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<div class="section" id="mupp-mgrsr-parameter-plotter">
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<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>
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<section id="mupp-mgrsr-parameter-plotter">
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<span id="mupp"></span><span id="index-0"></span><h1>mupp - μSR Parameter Plotter<a class="headerlink" href="#mupp-mgrsr-parameter-plotter" title="Link to this heading"></a></h1>
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<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,
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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.
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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
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@ -184,64 +105,54 @@ The <code class="docutils literal notranslate"><span class="pre">mupp</span></co
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A run is analyzed by a number of parameters (defined in the msr-files), and complemented by
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additional physical parameters as the temperature, magnetic field, implantation energy, etc.
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Hence parameters can be seen as vectors and can be plot against each other.</p>
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<div class="section" id="the-graphical-user-interface">
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<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>
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<section id="the-graphical-user-interface">
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<span id="index-1"></span><h2>The Graphical User Interface<a class="headerlink" href="#the-graphical-user-interface" title="Link to this heading"></a></h2>
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<p>A typical setting could look like this</p>
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<img alt="_images/mupp-gui-0.svg" src="_images/mupp-gui-0.svg" /><ol class="arabic">
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<li><p class="first">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
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<img alt="_images/mupp-gui-0.svg" src="_images/mupp-gui-0.svg" />
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<ol class="arabic">
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<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
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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
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<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>
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</li>
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<li><p class="first">in this list, the data-tags of the currently selected collection is presented. The data-tags can be
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<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>
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<li><p>in this list, the data-tags of the currently selected collection is presented. The data-tags can be
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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
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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
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for the <code class="docutils literal notranslate"><span class="pre">y</span></code>-axis.</p>
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</li>
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<li><p class="first"><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
|
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selection it corresponds to. The numbering of the collection is as given in the collection list.</p>
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</li>
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<li><p class="first"><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
|
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selection it corresponds to. The numbering of the collection is as given in the collection list.</p>
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</li>
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<li><p class="first"><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>
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</li>
|
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<li><p class="first"><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>
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</li>
|
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<li><p class="first"><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>
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</li>
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<li><p class="first"><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>
|
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</li>
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<li><p class="first">Often one would like to compare trends of different settings. In the above example each collections
|
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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
|
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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 <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>
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||||
<li><p class="first">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
|
||||
<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 alt="_images/mupp-plot-0.svg" height="600px" src="_images/mupp-plot-0.svg" /></a>
|
||||
<a class="reference internal image-reference" href="_images/mupp-plot-0.svg"><img alt="_images/mupp-plot-0.svg" src="_images/mupp-plot-0.svg" style="height: 600px;" />
|
||||
</a>
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||||
</li>
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||||
<li><p class="first"><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 class="first"><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 class="first">Command history window.</p>
|
||||
</li>
|
||||
<li><p class="first">This is the script command line. Currently it allows to perform the tasks without mouse gambling.
|
||||
<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>Command history window.</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>
|
||||
commands.</p></li>
|
||||
</ol>
|
||||
<div class="section" id="define-variable-dialog">
|
||||
<h3>Define Variable Dialog<a class="headerlink" href="#define-variable-dialog" title="Permalink to this headline">¶</a></h3>
|
||||
<img alt="_images/mupp-add-var.svg" src="_images/mupp-add-var.svg" /><ol class="arabic simple">
|
||||
<li>Variable text edit window.</li>
|
||||
<li>Collection link window.</li>
|
||||
<li>Shows the parameters of the selected collection.</li>
|
||||
<li>Check if the variable/error variable from the edit window is valid.</li>
|
||||
<li>Add the variable to the selected collection(s) if the parsing is successful.</li>
|
||||
<section id="define-variable-dialog">
|
||||
<h3>Define Variable Dialog<a class="headerlink" href="#define-variable-dialog" title="Link to this heading"></a></h3>
|
||||
<img alt="_images/mupp-add-var.svg" src="_images/mupp-add-var.svg" />
|
||||
<ol class="arabic simple">
|
||||
<li><p>Variable text edit window.</p></li>
|
||||
<li><p>Collection link window.</p></li>
|
||||
<li><p>Shows the parameters of the selected collection.</p></li>
|
||||
<li><p>Check if the variable/error variable from the edit window is valid.</p></li>
|
||||
<li><p>Add the variable to the selected collection(s) if the parsing is successful.</p></li>
|
||||
</ol>
|
||||
<p>A variable defined here is a mathematical expression defined by parameters of loaded collections.
|
||||
Since a parameter also has an associated error, also newly defined variables <strong>always</strong> need
|
||||
@ -249,48 +160,47 @@ to be defined together with a corresponding error variable. If the name of a var
|
||||
as <code class="docutils literal notranslate"><span class="pre">SigmaSC_10</span></code> (see the above snapshot), the error variable need to be named as <code class="docutils literal notranslate"><span class="pre">SigmaSC_10Err</span></code>.</p>
|
||||
<p>Currently the following mathematical functions are defined: <code class="docutils literal notranslate"><span class="pre">max</span></code>, <code class="docutils literal notranslate"><span class="pre">min</span></code>, <code class="docutils literal notranslate"><span class="pre">abs</span></code>, <code class="docutils literal notranslate"><span class="pre">sin</span></code>, <code class="docutils literal notranslate"><span class="pre">cos</span></code>,
|
||||
<code class="docutils literal notranslate"><span class="pre">tan</span></code>, <code class="docutils literal notranslate"><span class="pre">exp</span></code>, <code class="docutils literal notranslate"><span class="pre">log</span></code>, <code class="docutils literal notranslate"><span class="pre">ln</span></code>, <code class="docutils literal notranslate"><span class="pre">pow</span></code>.</p>
|
||||
</div>
|
||||
</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>
|
||||
</section>
|
||||
</section>
|
||||
<section id="the-scripting-interface">
|
||||
<span id="index-2"></span><h2>The Scripting Interface<a class="headerlink" href="#the-scripting-interface" title="Link to this heading"></a></h2>
|
||||
<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="docutils">
|
||||
<dt><strong>loadPath <dir></strong></dt>
|
||||
<dd>set the load path to <code class="docutils literal notranslate"><span class="pre"><dir></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).</dd>
|
||||
<dt><strong>load <coll></strong></dt>
|
||||
<dd>will load the collection <code class="docutils literal notranslate"><span class="pre"><coll></span></code>.</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 <nn></strong></dt>
|
||||
<dd>selects collection <code class="docutils literal notranslate"><span class="pre"><nn></span></code>, where <code class="docutils literal notranslate"><span class="pre"><nn></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.</dd>
|
||||
<dt><strong>x <label></strong></dt>
|
||||
<dd>add <code class="docutils literal notranslate"><span class="pre"><label></span></code> as a <em>x</em>-variable. Only <em>one</em> is allowed.</dd>
|
||||
<dt><strong>y <label(s)></strong></dt>
|
||||
<dd>add <code class="docutils literal notranslate"><span class="pre"><label(s)></span></code> as <em>y</em>-variable. <em>Multiple</em> labels are possible.</dd>
|
||||
<dt><strong>norm</strong></dt>
|
||||
<dd>this will normalize all the <em>y</em>-variables by their maximum.</dd>
|
||||
<dt><strong>savePath <dir></strong></dt>
|
||||
<dd>set the save path to <code class="docutils literal notranslate"><span class="pre"><dir></span></code>. The place where the macros, and/or the plot output will be saved.</dd>
|
||||
<dt><strong>plot <fln></strong></dt>
|
||||
<dd>where <code class="docutils literal notranslate"><span class="pre"><fln></span></code> is the file name with extension under which the plot should be saved.</dd>
|
||||
<dt><strong>macro <fln></strong></dt>
|
||||
<dd>where <code class="docutils literal notranslate"><span class="pre"><fln></span></code> is the file name under which the root macro should be saved.</dd>
|
||||
<dt><strong>var <var_name> = <expr></strong></dt>
|
||||
<dd><p class="first">defines a variable.
|
||||
<dl>
|
||||
<dt><strong>loadPath <dir></strong></dt><dd><p>set the load path to <code class="docutils literal notranslate"><span class="pre"><dir></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 <coll></strong></dt><dd><p>will load the collection <code class="docutils literal notranslate"><span class="pre"><coll></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 <nn></strong></dt><dd><p>selects collection <code class="docutils literal notranslate"><span class="pre"><nn></span></code>, where <code class="docutils literal notranslate"><span class="pre"><nn></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>x <label></strong></dt><dd><p>add <code class="docutils literal notranslate"><span class="pre"><label></span></code> as a <em>x</em>-variable. Only <em>one</em> is allowed.</p>
|
||||
</dd>
|
||||
<dt><strong>y <label(s)></strong></dt><dd><p>add <code class="docutils literal notranslate"><span class="pre"><label(s)></span></code> as <em>y</em>-variable. <em>Multiple</em> labels are possible.</p>
|
||||
</dd>
|
||||
<dt><strong>norm</strong></dt><dd><p>this will normalize all the <em>y</em>-variables by their maximum.</p>
|
||||
</dd>
|
||||
<dt><strong>savePath <dir></strong></dt><dd><p>set the save path to <code class="docutils literal notranslate"><span class="pre"><dir></span></code>. The place where the macros, and/or the plot output will be saved.</p>
|
||||
</dd>
|
||||
<dt><strong>plot <fln></strong></dt><dd><p>where <code class="docutils literal notranslate"><span class="pre"><fln></span></code> is the file name with extension under which the plot should be saved.</p>
|
||||
</dd>
|
||||
<dt><strong>macro <fln></strong></dt><dd><p>where <code class="docutils literal notranslate"><span class="pre"><fln></span></code> is the file name under which the root macro should be saved.</p>
|
||||
</dd>
|
||||
<dt><strong>var <var_name> = <expr></strong></dt><dd><p>defines a variable.
|
||||
<expr> is a mathematical expression where collection variables are addressed
|
||||
via the ‘$’, e.g. <code class="docutils literal notranslate"><span class="pre">dataT</span></code> is addressed by <code class="docutils literal notranslate"><span class="pre">$dataT</span></code>, etc. An example:</p>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">var</span> <span class="pre">invT</span> <span class="pre">=</span> <span class="pre">1000.0</span> <span class="pre">/</span> <span class="pre">$dataT</span></code></p>
|
||||
<p>Each variable has to be accompanied by its error variable. An error variable
|
||||
is defined by the <code class="docutils literal notranslate"><span class="pre"><var_name></span></code> followed by <code class="docutils literal notranslate"><span class="pre">Err</span></code>
|
||||
For the above example the error variable is</p>
|
||||
<p class="last"><code class="docutils literal notranslate"><span class="pre">var</span> <span class="pre">invTErr</span> <span class="pre">=</span> <span class="pre">$invT</span> <span class="pre">*</span> <span class="pre">$dataTErr</span> <span class="pre">/</span> <span class="pre">$dataT</span></code></p>
|
||||
<p><code class="docutils literal notranslate"><span class="pre">var</span> <span class="pre">invTErr</span> <span class="pre">=</span> <span class="pre">$invT</span> <span class="pre">*</span> <span class="pre">$dataTErr</span> <span class="pre">/</span> <span class="pre">$dataT</span></code></p>
|
||||
</dd>
|
||||
<dt><strong>col <nn> : <var_name></strong></dt><dd><p>links <var_name> to the collection <nn>, where <nn> is the number of the
|
||||
collection as defined by the order of load, starting with 0.</p>
|
||||
</dd>
|
||||
<dt><strong>col <nn> : <var_name></strong></dt>
|
||||
<dd>links <var_name> to the collection <nn>, where <nn> is the number of the
|
||||
collection as defined by the order of load, starting with 0.</dd>
|
||||
</dl>
|
||||
<p>An example script file <code class="docutils literal notranslate"><span class="pre">sigmaSC-vs-temp.txt</span></code> might look like this:</p>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># This is a comment
|
||||
@ -338,9 +248,9 @@ macro SigmaSCVsTemp.C
|
||||
# end
|
||||
</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>
|
||||
</section>
|
||||
<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="Link to this heading"></a></h2>
|
||||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>usage: mupp [OPTIONS] [[--path <fit-param-path>] <fit-param-file-names>]
|
||||
|
||||
OPTIONS:
|
||||
@ -384,73 +294,36 @@ SCRIPT COMMANDS:
|
||||
by the order of load, starting with 0.
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</section>
|
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<hr/>
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<div role="contentinfo">
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<p>
|
||||
© Copyright 2023, Andreas Suter.
|
||||
Last updated on Jun 24, 2024.
|
||||
|
||||
</p>
|
||||
<p>© Copyright 2025, Andreas Suter.
|
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<span class="lastupdated">Last updated on Jun 07, 2025.
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