update of the docu for version 1.6.0
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@ -4,7 +4,7 @@
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<html xmlns="http://www.w3.org/1999/xhtml">
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<head>
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<meta charset="utf-8" />
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<title>mupp - μSR Parameter Plotter — musrfit 1.5.2 documentation</title>
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<title>mupp - μSR Parameter Plotter — musrfit 1.6.0 documentation</title>
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<link rel="stylesheet" href="_static/nature.css" type="text/css" />
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<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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<script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
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@ -30,7 +30,7 @@
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<li class="right" >
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<a href="musredit.html" title="musredit: the GUI Based Interface to musrfit"
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accesskey="P">previous</a> |</li>
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<li class="nav-item nav-item-0"><a href="index.html">musrfit 1.5.2 documentation</a> »</li>
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<li class="nav-item nav-item-0"><a href="index.html">musrfit 1.6.0 documentation</a> »</li>
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</ul>
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</div>
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@ -47,6 +47,10 @@ Also a collection of <code class="docutils literal notranslate"><span class="pre
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<a class="reference external" href="http://musr.org/muview/">here</a>).</p>
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<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.
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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>
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<p>Each collection bundles a number of runs, where a run is a single μSR measurement.
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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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<p>A typical setting could look like this</p>
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@ -79,17 +83,34 @@ present the data, as shown here</p>
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<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>
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<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
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during beamtime where the collection is growing run-by-run.</p></li>
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<li><p>Command history window.</p></li>
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<li><p>This is the script command line. Currently it allows to perform the tasks without mouse gambling.
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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
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commands.</p></li>
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</ol>
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<div class="section" id="define-variable-dialog">
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<h3>Define Variable Dialog<a class="headerlink" href="#define-variable-dialog" title="Permalink to this headline">¶</a></h3>
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<img alt="_images/mupp-add-var.svg" src="_images/mupp-add-var.svg" /><ol class="arabic simple">
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<li><p>Variable text edit window.</p></li>
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<li><p>Collection link window.</p></li>
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<li><p>Shows the parameters of the selected collection.</p></li>
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<li><p>Check if the variable/error variable from the edit window is valid.</p></li>
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<li><p>Add the variable to the selected collection(s) if the parsing is successful.</p></li>
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</ol>
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<p>A variable defined here is a mathematical expression defined by parameters of loaded collections.
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Since a parameter also has an associated error, also newly defined variables <strong>always</strong> need
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to be defined together with a corresponding error variable. If the name of a variable is defined
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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>
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<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>,
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<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>
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</div>
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</div>
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<div class="section" id="the-scripting-interface">
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<span id="index-2"></span><h2>The Scripting Interface<a class="headerlink" href="#the-scripting-interface" title="Permalink to this headline">¶</a></h2>
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<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,
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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
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<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>
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<dl class="simple">
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<dl>
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<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>
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</dd>
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<dt><strong>load <coll></strong></dt><dd><p>will load the collection <code class="docutils literal notranslate"><span class="pre"><coll></span></code>.</p>
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@ -99,9 +120,11 @@ or web-based interaction which requests figures. A script is invoked by the comm
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<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>
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select YBCO-40nm-T5K-FC150mT-Escan.db.</p>
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</dd>
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<dt><strong>addX <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>
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<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>
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</dd>
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<dt><strong>addY <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>
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<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>
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</dd>
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<dt><strong>norm</strong></dt><dd><p>this will normalize all the <em>y</em>-variables by their maximum.</p>
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</dd>
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<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>
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</dd>
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@ -109,28 +132,63 @@ select YBCO-40nm-T5K-FC150mT-Escan.db.</p>
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</dd>
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<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>
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</dd>
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<dt><strong>var <var_name> = <expr></strong></dt><dd><p>defines a variable.
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<expr> is a mathematical expression where collection variables are addressed
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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">$dataT</span></code>, etc. An example:</p>
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<p><code class="docutils literal notranslate"><span class="pre">var</span> <span class="pre">invT</span> <span class="pre">=</span> <span class="pre">1000.0</span> <span class="pre">/</span> <span class="pre">$dataT</span></code></p>
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<p>Each variable has to be accompanied by its error variable. An error variable
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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>
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For the above example the error variable is</p>
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<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>
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</dd>
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<dt><strong>col <nn> : <var_name></strong></dt><dd><p>links <var_name> to the collection <nn>, where <nn> is the number of the
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collection as defined by the order of load, starting with 0.</p>
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</dd>
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</dl>
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<p>An example script file <code class="docutils literal notranslate"><span class="pre">field-vs-energy.txt</span></code> might look like this:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># This is a comment</span>
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<p>An example script file <code class="docutils literal notranslate"><span class="pre">sigmaSC-vs-temp.txt</span></code> might look like this:</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># This is a comment
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# Script: sigmaSC-vs-temp.txt
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<span class="n">loadPath</span> <span class="o">./</span>
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loadPath ./
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<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>
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<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>
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<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>
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<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>
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load YBCO-40nm-FC-E3p8keV-B10mT-Tscan.db # collection 0
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load YBCO-40nm-FC-E3p8keV-B150mT-Tscan.db # collection 1
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<span class="n">selectAll</span>
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# define variables: for each variable an associated error variable is needed.
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# B=10mT
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var SigmaSC_10 = pow(abs(pow($Sigma,2.0)-pow(0.11,2.0)), 0.5) # 0.11 (1/us) is the nuclear contribution (T>Tc)
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var SigmaSC_10Err = pow(pow($Sigma*$SigmaErr,2.0)+pow(0.11*0.0025,2.0), 0.5)/$SigmaSC_10
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# B=150mT
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var SigmaSC_150 = pow(abs(pow($Sigma,2.0)-pow(0.075,2.0)), 0.5) # 0.075 (1/us) is the nuclear contribution (T>Tc)
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var SigmaSC_150Err = pow(pow($Sigma*$SigmaErr,2.0)+pow(0.075*0.0025,2.0), 0.5)/$SigmaSC_150
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<span class="n">addX</span> <span class="n">dataE</span>
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<span class="n">addY</span> <span class="n">Field</span>
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# link variables to collections
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col 0 : SigmaSC_10 # error variable SigmaSC_10Err doesn't need to be given, it is automatically linked to SigmaSC_10
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col 1 : SigmaSC_150
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<span class="n">savePath</span> <span class="o">./</span>
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<span class="n">plot</span> <span class="n">FieldVsEnergy</span><span class="o">.</span><span class="n">pdf</span>
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norm # normalize the plot to the maximum of each y-data-set
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<span class="n">macro</span> <span class="n">FieldVsEnergy</span><span class="o">.</span><span class="n">C</span>
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# the next 3 cmds means the following: use collection 0, add dataT to the x-axis,
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# and SigmaSC_10 to the y-axis
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select 0
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x dataT
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y SigmaSC_10
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<span class="c1"># end</span>
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select 1
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x dataT
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y SigmaSC_150
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# where to save the output
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savePath ./
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# create a pdf output file of the above defined xy-data sets. Currently also
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# other file formats are supported, like png, jpg, etc.
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plot SigmaSCVsTemp.pdf
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# creates a ROOT macro which can be used for further refinement
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macro SigmaSCVsTemp.C
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# end
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</pre></div>
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</div>
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</div>
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@ -146,28 +204,37 @@ OPTIONS:
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<fit-param-file-names>: list of file name(s) to be loaded.
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allowed formats are: db, dat, msr
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SCRIPT COMMANDS:
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Lines starting with '#', '%', or '//' are comments and will be ignored.
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The same is true for empty lines. Comments are also allowed at the end
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for a command, i.e. loadPath ./ # the best place ever.
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loadPath <dir> : set the load path to <dir>. Bash variables like
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$HOME are accepted.
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load <coll> : will load a collection <coll>. Currently *.db and *.dat
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are handled.
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selectAll : will select all loaded collections. Thie means every plot
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of variable x/y will be carried out to ALL collections.
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select <nn> : selects collection <nn>, where <nn> is either the number
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of the collections, or its name, e.g.
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select YBCO-40nm-T5K-FC150mT-Escan.db
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addX <label> : add <label> as a x-variable. Only one is allowed.
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addY <label(s)>: add <label(s)> as y-variable. Multiple labls are possible.
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savePath <dir> : set the save path to <dir>. The place where the macros,
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and/or the plot output will be saved.
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plot <fln> : where <fln> is the file name with extension under which
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the plot should be saved.
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macro <fln> : where <fln> is the file name under which the root macro
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should be saved.
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SCRIPT COMMANDS:
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Lines starting with '#', '%', or '//' are comments and will be ignored.
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The same is true for empty lines. Comments are also allowed at the end
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for a command, i.e. loadPath ./ # the best place ever.
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load <coll> : load a collection. <coll> is the filename of the
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collection (*.db, *.dat)
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loadPath <path> : set the load path to <path>; accepting bash variables
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like $HOME, etc.
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x <var-name> : set a x-axis variable. <var-name> is a data tag of
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the db/dat-file.
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y <var-name> : set a y-axis variable. <var-name> is a data tag of
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the db/dat-file.
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select <nn> : select collection <nn>, where <nn> is the row-number
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or the name of the collection to be selected.
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selectAll : i.e. already set 'x', 'y' will apply to ALL collections
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present.
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savePath <path> : sets the save path to <path>; accepting bash variables
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like $HOME, etc.
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plot <fln> : where <fln> is the file name with extension under which
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the plot should be saved.
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macro <fln> : where <fln> is the file name under which the root macro
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should be saved.
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var <var_name> = <expr> : defines a variable.
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<expr> is a mathematical expression where
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collection variables are addressed via the '$',
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e.g. dataT is addressed by $dataT, etc.
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col <nn> : <var_name> : links <var_name> to the collection <nn>, where
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<nn> is the number of the collection as defined
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by the order of load, starting with 0.
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</pre></div>
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</div>
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</div>
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@ -182,7 +249,10 @@ SCRIPT COMMANDS:
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<h3><a href="index.html">Table of Contents</a></h3>
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<ul>
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<li><a class="reference internal" href="#">mupp - μSR Parameter Plotter</a><ul>
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<li><a class="reference internal" href="#the-graphical-user-interface">The Graphical User Interface</a></li>
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<li><a class="reference internal" href="#the-graphical-user-interface">The Graphical User Interface</a><ul>
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<li><a class="reference internal" href="#define-variable-dialog">Define Variable Dialog</a></li>
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</ul>
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</li>
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<li><a class="reference internal" href="#the-scripting-interface">The Scripting Interface</a></li>
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<li><a class="reference internal" href="#the-usage-summary">The Usage Summary</a></li>
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</ul>
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@ -228,13 +298,13 @@ SCRIPT COMMANDS:
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<li class="right" >
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<a href="musredit.html" title="musredit: the GUI Based Interface to musrfit"
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>previous</a> |</li>
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||||
<li class="nav-item nav-item-0"><a href="index.html">musrfit 1.5.2 documentation</a> »</li>
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<li class="nav-item nav-item-0"><a href="index.html">musrfit 1.6.0 documentation</a> »</li>
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</ul>
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</div>
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<div class="footer" role="contentinfo">
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© Copyright 2020, Andreas Suter.
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Last updated on Feb 04, 2020.
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Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.1.2.
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Last updated on May 15, 2020.
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Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.2.2.
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</div>
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</body>
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</html>
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