update of the docu including the SECTOR cmd.

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<div class="section" id="mupp-mgrsr-parameter-plotter">
<span id="mupp"></span><span id="index-0"></span><h1>mupp - μSR Parameter Plotter<a class="headerlink" href="#mupp-mgrsr-parameter-plotter" title="Permalink to this headline"></a></h1>
<p><tt class="docutils literal"><span class="pre">mupp</span></tt> is a little helper program which allows to quickly plot a collection of msr-file parameters,
as for instance generated by <a class="reference internal" href="msr2data.html#msr2data"><em>msr2data</em></a>. It can handle <tt class="docutils literal"><span class="pre">db</span></tt>- and <tt class="docutils literal"><span class="pre">dat</span></tt>-files.
Also a collection of <tt class="docutils literal"><span class="pre">msr</span></tt>-files can be invoked. <tt class="docutils literal"><span class="pre">mupp</span></tt> is heavily inspired by μView (see
<p><code class="docutils literal notranslate"><span class="pre">mupp</span></code> is a little helper program which allows to quickly plot a collection of msr-file parameters,
as for instance generated by <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>. It can handle <code class="docutils literal notranslate"><span class="pre">db</span></code>- and <code class="docutils literal notranslate"><span class="pre">dat</span></code>-files.
Also a collection of <code class="docutils literal notranslate"><span class="pre">msr</span></code>-files can be invoked. <code class="docutils literal notranslate"><span class="pre">mupp</span></code> is heavily inspired by μView (see
<a class="reference external" href="http://musr.org/muview/">here</a>).</p>
<p><tt class="docutils literal"><span class="pre">mupp</span></tt> can be operated from within as graphical user interface or via a command line scripting interface.
The <tt class="docutils literal"><span class="pre">mupp</span></tt> GUI can be invoked either directly from the command line or from within <a class="reference internal" href="musredit.html#musredit-sec"><em>musredit</em></a>.</p>
<p><code class="docutils literal notranslate"><span class="pre">mupp</span></code> can be operated from within as graphical user interface or via a command line scripting interface.
The <code class="docutils literal notranslate"><span class="pre">mupp</span></code> GUI can be invoked either directly from the command line or from within <a class="reference internal" href="musredit.html#musredit-sec"><span class="std std-ref">musredit</span></a>.</p>
<div class="section" id="the-graphical-user-interface">
<span id="index-1"></span><h2>The Graphical User Interface<a class="headerlink" href="#the-graphical-user-interface" title="Permalink to this headline"></a></h2>
<p>A typical setting could look like this</p>
<img src="_images/mupp-gui-0.svg" /><ol class="arabic">
<li><p class="first">shows the list of loaded collections. A collection is defined as <tt class="docutils literal"><span class="pre">db</span></tt>- or <tt class="docutils literal"><span class="pre">dat</span></tt>-file (typically the
output from <a class="reference internal" href="msr2data.html#msr2data"><em>msr2data</em></a>). If you call the open-dialog and select a collection of
<tt class="docutils literal"><span class="pre">msr</span></tt>-files, <tt class="docutils literal"><span class="pre">mupp</span></tt> will call <tt class="docutils literal"><span class="pre">msr2data</span></tt> and tries to generate a collection on-the-fly.</p>
</li>
<li><p class="first">in this list, the data-tags of the currently selected collection is presented. The data-tags can be
directly dragged over to the <tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis list. Another way is to select the data-tag
wished and click <tt class="docutils literal"><span class="pre">add</span> <span class="pre">X</span></tt> to add the selected data-tag to the <tt class="docutils literal"><span class="pre">x</span></tt>-axis list. Analogous it is done
for the <tt class="docutils literal"><span class="pre">y</span></tt>-axis.</p>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">x</span></tt>-axis list. The labels are followed by <tt class="docutils literal"><span class="pre">(-X-)</span></tt> where the number <tt class="docutils literal"><span class="pre">X</span></tt> corresponds to the
selection it corresponds to. The numbering of the collection is as given in the collection list.</p>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">y</span></tt>-axis list. The labels are followed by <tt class="docutils literal"><span class="pre">(-X-)</span></tt> where the number <tt class="docutils literal"><span class="pre">X</span></tt> corresponds to the
selection it corresponds to. The numbering of the collection is as given in the collection list.</p>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">add</span> <span class="pre">X</span></tt> allows to add the currently selected data-tag to the <tt class="docutils literal"><span class="pre">x</span></tt>-axis list.</p>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">add</span> <span class="pre">Y</span></tt> allows to add the currently selected data-tag to the <tt class="docutils literal"><span class="pre">y</span></tt>-axis list.</p>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">remove</span> <span class="pre">X</span></tt> will remove the selected <tt class="docutils literal"><span class="pre">x</span></tt>-axis tag.</p>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">remove</span> <span class="pre">Y</span></tt> will remove the selected <tt class="docutils literal"><span class="pre">y</span></tt>-axis tag.</p>
</li>
<li><p class="first">Often one would like to compare trends of different settings. In the above example each collections
<img alt="_images/mupp-gui-0.svg" src="_images/mupp-gui-0.svg" /><ol class="arabic">
<li><p>shows the list of loaded collections. A collection is defined as <code class="docutils literal notranslate"><span class="pre">db</span></code>- or <code class="docutils literal notranslate"><span class="pre">dat</span></code>-file (typically the
output from <a class="reference internal" href="msr2data.html#msr2data"><span class="std std-ref">msr2data</span></a>). If you call the open-dialog and select a collection of
<code class="docutils literal notranslate"><span class="pre">msr</span></code>-files, <code class="docutils literal notranslate"><span class="pre">mupp</span></code> will call <code class="docutils literal notranslate"><span class="pre">msr2data</span></code> and tries to generate a collection on-the-fly.</p></li>
<li><p>in this list, the data-tags of the currently selected collection is presented. The data-tags can be
directly dragged over to the <code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis list. Another way is to select the data-tag
wished and click <code class="docutils literal notranslate"><span class="pre">add</span> <span class="pre">X</span></code> to add the selected data-tag to the <code class="docutils literal notranslate"><span class="pre">x</span></code>-axis list. Analogous it is done
for the <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">x</span></code>-axis list. The labels are followed by <code class="docutils literal notranslate"><span class="pre">(-X-)</span></code> where the number <code class="docutils literal notranslate"><span class="pre">X</span></code> corresponds to the
selection it corresponds to. The numbering of the collection is as given in the collection list.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">y</span></code>-axis list. The labels are followed by <code class="docutils literal notranslate"><span class="pre">(-X-)</span></code> where the number <code class="docutils literal notranslate"><span class="pre">X</span></code> corresponds to the
selection it corresponds to. The numbering of the collection is as given in the collection list.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">add</span> <span class="pre">X</span></code> allows to add the currently selected data-tag to the <code class="docutils literal notranslate"><span class="pre">x</span></code>-axis list.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">add</span> <span class="pre">Y</span></code> allows to add the currently selected data-tag to the <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis list.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">remove</span> <span class="pre">X</span></code> will remove the selected <code class="docutils literal notranslate"><span class="pre">x</span></code>-axis tag.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">remove</span> <span class="pre">Y</span></code> will remove the selected <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis tag.</p></li>
<li><p>Often one would like to compare trends of different settings. In the above example each collections
holds an energy scans for a given temperature. Each collection is measured at a different temperature.
Now, instead of adding <tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis tags for each collection, you can do the following:
you add <tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis data-tags for the first collection. Afterwards you select all the other
collections of interest and click on <tt class="docutils literal"><span class="pre">Add</span> <span class="pre">Ditto</span></tt>. <tt class="docutils literal"><span class="pre">mupp</span></tt> will then add the corresponding
<tt class="docutils literal"><span class="pre">x</span></tt>- and <tt class="docutils literal"><span class="pre">y</span></tt>-axis data-tags accordingly. This is less error prone and quicker!</p>
</li>
<li><p class="first">Clicking the <tt class="docutils literal"><span class="pre">Plot</span></tt> button will invoke <tt class="docutils literal"><span class="pre">mupp_plot</span></tt> (a <tt class="docutils literal"><span class="pre">ROOT</span></tt> based application) which will
Now, instead of adding <code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis tags for each collection, you can do the following:
you add <code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis data-tags for the first collection. Afterwards you select all the other
collections of interest and click on <code class="docutils literal notranslate"><span class="pre">Add</span> <span class="pre">Ditto</span></code>. <code class="docutils literal notranslate"><span class="pre">mupp</span></code> will then add the corresponding
<code class="docutils literal notranslate"><span class="pre">x</span></code>- and <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis data-tags accordingly. This is less error prone and quicker!</p></li>
<li><p>Clicking the <code class="docutils literal notranslate"><span class="pre">Plot</span></code> button will invoke <code class="docutils literal notranslate"><span class="pre">mupp_plot</span></code> (a <code class="docutils literal notranslate"><span class="pre">ROOT</span></code> based application) which will
present the data, as shown here</p>
<a class="reference internal image-reference" href="_images/mupp-plot-0.svg"><img height="600px" src="_images/mupp-plot-0.svg" /></a>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">Remove</span> <span class="pre">Collection</span></tt>: will remove the selected collection</p>
</li>
<li><p class="first"><tt class="docutils literal"><span class="pre">Refresh</span> <span class="pre">Collection</span></tt>: will reload the collection (<tt class="docutils literal"><span class="pre">db</span></tt>- or <tt class="docutils literal"><span class="pre">dat</span></tt>-file). This is often useful
during beamtime where the collection is growing run-by-run.</p>
</li>
<li><p class="first">This is the script command line. Currently it allows to perform the tasks without mouse gambling.
In the future much more commands are planed. See the <tt class="docutils literal"><span class="pre">Help</span> <span class="pre">/</span> <span class="pre">Cmd's</span></tt> for the currently available
commands.</p>
<a class="reference internal image-reference" href="_images/mupp-plot-0.svg"><img alt="_images/mupp-plot-0.svg" height="600px" src="_images/mupp-plot-0.svg" /></a>
</li>
<li><p><code class="docutils literal notranslate"><span class="pre">Remove</span> <span class="pre">Collection</span></code>: will remove the selected collection</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Refresh</span> <span class="pre">Collection</span></code>: will reload the collection (<code class="docutils literal notranslate"><span class="pre">db</span></code>- or <code class="docutils literal notranslate"><span class="pre">dat</span></code>-file). This is often useful
during beamtime where the collection is growing run-by-run.</p></li>
<li><p>This is the script command line. Currently it allows to perform the tasks without mouse gambling.
In the future much more commands are planed. See the <code class="docutils literal notranslate"><span class="pre">Help</span> <span class="pre">/</span> <span class="pre">Cmd's</span></code> for the currently available
commands.</p></li>
</ol>
</div>
<div class="section" id="the-scripting-interface">
<span id="index-2"></span><h2>The Scripting Interface<a class="headerlink" href="#the-scripting-interface" title="Permalink to this headline"></a></h2>
<p><tt class="docutils literal"><span class="pre">mupp</span></tt> can also be operated in a scripting like manner. The use cases are plot updates during run time,
or web-based interaction which requests figures. A script is invoked by the command line option <tt class="docutils literal"><span class="pre">-s</span></tt> (see
<a class="reference internal" href="#mupp-usage"><em>mupp command line summary</em></a>. Currently the following scripting commands are available:</p>
<dl class="docutils">
<dt><strong>loadPath &lt;dir&gt;</strong></dt>
<dd>set the load path to <tt class="docutils literal"><span class="pre">&lt;dir&gt;</span></tt>. Bash variables like $HOME are accepted. This is the path where to look for collection files (<tt class="docutils literal"><span class="pre">db</span></tt>- and <tt class="docutils literal"><span class="pre">dat</span></tt>-files).</dd>
<dt><strong>load &lt;coll&gt;</strong></dt>
<dd>will load the collection <tt class="docutils literal"><span class="pre">&lt;coll&gt;</span></tt>.</dd>
<dt><strong>selectAll</strong></dt>
<dd>will select all loaded collections. This means every plot of variable x/y will be carried out to <em>ALL</em> collections.</dd>
<dt><strong>select &lt;nn&gt;</strong></dt>
<dd>selects collection <tt class="docutils literal"><span class="pre">&lt;nn&gt;</span></tt>, where <tt class="docutils literal"><span class="pre">&lt;nn&gt;</span></tt> is either the <em>number</em> of the collections, or its <em>name</em>, <em>e.g.</em>
select YBCO-40nm-T5K-FC150mT-Escan.db.</dd>
<dt><strong>addX &lt;label&gt;</strong></dt>
<dd>add <tt class="docutils literal"><span class="pre">&lt;label&gt;</span></tt> as a <em>x</em>-variable. Only <em>one</em> is allowed.</dd>
<dt><strong>addY &lt;label(s)&gt;</strong></dt>
<dd>add <tt class="docutils literal"><span class="pre">&lt;label(s)&gt;</span></tt> as <em>y</em>-variable. <em>Multiple</em> labels are possible.</dd>
<dt><strong>savePath &lt;dir&gt;</strong></dt>
<dd>set the save path to <tt class="docutils literal"><span class="pre">&lt;dir&gt;</span></tt>. The place where the macros, and/or the plot output will be saved.</dd>
<dt><strong>plot &lt;fln&gt;</strong></dt>
<dd>where <tt class="docutils literal"><span class="pre">&lt;fln&gt;</span></tt> is the file name with extension under which the plot should be saved.</dd>
<dt><strong>macro &lt;fln&gt;</strong></dt>
<dd>where <tt class="docutils literal"><span class="pre">&lt;fln&gt;</span></tt> is the file name under which the root macro should be saved.</dd>
<p><code class="docutils literal notranslate"><span class="pre">mupp</span></code> can also be operated in a scripting like manner. The use cases are plot updates during run time,
or web-based interaction which requests figures. A script is invoked by the command line option <code class="docutils literal notranslate"><span class="pre">-s</span></code> (see
<a class="reference internal" href="#mupp-usage"><span class="std std-ref">mupp command line summary</span></a>. Currently the following scripting commands are available:</p>
<dl class="simple">
<dt><strong>loadPath &lt;dir&gt;</strong></dt><dd><p>set the load path to <code class="docutils literal notranslate"><span class="pre">&lt;dir&gt;</span></code>. Bash variables like $HOME are accepted. This is the path where to look for collection files (<code class="docutils literal notranslate"><span class="pre">db</span></code>- and <code class="docutils literal notranslate"><span class="pre">dat</span></code>-files).</p>
</dd>
<dt><strong>load &lt;coll&gt;</strong></dt><dd><p>will load the collection <code class="docutils literal notranslate"><span class="pre">&lt;coll&gt;</span></code>.</p>
</dd>
<dt><strong>selectAll</strong></dt><dd><p>will select all loaded collections. This means every plot of variable x/y will be carried out to <em>ALL</em> collections.</p>
</dd>
<dt><strong>select &lt;nn&gt;</strong></dt><dd><p>selects collection <code class="docutils literal notranslate"><span class="pre">&lt;nn&gt;</span></code>, where <code class="docutils literal notranslate"><span class="pre">&lt;nn&gt;</span></code> is either the <em>number</em> of the collections, or its <em>name</em>, <em>e.g.</em>
select YBCO-40nm-T5K-FC150mT-Escan.db.</p>
</dd>
<dt><strong>addX &lt;label&gt;</strong></dt><dd><p>add <code class="docutils literal notranslate"><span class="pre">&lt;label&gt;</span></code> as a <em>x</em>-variable. Only <em>one</em> is allowed.</p>
</dd>
<dt><strong>addY &lt;label(s)&gt;</strong></dt><dd><p>add <code class="docutils literal notranslate"><span class="pre">&lt;label(s)&gt;</span></code> as <em>y</em>-variable. <em>Multiple</em> labels are possible.</p>
</dd>
<dt><strong>savePath &lt;dir&gt;</strong></dt><dd><p>set the save path to <code class="docutils literal notranslate"><span class="pre">&lt;dir&gt;</span></code>. The place where the macros, and/or the plot output will be saved.</p>
</dd>
<dt><strong>plot &lt;fln&gt;</strong></dt><dd><p>where <code class="docutils literal notranslate"><span class="pre">&lt;fln&gt;</span></code> is the file name with extension under which the plot should be saved.</p>
</dd>
<dt><strong>macro &lt;fln&gt;</strong></dt><dd><p>where <code class="docutils literal notranslate"><span class="pre">&lt;fln&gt;</span></code> is the file name under which the root macro should be saved.</p>
</dd>
</dl>
<p>An example script file <tt class="docutils literal"><span class="pre">field-vs-energy.txt</span></tt> might look like this:</p>
<div class="highlight-python"><div class="highlight"><pre><span></span># This is a comment
<p>An example script file <code class="docutils literal notranslate"><span class="pre">field-vs-energy.txt</span></code> might look like this:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># This is a comment</span>
loadPath ./
<span class="n">loadPath</span> <span class="o">./</span>
load YBCO-40nm-T5K-FC150mT-Escan.db
load YBCO-40nm-T30K-FC150mT-Escan.db
load YBCO-40nm-T60K-FC150mT-Escan.db
load YBCO-40nm-T120K-FC150mT-Escan.db
<span class="n">load</span> <span class="n">YBCO</span><span class="o">-</span><span class="mi">40</span><span class="n">nm</span><span class="o">-</span><span class="n">T5K</span><span class="o">-</span><span class="n">FC150mT</span><span class="o">-</span><span class="n">Escan</span><span class="o">.</span><span class="n">db</span>
<span class="n">load</span> <span class="n">YBCO</span><span class="o">-</span><span class="mi">40</span><span class="n">nm</span><span class="o">-</span><span class="n">T30K</span><span class="o">-</span><span class="n">FC150mT</span><span class="o">-</span><span class="n">Escan</span><span class="o">.</span><span class="n">db</span>
<span class="n">load</span> <span class="n">YBCO</span><span class="o">-</span><span class="mi">40</span><span class="n">nm</span><span class="o">-</span><span class="n">T60K</span><span class="o">-</span><span class="n">FC150mT</span><span class="o">-</span><span class="n">Escan</span><span class="o">.</span><span class="n">db</span>
<span class="n">load</span> <span class="n">YBCO</span><span class="o">-</span><span class="mi">40</span><span class="n">nm</span><span class="o">-</span><span class="n">T120K</span><span class="o">-</span><span class="n">FC150mT</span><span class="o">-</span><span class="n">Escan</span><span class="o">.</span><span class="n">db</span>
selectAll
<span class="n">selectAll</span>
addX dataE
addY Field
<span class="n">addX</span> <span class="n">dataE</span>
<span class="n">addY</span> <span class="n">Field</span>
savePath ./
plot FieldVsEnergy.pdf
<span class="n">savePath</span> <span class="o">./</span>
<span class="n">plot</span> <span class="n">FieldVsEnergy</span><span class="o">.</span><span class="n">pdf</span>
macro FieldVsEnergy.C
<span class="n">macro</span> <span class="n">FieldVsEnergy</span><span class="o">.</span><span class="n">C</span>
# end
<span class="c1"># end</span>
</pre></div>
</div>
</div>
<div class="section" id="the-usage-summary">
<span id="mupp-usage"></span><span id="index-3"></span><h2>The Usage Summary<a class="headerlink" href="#the-usage-summary" title="Permalink to this headline"></a></h2>
<div class="highlight-python"><div class="highlight"><pre><span></span>usage: mupp [OPTIONS] [[--path &lt;fit-param-path&gt;] &lt;fit-param-file-names&gt;]
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>usage: mupp [OPTIONS] [[--path &lt;fit-param-path&gt;] &lt;fit-param-file-names&gt;]
OPTIONS:
-h, --help: this help
@ -200,9 +177,9 @@ SCRIPT COMMANDS:
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<li><a class="reference internal" href="#">mupp - μSR Parameter Plotter</a><ul>
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