1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
|
<!DOCTYPE html>
<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>R interface — HARP 1.12 documentation</title>
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/custom.css" type="text/css" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="next" title="Command line tools" href="tools.html" />
<link rel="prev" title="Python interface" href="python.html" />
<script src="_static/js/modernizr.min.js"></script>
</head>
<body class="wy-body-for-nav">
<div class="wy-grid-for-nav">
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-scroll">
<div class="wy-side-nav-search">
<a href="index.html" class="icon icon-home"> HARP
</a>
<div class="version">
1.12
</div>
</div>
<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="conventions/index.html">Conventions</a></li>
<li class="toctree-l1"><a class="reference internal" href="algorithms/index.html">Algorithms</a></li>
<li class="toctree-l1"><a class="reference internal" href="operations.html">Operations</a></li>
<li class="toctree-l1"><a class="reference internal" href="ingestions/index.html">Ingestion definitions</a></li>
<li class="toctree-l1"><a class="reference internal" href="libharp.html">C library</a></li>
<li class="toctree-l1"><a class="reference internal" href="idl.html">IDL interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="matlab.html">MATLAB interface</a></li>
<li class="toctree-l1"><a class="reference internal" href="python.html">Python interface</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">R interface</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#dimension-types">Dimension types</a></li>
<li class="toctree-l2"><a class="reference internal" href="#data-types">Data types</a></li>
<li class="toctree-l2"><a class="reference internal" href="#unicode">Unicode</a></li>
<li class="toctree-l2"><a class="reference internal" href="#examples">Examples</a></li>
<li class="toctree-l2"><a class="reference internal" href="#api-reference">API reference</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="tools.html">Command line tools</a></li>
</ul>
</div>
</div>
</nav>
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
<nav class="wy-nav-top" aria-label="top navigation">
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
<a href="index.html">HARP</a>
</nav>
<div class="wy-nav-content">
<div class="rst-content">
<div role="navigation" aria-label="breadcrumbs navigation">
<ul class="wy-breadcrumbs">
<li><a href="index.html">Docs</a> »</li>
<li>R interface</li>
<li class="wy-breadcrumbs-aside">
</li>
</ul>
<hr/>
</div>
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
<div itemprop="articleBody">
<div class="section" id="r-interface">
<h1>R interface</h1>
<p>The R interface consists of an R package that provides the <cite>import</cite>, <cite>export</cite> and
<cite>version</cite> functions.</p>
<p>Products are represented in R as lists which can be manipulated freely
from within R. A product structure contains a sub-list field for each variable
contained in the product.</p>
<p>Products can be exported as HARP compliant products in any of the file formats
supported by the HARP C library (netCDF/HDF4/HDF5). Such exported products can
subsequently be processed further using the <a class="reference internal" href="tools.html"><span class="doc">HARP command line tools</span></a>.</p>
<div class="section" id="dimension-types">
<h2>Dimension types</h2>
<p>The HARP C library defines several dimension types (time, vertical, latitude
etc.). This information is stored in the <cite>dimension</cite> field of each variable
in R. If a variable is a scalar (which has no dimensions), the <cite>dimension</cite>
field is <cite>NULL</cite>.</p>
<p>Because of a mismatch in storage between the C and R side (row-major versus
column-major), the dimension order is reversed on the R side.</p>
</div>
<div class="section" id="data-types">
<h2>Data types</h2>
<p>The HARP R interface takes care of the conversion of product and variables
from the C domain to the R domain and back. This section describes the
relation between types in the C domain and types in the R domain.</p>
<p>The table below shows the type map that is used when importing or ingesting a
product, i.e. when translating from the C domain to the R domain.</p>
<p>Variable data arrays are converted to arrays in the product structure. The data
type used for the converted array is determined from the HARP data type of the
variable according to the type map shown below. Zero-dimensional arrays of
length 1 are converted to R arrays of 1x1. The resulting R type is also
shown in the type map.</p>
<table border="1" class="docutils">
<colgroup>
<col width="58%" />
<col width="42%" />
</colgroup>
<thead valign="bottom">
<tr class="row-odd"><th class="head">HARP data type</th>
<th class="head">R type</th>
</tr>
</thead>
<tbody valign="top">
<tr class="row-even"><td>harp_type_int8</td>
<td>integer</td>
</tr>
<tr class="row-odd"><td>harp_type_int16</td>
<td>integer</td>
</tr>
<tr class="row-even"><td>harp_type_int32</td>
<td>integer</td>
</tr>
<tr class="row-odd"><td>harp_type_float</td>
<td>real</td>
</tr>
<tr class="row-even"><td>harp_type_double</td>
<td>real</td>
</tr>
<tr class="row-odd"><td>harp_type_string</td>
<td>string</td>
</tr>
</tbody>
</table>
</div>
<div class="section" id="unicode">
<h2>Unicode</h2>
<p>Zero-terminated C strings received from the HARP C library are always converted
to arrays of mxCHAR in R which is a unicode string.</p>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-R notranslate"><div class="highlight"><pre><span></span><span class="c1"># Ingest a file and convert it to a HARP product (the</span>
<span class="c1"># file that is used in this example is an S5P L2 HCHO product).</span>
hcho_product <span class="o">=</span> harp<span class="o">::</span>import<span class="p">(</span><span class="s">"S5P_NRTI_L2__HCHO___20080808T224727_20080808T234211_21635_01_021797_00000000T000000.nc"</span><span class="p">,</span>
<span class="s">"solar_zenith_angle < 60 [degree]; latitude > 30 [degree_north]; latitude < 60 [degree_north]"</span><span class="p">)</span>
<span class="c1"># Print product</span>
<span class="kp">print</span><span class="p">(</span>hcho_product<span class="p">)</span>
<span class="c1"># Print variable 'tropospheric_HCHO_column_number_density'.</span>
<span class="kp">print</span><span class="p">(</span>hcho_product<span class="o">$</span>tropospheric_HCHO_column_number_density<span class="p">)</span>
<span class="c1"># Export the updated product as an HDF5 file (the format must be</span>
<span class="c1"># HDF4, HDF5 or netCDF, if no format is specified netCDF is used).</span>
harp<span class="o">::</span>export<span class="p">(</span>hcho_product<span class="p">,</span> <span class="s">"product.h5"</span><span class="p">,</span> <span class="s">"hdf5"</span><span class="p">)</span>
<span class="c1"># Import the HDF5 file and perform an operation to exclude the variable</span>
<span class="c1"># solar_azimuth_angle.</span>
hcho_product2 <span class="o">=</span> harp<span class="o">::</span>import<span class="p">(</span><span class="s">"product.h5"</span><span class="p">,</span> <span class="s">"exclude(solar_azimuth_angle)"</span><span class="p">);</span>
</pre></div>
</div>
</div>
<div class="section" id="api-reference">
<h2>API reference</h2>
<p>This section describes the functions defined by the HARP R interface.</p>
<dl class="function">
<dt>
<code class="descname">import</code><span class="sig-paren">(</span><em>filename</em>, <em>operations=""</em>, <em>options=""</em><span class="sig-paren">)</span></dt>
<dd><p>Import a product from a file.</p>
<p>This will first try to import the file as an HDF4, HDF5, or netCDF file that
complies to the HARP Data Format. If the file is not stored using the HARP
format then it will try to import it using one of the available ingestion
modules.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
<li><strong>filename</strong> (<em>str</em>) – Filename of the product to ingest</li>
<li><strong>operations</strong> (<em>str</em>) – Actions to apply as part of the import; should be
specified as a semi-colon separated string of operations.</li>
<li><strong>options</strong> (<em>str</em>) – Ingestion module specific options; should be specified as
a semi-colon separated string of key=value pairs; only
used if the file is not in HARP format.</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Ingested product.</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt>
<code class="descname">export</code><span class="sig-paren">(</span><em>product</em>, <em>filename</em>, <em>file_format="netcdf"</em><span class="sig-paren">)</span></dt>
<dd><p>Export a HARP compliant product.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
<tbody valign="top">
<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
<li><strong>product</strong> – Product to export.</li>
<li><strong>filename</strong> (<em>str</em>) – Filename of the exported product.</li>
<li><strong>file_format</strong> (<em>str</em>) – File format to use; one of ‘netcdf’, ‘hdf4’, or
‘hdf5’. If no format is specified, netcdf is used.</li>
</ul>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt>
<code class="descname">version</code><span class="sig-paren">(</span><span class="sig-paren">)</span></dt>
<dd><p>Returns the version number of HARP.</p>
</dd></dl>
</div>
</div>
</div>
</div>
<footer>
<div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
<a href="tools.html" class="btn btn-neutral float-right" title="Command line tools" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
<a href="python.html" class="btn btn-neutral" title="Python interface" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
</div>
<hr/>
<div role="contentinfo">
<p>
© Copyright 2015-2020 S[&]T, The Netherlands
</p>
</div>
</footer>
</div>
</div>
</section>
</div>
<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
<script type="text/javascript" src="_static/jquery.js"></script>
<script type="text/javascript" src="_static/underscore.js"></script>
<script type="text/javascript" src="_static/doctools.js"></script>
<script async="async" type="text/javascript" src="/usr/share/javascript/mathjax/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/js/theme.js"></script>
<script type="text/javascript">
jQuery(function () {
SphinxRtdTheme.Navigation.enable(true);
});
</script>
</body>
</html>
|
