
155
156 
157  <hr/>
158</div>
159          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
160           <div itemprop="articleBody">
161           
162  <h1>Source code for prepare_flexpart</h1><div class="highlight"><pre>
163<span></span><span class="ch">#!/usr/bin/env python3</span>
164<span class="c1"># -*- coding: utf-8 -*-</span>
165<span class="c1">#*******************************************************************************</span>
166<span class="c1"># @Author: Anne Fouilloux (University of Oslo)</span>
167<span class="c1">#</span>
168<span class="c1"># @Date: October 2014</span>
169<span class="c1">#</span>
170<span class="c1"># @Change History:</span>
171<span class="c1">#</span>
172<span class="c1">#    November 2015 - Leopold Haimberger (University of Vienna):</span>
173<span class="c1">#        - using the WebAPI also for general MARS retrievals</span>
174<span class="c1">#        - job submission on ecgate and cca</span>
175<span class="c1">#        - job templates suitable for twice daily operational dissemination</span>
176<span class="c1">#        - dividing retrievals of longer periods into digestable chunks</span>
177<span class="c1">#        - retrieve also longer term forecasts, not only analyses and</span>
178<span class="c1">#          short term forecast data</span>
179<span class="c1">#        - conversion into GRIB2</span>
180<span class="c1">#        - conversion into .fp format for faster execution of FLEXPART</span>
181<span class="c1">#</span>
182<span class="c1">#    February 2018 - Anne Philipp (University of Vienna):</span>
183<span class="c1">#        - applied PEP8 style guide</span>
184<span class="c1">#        - added documentation</span>
185<span class="c1">#        - minor changes in programming style for consistence</span>
186<span class="c1">#        - BUGFIX: removed call of clean_up-Function after call of</span>
187<span class="c1">#               prepareFlexpart in main since it is already called in</span>
188<span class="c1">#               prepareFlexpart at the end!</span>
189<span class="c1">#        - created function main and moved the two function calls for</span>
190<span class="c1">#          arguments and prepare_flexpart into it</span>
191<span class="c1">#</span>
192<span class="c1"># @License:</span>
193<span class="c1">#    (C) Copyright 2014-2019.</span>
194<span class="c1">#    Anne Philipp, Leopold Haimberger</span>
195<span class="c1">#</span>
196<span class="c1">#    SPDX-License-Identifier: CC-BY-4.0</span>
197<span class="c1">#</span>
198<span class="c1">#    This work is licensed under the Creative Commons Attribution 4.0</span>
199<span class="c1">#    International License. To view a copy of this license, visit</span>
200<span class="c1">#    http://creativecommons.org/licenses/by/4.0/ or send a letter to</span>
201<span class="c1">#    Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</span>
202<span class="c1"># *******************************************************************************</span>
203<span class="c1"># pylint: disable=ungrouped-imports</span>
204<span class="c1"># not necessary that we group the imports</span>
205<span class="sd">&#39;&#39;&#39;This script prepares the final version of the grib files which are</span>
206<span class="sd">then used by FLEXPART.</span>
207
208<span class="sd">It converts the bunch of grib files extracted via get_mars_data before,</span>
209<span class="sd">by doing the necessary conversion to get consistent grids or the</span>
210<span class="sd">disaggregation of flux data. Finally, the data fields are combined</span>
211<span class="sd">in files per available hour with the naming convention xxYYMMDDHH,</span>
212<span class="sd">where xx should be 2 arbitrary letters (mostly xx is chosen to be &quot;EN&quot;).</span>
213
214<span class="sd">This file can also be imported as a module which then contains the following</span>
215<span class="sd">functions:</span>
216
217<span class="sd">    * main</span>
218<span class="sd">    * prepare_flexpart</span>
219
220<span class="sd">Type: prepare_flexpart.py --help</span>
221<span class="sd">to get information about command line parameters.</span>
222<span class="sd">Read the documentation for usage instructions.</span>
223<span class="sd">&#39;&#39;&#39;</span>
224
225<span class="c1"># ------------------------------------------------------------------------------</span>
226<span class="c1"># MODULES</span>
227<span class="c1"># ------------------------------------------------------------------------------</span>
228<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">print_function</span>
229
230<span class="kn">import</span> <span class="nn">datetime</span>
231<span class="kn">import</span> <span class="nn">os</span>
232<span class="kn">import</span> <span class="nn">inspect</span>
233<span class="kn">import</span> <span class="nn">sys</span>
234
235<span class="c1"># software specific classes and modules from flex_extract</span>
236<span class="c1"># add path to local main python path for flex_extract to get full access</span>
237<span class="n">sys</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span>
238    <span class="n">inspect</span><span class="o">.</span><span class="n">getfile</span><span class="p">(</span><span class="n">inspect</span><span class="o">.</span><span class="n">currentframe</span><span class="p">())))</span> <span class="o">+</span> <span class="s1">&#39;/../&#39;</span><span class="p">)</span>
239<span class="c1"># pylint: disable=wrong-import-position</span>
240<span class="c1">#import _config</span>
241<span class="kn">from</span> <span class="nn">Mods.checks</span> <span class="k">import</span> <span class="n">check_ppid</span>
242<span class="kn">from</span> <span class="nn">Classes.UioFiles</span> <span class="k">import</span> <span class="n">UioFiles</span>
243<span class="c1">#from Classes.ControlFile import ControlFile</span>
244<span class="kn">from</span> <span class="nn">Mods.tools</span> <span class="k">import</span> <span class="p">(</span><span class="n">setup_controldata</span><span class="p">,</span> <span class="n">clean_up</span><span class="p">,</span> <span class="n">make_dir</span><span class="p">,</span> <span class="n">normal_exit</span><span class="p">)</span>
245<span class="kn">from</span> <span class="nn">Classes.EcFlexpart</span> <span class="k">import</span> <span class="n">EcFlexpart</span>
246<span class="c1"># pylint: enable=wrong-import-position</span>
247
248<span class="c1"># ------------------------------------------------------------------------------</span>
249<span class="c1"># FUNCTION</span>
250<span class="c1"># ------------------------------------------------------------------------------</span>
251<div class="viewcode-block" id="main"><a class="viewcode-back" href="../Documentation/Api/api_python.html#prepare_flexpart.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
252    <span class="sd">&#39;&#39;&#39;Controls the program to prepare flexpart input files from mars data.</span>
253
254<span class="sd">    This is done if it is called directly from command line.</span>
255<span class="sd">    Then it also takes program call arguments and control file input.</span>
256
257<span class="sd">    Parameters</span>
258<span class="sd">    ----------</span>
259
260<span class="sd">    Return</span>
261<span class="sd">    ------</span>
262
263<span class="sd">    &#39;&#39;&#39;</span>
264
265    <span class="n">c</span><span class="p">,</span> <span class="n">ppid</span><span class="p">,</span> <span class="n">_</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">setup_controldata</span><span class="p">()</span>
266    <span class="n">prepare_flexpart</span><span class="p">(</span><span class="n">ppid</span><span class="p">,</span> <span class="n">c</span><span class="p">)</span>
267    <span class="n">normal_exit</span><span class="p">(</span><span class="s1">&#39;Preparing FLEXPART output files: Done!&#39;</span><span class="p">)</span>
268
269    <span class="k">return</span></div>
270
271<div class="viewcode-block" id="prepare_flexpart"><a class="viewcode-back" href="../Documentation/Api/api_python.html#prepare_flexpart.prepare_flexpart">[docs]</a><span class="k">def</span> <span class="nf">prepare_flexpart</span><span class="p">(</span><span class="n">ppid</span><span class="p">,</span> <span class="n">c</span><span class="p">):</span>
272    <span class="sd">&#39;&#39;&#39;Converts the mars data into flexpart ready input files.</span>
273
274<span class="sd">    Specific data fields are converted to a different grid and the flux</span>
275<span class="sd">    data are going to be disaggregated. The data fields are collected by</span>
276<span class="sd">    hour and stored in a file with a specific FLEXPART relevant naming</span>
277<span class="sd">    convention.</span>
278
279<span class="sd">    Parameters</span>
280<span class="sd">    ----------</span>
281<span class="sd">    ppid : int</span>
282<span class="sd">        Contains the ppid number of the current ECMWF job. It will be None if</span>
283<span class="sd">        the method was called within this module.</span>
284
285<span class="sd">    c : ControlFile</span>
286<span class="sd">        Contains all the parameters of CONTROL file and</span>
287<span class="sd">        command line.</span>
288
289<span class="sd">    Return</span>
290<span class="sd">    ------</span>
291
292<span class="sd">    &#39;&#39;&#39;</span>
293    <span class="n">check_ppid</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">ppid</span><span class="p">)</span>
294
295    <span class="c1"># create the start and end date</span>
296    <span class="n">start</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">date</span><span class="p">(</span><span class="n">year</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">start_date</span><span class="p">[:</span><span class="mi">4</span><span class="p">]),</span>
297                          <span class="n">month</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">start_date</span><span class="p">[</span><span class="mi">4</span><span class="p">:</span><span class="mi">6</span><span class="p">]),</span>
298                          <span class="n">day</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">start_date</span><span class="p">[</span><span class="mi">6</span><span class="p">:]))</span>
299
300    <span class="n">end</span> <span class="o">=</span> <span class="n">datetime</span><span class="o">.</span><span class="n">date</span><span class="p">(</span><span class="n">year</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">end_date</span><span class="p">[:</span><span class="mi">4</span><span class="p">]),</span>
301                        <span class="n">month</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">end_date</span><span class="p">[</span><span class="mi">4</span><span class="p">:</span><span class="mi">6</span><span class="p">]),</span>
302                        <span class="n">day</span><span class="o">=</span><span class="nb">int</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">end_date</span><span class="p">[</span><span class="mi">6</span><span class="p">:]))</span>
303
304    <span class="c1"># if basetime is 00</span>
305    <span class="c1"># assign starting date minus 1 day</span>
306    <span class="c1"># since we need the 12 hours upfront</span>
307    <span class="c1"># (the day before from 12 UTC to current day 00 UTC)</span>
308    <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">basetime</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
309        <span class="n">start</span> <span class="o">=</span> <span class="n">start</span> <span class="o">-</span> <span class="n">datetime</span><span class="o">.</span><span class="n">timedelta</span><span class="p">(</span><span class="n">days</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
310
311    <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;Prepare &#39;</span> <span class="o">+</span> <span class="n">start</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">&quot;%Y%m</span><span class="si">%d</span><span class="s2">&quot;</span><span class="p">)</span> <span class="o">+</span>
312          <span class="s1">&#39;/to/&#39;</span> <span class="o">+</span> <span class="n">end</span><span class="o">.</span><span class="n">strftime</span><span class="p">(</span><span class="s2">&quot;%Y%m</span><span class="si">%d</span><span class="s2">&quot;</span><span class="p">))</span>
313
314    <span class="c1"># create output dir if necessary</span>
315    <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">outputdir</span><span class="p">):</span>
316        <span class="n">make_dir</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">outputdir</span><span class="p">)</span>
317
318    <span class="c1"># get all files with flux data to be deaccumulated</span>
319    <span class="n">inputfiles</span> <span class="o">=</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">,</span> <span class="s1">&#39;*OG_acc_SL*.&#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">ppid</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;.*&#39;</span><span class="p">)</span>
320
321    <span class="c1"># deaccumulate the flux data</span>
322    <span class="n">flexpart</span> <span class="o">=</span> <span class="n">EcFlexpart</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">fluxes</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
323    <span class="n">flexpart</span><span class="o">.</span><span class="n">write_namelist</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
324    <span class="n">flexpart</span><span class="o">.</span><span class="n">deacc_fluxes</span><span class="p">(</span><span class="n">inputfiles</span><span class="p">,</span> <span class="n">c</span><span class="p">)</span>
325
326    <span class="c1"># get a list of all other files</span>
327    <span class="n">inputfiles</span> <span class="o">=</span> <span class="n">UioFiles</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">,</span> <span class="s1">&#39;????__??.*&#39;</span> <span class="o">+</span> <span class="nb">str</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">ppid</span><span class="p">)</span> <span class="o">+</span> <span class="s1">&#39;.*&#39;</span><span class="p">)</span>
328
329    <span class="c1"># produce FLEXPART-ready GRIB files and process them -</span>
330    <span class="c1"># copy/transfer/interpolate them or make them GRIB2</span>
331    <span class="n">flexpart</span> <span class="o">=</span> <span class="n">EcFlexpart</span><span class="p">(</span><span class="n">c</span><span class="p">,</span> <span class="n">fluxes</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
332    <span class="n">flexpart</span><span class="o">.</span><span class="n">create</span><span class="p">(</span><span class="n">inputfiles</span><span class="p">,</span> <span class="n">c</span><span class="p">)</span>
333    <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">stream</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s1">&#39;elda&#39;</span> <span class="ow">and</span> <span class="n">c</span><span class="o">.</span><span class="n">doubleelda</span><span class="p">:</span>
334        <span class="n">flexpart</span><span class="o">.</span><span class="n">calc_extra_elda</span><span class="p">(</span><span class="n">c</span><span class="o">.</span><span class="n">inputdir</span><span class="p">,</span> <span class="n">c</span><span class="o">.</span><span class="n">prefix</span><span class="p">)</span>
335    <span class="n">flexpart</span><span class="o">.</span><span class="n">process_output</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
336
337    <span class="c1"># check if in debugging mode, then store all files</span>
338    <span class="c1"># otherwise delete temporary files</span>
339    <span class="k">if</span> <span class="n">c</span><span class="o">.</span><span class="n">debug</span><span class="p">:</span>
340        <span class="nb">print</span><span class="p">(</span><span class="s1">&#39;</span><span class="se">\n</span><span class="s1">Temporary files left intact&#39;</span><span class="p">)</span>
341    <span class="k">else</span><span class="p">:</span>
342        <span class="n">clean_up</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
343
344    <span class="k">return</span></div>
345
346<span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>
347    <span class="n">main</span><span class="p">()</span>
348</pre></div>
349
350           </div>
351           
352          </div>
353          <footer>
354 
355
356  <hr/>
357
358  <div role="contentinfo">
359    <p>
360        &copy; Copyright 2019, Anne Philipp and Leopold Haimberger
361
362    </p>
363  </div>
364  Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
365
366</footer>
367
368        </div>
369      </div>
370
371    </section>
372
373  </div>
374 
375
376
377  <script type="text/javascript">
378      jQuery(function () {
379          SphinxRtdTheme.Navigation.enable(true);
380      });
381  </script>
382
383 
384 
385   
386   
387
388</body>
389</html>
Note: See TracBrowser for help on using the repository browser.
hosted by ZAMG