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
|
<!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="X-UA-Compatible" content="IE=Edge" />
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<title>esys.weipa Package — esys.escript 5.6 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" 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 type="text/javascript" src="_static/language_data.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="prev" title="esys.speckley Package" href="esys.speckley.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="esys.speckley.html" title="esys.speckley Package"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">esys.escript 5.6 documentation</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="module-esys.weipa">
<span id="esys-weipa-package"></span><h1>esys.weipa Package<a class="headerlink" href="#module-esys.weipa" title="Permalink to this headline">¶</a></h1>
<ul class="simple">
<li></li>
</ul>
<div class="section" id="classes">
<h2>Classes<a class="headerlink" href="#classes" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><a class="reference internal" href="#esys.weipa.EscriptToTVTK" title="esys.weipa.EscriptToTVTK"><code class="xref py py-obj docutils literal notranslate"><span class="pre">EscriptToTVTK</span></code></a></li>
</ul>
<dl class="class">
<dt id="esys.weipa.EscriptToTVTK">
<em class="property">class </em><code class="descclassname">esys.weipa.</code><code class="descname">EscriptToTVTK</code><span class="sig-paren">(</span><em>domain=None</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.EscriptToTVTK" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>a simple interface from escript to TVTK for rendering with mayavi.mlab</p>
<dl class="method">
<dt id="esys.weipa.EscriptToTVTK.__init__">
<code class="descname">__init__</code><span class="sig-paren">(</span><em>domain=None</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.EscriptToTVTK.__init__" title="Permalink to this definition">¶</a></dt>
<dd><p>sets up driver for translating Data objects in domain to TVTK object.</p>
</dd></dl>
<dl class="method">
<dt id="esys.weipa.EscriptToTVTK.getDomain">
<code class="descname">getDomain</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.EscriptToTVTK.getDomain" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="esys.weipa.EscriptToTVTK.getTVTK">
<code class="descname">getTVTK</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.EscriptToTVTK.getTVTK" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="method">
<dt id="esys.weipa.EscriptToTVTK.setData">
<code class="descname">setData</code><span class="sig-paren">(</span><em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.EscriptToTVTK.setData" title="Permalink to this definition">¶</a></dt>
<dd><p>set the scalar data set:</p>
</dd></dl>
<dl class="method">
<dt id="esys.weipa.EscriptToTVTK.setDomain">
<code class="descname">setDomain</code><span class="sig-paren">(</span><em>domain</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.EscriptToTVTK.setDomain" title="Permalink to this definition">¶</a></dt>
<dd><p>resets the domain</p>
</dd></dl>
</dd></dl>
</div>
<div class="section" id="functions">
<h2>Functions<a class="headerlink" href="#functions" title="Permalink to this headline">¶</a></h2>
<dl class="function">
<dt id="esys.weipa.convertToNumpy">
<code class="descclassname">esys.weipa.</code><code class="descname">convertToNumpy</code><span class="sig-paren">(</span><em>data</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.convertToNumpy" title="Permalink to this definition">¶</a></dt>
<dd><p>Writes <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects to a numpy array.</p>
<p>The keyword args are Data objects to save.
If a scalar <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> object is passed with the name <code class="docutils literal notranslate"><span class="pre">mask</span></code>, then only
samples which correspond to positive values in <code class="docutils literal notranslate"><span class="pre">mask</span></code> will be output.</p>
<p>Example usage:</p>
<p>s=Scalar(..)
v=Vector(..)
t=Tensor(..)
f=float()
array = getNumpy(a=s, b=v, c=t, d=f)</p>
</dd></dl>
<dl class="function">
<dt id="esys.weipa.createDataset">
<code class="descclassname">esys.weipa.</code><code class="descname">createDataset</code><span class="sig-paren">(</span><em>domain=None</em>, <em>**data</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.createDataset" title="Permalink to this definition">¶</a></dt>
<dd><p>Creates and returns an esys.weipa dataset consisting of a Domain and Data
objects. The returned object provides methods to access and export data.</p>
</dd></dl>
<dl class="function">
<dt id="esys.weipa.hasFeature">
<code class="descclassname">esys.weipa.</code><code class="descname">hasFeature</code><span class="sig-paren">(</span><em>(str)name</em><span class="sig-paren">)</span> → bool :<a class="headerlink" href="#esys.weipa.hasFeature" title="Permalink to this definition">¶</a></dt>
<dd><p>Check if escript was compiled with a certain feature</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"><strong>name</strong> (<code class="docutils literal notranslate"><span class="pre">string</span></code>) – feature to lookup</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="esys.weipa.interpolateEscriptData">
<code class="descclassname">esys.weipa.</code><code class="descname">interpolateEscriptData</code><span class="sig-paren">(</span><em>domain</em>, <em>data</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.interpolateEscriptData" title="Permalink to this definition">¶</a></dt>
<dd><p>esys.weipa does not support the function spaces Solution and
ReducedSolution. This function interpolates Data defined on those function
spaces to compatible alternatives.</p>
</dd></dl>
<dl class="function">
<dt id="esys.weipa.saveSilo">
<code class="descclassname">esys.weipa.</code><code class="descname">saveSilo</code><span class="sig-paren">(</span><em>filename</em>, <em>domain=None</em>, <em>write_meshdata=False</em>, <em>time=0.0</em>, <em>cycle=0</em>, <em>**data</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.saveSilo" title="Permalink to this definition">¶</a></dt>
<dd><p>Writes <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects and their mesh to a file using the SILO file format.</p>
<p>Example:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">temp</span><span class="o">=</span><span class="n">Scalar</span><span class="p">(</span><span class="o">..</span><span class="p">)</span>
<span class="n">v</span><span class="o">=</span><span class="n">Vector</span><span class="p">(</span><span class="o">..</span><span class="p">)</span>
<span class="n">saveSilo</span><span class="p">(</span><span class="s2">"solution.silo"</span><span class="p">,</span> <span class="n">temperature</span><span class="o">=</span><span class="n">temp</span><span class="p">,</span> <span class="n">velocity</span><span class="o">=</span><span class="n">v</span><span class="p">)</span>
</pre></div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">temp</span></code> and <code class="docutils literal notranslate"><span class="pre">v</span></code> are written to “solution.silo” where <code class="docutils literal notranslate"><span class="pre">temp</span></code> is named
“temperature” and <code class="docutils literal notranslate"><span class="pre">v</span></code> is named “velocity”.</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> (<code class="docutils literal notranslate"><span class="pre">str</span></code>) – name of the output file (‘.silo’ is added if required)</li>
<li><strong>domain</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">escript.Domain</span></code>) – domain of the <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects. If not specified, the domain
of the given <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects is used.</li>
<li><strong>write_meshdata</strong> (<code class="docutils literal notranslate"><span class="pre">bool</span></code>) – whether to save mesh-related data such as element
identifiers, ownership etc. This is mainly useful
for debugging.</li>
<li><strong>time</strong> (<code class="docutils literal notranslate"><span class="pre">float</span></code>) – the timestamp to save within the file</li>
<li><strong>cycle</strong> (<code class="docutils literal notranslate"><span class="pre">int</span></code>) – the cycle (or timestep) of the data</li>
<li><strong><name></strong> – writes the assigned value to the Silo file using <name> as
identifier</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Note:</th><td class="field-body"><p class="first last">All data objects have to be defined on the same domain but they may
be defined on separate <code class="xref py py-obj docutils literal notranslate"><span class="pre">FunctionSpace</span></code> s.</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="esys.weipa.saveVTK">
<code class="descclassname">esys.weipa.</code><code class="descname">saveVTK</code><span class="sig-paren">(</span><em>filename</em>, <em>domain=None</em>, <em>metadata=''</em>, <em>metadata_schema=None</em>, <em>write_meshdata=False</em>, <em>time=0.0</em>, <em>cycle=0</em>, <em>**data</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.saveVTK" title="Permalink to this definition">¶</a></dt>
<dd><p>Writes <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects and their mesh to a file using the VTK XML file
format.</p>
<p>Example:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">temp</span><span class="o">=</span><span class="n">Scalar</span><span class="p">(</span><span class="o">..</span><span class="p">)</span>
<span class="n">v</span><span class="o">=</span><span class="n">Vector</span><span class="p">(</span><span class="o">..</span><span class="p">)</span>
<span class="n">saveVTK</span><span class="p">(</span><span class="s2">"solution.vtu"</span><span class="p">,</span> <span class="n">temperature</span><span class="o">=</span><span class="n">temp</span><span class="p">,</span> <span class="n">velocity</span><span class="o">=</span><span class="n">v</span><span class="p">)</span>
</pre></div>
</div>
<p><code class="docutils literal notranslate"><span class="pre">temp</span></code> and <code class="docutils literal notranslate"><span class="pre">v</span></code> are written to “solution.vtu” where <code class="docutils literal notranslate"><span class="pre">temp</span></code> is named
“temperature” and <code class="docutils literal notranslate"><span class="pre">v</span></code> is named “velocity”.</p>
<p>Meta tags, e.g. a timeStamp, can be added to the file, for instance:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">tmp</span><span class="o">=</span><span class="n">Scalar</span><span class="p">(</span><span class="o">..</span><span class="p">)</span>
<span class="n">v</span><span class="o">=</span><span class="n">Vector</span><span class="p">(</span><span class="o">..</span><span class="p">)</span>
<span class="n">saveVTK</span><span class="p">(</span><span class="s2">"solution.vtu"</span><span class="p">,</span> <span class="n">temperature</span><span class="o">=</span><span class="n">tmp</span><span class="p">,</span> <span class="n">velocity</span><span class="o">=</span><span class="n">v</span><span class="p">,</span>
<span class="n">metadata</span><span class="o">=</span><span class="s2">"<timeStamp>1.234</timeStamp>"</span><span class="p">,</span>
<span class="n">metadata_schema</span><span class="o">=</span><span class="p">{</span><span class="s2">"gml"</span><span class="p">:</span><span class="s2">"http://www.opengis.net/gml"</span><span class="p">})</span>
</pre></div>
</div>
<p>The argument <code class="docutils literal notranslate"><span class="pre">metadata_schema</span></code> allows the definition of name spaces with
a schema used in the definition of meta tags.</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> (<code class="docutils literal notranslate"><span class="pre">str</span></code>) – name of the output file (‘.vtu’ is added if required)</li>
<li><strong>domain</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">escript.Domain</span></code>) – domain of the <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects. If not specified, the domain
of the given <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects is used.</li>
<li><strong><name></strong> – writes the assigned value to the VTK file using <name> as
identifier</li>
<li><strong>metadata</strong> (<code class="docutils literal notranslate"><span class="pre">str</span></code>) – additional XML meta data which are inserted into the VTK
file. The meta data are marked by the tag <code class="docutils literal notranslate"><span class="pre"><MetaData></span></code>.</li>
<li><strong>metadata_schema</strong> (<code class="docutils literal notranslate"><span class="pre">dict</span></code> with <code class="docutils literal notranslate"><span class="pre">metadata_schema[<namespace>]=<URI></span></code>
to assign the scheme <code class="docutils literal notranslate"><span class="pre"><URI></span></code> to the name space
<code class="docutils literal notranslate"><span class="pre"><namespace></span></code>.) – assigns schemas to namespaces which have been used
to define meta data.</li>
<li><strong>write_meshdata</strong> (<code class="docutils literal notranslate"><span class="pre">bool</span></code>) – whether to save mesh-related data such as element
identifiers, ownership etc. This is mainly useful
for debugging.</li>
<li><strong>time</strong> (<code class="docutils literal notranslate"><span class="pre">float</span></code>) – the timestamp to save within the file, seperate to metadata</li>
<li><strong>cycle</strong> (<code class="docutils literal notranslate"><span class="pre">int</span></code>) – the cycle (or timestep) of the data</li>
</ul>
</td>
</tr>
<tr class="field-even field"><th class="field-name">Note:</th><td class="field-body"><p class="first last">All data objects have to be defined on the same domain. They may not
be in the same <code class="xref py py-obj docutils literal notranslate"><span class="pre">FunctionSpace</span></code> but not all combinations of
<code class="xref py py-obj docutils literal notranslate"><span class="pre">FunctionSpace</span></code> s can be written to a single VTK file.
Typically, data on the boundary and on the interior cannot be mixed.</p>
</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="esys.weipa.saveVoxet">
<code class="descclassname">esys.weipa.</code><code class="descname">saveVoxet</code><span class="sig-paren">(</span><em>filename</em>, <em>**data</em><span class="sig-paren">)</span><a class="headerlink" href="#esys.weipa.saveVoxet" title="Permalink to this definition">¶</a></dt>
<dd><p>Writes <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> objects to a file using the GOCAD Voxet file format as
separate properties on the same grid.
At the moment only Data on a <code class="xref py py-obj docutils literal notranslate"><span class="pre">ripley</span></code> domain can be saved in this format.
Note that this function will produce one header file (ending in .vo) and
a separate property file for each <code class="xref py py-obj docutils literal notranslate"><span class="pre">Data</span></code> object.</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"><strong>filename</strong> (<code class="docutils literal notranslate"><span class="pre">str</span></code>) – name of the output file (‘.vo’ is added if required)</td>
</tr>
<tr class="field-even field"><th class="field-name">Note:</th><td class="field-body">All data objects have to be defined on the same ripley domain and
either defined on reduced Function or on a <code class="xref py py-obj docutils literal notranslate"><span class="pre">FunctionSpace</span></code> that
allows interpolation to reduced Function.</td>
</tr>
</tbody>
</table>
</dd></dl>
<dl class="function">
<dt id="esys.weipa.visitInitialize">
<code class="descclassname">esys.weipa.</code><code class="descname">visitInitialize</code><span class="sig-paren">(</span><em>(str)simFile</em><span class="optional">[</span>, <em>(str)comment=''</em><span class="optional">]</span><span class="sig-paren">)</span> → bool<a class="headerlink" href="#esys.weipa.visitInitialize" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="function">
<dt id="esys.weipa.visitPublishData">
<code class="descclassname">esys.weipa.</code><code class="descname">visitPublishData</code><span class="sig-paren">(</span><em>(EscriptDataset)dataset</em><span class="sig-paren">)</span> → bool<a class="headerlink" href="#esys.weipa.visitPublishData" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</div>
<div class="section" id="others">
<h2>Others<a class="headerlink" href="#others" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>HAVE_TVTK</li>
</ul>
</div>
<div class="section" id="packages">
<h2>Packages<a class="headerlink" href="#packages" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
</div>
</div>
</div>
</div>
</div>
</div>
<div class="sphinxsidebar" role="navigation" aria-label="main navigation">
<div class="sphinxsidebarwrapper">
<h3><a href="index.html">Table of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">esys.weipa Package</a><ul>
<li><a class="reference internal" href="#classes">Classes</a></li>
<li><a class="reference internal" href="#functions">Functions</a></li>
<li><a class="reference internal" href="#others">Others</a></li>
<li><a class="reference internal" href="#packages">Packages</a></li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
<p class="topless"><a href="esys.speckley.html"
title="previous chapter">esys.speckley Package</a></p>
</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="esys.speckley.html" title="esys.speckley Package"
>previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">esys.escript 5.6 documentation</a> »</li>
</ul>
</div>
<div class="footer" role="contentinfo">
© Copyright 2012-2014, Author.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.8.4.
</div>
</body>
</html>
|
