update of the docu which now describes the RRF option.
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<div id="patternMainContents"><div class="patternTop"><span class="patternHomePath foswikiLeft"></span><span class="patternToolBar foswikiRight"><span><a href='TutorialSingleHistoc99a.html?cover=print;cover=print' rel='nofollow' title='Printable version of this topic' accesskey='p'><span class='foswikiAccessKey'>P</span>rint version</a></span><a href="https://intranet.psi.ch/MUSR/TutorialSingleHisto?restrictions=on" id="restriction_link"><img src='../pub/System/PsiSkin/lock_open.png' class='lock' height='16' width='23' title='open in PSI - click for more information'/></a></span><div class="foswikiClear"></div></div><div class="foswikiContentHeader">
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</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="A_61_61musrfit_61_61_Single_45Histogram_45Fit_Tutorial"></a> <code><b>musrfit</b></code> Single-Histogram-Fit Tutorial </h1>
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<div class="patternContent"><div class="foswikiTopic"> <h1 id="A_61_61musrfit_61_61_Single_45Histogram_45Fit_Tutorial"> <code><b>musrfit</b></code> Single-Histogram-Fit Tutorial </h1>
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<p></p>
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The μSR-data-analysis process using <code>musrfit</code> is based on so-called <code>msr</code> files. These files contain all information needed for the analysis such as names of the data files, a theory function, fit and plot parameters, and so on. It is the idea of this page to explain the basic use of an <code>msr</code> file and the different programs of the <code>musrfit</code> suite using the example of a single-histogram fit to time-differential transverse-field μSR data. For a complete description of all options please refer to the <a href="MusrFit.html">manual</a>.
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<p></p>
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The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html" target="_top">GPS spectrometer</a> at <a href="http://www.psi.ch/" target="_top">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50° up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.
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The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html">GPS spectrometer</a> at <a href="http://www.psi.ch/">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50° up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.
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<p></p>
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To analyze these data (in a simple way) one starts out from the <code>msr</code> file <strong>3110_tutorial.msr</strong> provided together with the source-code distribution in the sub-directory <strong>doc/examples/</strong>. This ASCII file can be edited using any text editor. For convenience the editors <code>musredit</code>/<code>musrgui</code> are provided which offer some <code>msr</code>-file-specific functionalities and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is open within <code>musredit</code>.
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<p></p>
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<h1><a name="A_1_The_61msr_61_file"></a> 1 The <code>msr</code> file </h1>
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<h1 id="A_1_The_61msr_61_file"> 1 The <code>msr</code> file </h1>
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<p></p>
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The <code>msr</code> file itself is divided into different blocks—a full description of the format can be found <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">here</a>.
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In the file <strong>3110_tutorial.msr</strong> these blocks are successively: <ul>
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@ -232,129 +269,138 @@ STATISTIC --- 2011-07-09 10:58:44
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</pre> This block is the last block of a <code>msr</code> file. It contains some information on the fit: the date and time as well as the absolute and normalized values of χ<sup>2</sup> and the number of degrees of freedom in the fit.<br> These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged!
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</li></ul>
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<p></p>
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<h1><a name="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"></a> 2 Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1>
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<h1 id="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"> 2 Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1>
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Before the given model can be fitted to the data, the data ranges and time zeros of the different RUN blocks have to be set correctly. This can be achieved using <code><a href="MusrFit.html#MusrT0">musrt0</a></code>. Starting this program by selecting the <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrt0 3110_tutorial.msr</pre> opens an interactive window plotting the data of the first RUN block:<br />
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<img src="../pub/MUSR/TutorialSingleHisto/musrt0-1.png" alt="musrt0-1" align="center" /><br />
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<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrt0-1.png' alt='musrt0-1' title='musrt0-1.png' width='708' height='529' style='' /><br />
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The green line (at bin 1) represents time zero, the blue lines the start (at bin 1) and end (at bin 8000) of the data range and the optional red lines give the limits of the background range (if the background shall not be determined by the fit). All lines can be either dragged to reasonable locations or set by pressing the corresponding keyboard shortcuts. In the example the time zero can be set by pressing <strong>T</strong> (which moves the green line to the bin containing the maximum number of counts), the start of the data range should be set to about five bins later by zooming into the graph around bin 250 and pressing <strong>d</strong> when the cursor is found at a suitable location:<br />
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<img src="../pub/MUSR/TutorialSingleHisto/musrt0-2.png" alt="musrt0-2" width='708' height='529' align="center" /><br />
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<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/igp_dabb07604d494aa45c41710849314460_musrt0-2.png' alt='musrt0-2' title='musrt0-2.png' width='688' height='529' style='' /><br />
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After all lines have been adjusted for the first histogram, one can go on to the second by pressing <strong>q</strong>. This procedure is repeated until all ranges have been set correctly. When finished with the last histogram the new <i>t</i><sub>0</sub> and data-range values will be written to the <code>msr</code> file.
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A full description of <code>musrt0</code> can be found <a href="MusrFit.html#MusrT0">here</a>.
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<p></p>
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<h1><a name="A_3_Fit_the_model_to_the_data_using_61musrfit_61"></a> 3 Fit the model to the data using <code>musrfit</code> </h1>
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Now that the basics of the <code>msr</code> file have been introduced and the necessary adjustments have been done one can proceed with fitting the specified model to the data. This is done by selecting the <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrfit 3110_tutorial.msr</pre>
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<h1 id="A_3_Fit_the_model_to_the_data_using_61musrfit_61"> 3 Fit the model to the data using <code>musrfit</code> </h1>
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Now that the basics of the <code>msr</code> file have been introduced and the necessary adjustments have been done one can proceed with fitting the specified model to the data. This is done by selecting the <img src="../pub/MUSR/MusrGui/musrfit.png" alt="musrfit.png" /> button in <code>musredit</code> or calling from a terminal <pre>musrfit 3110_tutorial.msr</pre>
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<p></p>
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After the fitting procedure has finished the <code>msr</code> file is updated and contains the newly determined values of the fit parameters.
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<p></p>
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<h1><a name="A_4_View_the_data_and_the_fit_using_61musrview_61"></a> 4 View the data and the fit using <code>musrview</code> </h1>
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<h1 id="A_4_View_the_data_and_the_fit_using_61musrview_61"> 4 View the data and the fit using <code>musrview</code> </h1>
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The data and the corresponding fit can be visualized by choosing <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> in <code>musredit</code> or calling from a terminal <pre>musrview 3110_tutorial.msr</pre> This creates the windows according to the given PLOT blocks in the <code>msr</code> file:<br />
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<img src="../pub/MUSR/TutorialSingleHisto/musrview-1.png" alt="musrview-1" align="center" /><br />
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<img src="../pub/MUSR/TutorialSingleHisto/musrview-2.png" alt="musrview-2" align="center" /><br />
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<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-1.png' alt='musrview-1' title='musrview-1.png' width='808' height='629' style='' /><br />
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<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-2.png' alt='musrview-2' title='musrview-2.png' width='808' height='629' style='' /><br />
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The basic features of <code>musrview</code> can be found in the Musrfit menu. They include: <ul>
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<li> export the shown data and the model to an ASCII file with comma-separated values
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</li> <li> presenting the difference between the shown data and the model (keyboard shortcut: <strong>d</strong>)
|
||||
</li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br /> <img src="../pub/MUSR/TutorialSingleHisto/musrview-3.png" alt="musrview-3" align="center" /><br />
|
||||
</li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br /> <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-3.png' alt='musrview-3' title='musrview-3.png' width='808' height='629' style='' /><br />
|
||||
</li></ul>
|
||||
<p></p>
|
||||
<h1><a name="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"></a> 5 Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
|
||||
<h1 id="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"> 5 Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
|
||||
This short introduction is concluded by calling attention to the program <code><a href="Msr2Data.html">msr2data</a></code>. As the name indicates the main purpose of this program is to extract the FITPARAMETER-block information from multiple <code>msr</code> files with the same structure and to summarize them in a single ASCII file (either in TRIUMF DB format or simple columns). However, as described in detail in the <code><a href="Msr2Data.html">manual</a></code>, it is not only possible to collect data from <code>msr</code> files but also to create new <code>msr</code> files from a template and to process these files using <code>musrfit</code> on the fly.<br>
|
||||
Assuming the successive runs <strong>3111</strong> through <strong>3114</strong> can be analyzed using the same model introduced above for run <strong>3110</strong> (e.g. in the case one has done measurements at different temperatures) one can use the file <strong>3110_tutorial.msr</strong> as template, generate the files <strong>3111_tutorial.msr</strong> through <strong>3114_tutorial.msr</strong> with the corresponding updates in the RUN blocks, call for each one <code>musrfit</code> and finally summarize the FITPARAMETER-block information of all processed files in an ASCII output file <strong>tutorial-T-dependence.dat</strong> (simple columns). If further information on the temperature or the applied field is available in the data files these will be included as well in the resulting ASCII file.<br>
|
||||
From the terminal this would be done as follows:<pre>
|
||||
msr2data 3110 3114 _tutorial fit-3110 -o tutorial-T-dependence.dat data
|
||||
</pre>
|
||||
To achieve the same in <code>musredit</code> one selects <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> and fills the form accordingly:<br />
|
||||
<img src="../pub/MUSR/TutorialSingleHisto/msr2data.png" alt="msr2data" align="center" />
|
||||
<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/msr2data.png' alt='msr2data' title='msr2data.png' width='612' height='605' style='' />
|
||||
<p></p>
|
||||
<h1><a name="A_6_Further_reading"></a> 6 Further reading </h1>
|
||||
<h1 id="A_6_Further_reading"> 6 Further reading </h1>
|
||||
This page only summarizes the very basic features and options of the programs contained in the <code>musrfit</code> suite. For a complete description please refer to the manuals of <ul>
|
||||
<li> <code><a href="MusrFit.html">musrfit</a></code> (including <code><a href="MusrFit.html#MusrFit">musrfit</a></code>, <code><a href="MusrFit.html#MusrView">musrview</a></code>, <code><a href="MusrFit.html#MusrT0">musrt0</a></code> and the full description of the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat"><code>msr</code>-file format</a>)
|
||||
</li> <li> <code><a href="MusrGui.html">musredit</a></code>
|
||||
</li> <li> <code><a href="Msr2Data.html">msr2data</a></code>.
|
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<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-3.png' /></span><span class="foswikiHidden">png</span> </td>
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<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-3.png">musrview-3.png</a> </td>
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<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-3.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
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<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 42 K </td>
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<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">09 Jul 2011 - 16:01</span> </td>
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<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
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<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> </td>
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</tr>
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<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'> > </span>TutorialSingleHisto <br />
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Topic revision: <span class='patternRevInfo'>02 Sep 2011, wojek</span></div>
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</div>
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</div></div><!-- /endWrap -->
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Reference in New Issue
Block a user