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<section id="data-visualisation-and-post-processing">
<span id="secpythonpostproc"></span><h1>Data visualisation and post-processing<a class="headerlink" href="#data-visualisation-and-post-processing" title="Link to this heading">¶</a></h1>
<p>Most of the <a class="reference internal" href="outputFiles/outFiles.html#secoutputfiles"><span class="std std-ref">output files</span></a> written during a run of MagIC
can be treated with the python post-processing classes and functions present in the
<code class="docutils literal notranslate"><span class="pre">$MAGIC_HOME/python/magic</span></code> directory. These classes depend on several python libraries
that can be usually found in most of the Linux distributions.</p>
<section id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Link to this heading">¶</a></h2>
<section id="hard-dependencies">
<h3>Hard dependencies<a class="headerlink" href="#hard-dependencies" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p><a class="reference external" href="https://www.python.org">python</a> 2.7/3.3 or higher.</p></li>
<li><p><a class="reference external" href="http://matplotlib.org">matplotlib</a> 1.0 or higher.</p></li>
<li><p><a class="reference external" href="http://www.scipy.org/">scipy</a> 0.10 or higher.</p></li>
</ul>
</section>
<section id="optional-dependencies">
<h3>Optional dependencies<a class="headerlink" href="#optional-dependencies" title="Link to this heading">¶</a></h3>
<ul class="simple">
<li><p>Although entirely optional, the installation of <a class="reference external" href="http://ipython.org/">ipython</a> makes the interactive use of the post-processing python
functions much more pleasant. Installing it is therefore recommanded for a smoother
interactive usage of the python functions.</p></li>
<li><p>The installation of the <a class="reference external" href="http://matplotlib.org/basemap/">basemap toolkit</a>
is optional. If installed, additional projections for the
<a class="reference internal" href="apiPython/graphMovCoeff.html#magic.Surf" title="magic.Surf"><code class="xref py py-class docutils literal notranslate"><span class="pre">magic.Surf</span></code></a> (<a class="reference external" href="https://en.wikipedia.org/wiki/Aitoff_projection">Aitoff</a>,
<a class="reference external" href="https://en.wikipedia.org/wiki/Orthographic_projection">orthographic</a>,
<a class="reference external" href="https://en.wikipedia.org/wiki/Mollweide_projection">Mollweide</a>, etc.) class
will be provided for 2-D surface plotting. Otherwise, the usage of
<a class="reference internal" href="apiPython/graphMovCoeff.html#magic.Surf" title="magic.Surf"><code class="xref py py-class docutils literal notranslate"><span class="pre">magic.Surf</span></code></a> is limited to the standalone
<a class="reference external" href="https://en.wikipedia.org/wiki/Hammer_projection">Hammer projection</a>.</p></li>
</ul>
</section>
</section>
<section id="configuration-magic-cfg-file">
<h2>Configuration: <code class="docutils literal notranslate"><span class="pre">magic.cfg</span></code> file<a class="headerlink" href="#configuration-magic-cfg-file" title="Link to this heading">¶</a></h2>
<p>A file named <strong>magic.cfg</strong> located in <code class="docutils literal notranslate"><span class="pre">$MAGIC_HOME/python/magic/magic.cfg</span></code> should have
been created when you used the <code class="docutils literal notranslate"><span class="pre">source</span> <span class="pre">path/sourceme.sh</span></code> command for the first time on
your machine. At that stage, it tried to <strong>automatically fill the best options</strong> that
correspond to your setup. Although tested on several various machine configurations, the
auto-configuration script might however fail on your setup. The paragraph below details
the possible options that you may want to adjust in the <code class="docutils literal notranslate"><span class="pre">magic.cfg</span></code> file.</p>
<section id="detailed-options">
<h3>Detailed options<a class="headerlink" href="#detailed-options" title="Link to this heading">¶</a></h3>
<p>In case, the file <code class="docutils literal notranslate"><span class="pre">magic.cfg</span></code> doesn’t exist in the directory <code class="docutils literal notranslate"><span class="pre">$MAGIC_HOME/python/magic</span></code>,
you can easily copy it from the default configuration <code class="docutils literal notranslate"><span class="pre">magic.cfg.default</span></code> and then adjust
the options manually:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$<span class="w"> </span>cp<span class="w"> </span><span class="nv">$MAGIC_HOME</span>/python/magic/magic.cfg.default<span class="w"> </span><span class="nv">$MAGIC_HOME</span>/python/magic/magic.cfg
</pre></div>
</div>
<p>In that file, you can set up the default <a class="reference external" href="http://matplotlib.org">matplotlib</a>
rendering backend (among the possible options: <code class="docutils literal notranslate"><span class="pre">TkAgg</span></code>, <code class="docutils literal notranslate"><span class="pre">GTKAgg</span></code>, <code class="docutils literal notranslate"><span class="pre">Qt5Agg</span></code>, <code class="docutils literal notranslate"><span class="pre">Qt4Agg</span></code>, …).
The default configuration is</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">backend</span> <span class="o">=</span> <span class="n">TkAgg</span>
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>This is usually the default configuration which is the most likely to work on
supercomputing clusters.</p>
</div>
<p>If <a class="reference external" href="http://www.latex-project.org/">LaTeX</a> is installed on your work station, you
might also want to make use of the better looking LaTeX fonts for all your
displayed matplotlib figures (labels, caption, ticks, etc.). Be careful though that
most of the time LaTeX is <strong>not installed</strong> on supercomputers. The default
configuration is thus:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">labTex</span> <span class="o">=</span> <span class="kc">False</span>
</pre></div>
</div>
<p>You can change the default colormap that will be used in the plotting routines.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">defaultCm</span> <span class="o">=</span> <span class="n">seismic</span>
</pre></div>
</div>
<p>You cant change the default number of contours that will be used in the plotting routines.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">defaultLevels</span> <span class="o">=</span> <span class="mi">65</span>
</pre></div>
</div>
<p>If you want to enable all the features of the python functions (faster reading the
<a class="reference internal" href="outputFiles/outGraph.html#secgraphfile"><span class="std std-ref">G_#.TAG</span></a>, conversion to the <a class="reference external" href="http://www.vtk.org/">VTK/VTS</a>
file format, potential extrapolation of the field lines, etc.), some fortran libraries
present in the <cite>$MAGIC_HOME/python/magic/fortranLib</cite> directory need to be built using
the <a class="reference external" href="http://www.f2py.com/">f2py</a>, which should be available on your Linux workstation
if all the required python libraries have been correctly installed. The boolean
<code class="docutils literal notranslate"><span class="pre">buildLib</span></code> can control whether you want to try building the fortran libraries
with <a class="reference external" href="http://www.f2py.com/">f2py</a>. The following configuration will try to build
the libraries:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">buildLib</span> <span class="o">=</span> <span class="kc">True</span>
</pre></div>
</div>
<p>The exact name of the executable <a class="reference external" href="http://www.f2py.com/">f2py</a>
however varies from one Linux distribution to the other. Among possible
options, one frequently finds: <code class="docutils literal notranslate"><span class="pre">f2py</span></code>, <code class="docutils literal notranslate"><span class="pre">f2py2</span></code>, <code class="docutils literal notranslate"><span class="pre">f2py3</span></code>. This can be set to
your proper configuration using the <code class="docutils literal notranslate"><span class="pre">f2pyexec</span></code> option of the <code class="docutils literal notranslate"><span class="pre">magic.cfg</span></code> file.
The default configuration is:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">f2pyexec</span> <span class="o">=</span> <span class="n">f2py2</span>
</pre></div>
</div>
<p>You can also choose the fortran compiler you want to use on your machine. A list
of the installed compilers can be obtained by using (where <code class="docutils literal notranslate"><span class="pre">f2py</span></code> has to be
replaced by your own executable):</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>$<span class="w"> </span>f2py<span class="w"> </span>-c<span class="w"> </span>--help-fcompiler
</pre></div>
</div>
<p>The most frequent options are:</p>
<blockquote>
<div><ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">gnu95</span></code> for the GNU gfortran compiler.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">intelem</span></code> for the Intel ifort compiler.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">pg</span></code> for the Portlang group pgf compiler.</p></li>
</ul>
</div></blockquote>
<p>Once you’ve decided the ideal configuration for your machine, set it up via the option
<code class="docutils literal notranslate"><span class="pre">fcompiler</span></code>:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">fcompiler</span> <span class="o">=</span> <span class="n">intelem</span>
</pre></div>
</div>
<p>Finally, he same configuration procedure can be applied to the C compiler using
the variable named <code class="docutils literal notranslate"><span class="pre">ccompiler</span></code>. The possible options are:</p>
<blockquote>
<div><ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">unix</span></code> for the GNU gcc compiler.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">intelem</span></code> for the Intel icc compiler.</p></li>
</ul>
</div></blockquote>
<p>In most of the configurations, the default configuration should do a good job:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">ccompiler</span> <span class="o">=</span> <span class="n">unix</span>
</pre></div>
</div>
<p>If you encounter any problem during the building stage, you can try playing with
this parameter though.</p>
</section>
<section id="ready">
<h3>Ready?!<a class="headerlink" href="#ready" title="Link to this heading">¶</a></h3>
<p>Once you think you set up your <code class="docutils literal notranslate"><span class="pre">magic.cfg</span></code> file correctly, you can test your
configuration. If you decided to build the fortran libraries (i.e. <code class="docutils literal notranslate"><span class="pre">buildLib=True</span></code>),
you can easily test it with any python shell by typing the following command:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">>>> </span><span class="kn">from</span> <span class="nn">magic</span> <span class="kn">import</span> <span class="o">*</span>
</pre></div>
</div>
<p>If the build was successful, it should display:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">Please</span> <span class="n">wait</span><span class="p">:</span> <span class="n">building</span> <span class="n">greader_single</span><span class="o">...</span>
<span class="n">Please</span> <span class="n">wait</span><span class="p">:</span> <span class="n">building</span> <span class="n">greader_double</span><span class="o">...</span>
<span class="n">Please</span> <span class="n">wait</span><span class="p">:</span> <span class="n">building</span> <span class="n">lmrreader_single</span><span class="o">...</span>
<span class="n">Please</span> <span class="n">wait</span><span class="p">:</span> <span class="n">building</span> <span class="n">Legendre</span> <span class="n">transforms</span><span class="o">...</span>
<span class="n">Please</span> <span class="n">wait</span><span class="p">:</span> <span class="n">building</span> <span class="n">vtklib</span><span class="o">...</span>
<span class="n">Please</span> <span class="n">wait</span><span class="p">:</span> <span class="n">building</span> <span class="n">cylavg</span><span class="o">...</span>
</pre></div>
</div>
<p>Once the libraries have been successfully installed, this message won’t be displayed
again, except if you remove the <code class="docutils literal notranslate"><span class="pre">*.so</span></code> files that are now present in the
<code class="docutils literal notranslate"><span class="pre">$MAGIC_HOME/python/magic/</span></code> directory.</p>
</section>
</section>
<section id="python-functions-and-classes">
<span id="secpythonclasses"></span><h2>Python functions and classes<a class="headerlink" href="#python-functions-and-classes" title="Link to this heading">¶</a></h2>
<p>Once the python environment is correctly configured you can use the available functions and
classes to analyse and post-process your data. The following pages will give you the detailed
API of the available classes, as well as some practical examples:</p>
<aside class="topic">
<p class="topic-title">Python classes</p>
<ol class="arabic simple">
<li><p>To read the <strong>log.TAG</strong> files , see <a class="reference internal" href="apiPython/timeSeries.html#secpythonlogfile"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse the time series, see <a class="reference internal" href="apiPython/timeSeries.html#secpythontimeseries"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse the radial profiles, see <a class="reference internal" href="apiPython/radial.html#secpythonradial"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse spectra <strong>_spec_#.TAG</strong>, see <a class="reference internal" href="apiPython/spectra.html#secpythonspectra"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse the <strong>G_#.TAG</strong> files, see <a class="reference internal" href="apiPython/graphMovCoeff.html#secpythongraphfile"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse the <strong>checkpoint_#.TAG</strong> files, see <a class="reference internal" href="apiPython/graphMovCoeff.html#secpythoncheckpointfile"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse movie files <strong>_mov.TAG</strong>, see <a class="reference internal" href="apiPython/graphMovCoeff.html#secpythonmoviefiles"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse coeff files <strong>[V|B|T]_coeff.TAG</strong>, see <a class="reference internal" href="apiPython/graphMovCoeff.html#secpythoncoeffs"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse potential files <strong>[V|B|T]_lmr_#.TAG</strong>, see <a class="reference internal" href="apiPython/graphMovCoeff.html#secpythonpot"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse radial spectra <strong>B[r|p]Spec.TAG</strong>, see <a class="reference internal" href="apiPython/graphMovCoeff.html#secpythonrspec"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To read and analyse TO outputs, see <a class="reference internal" href="apiPython/outTO.html#secpythonto"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To compare several runs simultaneously, see <a class="reference internal" href="apiPython/runComparison.html#secpythoncomp"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To transform the graphic files <strong>G_#.TAG</strong> to a file format readable by <a class="reference external" href="http://www.paraview.org/">paraview</a>, <a class="reference external" href="https://visit.llnl.gov/">VisIt</a> or <a class="reference external" href="http://code.enthought.com/projects/mayavi/">mayavi</a> and do some fancy 3-D visualisation, see <a class="reference internal" href="apiPython/toParaview.html#secpythonparaview"><span class="std std-ref">here</span></a>.</p></li>
<li><p>For additional diagnostics (boundary layer, heat transport, interpolation on cylindrical grids, etc.), see <a class="reference internal" href="apiPython/misc.html#secpythonmisc"><span class="std std-ref">here</span></a>.</p></li>
<li><p>To take a look at the additional useful functions available (derivation, integration, interpolation, etc.), see <a class="reference internal" href="apiPython/libs.html#secpythonlibs"><span class="std std-ref">here</span></a>.</p></li>
</ol>
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