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<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>BmwLibs <br />
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Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
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<h1 id="libFitPofB"> libFitPofB </h1>
<div id="foswikiTOC" class="foswikiToc"> <ul>
<div class="foswikiToc" id="foswikiTOC"> <ul>
<li> <a href="LibFitPofB.html#libFitPofB"> libFitPofB </a>
</li> <li> <a href="LibFitPofB.html#A_1_Introduction"> 1 Introduction </a>
</li> <li> <a href="LibFitPofB.html#A_2_LE_45SR"> 2 LE-&mu;SR </a> <ul>
@ -148,7 +148,7 @@ where <img alt="\gamma&#95;{\mu} &#61; 2\pi\times 135.54~\mathrm{MHz/T}" class="
At the moment the only available implementations deal with field distributions measured in local isotropic superconductors, either by means of <a href="http://lmu.web.psi.ch/lem/">low-energy &mu;SR</a> in the Meissner state or by conventional &mu;SR in the mixed state. In the following the basic usage of the library in <code>musrfit</code> is explained&mdash;the calculations by themselves are only outlined. For further information please refer to the original literature and/or the source code of the implementation.
<p></p>
<hr />
<strong><span class='foswikiBlackFG'>Remark 1:</span></strong> In order to supply certain information needed for the calculations but not suited to be stored in the <code>musrfit</code> msr files an XML configuration file in the working directory is used. For details, see <a href="#XmlFile" class="foswikiCurrentTopicLink">below</a>.
<strong><span class='foswikiBlackFG'>Remark 1:</span></strong> In order to supply certain information needed for the calculations but not suited to be stored in the <code>musrfit</code> msr files an XML configuration file in the working directory is used. For details, see <a class="foswikiCurrentTopicLink" href="#XmlFile">below</a>.
<p></p>
<strong><span class='foswikiBlackFG'>Remark 2:</span></strong> The implementations in this library heavily rely on <code><a href="http://www.fftw.org/">FFTW3</a></code>. In principle, it always checks what is the best way to do efficient Fourier transforms for a given machine before the transforms are actually done. If repeatedly Fourier transforms of the same (sizable) length should be done, it might be worth storing the once obtained information in an external file and just load it the next time this information is needed (<a href="http://fftw.org/fftw3_doc/Wisdom.html">"wisdom handling"</a>). In case this feature shall be used, a valid wisdom file has to be specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML file</a>.
<p></p>
@ -262,7 +262,7 @@ The optional parameters are: <ol>
<p></p>
Notes
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<a name="FootNote1note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="LibFitPofB.html#FootNote1text"> <strong>1</strong> </a></span>: <span class="FootNote">F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34</span>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>1</b></a></span>: <span class="FootNote">F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34</span>
<p></p>
<p></p>
<p></p>
@ -277,8 +277,8 @@ When investigating superconductors in the mixed state by means of conventional &
</p>
where <img alt="\mathbf{r}&#61;(x,y)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e47f33589d28eaa3f9baccb7a80fdbaa.png" title="r" />, <img alt="\mathbf{K}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e6688a12ee4e821abc31b4c1dd511539.png" title="K" /> are the reciprocal lattice vectors of a two-dimensional vortex lattice and the <img alt="B&#95;{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> are the Fourier coefficients depending on the magnetic penetration depth <img alt="\lambda" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_28f3ed750a4819b4256c2f9be649f594.png" title="lambda" /> and the superconducting coherence length <img alt="\xi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e8414d477977d226317c020980b7d34f.png" title="xi" />. The <img alt="B&#95;{\mathbf{K}}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_8fa3ac8f18b7bc49eb89163d6528684c.png" title="Bk" /> for some specific models are as follows: <dl>
<dt> London model with Gaussian cutoff<a name="FootNote2text"></a><span class="FootNoteTextLink" title="E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1007&#47;BF00683568&#93;&#91;J&#46; Low Temp&#46; Phys&#46; &#42;73&#42;&#44; 355 &#40;1988&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote2note">(2)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2}\right)}{1 + K^2\lambda^2}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_469d5d1b83125e4915e2f073d8150b12.png" title="BkLondon" /></p>
</dd> <dt> Modified London model<a name="FootNote3text"></a><span class="FootNoteTextLink" title="T&#46;M&#46; Riseman _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;52&#46;10569&#93;&#91;Phys&#46; Rev&#46; B &#42;52&#42;&#44; 10569 &#40;1995&#41;&#93;&#93;&#46;"><a href="#FootNote3note" class="foswikiCurrentTopicLink">(3)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_b6719fad8e30208538b34bc94040b7a5.png" title="BkML" /></p> where <img alt="b &#61; \langle B \rangle/\mu&#95;0H&#95;{\mathrm{c}2}." class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_039b3b38df7c6f284089c14f1efdf643.png" title="b" />
</dd> <dt> Analytical Ginzburg-Landau model<a name="FootNote4text"></a><span class="FootNoteTextLink" title="A&#46; Yaouanc&#44; P&#46; Dalmas de R&#38;eacute&#59;otier and E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;55&#46;11107&#93;&#91;Phys&#46; Rev&#46; B &#42;55&#42;&#44; 11107 &#40;1997&#41;&#93;&#93;&#46;"><a href="#FootNote4note" class="foswikiCurrentTopicLink">(4)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{f&#95;{\infty}K&#95;1\left(\frac{\xi&#95;v}{\lambda}\sqrt{f&#95;{\infty}^2+\lambda^2K^2}\right)}{K&#95;1\left(\frac{\xi&#95;v}{\lambda}f&#95;{\infty}\right)\sqrt{f&#95;{\infty}^2+\lambda^2K^2}}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3146cb17887e3a20cc2078f103605af5.png" title="BkAGL" /></p> where <img alt="f&#95;{\infty} &#61; 1 - b^4,~\xi&#95;v &#61; \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e0b0e98f9a3974249b42b6910523c8a4.png" title="f_inf_and_xi_v" /> and <img alt="K&#95;1" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3cee3cc69dbe918398ec39a72a465014.png" title="K1" /> is a modified Bessel function.
</dd> <dt> Modified London model<a name="FootNote3text"></a><span class="FootNoteTextLink" title="T&#46;M&#46; Riseman _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;52&#46;10569&#93;&#91;Phys&#46; Rev&#46; B &#42;52&#42;&#44; 10569 &#40;1995&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote3note">(3)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{\exp\left({-K^2\xi^2/2(1-b)}\right)}{1 + K^2\lambda^2/(1-b)}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_b6719fad8e30208538b34bc94040b7a5.png" title="BkML" /></p> where <img alt="b &#61; \langle B \rangle/\mu&#95;0H&#95;{\mathrm{c}2}." class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_039b3b38df7c6f284089c14f1efdf643.png" title="b" />
</dd> <dt> Analytical Ginzburg-Landau model<a name="FootNote4text"></a><span class="FootNoteTextLink" title="A&#46; Yaouanc&#44; P&#46; Dalmas de R&#38;eacute&#59;otier and E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;55&#46;11107&#93;&#91;Phys&#46; Rev&#46; B &#42;55&#42;&#44; 11107 &#40;1997&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote4note">(4)</a></span> </dt><dd> <p style="text-align:center"><img alt="B&#95;{\mathbf{K}} &#61; \frac{f&#95;{\infty}K&#95;1\left(\frac{\xi&#95;v}{\lambda}\sqrt{f&#95;{\infty}^2+\lambda^2K^2}\right)}{K&#95;1\left(\frac{\xi&#95;v}{\lambda}f&#95;{\infty}\right)\sqrt{f&#95;{\infty}^2+\lambda^2K^2}}," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3146cb17887e3a20cc2078f103605af5.png" title="BkAGL" /></p> where <img alt="f&#95;{\infty} &#61; 1 - b^4,~\xi&#95;v &#61; \xi\left(\sqrt{2}-{3\xi}/\left({4\lambda}\right)\right)\sqrt{(1+b^4)(1-2b(1-b)^2)}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_e0b0e98f9a3974249b42b6910523c8a4.png" title="f_inf_and_xi_v" /> and <img alt="K&#95;1" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_3cee3cc69dbe918398ec39a72a465014.png" title="K1" /> is a modified Bessel function.
</dd></dl>
Apart from the mentioned analytical models the <strong>numerical Ginzburg-Landau model</strong> <a name="FootNote5text"></a><span class="FootNoteTextLink" title="E&#46;H&#46; Brandt&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1103&#47;PhysRevB&#46;68&#46;054506&#93;&#91;Phys&#46; Rev&#46; B &#42;68&#42;&#44; 054506 &#40;2003&#41;&#93;&#93;&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote5note">(5)</a></span> is available. In this case <img alt="B(\mathbf{r})" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_373e9bf1fc97e2c6aacf93bcc090402c.png" title="BofR" /> is obtained by an iterative minimization of the free energy of the vortex lattice.
<p></p>
@ -343,13 +343,13 @@ SAVE
<p></p>
Notes
<p></p>
<a name="FootNote2note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="LibFitPofB.html#FootNote2text"> <strong>2</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span>
<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text"><b>2</b></a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span>
<p></p>
<a name="FootNote3note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="LibFitPofB.html#FootNote3text"> <strong>3</strong> </a></span>: <span class="FootNote">T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span>
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text"><b>3</b></a></span>: <span class="FootNote">T.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span>
<p></p>
<a name="FootNote4note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="LibFitPofB.html#FootNote4text"> <strong>4</strong> </a></span>: <span class="FootNote">A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span>
<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="#FootNote4text"><b>4</b></a></span>: <span class="FootNote">A. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span>
<p></p>
<a name="FootNote5note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="LibFitPofB.html#FootNote5text"> <strong>5</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span>
<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="#FootNote5text"><b>5</b></a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span>
<p></p>
<p></p>
<p></p>
@ -409,12 +409,12 @@ An example XML file looks as follows:
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Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
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</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:andre.lichtsteiner@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.LibFitPofB'>Send feedback</a></div></div></div>
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@ -428,6 +428,6 @@ Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
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@ -1,6 +1,6 @@
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@ -14,14 +14,14 @@
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<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
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@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -104,15 +104,15 @@
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@ -125,7 +125,7 @@
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<span id="TopIc"></span>
<h1 id="libZFRelaxation"> libZFRelaxation </h1>
<div id="foswikiTOC" class="foswikiToc"> <ul>
<div class="foswikiToc" id="foswikiTOC"> <ul>
<li> <a href="LibZFRelaxation.html#libZFRelaxation"> libZFRelaxation </a>
</li> <li> <a href="LibZFRelaxation.html#A_1_Introduction"> 1 Introduction </a>
</li> <li> <a href="LibZFRelaxation.html#A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"> 2 Isotropic static Gaussian broadened randomly oriented internal fields </a>
@ -214,12 +214,12 @@ The parameters are: <ol>
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@ -233,6 +233,6 @@ Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
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78
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@ -1,6 +1,6 @@
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<h1 id="A_61_61msr2data_61_61"> <code><b>msr2data</b></code> </h1>
<p></p>
<div id="foswikiTOC" class="foswikiToc"> <ul>
<div class="foswikiToc" id="foswikiTOC"> <ul>
<li> <a href="Msr2Data.html#A_61_61msr2data_61_61"> msr2data </a>
</li> <li> <a href="Msr2Data.html#A_1_Introduction"> 1 Introduction </a>
</li> <li> <a href="Msr2Data.html#A_2_Basic_Types_of_Usage"> 2 Basic Types of Usage </a>
@ -178,18 +178,18 @@ body .foswikiTable#tableMsr2Data1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol
<p></p>
<span id="IntroDuction"></span>
<h1 id="A_1_Introduction"> 1 Introduction </h1>
<code>msr2data</code> (originally written by B. M. Wojek) is a program implemented in <code>C++</code>. Its purpose is to process multiple <code><a href="MusrFit.html">musrfit</a></code> msr files with the same parameters and summarize the fitting results either in a TRIUMF <strong>DB</strong> <a name="FootNote1text"></a><span class="FootNoteTextLink" title=" For an abridged description of this format see &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;xyfit&#47;dbformat&#46;html&#93;&#91;here&#93;&#93;&#46; The &#42;DB&#42; files produced by &#61;msr2data&#61; can be viewed for instance with &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;muview&#47;&#93;&#91;&#38;mu&#59;View&#93;&#93;&#44; however&#44; they are <em>not completely</em> backward&#45;compatible to the original &#34;db language&#34; since the parameter names can be longer than five or six characters&#33; In order to establish this backward compatibility &#40;if needed&#41; the user has to ensure the correct length of the parameter names in the msr files&#33;"><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span> or a <strong>column ASCII</strong> file. It evolved from a script called <code>mlog2db</code> which has been written only for collecting fit results of <a href="http://lmu.web.psi.ch/lem/">LEM</a> data stored in mlog files generated by <code>musrfit</code> and putting them together in a file with the <strong>DB</strong> format for further analysis. Therefore, any peculiarities, e.g. in supplying options to <code>msr2data</code> are owed its original purpose.
<code>msr2data</code> (originally written by B. M. Wojek) is a program implemented in <code>C++</code>. Its purpose is to process multiple <code><a href="MusrFit.html">musrfit</a></code> msr files with the same parameters and summarize the fitting results either in a TRIUMF <strong>DB</strong> <a name="FootNote1text"></a><span class="FootNoteTextLink" title=" For an abridged description of this format see &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;xyfit&#47;dbformat&#46;html&#93;&#91;here&#93;&#93;&#46; The &#42;DB&#42; files produced by &#61;msr2data&#61; can be viewed for instance with &#91;&#91;http&#58;&#47;&#47;musr&#46;org&#47;muview&#47;&#93;&#91;&#38;mu&#59;View&#93;&#93;&#44; however&#44; they are <em>not completely</em> backward&#45;compatible to the original &#34;db language&#34; since the parameter names can be longer than five or six characters&#33; In order to establish this backward compatibility &#40;if needed&#41; the user has to ensure the correct length of the parameter names in the msr files&#33;"><a class="foswikiCurrentTopicLink" href="#FootNote1note">(1)</a></span> or a <strong>column ASCII</strong> file. It evolved from a script called <code>mlog2db</code> which has been written only for collecting fit results of <a href="http://lmu.web.psi.ch/lem/">LEM</a> data stored in mlog files generated by <code>musrfit</code> and putting them together in a file with the <strong>DB</strong> format for further analysis. Therefore, any peculiarities, e.g. in supplying options to <code>msr2data</code> are owed its original purpose.
<code>msr2data</code> is <a href="http://www.gnu.org/philosophy/free-sw.html">free software</a> and licensed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GNU GPL version 2</a> or any later version (at your option).
<p></p>
Before the usage of msr2data will be explained in greater detail first be aware of the following:
<p></p>
<strong><span class='foswikiRedFG'>If using msr2data always bear in mind <a href="#KnownLimitations" class="foswikiCurrentTopicLink">its limitations</a>!</span></strong>
<strong><span class='foswikiRedFG'>If using msr2data always bear in mind <a class="foswikiCurrentTopicLink" href="#KnownLimitations">its limitations</a>!</span></strong>
<p></p>
<p></p>
<p></p>
Notes
<p></p>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="Msr2Data.html#FootNote1text" class="foswikiCurrentWebHomeLink"> <strong>1</strong> </a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!</span>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>1</b></a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/">&mu;View</a>, however, they are <em>not completely</em> backward-compatible to the original "db language" since the parameter names can be longer than five or six characters! In order to establish this backward compatibility (if needed) the user has to ensure the correct length of the parameter names in the msr files!</span>
<p></p>
<p></p>
<p></p>
@ -197,19 +197,19 @@ Notes
<p></p>
<span id="BasicTypesOfUsage"></span>
<h1 id="A_2_Basic_Types_of_Usage"> 2 Basic Types of Usage </h1>
Apart from numerous <a href="#OptionalParameters" class="foswikiCurrentTopicLink">optional parameters</a> that might be set or not, in principle there are four different ways of calling <code>msr2data</code>. These differ in how the list of runs which should be processed is supplied: <dl>
Apart from numerous <a class="foswikiCurrentTopicLink" href="#OptionalParameters">optional parameters</a> that might be set or not, in principle there are four different ways of calling <code>msr2data</code>. These differ in how the list of runs which should be processed is supplied: <dl>
<dt> msr2data &lt;run&gt; &lt;extension&gt; [optional parameters] </dt><dd> A single run number.
</dd> <dt> msr2data &lt;firstRunNo&gt; &lt;lastRunNo&gt; &lt;extension&gt; [optional parameters] </dt><dd> An interval of run numbers is specified through the first and the last run number. The condition <strong>&lt;firstRunNo&gt; &lt; &lt;lastRunNo&gt;</strong> is <em>not</em> necessary.
</dd> <dt> msr2data \[ &lt;runList&gt; \] &lt;extension&gt; [optional parameters] </dt><dd> Where &lt;runList&gt; is one or a combination of the following:(i) <strong>&lt;run0&gt;, &lt;run1&gt;, &lt;run2&gt;, ... &lt;runN&gt;</strong> : run numbers, e.g. 123 124, (ii) <strong>&lt;run0&gt;-&lt;runN&gt;</strong> : a range, e.g. 123-125 -&gt; 123 124 125, (iii) <strong>&lt;run0&gt;:&lt;runN&gt;:&lt;step&gt;</strong> : a sequence, e.g. 123:127:2 -&gt; 123 125 127. &lt;step&gt; has to be a <strong>positive</strong> integer. A &lt;runList&gt; can also combine (i)-(iii), e.g. 123 128-130 133, etc.
</dd> <dt> msr2data &lt;runListFileName&gt; &lt;extension&gt; [optional parameters] </dt><dd> An ASCII file containing a list of run numbers and optional external parameters is passed to <code>msr2data</code>. For the structure of the ASCII file see <a href="#RunListStructure" class="foswikiCurrentTopicLink">below</a>.
</dd> <dt> msr2data &lt;runListFileName&gt; &lt;extension&gt; [optional parameters] </dt><dd> An ASCII file containing a list of run numbers and optional external parameters is passed to <code>msr2data</code>. For the structure of the ASCII file see <a class="foswikiCurrentTopicLink" href="#RunListStructure">below</a>.
</dd></dl>
<p></p>
All four basic types of calling <code>msr2data</code> contain the <em>mandatory</em> file-name <strong>&lt;extension&gt;</strong> passed right after the list of runs. The meaning of this <strong>&lt;extension&gt;</strong> should become clear after giving examples for all four cases:
<pre class="bash">msr2data 8472 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>.
<pre class="bash">msr2data 8472 8474 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>, <code><b>8473_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
<pre class="bash">msr2data 8472 8474 &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>, <code><b>8473_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
<pre class="bash">msr2data &#91;8472 8470&#93; &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code> and <code><b>8470_tf_h13.msr</b></code>.
<pre class="bash">msr2data &#91;8470:8474:2&#93; &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from <code><b>8470_tf_h13.msr</b></code>, <code><b>8472_tf_h13.msr</b></code>, and <code><b>8474_tf_h13.msr</b></code>.
<pre class="bash">msr2data run.list &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from all runs listed in the ASCII file <code><b>run.list</b></code> in the working directory. In this file it is also possible to include external parameters which should be put in the resulting <strong>DB</strong> file. The structure of the <code><b>run.list</b></code> is the following:
<pre class="bash">msr2data run.list &#95;tf&#95;h13</pre> generates the <strong>DB</strong> file <code><b>out.db</b></code> (can be changed by using <a class="foswikiCurrentTopicLink" href="#OptionalParameters">the -o option</a>) from all runs listed in the ASCII file <code><b>run.list</b></code> in the working directory. In this file it is also possible to include external parameters which should be put in the resulting <strong>DB</strong> file. The structure of the <code><b>run.list</b></code> is the following:
<span id="RunListStructure"></span>
<pre>
RUN VAR1 VAR2 VAR3 ...
@ -225,7 +225,7 @@ It is allowed to add comments (with a preceding <strong>#</strong>) or empty lin
<p></p>
The following should be mentioned together with the above examples: <ul>
<li> The output files in the examples above are only newly created if they did not exist before invoking <strong>msr2data</strong>. If the files were already present the msr-file data would be appended!
</li> <li> If the files have been newly created, also the <strong>DB</strong> file header is written. If the files were present before, only the data blocks are appended. The output of the header can either be forced or completely suppressed with the <a href="#OptionalParameters" class="foswikiCurrentTopicLink">header and noheader options</a> as shall be seen later.
</li> <li> If the files have been newly created, also the <strong>DB</strong> file header is written. If the files were present before, only the data blocks are appended. The output of the header can either be forced or completely suppressed with the <a class="foswikiCurrentTopicLink" href="#OptionalParameters">header and noheader options</a> as shall be seen later.
</li></ul>
<span id="NoExtension"></span> <ul>
<li> <span class='foswikiRedFG'>If the <code>musrfit</code> output files do not have an &lt;extension&gt; as specified above like <code><b>8472.msr</b></code> one has to call <code>msr2data</code> like in the following example:</span> <pre class="bash">
@ -273,7 +273,7 @@ Using <code><b>8471_tf_h13.msr</b></code> as template for <em>all</em> runs, <co
<p></p>
<span id="TheGlobalMode"></span>
<h1 id="A_4_The_Global_Mode"> 4 The Global Mode </h1>
Apart from all the options described <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a> there is another program option: <strong>global</strong>. This option changes the general behavior of <code>msr2data</code> in that way that instead of processing one msr file for each run it combines all specified runs in one single msr file with the possibility to define common parameters for all runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured ASCII file that single msr file is read and the parameters valid for each run are extracted. The <strong>global</strong> option can be used in conjunction with any of the described <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">invocations</a> of <code>msr2data</code> and together with all options stated <a href="#OptionalParameters" class="foswikiCurrentTopicLink">above</a>.
Apart from all the options described <a class="foswikiCurrentTopicLink" href="#OptionalParameters">above</a> there is another program option: <strong>global</strong>. This option changes the general behavior of <code>msr2data</code> in that way that instead of processing one msr file for each run it combines all specified runs in one single msr file with the possibility to define common parameters for all runs as well as run-specific parameters. When writing the obtained parameters to a DB file or a column-structured ASCII file that single msr file is read and the parameters valid for each run are extracted. The <strong>global</strong> option can be used in conjunction with any of the described <a class="foswikiCurrentTopicLink" href="#BasicTypesOfUsage">invocations</a> of <code>msr2data</code> and together with all options stated <a class="foswikiCurrentTopicLink" href="#OptionalParameters">above</a>.
<p></p>
<span id="GlobalFileGeneration"></span>
<h2 id="A_4.1_File_Generation"> 4.1 File Generation </h2>
@ -322,9 +322,9 @@ During this reorganization all the affected parameter occurrences are changed ac
<span class='foswikiRedFG'>Please be aware of the fact that comments in the template msr file are <em>not</em> propagated to the newly generated global msr file!</span>
<p></p>
<h2 id="A_4.2_Parameter_Extraction"> 4.2 Parameter Extraction </h2>
After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a <strong>DB</strong> or column-structured ASCII file&mdash;as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a href="#RunListStructure" class="foswikiCurrentTopicLink">run-list file</a>.
After fitting some model to the specified data the fit parameters can be extracted from the global msr file to a <strong>DB</strong> or column-structured ASCII file&mdash;as usual this includes also parameters stored in the run data files or externally specified parameters given in a <a class="foswikiCurrentTopicLink" href="#RunListStructure">run-list file</a>.
In order to reach this goal the global msr file has to obey certain rules: <ul>
<li> The order of the parameters has to match the one described <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>, meaning the common parameters are listed first followed by the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and having the same order as the specified list of runs.
<li> The order of the parameters has to match the one described <a class="foswikiCurrentTopicLink" href="#GlobalFileGeneration">above</a>, meaning the common parameters are listed first followed by the same number of parameters specific to each run tagged by the according run numbers at the end of the parameter names and having the same order as the specified list of runs.
</li> <li> The RUN blocks have to be ordered according to the list of runs to be processed.
</li></ul>
Following these rules&mdash;which is achieved most easily by generating the global msr file using <code>msr2data</code> as shown <a class="foswikiCurrentTopicLink" href="#GlobalFileGeneration">above</a>&mdash;the parameters can be extracted e.g. like <pre class="bash">
@ -338,7 +338,7 @@ If a new global input file is generated, it is also possible to do an automatic
msr2data 8471 8470 &#95;example global+ msr-8472
</pre>
Here, <code><b>8472_example.msr</b></code> is first used as template to generate the file <code><b>8471-OneRunFit_example.msr</b></code>, then <code>musrfit</code> is called for it, the result is used to generate <code><b>8470-OneRunFit_example.msr</b></code> and <code>musrfit</code> is called for that file. Finally, the global fit file <code><b>8471+global_example.msr</b></code> is produced&mdash;including the fit results of the OneRunFit files for the run-specific parameters.<br>
By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the <strong>fit</strong> option explained <a href="#OptionalParameters" class="foswikiCurrentTopicLink">before</a>). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.<br>
By appending an exclamation mark <strong>!</strong> to the <strong>global+</strong> option, the given template will be used for every new file generation (similar to the <strong>fit</strong> option explained <a class="foswikiCurrentTopicLink" href="#OptionalParameters">before</a>). The <strong>+[!]</strong> extension will be ignored, if no new global input file is generated.<br>
The single run msr files are not deleted at the moment. The information contained in them might be useful for some people. Of course the data can also be collected by <code>msr2data</code>. E.g. in order to produce a <strong>DB</strong> file <code><b>OneRunFits.db</b></code> one could call <pre class="bash">
msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
</pre>
@ -357,9 +357,9 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
<span id="MusrGuiInterface"></span>
<h1 id="A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"> 6 The Graphical User Interface Provided by <code><b>musrgui</b></code> / <code><b>musredit</b></code> </h1>
<code><a href="MusrGui.html">musrgui/musredit</a></code>, editors designed especially for the manipulation of <code>musrfit</code> msr files and graphical front ends to <code><a href="MusrFit.html">musrfit</a></code>, offer an almost self-explanatory graphical user interface to <code>msr2data</code> depicted below:<br>
<img class='imagePlain imagePlain_right ' src='../pub/MUSR/Msr2Data/igp_1c17a5bfb1fd01add8e3c7933ca421d5_msr2data-input-tabs.png' alt='msr2data-input-tabs.png' title='msr2data-input-tabs.png' width='612' height='605' style='' /> <dl>
<img class='imagePlain imagePlain_right ' src='../pub/MUSR/Msr2Data/igp_589e1dc22ab7bf8fd9d5889da6e407f1_msr2data-input-tabs.png' alt='msr2data-input-tabs.png' title='msr2data-input-tabs.png' width='612' height='605' style='' /> <dl>
<dt> <span class='foswikiRedFG'>1&ndash;3</span> </dt><dd> Choose one of the <a class="foswikiCurrentTopicLink" href="#BasicTypesOfUsage">ways</a> to specify your list of runs.
</dd> <dt> <span class='foswikiRedFG'>4</span> </dt><dd> Give the file extension here, e.g. <strong>_zf</strong> for files like <code><b>8472_zf.msr</b></code>. If the files do not have an extension this field stays empty. <code>musrgui</code> / <code>musredit</code> take care of passing the <strong>""</strong> to <code>msr2data</code> as mentioned <a href="#NoExtension" class="foswikiCurrentTopicLink">above</a>.
</dd> <dt> <span class='foswikiRedFG'>4</span> </dt><dd> Give the file extension here, e.g. <strong>_zf</strong> for files like <code><b>8472_zf.msr</b></code>. If the files do not have an extension this field stays empty. <code>musrgui</code> / <code>musredit</code> take care of passing the <strong>""</strong> to <code>msr2data</code> as mentioned <a class="foswikiCurrentTopicLink" href="#NoExtension">above</a>.
</dd> <dt> <span class='foswikiRedFG'>5</span> </dt><dd> Activates the <strong>fit-&lt;template&gt;</strong> option if <strong>&lt;template&gt;</strong> is entered. In case the option "Chain Fit" is <em>not</em> set the given template will be used for the input-file generation for <em>all</em> runs to be fitted&mdash;otherwise the output of the first fit serves as template for the second and so on. The template field stays empty if no fits should be performed!
</dd> <dt> <span class='foswikiRedFG'>6</span> </dt><dd> Activates the <strong>-o&lt;outputFileName&gt;</strong> option if <strong>&lt;outputFileName&gt;</strong> is entered. If nothing is entered the default output file <code><b>out.db</b></code> or <code><b>out.dat</b></code> is used.
</dd> <dt> <span class='foswikiRedFG'>7</span> </dt><dd> If <em>not</em> set, the <strong>noheader</strong> option is passed to <code>msr2data</code>.
@ -372,7 +372,7 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
</dd> <dt> <span class='foswikiRedFG'>14</span> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>msr-&lt;template&gt;</strong> (instead of <strong>fit-&lt;template&gt;</strong>) and hence is only producing the msr input files without any fitting.
</dd> <dt> <span class='foswikiRedFG'>15</span> </dt><dd> If set, <code>msr2data</code> is called with the option <strong>fit</strong>, i.e. no template will be used to generate new msr input files; only existing files are fed to <code>musrfit</code>.
</dd> <dt> <span class='foswikiRedFG'>16</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a class="foswikiCurrentTopicLink" href="#TheGlobalMode">global mode</a>.
</dd> <dt> <span class='foswikiRedFG'>17</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a href="#GlobalPlus" class="foswikiCurrentTopicLink">extended global mode</a>.
</dd> <dt> <span class='foswikiRedFG'>17</span> </dt><dd> If set, <code>msr2data</code> is operating in the <a class="foswikiCurrentTopicLink" href="#GlobalPlus">extended global mode</a>.
</dd></dl>
<p></p>
<span id="BugTracking"></span>
@ -384,17 +384,17 @@ For reporting bugs or requesting new features and improvements please use the <a
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@ -402,19 +402,19 @@ For reporting bugs or requesting new features and improvements please use the <a
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='msr2data-input-tabs.png' /></span><span class="foswikiHidden">png</span> </td>
<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/Msr2Data/msr2data-input-tabs.png">msr2data-input-tabs.png</a> </td>
<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/Msr2Data?filename=msr2data-input-tabs.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
<td style="text-align:right" class="foswikiTableCol3 foswikiLast"> 36 K </td>
<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 36 K </td>
<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">20 Jul 2011 - 12:13</span> </td>
<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> graphical interface to msr2data </td>
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<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>Msr2Data <br />
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Topic revision: <span class='patternRevInfo'>16 Aug 2015, suter_a</span></div>
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@ -428,6 +428,6 @@ Topic revision: <span class='patternRevInfo'>16 Aug 2015, suter_a</span></div>
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@ -209,7 +209,7 @@ If called from within a shell it accepts several parameters: <dl>
<p></p>
If called with a msr input file, e.g.
<pre class="bash">musrfit 8472.msr</pre>
the fit described in the input file will be executed and the results will be written to a mlog output file&mdash;in the example <code><b>8472.mlog</b></code>. When the fitting has terminated the msr file and the mlog file are swapped, so that the resultant parameter values can be found in the msr file and the mlog file contains a copy of the input file. The format of the mlog file is the same as that of the msr file. For a detailed description of the msr file format refer to <a href="#DescriptionOfTheMsrFileFormat" class="foswikiCurrentTopicLink">the corresponding section</a>.
the fit described in the input file will be executed and the results will be written to a mlog output file&mdash;in the example <code><b>8472.mlog</b></code>. When the fitting has terminated the msr file and the mlog file are swapped, so that the resultant parameter values can be found in the msr file and the mlog file contains a copy of the input file. The format of the mlog file is the same as that of the msr file. For a detailed description of the msr file format refer to <a class="foswikiCurrentTopicLink" href="#DescriptionOfTheMsrFileFormat">the corresponding section</a>.
<p></p>
<span id="MusrView"></span>
<h2 id="A_2.2_musrview"> 2.2 musrview </h2>
@ -310,7 +310,7 @@ Additionally, some functions can be accessed using key-shortcuts: <dl>
The interactive mode of <code>musrt0</code> is started if the program is called with a sole msr-file argument, e.g.
<pre class="bash">musrt0 8472.msr</pre>
Then a <code>ROOT</code> canvas depicting the histogram of the data set mentioned first in the <a class="foswikiCurrentTopicLink" href="#TheRunBlock">RUN block</a> is drawn in different colors:<br />
<img class='imagePlain imagePlain_center ' src='../pub/MUSR/MusrFit/igp_30b1bd03f016c26e55e7a3979538e223_musrt0.png' alt='musrt0' title='musrt0.png' width='626' height='424' style='' /><br />
<img class='imagePlain imagePlain_center ' src='../pub/MUSR/MusrFit/igp_a66e7f65af64996b805ac54a0eba1f8c_musrt0.png' alt='musrt0' title='musrt0.png' width='626' height='424' style='' /><br />
The colors of the data points represent the choice of the time windows of <strong><span class='foswikiBlueFG'>data (blue)</span></strong> and <strong><span class='foswikiRedFG'>background (red)</span></strong>, as well as <strong><span class='foswikiGreenFG'>t0 (green line)</span></strong>. In order to change these ranges the mouse cross-hair is moved to a channel of choice and one of the following keys is pressed: <dl>
<dt> q </dt><dd> close the currently open histogram and opens the next (see also below)
</dd> <dt> Q </dt><dd> quit <code>musrt0</code> without writing into the msr file
@ -332,8 +332,8 @@ Closing a window by clicking the <strong>X</strong> button is equivalent to pres
<h2 id="A_2.5_musrfit_startup.xml"> 2.5 musrfit_startup.xml </h2>
<code><b>musrfit_startup.xml</b></code> is a configuration file located at the <code>musrfit</code> binary path. In this file the following XML tags are allowed to define settings: <dl>
<dt> &lt;data_path&gt;PATH_TO_DATA&lt;/data_path&gt; </dt><dd> add the new path <strong>PATH_TO_DATA</strong> where <code>musrfit</code> and <code>musrview</code> will search for data files
</dd> <dt> &lt;write_per_run_block_chisq&gt;<b>y/n</b>&lt;/write_per_run_block_chisq&gt; </dt><dd> if enabled &chi;<sup>2</sup> for each RUN block will be written to the <a class="foswikiCurrentTopicLink" href="#TheStatisticBlock">STATISTIC block</a> of the resulting <code>msr</code> file. Additionally, in case a &chi;<sup>2</sup> <a href="#SingleHistogramFit" class="foswikiCurrentTopicLink">single-histogram fit</a> is done, also <a href="http://en.wikipedia.org/wiki/Pearson's_chi-square_test">Pearson's &chi;<sup>2</sup></a> will be added.
</dd> <dt> &lt;fourier_settings&gt;&lt;/fourier_settings&gt; </dt><dd> set the default parameters for the Fourier transform in <code>musrview</code>. For further details refer to <a href="#TheFourierBlock" class="foswikiCurrentTopicLink">the description of the msr file</a>. <dl>
</dd> <dt> &lt;write_per_run_block_chisq&gt;<b>y/n</b>&lt;/write_per_run_block_chisq&gt; </dt><dd> if enabled &chi;<sup>2</sup> for each RUN block will be written to the <a class="foswikiCurrentTopicLink" href="#TheStatisticBlock">STATISTIC block</a> of the resulting <code>msr</code> file. Additionally, in case a &chi;<sup>2</sup> <a class="foswikiCurrentTopicLink" href="#SingleHistogramFit">single-histogram fit</a> is done, also <a href="http://en.wikipedia.org/wiki/Pearson's_chi-square_test">Pearson's &chi;<sup>2</sup></a> will be added.
</dd> <dt> &lt;fourier_settings&gt;&lt;/fourier_settings&gt; </dt><dd> set the default parameters for the Fourier transform in <code>musrview</code>. For further details refer to <a class="foswikiCurrentTopicLink" href="#TheFourierBlock">the description of the msr file</a>. <dl>
<dt> &lt;units&gt;UNITS&lt;/units&gt; </dt><dd> specify the units of the frequency or field-domain. Valid units are <strong>Gauss</strong>, <strong>MHz</strong> and <strong>Mc/s</strong> (inside a &lt;fourier_settings&gt; environment)
</dd> <dt> &lt;fourier_power&gt;<i>n</i>&lt;/fourier_power&gt; </dt><dd> specify the number of points 2<sup><b><i>n</i></b></sup> (<b><i>n</i></b> &lt; 21) to be used for the Fourier transform (inside a &lt;fourier_settings&gt; environment)
</dd> <dt> &lt;apodization&gt;APOD&lt;/apodization&gt; </dt><dd> set the default apodization method. Valid apodizations are <strong>none</strong>, <strong>weak</strong>, <strong>medium</strong> and <strong>strong</strong> (inside a &lt;fourier_settings&gt; environment)
@ -470,7 +470,7 @@ are various possible parameter definitions which are listed here:
2. &#60;no&#62; &#60;name&#62; &#60;value&#62; &#60;step&#62; &#60;lower&#95;boundary&#62; &#60;upper&#95;boundary&#62;
3. &#60;no&#62; &#60;name&#62; &#60;value&#62; &#60;step&#62; &#60;pos&#95;error&#62; &#60;lower&#95;boundary&#62; &#60;upper&#95;boundary&#62;
</pre>
where <strong>&lt;no&gt;</strong> is the parameter number, <strong>&lt;name&gt;</strong> is the parameter name <a name="FootNote1text"></a><span class="FootNoteTextLink" title=" a standard string without whitespace "><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span>, <strong>&lt;value&gt;</strong> is the initial guess of the parameter, <strong>&lt;step&gt;</strong> the inital step width, <strong>&lt;lower/upper_boundary&gt;</strong> is the lower/upper boundary for the parameter <a name="FootNote2text"></a><span class="FootNoteTextLink" title=" According to the &#61;MINUIT&#61; manual this should be avoided whenever possible&#33; "><a class="foswikiCurrentTopicLink" href="#FootNote2note">(2)</a></span>.
where <strong>&lt;no&gt;</strong> is the parameter number, <strong>&lt;name&gt;</strong> is the parameter name <a name="FootNote1text"></a><span class="FootNoteTextLink" title=" a standard string without whitespace "><a class="foswikiCurrentTopicLink" href="#FootNote1note">(1)</a></span>, <strong>&lt;value&gt;</strong> is the initial guess of the parameter, <strong>&lt;step&gt;</strong> the inital step width, <strong>&lt;lower/upper_boundary&gt;</strong> is the lower/upper boundary for the parameter <a name="FootNote2text"></a><span class="FootNoteTextLink" title=" According to the &#61;MINUIT&#61; manual this should be avoided whenever possible&#33; "><a class="foswikiCurrentTopicLink" href="#FootNote2note">(2)</a></span>.
<p></p>
In the output file, <strong>&lt;value&gt;</strong> will be the <code>MINUIT</code> fit value, <strong>&lt;step&gt;</strong> will contain the error estimate (or the negative error estimate if <code>MINOS</code> was successfully used), <strong>&lt;pos_error&gt;</strong> will have the value <strong>none</strong> if <code>MINOS</code> has not been used, otherwise it will show the positive error estimate.
<p></p>
@ -507,9 +507,9 @@ There is also the possibility to constrain the parameters to semi-defined interv
<p></p>
Notes
<p></p>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="MusrFit.html#FootNote1text" class="foswikiCurrentWebHomeLink"> <strong>1</strong> </a></span>: <span class="FootNote"> a standard string without whitespace </span>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>1</b></a></span>: <span class="FootNote"> a standard string without whitespace </span>
<p></p>
<a name="FootNote2note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="MusrFit.html#FootNote2text"> <strong>2</strong> </a></span>: <span class="FootNote"> According to the <code>MINUIT</code> manual this should be avoided whenever possible! </span>
<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text"><b>2</b></a></span>: <span class="FootNote"> According to the <code>MINUIT</code> manual this should be avoided whenever possible! </span>
<p></p>
<p></p>
<p></p>
@ -523,11 +523,11 @@ The THEORY block is used to define the fit function. There is a set of predefine
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<th class="foswikiTableCol0 foswikiFirstCol"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=0;table=1;up=0#sorted_table">name</a> </th>
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<th class="foswikiTableCol2"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=2;table=1;up=0#sorted_table">parameters</a> </th>
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<th rowspan="6" class="foswikiTableCol4 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=4;table=1;up=0#sorted_table" title="Sort by this column" rel="nofollow">reference</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=0;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">name</a> </th>
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<th class="foswikiTableCol2"> <a href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=2;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">parameters</a> </th>
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<th class="foswikiTableCol4 foswikiLastCol" rowspan="6"> <a href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=4;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">reference</a> </th>
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<tbody>
@ -580,14 +580,14 @@ The THEORY block is used to define the fit function. There is a set of predefine
<td class="foswikiTableCol1"> dgktlf </td>
<td class="foswikiTableCol2"> <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png" />, <img alt="\sigma\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_6b6bbc4add4da0bde8220c54594658f3.png" />, <img alt="\Gamma\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_f87b1352f663a35bf263bc7e9a214ca3.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\frac{1}{2\pi \imath}\int&#95;{\gamma-\imath\infty}^{\gamma+\imath\infty} \frac{f&#95;{\mathrm{G}}(s+\Gamma)}{1-\Gamma f&#95;{\mathrm{G}}(s+\Gamma)} \exp(s t) \mathrm{d}s,\mathrm{where}\,f&#95;{\mathrm{G}}(s)\equiv \int&#95;0^{\infty}G&#95;{\mathrm{G,LF}}(t)\exp(-s t) \mathrm{d}t" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_cb688f85a062f09bfaff5cf9144860a9.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote4text"></a><span class="FootNoteTextLink" title=" R&#46; S&#46; Hayano _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;20&#46;850&#93;&#91;Phys&#46; Rev&#46; B &#42;20&#42; &#40;1979&#41; 850&#93;&#93;&#59; P&#46; Dalmas de R&#38;eacute&#59;otier and A&#46; Yaouanc&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1088&#47;0953&#45;8984&#47;4&#47;18&#47;020&#93;&#91;J&#46; Phys&#46;&#58; Condens&#46; Matter &#42;4&#42; &#40;1992&#41; 4533&#93;&#93;&#59; A&#46; Keren&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;50&#46;10039&#93;&#91;Phys&#46; Rev&#46; B &#42;50&#42; &#40;1994&#41; 10039&#93;&#93; "><a href="#FootNote4note" class="foswikiCurrentTopicLink">(5)</a></span> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote4text"></a><span class="FootNoteTextLink" title=" R&#46; S&#46; Hayano _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;20&#46;850&#93;&#91;Phys&#46; Rev&#46; B &#42;20&#42; &#40;1979&#41; 850&#93;&#93;&#59; P&#46; Dalmas de R&#38;eacute&#59;otier and A&#46; Yaouanc&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1088&#47;0953&#45;8984&#47;4&#47;18&#47;020&#93;&#91;J&#46; Phys&#46;&#58; Condens&#46; Matter &#42;4&#42; &#40;1992&#41; 4533&#93;&#93;&#59; A&#46; Keren&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;50&#46;10039&#93;&#91;Phys&#46; Rev&#46; B &#42;50&#42; &#40;1994&#41; 10039&#93;&#93; "><a class="foswikiCurrentTopicLink" href="#FootNote4note">(5)</a></span> </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> statExpKT </td>
<td class="foswikiTableCol1"> sekt </td>
<td class="foswikiTableCol2"> <img alt="\lambda\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_020e973cf5b1293c76cb3ecef5a269f8.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\frac{1}{3} + \frac{2}{3} \left&#91;1-\lambda t\right] \exp\left(-\lambda t\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_6466a97e4b7c510909bffce51d31c4b9.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote5text"></a><span class="FootNoteTextLink" title=" Y&#46; J&#46; Uemura _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;31&#46;546&#93;&#91;Phys&#46; Rev&#46; B &#42;31&#42; &#40;1985&#41; 546&#93;&#93; "><a href="#FootNote5note" class="foswikiCurrentTopicLink">(6)</a></span> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote5text"></a><span class="FootNoteTextLink" title=" Y&#46; J&#46; Uemura _et al&#46;_&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;31&#46;546&#93;&#91;Phys&#46; Rev&#46; B &#42;31&#42; &#40;1985&#41; 546&#93;&#93; "><a class="foswikiCurrentTopicLink" href="#FootNote5note">(6)</a></span> </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> statExpKTLF </td>
@ -615,7 +615,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
<td class="foswikiTableCol1"> skt </td>
<td class="foswikiTableCol2"> <img alt="\sigma\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_6b6bbc4add4da0bde8220c54594658f3.png" />, <img alt="\beta\,(1)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_aad467dd15ac57481f24ada5fbe5d85f.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\frac{1}{3}+\frac{2}{3}\left&#91;1-(\sigma t)^\beta\right] \exp\left&#91;-(\sigma t)^\beta / \beta \right]" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_63b1658426cdac24a0730149c3b5ea80.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote8text"></a><span class="FootNoteTextLink" title=" M&#46;R&#46; Crook and R&#46; Cywinski&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1088&#47;0953&#45;8984&#47;9&#47;5&#47;018&#93;&#91;J&#46; Phys&#46;&#58; Condens&#46; Matter &#42;9&#42; &#40;1997&#41; 1149&#93;&#93; "><a href="#FootNote8note" class="foswikiCurrentTopicLink">(9)</a></span> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote8text"></a><span class="FootNoteTextLink" title=" M&#46;R&#46; Crook and R&#46; Cywinski&#44; &#91;&#91;http&#58;&#47;&#47;dx&#46;doi&#46;org&#47;10&#46;1088&#47;0953&#45;8984&#47;9&#47;5&#47;018&#93;&#91;J&#46; Phys&#46;&#58; Condens&#46; Matter &#42;9&#42; &#40;1997&#41; 1149&#93;&#93; "><a class="foswikiCurrentTopicLink" href="#FootNote8note">(9)</a></span> </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> spinGlass </td>
@ -629,7 +629,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
<td class="foswikiTableCol1"> rahf </td>
<td class="foswikiTableCol2"> <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png" />, <img alt="\lambda\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_020e973cf5b1293c76cb3ecef5a269f8.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\frac{1}{6}\left(1-\frac{\nu t}{2}\right)\exp\left(-\frac{\nu t}{2}\right)+\frac{1}{3}\left(1-\frac{\nu t}{4}\right)\exp\left(-\frac{\nu t + 2.44949\lambda t}{4}\right)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_f91ff8255a7b8a99c5eefcb2c29f9262.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote9text"></a><span class="FootNoteTextLink" title=" R&#46; E&#46; Turner and D&#46; R&#46; Harshman&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;34&#46;4467&#93;&#91;Phys&#46; Rev&#46; B &#42;34&#42; &#40;1986&#41; 4467&#93;&#93; "><a href="#FootNote9note" class="foswikiCurrentTopicLink">(9)</a></span> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote9text"></a><span class="FootNoteTextLink" title=" R&#46; E&#46; Turner and D&#46; R&#46; Harshman&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;34&#46;4467&#93;&#91;Phys&#46; Rev&#46; B &#42;34&#42; &#40;1986&#41; 4467&#93;&#93; "><a class="foswikiCurrentTopicLink" href="#FootNote9note">(9)</a></span> </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> TFieldCos </td>
@ -678,7 +678,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
<td class="foswikiTableCol1"> snkzf </td>
<td class="foswikiTableCol2"> <img alt="\Delta&#95;0\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_30b87ca180341a9f8f9a15c1082f7f29.png" />, <img alt="R&#95;b &#61; \Delta&#95;{\mathrm{GbG}}/\Delta&#95;0 \,(\text{1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_5563541e58443a8d18e5bd40d2746e9a.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\frac{1}{3}+\frac{2}{3}\left(\frac{1}{1+R&#95;b^2\Delta&#95;0^2 t^2}\right)^{3/2} \left(1-\frac{\Delta&#95;0^2 t^2}{1+R&#95;b^2\Delta&#95;0^2 t^2}\right)\,\exp\left&#91;-\frac{\Delta&#95;0^2 t^2}{2(1+R&#95;b^2\Delta&#95;0^2 t^2)}\right]" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_d5edc50e5c0ce856d632a5a682e0347f.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote10text"></a><span class="FootNoteTextLink" title=" D&#46;R&#46; Noakes and G&#46;M&#46; Kalvius&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;56&#46;2352&#93;&#91;Phys&#46; Rev&#46; B &#42;56&#42; &#40;1997&#41; 2352&#93;&#93;&#59; A&#46; Yaouanc and P&#46; Dalmas de R&#38;eacute&#59;otier &#34;Muon Spin Rotation&#44; Relaxation&#44; and Resonance&#34; Oxford Scientific Publication&#59; simplifying the original formulae by eliminating &#60;latex&#62;&#92;Delta_&#123;&#92;rm eff&#125;&#60;&#47;latex&#62; via the identity &#60;latex&#62;&#92;Delta_&#123;&#92;rm eff&#125;&#94;2 &#61; &#40;1&#43;R_b&#94;2&#41; &#92;Delta_0&#60;&#47;latex&#62; "><a href="#FootNote10note" class="foswikiCurrentTopicLink">(10)</a></span> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote10text"></a><span class="FootNoteTextLink" title=" D&#46;R&#46; Noakes and G&#46;M&#46; Kalvius&#44; &#91;&#91;http&#58;&#47;&#47;link&#46;aps&#46;org&#47;doi&#47;10&#46;1103&#47;PhysRevB&#46;56&#46;2352&#93;&#91;Phys&#46; Rev&#46; B &#42;56&#42; &#40;1997&#41; 2352&#93;&#93;&#59; A&#46; Yaouanc and P&#46; Dalmas de R&#38;eacute&#59;otier &#34;Muon Spin Rotation&#44; Relaxation&#44; and Resonance&#34; Oxford Scientific Publication&#59; simplifying the original formulae by eliminating &#60;latex&#62;&#92;Delta_&#123;&#92;rm eff&#125;&#60;&#47;latex&#62; via the identity &#60;latex&#62;&#92;Delta_&#123;&#92;rm eff&#125;&#94;2 &#61; &#40;1&#43;R_b&#94;2&#41; &#92;Delta_0&#60;&#47;latex&#62; "><a class="foswikiCurrentTopicLink" href="#FootNote10note">(10)</a></span> </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> staticNKTF </td>
@ -692,16 +692,23 @@ The THEORY block is used to define the fit function. There is a set of predefine
<td class="foswikiTableCol1"> dnkzf </td>
<td class="foswikiTableCol2"> <img alt="\Delta&#95;0\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_30b87ca180341a9f8f9a15c1082f7f29.png" />, <img alt="R&#95;b &#61; \Delta&#95;{\mathrm{GbG}}/\Delta&#95;0\,(\text{1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_b7d61ac387fd12b956816be1c6c9a577.png" />, <img alt="\nu&#95;c\,(\text{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_c4bdea6bbc03bcca6d713519e7bab071.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\sqrt{\frac{1}{1+4 R&#95;b^2\Delta&#95;0^2 \Theta(t)}}\,\exp\left&#91;-\frac{2 \Delta&#95;0^2 \Theta(t)}{1+4 R&#95;b^2\Delta&#95;0^2 \Theta(t)}\right]\quad,\, \Theta(t) &#61; \frac{\exp(-\nu&#95;c t) - 1 - \nu&#95;c t}{\nu&#95;c^2}" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_af36b27f661f5b8a569f5672d18f8844.png" /> </td>
<td class="foswikiTableCol4"> see note 10 </td>
<td class="foswikiTableCol4 foswikiLastCol"> see note 10 </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> dynamicNKTF </td>
<td class="foswikiTableCol1"> dnktf </td>
<td class="foswikiTableCol2"> <img alt="\varphi\,(^{\circ})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_61136f20673ad20f955c43e43b8cec9d.png" />, <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png" />, <img alt="\Delta&#95;0\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_30b87ca180341a9f8f9a15c1082f7f29.png" />, <img alt="R&#95;b &#61; \Delta&#95;{\mathrm{GbG}}/\Delta&#95;0\,(\text{1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_b7d61ac387fd12b956816be1c6c9a577.png" />, <img alt="\nu&#95;c\,(\text{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_c4bdea6bbc03bcca6d713519e7bab071.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\sqrt{\frac{1}{1+2 R&#95;b^2\Delta&#95;0^2 \Theta(t)}}\,\exp\left&#91;-\frac{\Delta&#95;0^2 \Theta(t)}{1+2 R&#95;b^2\Delta&#95;0^2 \Theta(t)}\right]\, \cos(\nu t + \varphi) \quad,\, \Theta(t) &#61; \frac{\exp(-\nu&#95;c t) - 1 - \nu&#95;c t}{\nu&#95;c^2}" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_c7fe4fcfd08f7d4ca8638228bb83b4f9.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> see note 10 </td>
<td class="foswikiTableCol3"> <img alt="\sqrt{\frac{1}{1+2 R&#95;b^2\Delta&#95;0^2 \Theta(t)}}\,\exp\left&#91;-\frac{\Delta&#95;0^2 \Theta(t)}{1+2 R&#95;b^2\Delta&#95;0^2 \Theta(t)}\right]\, \cos(2\pi \nu t + \varphi) \quad,\, \Theta(t) &#61; \frac{\exp(-\nu&#95;c t) - 1 - \nu&#95;c t}{\nu&#95;c^2}" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_466fcb53c3da4f84fb2d12e03eef9439.png" /> </td>
<td class="foswikiTableCol4"> see note 10 </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> muMinusExpTF </td>
<td class="foswikiTableCol1"> mmsetf </td>
<td class="foswikiTableCol2"> <img alt="N&#95;0\,(1)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_fcadee367bc447abe1119778b6fa1a14.png" />, <img alt="\tau\,(\mu s)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_545dca52882440763fc3ac973a36852a.png" />, <img alt="A\,(1)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_facd1d42ae8b62aa1043316d525d3af4.png" />, <img alt="\lambda\,(\mu s^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_319772b46bc6861fbe24a28e59530ade.png" />, <img alt="\varphi\,(^{\circ})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_61136f20673ad20f955c43e43b8cec9d.png" />, <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png" /> </td>
<td class="foswikiTableCol3"> <img alt="N&#95;0 \exp(-t/\tau) \left&#91; 1 + A \exp(-\lambda t) \cos(2\pi \nu t + \varphi) \right]" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_57316547e3b34dd9d537b722e4a0e176.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a name="FootNote11text"></a><span class="FootNoteTextLink" title=" This function is explicit for &#60;latex&#62;&#92;mu&#94;&#45;&#60;&#47;latex&#62;&#33; Do not try to use it for &#60;latex&#62;&#92;mu&#94;&#43;&#60;&#47;latex&#62;&#46; "><a class="foswikiCurrentTopicLink" href="#FootNote11note">(11)</a></span> </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> polynom </td>
<td class="foswikiTableCol1 foswikiLast"> p </td>
<td class="foswikiTableCol2 foswikiLast"> <img alt="t&#95;0\,(&#91;t])" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_20651e8230c7eb66c452bb1f01dc4633.png" />, <img alt="a&#95;0\,(1),\,a&#95;1\,(1),\,\dots,\,a&#95;{n}\,(1)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_03095d51eca2bcb1dda113e995238fc0.png" /> </td>
@ -711,7 +718,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
</tbody></table>
<p></p>
<p></p>
Every theory function has to be written on a single line. It starts with the theory function name or its abbreviation followed by the parameters. Consecutive lines of theory functions will be multiplied. If theory functions need to be added, a line with a <strong>+</strong> has to separate them. The parameters are given as the numbers assigned to them in the <a href="#TheFitparameterBlock" class="foswikiCurrentTopicLink">FITPARAMETER block</a>. The order of the parameters is given in the <a class="foswikiCurrentTopicLink" href="#TheoryTable">table above</a>. As an example
Every theory function has to be written on a single line. It starts with the theory function name or its abbreviation followed by the parameters. Consecutive lines of theory functions will be multiplied. If theory functions need to be added, a line with a <strong>+</strong> has to separate them. The parameters are given as the numbers assigned to them in the <a class="foswikiCurrentTopicLink" href="#TheFitparameterBlock">FITPARAMETER block</a>. The order of the parameters is given in the <a class="foswikiCurrentTopicLink" href="#TheoryTable">table above</a>. As an example
<pre>
simplExpo 4
</pre>
@ -731,19 +738,21 @@ which means <i>A</i>(<i>t</i>) = <i>p</i><sub>2</sub> e<sup>-<i>p</i><sub>3</sub
<p></p>
Notes
<p></p>
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="MusrFit.html#FootNote3text" class="foswikiCurrentWebHomeLink"> <strong>4</strong> </a></span>: <span class="FootNote"> R. S. Hayano <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.20.850">Phys. Rev. B <strong>20</strong> (1979) 850</a> </span>
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text"><b>4</b></a></span>: <span class="FootNote"> R. S. Hayano <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.20.850">Phys. Rev. B <strong>20</strong> (1979) 850</a> </span>
<p></p>
<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="MusrFit.html#FootNote4text" class="foswikiCurrentWebHomeLink"> <strong>5</strong> </a></span>: <span class="FootNote"> R. S. Hayano <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.20.850">Phys. Rev. B <strong>20</strong> (1979) 850</a>; P. Dalmas de R&eacute;otier and A. Yaouanc, <a href="http://dx.doi.org/10.1088/0953-8984/4/18/020">J. Phys.: Condens. Matter <strong>4</strong> (1992) 4533</a>; A. Keren, <a href="http://link.aps.org/doi/10.1103/PhysRevB.50.10039">Phys. Rev. B <strong>50</strong> (1994) 10039</a> </span>
<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="#FootNote4text"><b>5</b></a></span>: <span class="FootNote"> R. S. Hayano <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.20.850">Phys. Rev. B <strong>20</strong> (1979) 850</a>; P. Dalmas de R&eacute;otier and A. Yaouanc, <a href="http://dx.doi.org/10.1088/0953-8984/4/18/020">J. Phys.: Condens. Matter <strong>4</strong> (1992) 4533</a>; A. Keren, <a href="http://link.aps.org/doi/10.1103/PhysRevB.50.10039">Phys. Rev. B <strong>50</strong> (1994) 10039</a> </span>
<p></p>
<a name="FootNote5note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="MusrFit.html#FootNote5text"> <strong>6</strong> </a></span>,<a name="FootNote6note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="MusrFit.html#FootNote6text"> <strong>7</strong> </a></span>: <span class="FootNote"> Y. J. Uemura <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.31.546">Phys. Rev. B <strong>31</strong> (1985) 546</a> </span>
<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="#FootNote5text"><b>6</b></a></span>,<a name="FootNote6note"></a><span class="FootNoteLabel"><a href="#FootNote6text"><b>7</b></a></span>: <span class="FootNote"> Y. J. Uemura <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.31.546">Phys. Rev. B <strong>31</strong> (1985) 546</a> </span>
<p></p>
<a name="FootNote7note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="MusrFit.html#FootNote7text"> <strong>8</strong> </a></span>: <span class="FootNote"> R. S. Hayano <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.20.850">Phys. Rev. B <strong>20</strong> (1979) 850</a>; P. Dalmas de R&eacute;otier and A. Yaouanc, <a href="http://dx.doi.org/10.1088/0953-8984/4/18/020">J. Phys.: Condens. Matter <strong>4</strong> (1992) 4533</a> </span>
<a name="FootNote7note"></a><span class="FootNoteLabel"><a href="#FootNote7text"><b>8</b></a></span>: <span class="FootNote"> R. S. Hayano <em>et al.</em>, <a href="http://link.aps.org/doi/10.1103/PhysRevB.20.850">Phys. Rev. B <strong>20</strong> (1979) 850</a>; P. Dalmas de R&eacute;otier and A. Yaouanc, <a href="http://dx.doi.org/10.1088/0953-8984/4/18/020">J. Phys.: Condens. Matter <strong>4</strong> (1992) 4533</a> </span>
<p></p>
<a name="FootNote8note"></a><span class="FootNoteLabel"><a href="MusrFit.html#FootNote8text" class="foswikiCurrentWebHomeLink"> <strong>9</strong> </a></span>: <span class="FootNote"> M.R. Crook and R. Cywinski, <a href="http://dx.doi.org/10.1088/0953-8984/9/5/018">J. Phys.: Condens. Matter <strong>9</strong> (1997) 1149</a> </span>
<a name="FootNote8note"></a><span class="FootNoteLabel"><a href="#FootNote8text"><b>9</b></a></span>: <span class="FootNote"> M.R. Crook and R. Cywinski, <a href="http://dx.doi.org/10.1088/0953-8984/9/5/018">J. Phys.: Condens. Matter <strong>9</strong> (1997) 1149</a> </span>
<p></p>
<a name="FootNote9note"></a><span class="FootNoteLabel"><a href="MusrFit.html#FootNote9text" class="foswikiCurrentWebHomeLink"> <strong>9</strong> </a></span>: <span class="FootNote"> R. E. Turner and D. R. Harshman, <a href="http://link.aps.org/doi/10.1103/PhysRevB.34.4467">Phys. Rev. B <strong>34</strong> (1986) 4467</a> </span>
<a name="FootNote9note"></a><span class="FootNoteLabel"><a href="#FootNote9text"><b>9</b></a></span>: <span class="FootNote"> R. E. Turner and D. R. Harshman, <a href="http://link.aps.org/doi/10.1103/PhysRevB.34.4467">Phys. Rev. B <strong>34</strong> (1986) 4467</a> </span>
<p></p>
<a name="FootNote10note"></a><span class="FootNoteLabel"><a href="MusrFit.html#FootNote10text" class="foswikiCurrentWebHomeLink"> <strong>10</strong> </a></span>: <span class="FootNote"> D.R. Noakes and G.M. Kalvius, <a href="http://link.aps.org/doi/10.1103/PhysRevB.56.2352">Phys. Rev. B <strong>56</strong> (1997) 2352</a>; A. Yaouanc and P. Dalmas de R&eacute;otier "Muon Spin Rotation, Relaxation, and Resonance" Oxford Scientific Publication; simplifying the original formulae by eliminating <img alt="\Delta&#95;{\rm eff}" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_663c0beda820045042826686eaeefb6a.png" /> via the identity <img alt="\Delta&#95;{\rm eff}^2 &#61; (1+R&#95;b^2) \Delta&#95;0" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_81abadaf16877e78e8bb9317a16cd704.png" /> </span>
<a name="FootNote10note"></a><span class="FootNoteLabel"><a href="#FootNote10text"><b>10</b></a></span>: <span class="FootNote"> D.R. Noakes and G.M. Kalvius, <a href="http://link.aps.org/doi/10.1103/PhysRevB.56.2352">Phys. Rev. B <strong>56</strong> (1997) 2352</a>; A. Yaouanc and P. Dalmas de R&eacute;otier "Muon Spin Rotation, Relaxation, and Resonance" Oxford Scientific Publication; simplifying the original formulae by eliminating <img alt="\Delta&#95;{\rm eff}" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_663c0beda820045042826686eaeefb6a.png" /> via the identity <img alt="\Delta&#95;{\rm eff}^2 &#61; (1+R&#95;b^2) \Delta&#95;0" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_81abadaf16877e78e8bb9317a16cd704.png" /> </span>
<p></p>
<a name="FootNote11note"></a><span class="FootNoteLabel"><a href="#FootNote11text"><b>11</b></a></span>: <span class="FootNote"> This function is explicit for <img alt="\mu^-" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_d65298a2553c29f00e58481f3465086a.png" />! Do not try to use it for <img alt="\mu^+" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_8eb55dc360ede9ff12fa65dc47046bc0.png" />. </span>
<p></p>
<p></p>
<p></p>
@ -751,7 +760,7 @@ Notes
<p></p>
<span id="MaPs"></span>
<h3 id="A_4.3.1_Maps"> 4.3.1 Maps </h3>
In case different runs are fitted simultaneously, it is very often necessary that for a given theory function, some parameters are run-dependent. An example could be a temperature scan, where the parameters (asymmetry, depolarization rates, etc.) will depend on the temperature. In order to handle such situations, a mapping of parameters in the THEORY block is possible. That means, instead of a parameter number, the mapping of the parameter is given. The definition of the mapping block is part of the <a href="#TheRunBlock" class="foswikiCurrentTopicLink">RUN block</a> and will be described there. For example
In case different runs are fitted simultaneously, it is very often necessary that for a given theory function, some parameters are run-dependent. An example could be a temperature scan, where the parameters (asymmetry, depolarization rates, etc.) will depend on the temperature. In order to handle such situations, a mapping of parameters in the THEORY block is possible. That means, instead of a parameter number, the mapping of the parameter is given. The definition of the mapping block is part of the <a class="foswikiCurrentTopicLink" href="#TheRunBlock">RUN block</a> and will be described there. For example
<pre>
THEORY
asymmetry 2
@ -783,7 +792,7 @@ A THEORY block including a user function may then look like
<p></p>
<span id="TheFunctionsBlock"></span>
<h2 id="A_4.4_The_FUNCTIONS_Block"> 4.4 The FUNCTIONS Block </h2>
<code>musrfit</code> utilizes a <a href="http://boost-spirit.com/home/">powerful parser</a>. Therefore, it is possible to define even rather complicated functional relations between the fit parameters and use these in the THEORY block (and <a href="#NormFun" class="foswikiCurrentTopicLink">in one exceptional case</a> also in the RUN-block). Supported is the use of basic arithmetics: <dl>
<code>musrfit</code> utilizes a <a href="http://boost-spirit.com/home/">powerful parser</a>. Therefore, it is possible to define even rather complicated functional relations between the fit parameters and use these in the THEORY block (and <a class="foswikiCurrentTopicLink" href="#NormFun">in one exceptional case</a> also in the RUN-block). Supported is the use of basic arithmetics: <dl>
<dt> + </dt><dd> Addition
</dd> <dt> - </dt><dd> Subtraction
</dd> <dt> * </dt><dd> Multiplication
@ -798,9 +807,9 @@ Furthermore, some constants are predefined and might also be used: <ul>
</li> <li> <strong>pi</strong> = &#960; = 3.14159265358979323846
</li></ul>
<p></p>
The fit parameters are accessed either directly through <code><b>par&alpha;</b></code>, where &alpha; is the number of the parameter in the FITPARAMETER block, e.g. <code><b>par5</b></code> or through a mapping with <code><b>map&delta;</b></code>, where &delta; specifies the mapping number in the RUN block as explained <a href="#TheRunBlock" class="foswikiCurrentTopicLink">below</a>.
The fit parameters are accessed either directly through <code><b>par&alpha;</b></code>, where &alpha; is the number of the parameter in the FITPARAMETER block, e.g. <code><b>par5</b></code> or through a mapping with <code><b>map&delta;</b></code>, where &delta; specifies the mapping number in the RUN block as explained <a class="foswikiCurrentTopicLink" href="#TheRunBlock">below</a>.
<p></p>
The defined functions are denoted as <code><b>fun&alpha;</b></code>, where &alpha; is the function number, i.e. <code><b>fun1</b></code>, <code><b>fun2</b></code>, etc. and have to be placed separately on one line each. Afterwards they might be used in the <a href="#TheTheoryBlock" class="foswikiCurrentTopicLink">THEORY block</a>.
The defined functions are denoted as <code><b>fun&alpha;</b></code>, where &alpha; is the function number, i.e. <code><b>fun1</b></code>, <code><b>fun2</b></code>, etc. and have to be placed separately on one line each. Afterwards they might be used in the <a class="foswikiCurrentTopicLink" href="#TheTheoryBlock">THEORY block</a>.
<p></p>
It follows an example to illustrate the usage of functions in the THEORY block. The total asymmetry of a signal consisting of two parts should be a fit parameter. The fraction of each of the parts will then be expressed as a function of the total asymmetry.
<p></p>
@ -829,7 +838,7 @@ It follows an example to illustrate the usage of functions in the THEORY block.
</pre>
<p></p>
In the case that functions have to be fitted which cannot be defined in the FUNCTIONS block, the functions can be implemented externally and made usable through the <a href="#UserFunctions" class="foswikiCurrentTopicLink">userFunc mechanism</a>.
In the case that functions have to be fitted which cannot be defined in the FUNCTIONS block, the functions can be implemented externally and made usable through the <a class="foswikiCurrentTopicLink" href="#UserFunctions">userFunc mechanism</a>.
<p></p>
<span id="TheGlobalBlock"></span>
<h2 id="A_4.5_The_GLOBAL_Block"> 4.5 The GLOBAL Block </h2>
@ -940,8 +949,8 @@ The RUN block is used to collect the data needed for a particular run to be fitt
<table border="1" class="foswikiTable" rules="none">
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=0;table=2;up=0#sorted_table">RUN-block tag</a> </th>
<th class="foswikiTableCol1 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=1;table=2;up=0#sorted_table" title="Sort by this column" rel="nofollow">comment</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=0;table=2;up=0#sorted_table" rel="nofollow" title="Sort by this column">RUN-block tag</a> </th>
<th class="foswikiTableCol1 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrFit?cover=print;sortcol=1;table=2;up=0#sorted_table" rel="nofollow" title="Sort by this column">comment</a> </th>
</tr>
</thead>
<tbody>
@ -1008,7 +1017,7 @@ etc.
<span id="FitTypes"></span> <dl>
<dt> fittype (required if not already defined in the GLOBAL block) </dt><dd> This tag is used to indicate which type of fit is wished. The supported fit types are: <dl>
<dt> 0 </dt><dd> Single Histogram Fit
</dd> <dt> 1 </dt><dd> Single Histogram RRF Fit (only for online analysis<a name="FootNote11text"></a><span class="FootNoteTextLink" title="for a more detailed discussion about the shortcomings of RRF fits see the RRF memo found under &#38;lt&#59;musrfit&#38;gt&#59;&#47;doc&#47;memo&#47;rrf"><a class="foswikiCurrentTopicLink" href="#FootNote11note">(l)</a></span> )
</dd> <dt> 1 </dt><dd> Single Histogram RRF Fit (only for online analysis<a name="FootNote12text"></a><span class="FootNoteTextLink" title="for a more detailed discussion about the shortcomings of RRF fits see the RRF memo found under &#38;lt&#59;musrfit&#38;gt&#59;&#47;doc&#47;memo&#47;rrf"><a class="foswikiCurrentTopicLink" href="#FootNote12note">(l)</a></span> )
</dd> <dt> 2 </dt><dd> Asymmetry Fit
</dd> <dt> 3 </dt><dd> Asymmetry RRF Fit (only for online analysis. See comment added for Single Histogram RRF Fit)
</dd> <dt> 4 </dt><dd> MuMinus Fit. This is a single histogram fit especially for negative muon &mu;SR
@ -1027,7 +1036,7 @@ alpha 1
</dd></dl>
<p></p>
<span id="NormFun"></span> <dl>
<dt> norm (fit type 0) </dt><dd> Number of the fit parameter that represents the normalization constant <i>N</i><sub>0</sub> of the histogram; the value of this parameter is given either per nanosecond or per bin (see <a href="#ScaleNzero" class="foswikiCurrentTopicLink">below</a>). It is possible to substitute the parameter number by a function here (<u>and only here in a RUN block</u>), for instance to relate <i>N</i><sub>0</sub>s of different histograms through an &alpha; parameter. Example for a norm defined by fit parameter number 12:<pre>
<dt> norm (fit type 0) </dt><dd> Number of the fit parameter that represents the normalization constant <i>N</i><sub>0</sub> of the histogram; the value of this parameter is given either per nanosecond or per bin (see <a class="foswikiCurrentTopicLink" href="#ScaleNzero">below</a>). It is possible to substitute the parameter number by a function here (<u>and only here in a RUN block</u>), for instance to relate <i>N</i><sub>0</sub>s of different histograms through an &alpha; parameter. Example for a norm defined by fit parameter number 12:<pre>
norm 12
</pre> Example for a norm defined in function number 3:<pre>
norm fun3
@ -1040,7 +1049,7 @@ norm fun3
<dt> lifetime (fit type 0) </dt><dd> Fit parameter representing the lifetime of the muon. If it is not specified the value &#964;<sub>&#956;</sub>=2.197019 &#956;s is used in the calculations.
</dd></dl>
<p></p> <dl>
<dt> lifetimecorrection (fit type 0) <img class='smily' src='../pub/Main/SmiliesPluginPSI_/eek.gif' alt='eek!' title='eek!' /> <strong>obsolete</strong> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/eek.gif' alt='eek!' title='eek!' /> </dt><dd> Does not accept any arguments. If present, the output in <code>musrview</code> is corrected for the exponential decay of the muon. This item is <strong>obsolete</strong> in the RUN block and will be transferred to the <a href="#ThePlotBlock" class="foswikiCurrentTopicLink">PLOT block</a>, which allows switching between histogram view and asymmetry view much quicker.
<dt> lifetimecorrection (fit type 0) <img class='smily' src='../pub/Main/SmiliesPluginPSI_/eek.gif' alt='eek!' title='eek!' /> <strong>obsolete</strong> <img class='smily' src='../pub/Main/SmiliesPluginPSI_/eek.gif' alt='eek!' title='eek!' /> </dt><dd> Does not accept any arguments. If present, the output in <code>musrview</code> is corrected for the exponential decay of the muon. This item is <strong>obsolete</strong> in the RUN block and will be transferred to the <a class="foswikiCurrentTopicLink" href="#ThePlotBlock">PLOT block</a>, which allows switching between histogram view and asymmetry view much quicker.
</dd></dl>
<p></p> <dl>
<dt> map </dt><dd> On this line the mapping of run-dependent parameters is done. Parameter numbers given here may be accessed through <code><b>map1</b></code>, <code><b>map2</b></code>, etc. in the THEORY and FUNCTIONS blocks (see also <a class="foswikiCurrentTopicLink" href="#MaPs">here</a>). The first ten maps are always present and have the value 0 if not used; however, the total number of maps is not restricted!
@ -1067,7 +1076,7 @@ norm fun3
</pre>
</dd></dl>
<p></p> <dl>
<dt> backgr.fix (fit types 0, 1, 2) </dt><dd> A fixed constant background in counts per nanosecond or per bin (see <a href="#ScaleNzero" class="foswikiCurrentTopicLink">below</a>) may be given at this point. The background is specified for all histograms in the order <i>B</i><sub>f</sub> <i>B</i><sub>b</sub> [<i>B</i><sub>r</sub> <i>B</i><sub>l</sub>]. If this keyword is present, any information on a <strong>background</strong> line is ignored.
<dt> backgr.fix (fit types 0, 1, 2) </dt><dd> A fixed constant background in counts per nanosecond or per bin (see <a class="foswikiCurrentTopicLink" href="#ScaleNzero">below</a>) may be given at this point. The background is specified for all histograms in the order <i>B</i><sub>f</sub> <i>B</i><sub>b</sub> [<i>B</i><sub>r</sub> <i>B</i><sub>l</sub>]. If this keyword is present, any information on a <strong>background</strong> line is ignored.
</dd></dl>
<p></p> <dl>
<dt> background (fit type 0, 1) </dt><dd> The numbers of the first and the last channel of an interval from which the constant background should be calculated are specified here. In case histograms are being grouped, the specified channels are interpreted with respect to the first histogram. Example:<pre>
@ -1105,7 +1114,7 @@ data 207 7994 167 8009
</dd></dl>
<p></p>
<span id="AddTimeZero"></span> <dl>
<dt> addt0 (fit type 0, 1, 4) </dt><dd> The number of the time-zero channel of the histogram. If grouping of histograms is present (see <a href="#ForwardHisto" class="foswikiCurrentTopicLink">forward</a>) the same syntax as for <a href="#TimeZero" class="foswikiCurrentTopicLink">t0</a> applies. If one addt0 is given, the total number of addt0's needs to be equal to the total number of ADDRUN's!
<dt> addt0 (fit type 0, 1, 4) </dt><dd> The number of the time-zero channel of the histogram. If grouping of histograms is present (see <a class="foswikiCurrentTopicLink" href="#ForwardHisto">forward</a>) the same syntax as for <a class="foswikiCurrentTopicLink" href="#TimeZero">t0</a> applies. If one addt0 is given, the total number of addt0's needs to be equal to the total number of ADDRUN's!
</dd></dl>
<p></p> <dl>
<dt> addt0 (fit types 2) </dt><dd> The numbers of time-zero channels of the histograms in the order <i>t</i><sub>0,f</sub> <i>t</i><sub>0,b</sub> [<i>t</i><sub>0,r</sub> <i>t</i><sub>0,l</sub>]. If grouping of histograms is present (see <a class="foswikiCurrentTopicLink" href="#ForwardHisto">forward</a>) the same syntax as for <a class="foswikiCurrentTopicLink" href="#TimeZero">t0</a> applies. If one addt0 is given, the total number of addt0's needs to be equal to the total number of ADDRUN's!
@ -1114,7 +1123,7 @@ data 207 7994 167 8009
<dt> xy-data (fit type 8) </dt><dd> Specification of the data from an ASCII or DB file which should be used as <i>x</i> and <i>y</i> data (in this order). For a simple ASCII file the column numbers are used, in the case of a DB file one can either specify the variable numbers or the name of the variables as given in the DB header.
</dd></dl>
<p></p> <dl>
<dt> fit </dt><dd> The range of data that should be considered when the fitting is done. For the &mu;SR fit types <strong>0</strong>, <strong>2</strong>, and <strong>4</strong> here the starting and end times are given in microseconds. For the non-&mu;SR fit type <strong>8</strong> the starting and end points of the fitting range are given in the units of the <i>x</i> data.<br><span class='foswikiRedFG'>In case the fit range specified here is larger than the <a href="#DataRange" class="foswikiCurrentTopicLink">data range</a> (in any direction), eventually the <a class="foswikiCurrentTopicLink" href="#DataRange">data range</a> will be used as fit range.</span> An example for a &mu;SR fit:<pre>
<dt> fit </dt><dd> The range of data that should be considered when the fitting is done. For the &mu;SR fit types <strong>0</strong>, <strong>2</strong>, and <strong>4</strong> here the starting and end times are given in microseconds. For the non-&mu;SR fit type <strong>8</strong> the starting and end points of the fitting range are given in the units of the <i>x</i> data.<br><span class='foswikiRedFG'>In case the fit range specified here is larger than the <a class="foswikiCurrentTopicLink" href="#DataRange">data range</a> (in any direction), eventually the <a class="foswikiCurrentTopicLink" href="#DataRange">data range</a> will be used as fit range.</span> An example for a &mu;SR fit:<pre>
fit 0.2 8.5
</pre>Which means that the fitting window will span from 0.2 to 8.5 microseconds.<br> Another possibility for the &mu;SR fits is to give the fit range in bins, rather than time. The syntax is then: <pre>fit fgb+&#60;n0&#62; lgb-&#60;n1&#62;,</pre> where <strong>fgb</strong> and <strong>lgb</strong> are label tags which refer to the 'first good bin' and the 'last good bin' defined either in the <code><b>data</b></code> tag of the run block, data file, are estimated based on T0. &lt;n0&gt; and &lt;n1&gt; are offsets (given in bins) allowing to change the fit window compared to the data window. An example: <pre>fit fgb+150 lgb-1332</pre>
</dd></dl>
@ -1162,7 +1171,7 @@ Sometimes it is necessary to guide <code>MINUIT2</code> to the global optimum. F
<p></p>
It is important to understand that before <strong>MINOS</strong> is called, all the fixed parameters need to be released and another minimizer command (<strong>MINIMIZE</strong>, <strong>MIGRAD</strong>, or <strong>SIMPLEX</strong>) needs to be in place, otherwise <code>musrfit</code> will assume that the still fixed parameters have to be handled as constant parameters, i.e. setting the &lt;step&gt; value of the parameter to zero.
<p></p>
For even more complex fitting the additional command <strong>FIT_RANGE RESET | <i>t</i><sub>start</sub> <i>t</i><sub>end</sub> | <i>t</i><sub>s1</sub> <i>t</i><sub>e1</sub> <i>t</i><sub>s2</sub> <i>t</i><sub>e2</sub> ... <i>t</i><sub>s<i>n</i></sub> <i>t</i><sub>e<i>n</i></sub></strong> is provided. It allows to change the fit range during different iterations. The command <strong>FIT_RANGE <i>t</i><sub>start</sub> <i>t</i><sub>end</sub></strong> changes the current fit range for <code>all</code> the runs present in the msr file. <strong>FIT_RANGE RESET</strong> will restore to the original fit ranges as provided in the <a href="#TheRunBlock" class="foswikiCurrentTopicLink">RUN block</a>. If for each run of the msr file an individual fit range should be used, the third option applies. Here <strong><i>n</i></strong> has to correspond to the number of runs in the RUN block.
For even more complex fitting the additional command <strong>FIT_RANGE RESET | <i>t</i><sub>start</sub> <i>t</i><sub>end</sub> | <i>t</i><sub>s1</sub> <i>t</i><sub>e1</sub> <i>t</i><sub>s2</sub> <i>t</i><sub>e2</sub> ... <i>t</i><sub>s<i>n</i></sub> <i>t</i><sub>e<i>n</i></sub></strong> is provided. It allows to change the fit range during different iterations. The command <strong>FIT_RANGE <i>t</i><sub>start</sub> <i>t</i><sub>end</sub></strong> changes the current fit range for <code>all</code> the runs present in the msr file. <strong>FIT_RANGE RESET</strong> will restore to the original fit ranges as provided in the <a class="foswikiCurrentTopicLink" href="#TheRunBlock">RUN block</a>. If for each run of the msr file an individual fit range should be used, the third option applies. Here <strong><i>n</i></strong> has to correspond to the number of runs in the RUN block.
<p></p>
As for the run block, there is a 2nd flavor how the <strong>FIT_RANGE</strong> can be changed, namely giving the fit range in bins, i.e. <strong>FIT_RANGE RESET | fgb+&lt;n0&gt; lgb-&lt;n1&gt; | fgb+&lt;n00&gt; lgb-&lt;n01&gt; fgb+&lt;n10&gt; lgb-&lt;n11&gt; ... fgb+&lt;nN0&gt; lgb-&lt;nN1&gt;</strong> where <strong>N</strong> is the number of available run blocks. The idea is inline with the above syntax and the syntax describe for the fit range (<strong>fit</strong>) of the <a class="foswikiCurrentTopicLink" href="#TheRunBlock">RUN block</a>.
<p></p>
@ -1201,7 +1210,7 @@ Here the <code>MINOS</code> command will print out lot of additional information
<p></p>
<span id="TheFourierBlock"></span>
<h2 id="A_4.8_The_FOURIER_Block"> 4.8 The FOURIER Block </h2>
The Fourier transform is done and the results are plotted within <code>musrview</code> &mdash;as input data the actual data shown in <code>musrview</code> is used. In the FOURIER block of the msr file all necessary parameters for calculating and presenting the Fourier transform of the data specified in the <a href="#ThePlotBlock" class="foswikiCurrentTopicLink">PLOT block</a> is given. If the FOURIER block is not present in the msr file, either the parameters set in the <a class="foswikiCurrentTopicLink" href="#MusrfitStartupXml">XML startup file</a> or the system defaults are taken when the Fourier transform is performed. The block starts with the FOURIER keyword and may contain the following entries on the successive lines: <dl>
The Fourier transform is done and the results are plotted within <code>musrview</code> &mdash;as input data the actual data shown in <code>musrview</code> is used. In the FOURIER block of the msr file all necessary parameters for calculating and presenting the Fourier transform of the data specified in the <a class="foswikiCurrentTopicLink" href="#ThePlotBlock">PLOT block</a> is given. If the FOURIER block is not present in the msr file, either the parameters set in the <a class="foswikiCurrentTopicLink" href="#MusrfitStartupXml">XML startup file</a> or the system defaults are taken when the Fourier transform is performed. The block starts with the FOURIER keyword and may contain the following entries on the successive lines: <dl>
<dt> units </dt><dd> Here is specified in which domain the Fourier-transformed data is presented. One may choose between the fields (<strong>Gauss</strong>) or (<strong>Tesla</strong>), the frequency (<strong>MHz</strong>), and the angular-frequency domain (<strong>Mc/s</strong>).
</dd> <dt> fourier_power </dt><dd> It is possible (but not necessary) to set the number of data points used for the Fourier transform here. As argument the exponent <i>n</i>&lt;21 of a power of 2 is accepted. The number of data points is then 2<sup><i>n</i></sup>. <strong>Attention:</strong> If the number of points given here is bigger than the actual number of available data points, the input data vector is filled with zeros until the number of requested points is reached (zero padding)!
</dd> <dt> dc-corrected </dt><dd> a flag to remove a potential DC-offset of the signal. Allowed entries are <code>dc-corrected true | 1 | false | 0</code>.
@ -1238,7 +1247,7 @@ Altogether, a possible FOURIER block might look like that:
<p></p>
Notes
<p></p>
<a name="FootNote11note"></a><span class="FootNoteLabel"><a href="MusrFit.html#FootNote11text" class="foswikiCurrentWebHomeLink"> <strong>l</strong> </a></span>: <span class="FootNote">for a more detailed discussion about the shortcomings of RRF fits see the RRF memo found under &lt;musrfit&gt;/doc/memo/rrf</span>
<a name="FootNote12note"></a><span class="FootNoteLabel"><a href="#FootNote12text"><b>l</b></a></span>: <span class="FootNote">for a more detailed discussion about the shortcomings of RRF fits see the RRF memo found under &lt;musrfit&gt;/doc/memo/rrf</span>
<p></p>
<p></p>
<p></p>
@ -1246,7 +1255,7 @@ Notes
<p></p>
<span id="ThePlotBlock"></span>
<h2 id="A_4.9_The_PLOT_Block"> 4.9 The PLOT Block </h2>
The PLOT block is intended to collect all the information needed for the graphical presentation of the data and fits using <code>musrview</code>. The PLOT keyword at the beginning of the block is followed by a number which indicates the plot type. The plot types match the <a href="#FitTypes" class="foswikiCurrentTopicLink">fit types</a>. Additionally, it is possible to provide information using the following keywords: <dl>
The PLOT block is intended to collect all the information needed for the graphical presentation of the data and fits using <code>musrview</code>. The PLOT keyword at the beginning of the block is followed by a number which indicates the plot type. The plot types match the <a class="foswikiCurrentTopicLink" href="#FitTypes">fit types</a>. Additionally, it is possible to provide information using the following keywords: <dl>
<dt> lifetimecorrection </dt><dd> Does not accept any arguments. If present, the output in <code>musrview</code> is corrected for the exponential decay of the muon. Only relevant for (type 0).
</dd> <dt> runs </dt><dd> The numbers of the runs to be plotted have to be put here. The runs are numbered according to their appearance in the RUN block.
</dd> <dt> range </dt><dd> Here it is possible to define the plotting range explicitly. Depending on the plot type the following settings are allowed where the times are given in microseconds and the <i>N</i> in counts (type 0, 4) or in counts/nsec (type 0): <dl>
@ -1286,7 +1295,7 @@ The PLOT block is intended to collect all the information needed for the graphic
<span id="TheStatisticBlock"></span>
<h2 id="A_4.10_The_STATISTIC_Block"> 4.10 The STATISTIC Block </h2>
The STATISTIC block is the last block of a msr file. It contains some information on the fit: the date and time as well as the absolute and normalized values of &#967;<sup>2</sup> and the number of degrees of freedom in the fit.<br>
If enabled in the <a class="foswikiCurrentTopicLink" href="#MusrfitStartupXml">XML file</a> for &chi;<sup>2</sup>-<a href="#SingleHistogramFit" class="foswikiCurrentTopicLink">single-histogram fits</a> also <a href="http://en.wikipedia.org/wiki/Pearson's_chi-square_test">Pearson's &chi;<sup>2</sup></a> will be written to the STATISTIC block.<br>
If enabled in the <a class="foswikiCurrentTopicLink" href="#MusrfitStartupXml">XML file</a> for &chi;<sup>2</sup>-<a class="foswikiCurrentTopicLink" href="#SingleHistogramFit">single-histogram fits</a> also <a href="http://en.wikipedia.org/wiki/Pearson's_chi-square_test">Pearson's &chi;<sup>2</sup></a> will be written to the STATISTIC block.<br>
These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged!
<p></p>
<span id="TheFitTypes"></span>
@ -1359,7 +1368,7 @@ and plotted together with the function given in the THEORY block.
<p></p>
<span id="AsymmetryRrfFit"></span>
<h2 id="A_5.4_Asymmetry_RRF_Fit"> 5.4 Asymmetry RRF Fit </h2>
In a first step, the unbinned asymmetry is formed as described for the asymmetry fit. Afterwards the RRF transformation is carried out, i.e. point 4. and 5. as sketched in the single histogramm RRF fit. The same reservations as for the single histogram RRF fit apply: <strong>if you not urgently need it: do not use it! There are better ways to deal with the analysis of high frequency data!</strong>
For asymmetry RRF Fit (fit type <strong>3</strong>) two histograms are needed. In a first step, the unbinned asymmetry is formed as described for the asymmetry fit. Afterwards the RRF transformation is carried out, i.e. point 4. and 5. as sketched in the single histogramm RRF fit. The same reservations as for the single histogram RRF fit apply: <strong>if you not urgently need it: do not use it! There are better ways to deal with the analysis of high frequency data!</strong>
<p></p>
<span id="MuMinusFit"></span>
<h2 id="A_5.5_Negative_Muon_SR_Fit"> 5.5 Negative Muon &mu;SR Fit </h2>
@ -1374,7 +1383,7 @@ where <img alt="i" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_c46
</dd> <dt> <img alt="N&#95;{\rm bkg}(t)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_5e07a020de661906573e8fed8eff32bf.png" /> </dt><dd> <img alt="N&#95;{\rm bkg}(t)&#61; N&#95;{\rm bkg,0} + \sum&#95;k N&#95;{\rm bkg,k} \cos(k \omega&#95;{\rm cyclotron} t)" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_53e41adf70ef506cc7668f8593a1b501.png" /> the background
</dd></dl>
<p></p>
Since MuMinus is quite generic, the full functional depends has to be written in the <a href="#TheTheoryBlock" class="foswikiCurrentTopicLink">THEORY Block</a>.
Since MuMinus is quite generic, the full functional depends has to be written in the <a class="foswikiCurrentTopicLink" href="#TheTheoryBlock">THEORY Block</a>.
<p></p>
<span id="NonMusrFit"></span>
<h2 id="A_5.6_Non_45SR_Fit"> 5.6 Non-&mu;SR Fit </h2>
@ -1501,11 +1510,11 @@ make -f Makefile.TMyLibrary install
</pre>
In case of a custom installation some paths in the Makefile might have to be changed. For further information about the <code>ROOT</code> dictionary mechanism please refer to the <a href="http://root.cern.ch/drupal/content/interacting-shared-libraries-rootcint">documentation</a>.
<p></p>
After installing the shared library the defined user function might be used in <code>musrfit</code> as described <a href="#UserFunctions" class="foswikiCurrentTopicLink">above</a>.
After installing the shared library the defined user function might be used in <code>musrfit</code> as described <a class="foswikiCurrentTopicLink" href="#UserFunctions">above</a>.
<p></p>
Good luck! <img class='smily' src='../pub/Main/SmiliesPluginPSI_/wink.gif' alt='wink' title='wink' />
<p></p>
Finally, please be aware of the <a href="#UserFunctionRemark" class="foswikiCurrentTopicLink">remark</a> at the end of this section.
Finally, please be aware of the <a class="foswikiCurrentTopicLink" href="#UserFunctionRemark">remark</a> at the end of this section.
<p></p>
<span id="UserFcnWithGlobal"></span>
<h2 id="A_6.2_User_Function_with_global_user_45function_45object_access"> 6.2 User Function with global user-function-object access </h2>
@ -1517,7 +1526,7 @@ are independent entities. This means if the msr file contains <em>n</em> run blo
If the user function is performing CPU-demanding calculations this is rather inefficient.
<p></p>
<span id="GlobalUserFunctionFigure"></span>
<img class='imagePlain imagePlain_none ' src='../pub/MUSR/MusrFit/igp_9eac78831993c6c274146a8f75bc15fe_Theory-Tree-with-UserFcn.png' alt='theory tree with user function and global user function objects' title='Theory-Tree-with-UserFcn.png' width='800' height='566' style='' />
<img class='imagePlain imagePlain_none ' src='../pub/MUSR/MusrFit/igp_96bafe0a153bdf59fbc40ada0300f686_Theory-Tree-with-UserFcn.png' alt='theory tree with user function and global user function objects' title='Theory-Tree-with-UserFcn.png' width='800' height='566' style='' />
<p></p>
Therefore, it is possible to associate to each user function (<code>uFx</code>) a global user-function object (<code>g_uFx</code>). The idea is the following: If <code>uFx</code> needs to
perform very time-consuming calculations (e.g. calculate an Abrikosov vortex lattice or the nonlocal response of a superconductor in the Meissner state) this can be
@ -1593,7 +1602,7 @@ private:
};
</pre>
<p></p>
Compared to the <a href="#UserFcnWithoutGlobal" class="foswikiCurrentTopicLink">user function <strong>without</strong> global objects</a>, here the <code>NeedGlobalPart()</code> method returns <code>true</code> meaning that a global user-function object will be needed. Furthermore, the methods <code>SetGlobalPart(vector&lt;void*&gt; &amp;globalPart, UInt_t idx)</code> and <code>GlobalPartIsValid()</code> now need to be implemented.
Compared to the <a class="foswikiCurrentTopicLink" href="#UserFcnWithoutGlobal">user function <strong>without</strong> global objects</a>, here the <code>NeedGlobalPart()</code> method returns <code>true</code> meaning that a global user-function object will be needed. Furthermore, the methods <code>SetGlobalPart(vector&lt;void*&gt; &amp;globalPart, UInt_t idx)</code> and <code>GlobalPartIsValid()</code> now need to be implemented.
The method <code>SetGlobalPart(vector&lt;void*&gt; &amp;globalPart, UInt_t idx)</code> is used to link the <code>fGlobalUserFcn</code> to the global user object. This routine will look like:
<p></p>
<pre class="cplusplus">
@ -1650,7 +1659,7 @@ This way the efficiency of the user function can be increased by almost a factor
<p></p>
<hr />
<span id="UserFunctionRemark"></span>
<span class='foswikiRedFG'><b>Important remark:</b></span> If <code>musrfit</code> <a href="MusrFitSetup.html#MusrFitInstallation">has been built</a> with parallelization support (default for <code>GCC</code> &ge; 4.2) it should be taken care of the thread safety of the user-function <strong>operator()</strong>. During the function optimization of <code>musrfit</code> the <strong>operator()</strong> is called once for any given set of parameters in order to allow the safe execution of any calculation. Within the <a href="#SingleHistogramFit" class="foswikiCurrentTopicLink">single-histogram</a> and <a class="foswikiCurrentTopicLink" href="#AsymmetryFit">asymmetry</a> fits the calculation of &chi;<sup>2</sup> or the log-likelihood is parallelized and the <strong>operator()</strong> is expected to evaluate to reasonable values for a fixed set of parameters (but changing <i>t</i>) beginning with the second function call.
<span class='foswikiRedFG'><b>Important remark:</b></span> If <code>musrfit</code> <a href="MusrFitSetup.html#MusrFitInstallation">has been built</a> with parallelization support (default for <code>GCC</code> &ge; 4.2) it should be taken care of the thread safety of the user-function <strong>operator()</strong>. During the function optimization of <code>musrfit</code> the <strong>operator()</strong> is called once for any given set of parameters in order to allow the safe execution of any calculation. Within the <a class="foswikiCurrentTopicLink" href="#SingleHistogramFit">single-histogram</a> and <a class="foswikiCurrentTopicLink" href="#AsymmetryFit">asymmetry</a> fits the calculation of &chi;<sup>2</sup> or the log-likelihood is parallelized and the <strong>operator()</strong> is expected to evaluate to reasonable values for a fixed set of parameters (but changing <i>t</i>) beginning with the second function call.
In case this cannot be ensured, the parallelization can be disabled by <strong>--disable-omp</strong> on the <a href="MusrFitSetup.html#MusrFitInstallation">configure level</a> of the program installation.
<hr />
<p></p>
@ -1669,11 +1678,11 @@ For reporting bugs or requesting new features and improvements please use the <a
<p></p>
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@ -1687,6 +1696,6 @@ Topic revision: <span class='patternRevInfo'>22 Jan 2016, <a href="https://intr
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@ -225,7 +225,7 @@ In order to obtain some information about the possible options for the installat
For any further information on the standard installation of software, please refer to the web search engine of choice and ask for "install software on linux"...
<p></p>
<h3 id="A_3.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"> 3.1.2 Installation of <code><b>NeXus</b></code> requirements (optional) </h3>
<span class='foswikiRedFG'>Only if</span> <code>musrfit</code> should support reading/writing data files in the <code>NeXus</code> format the further <a href="#ReqSwNeXus" class="foswikiCurrentTopicLink">required</a> software has to be set up. The required libraries and header files could either be available through the user's GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. E.g. on Red Hat-like systems binary packages for <code>MXML</code>, <code>HDF4</code>, and <code>HDF5</code> might be called <code><b>mxml, mxml-devel, hdf, hdf-devel, hdf5, hdf5-devel</b></code>, on Debian-like systems <code><b>libmxml1, libmxml-dev, libhdf4-dev, libhdf5-dev</b></code>.
<span class='foswikiRedFG'>Only if</span> <code>musrfit</code> should support reading/writing data files in the <code>NeXus</code> format the further <a class="foswikiCurrentTopicLink" href="#ReqSwNeXus">required</a> software has to be set up. The required libraries and header files could either be available through the user's GNU/Linux distribution or if this is not the case, the packages can be installed from the source code. E.g. on Red Hat-like systems binary packages for <code>MXML</code>, <code>HDF4</code>, and <code>HDF5</code> might be called <code><b>mxml, mxml-devel, hdf, hdf-devel, hdf5, hdf5-devel</b></code>, on Debian-like systems <code><b>libmxml1, libmxml-dev, libhdf4-dev, libhdf5-dev</b></code>.
<p></p>
Even though there might exist binary packages for the <code>NeXus</code> library, it is best to build and install it directly from the source code which can be found <a href="http://download.nexusformat.org/kits/">here</a>.
<p></p>
@ -328,7 +328,7 @@ After the source-code extraction the <strong>autogen.sh</strong> script is calle
</dd></dl>
<p></p>
Normally it should not be necessary to make use of any of the options except for specifying the installation path with <strong>--prefix</strong>. The other paths should be detected automatically. If this does not work for some reason the <strong>configure</strong> script will terminate and ask for the information.
When the <strong>configure</strong> script has been called successfully everything is ready for building the <code>musrfit</code> libraries and executables. A standard installation sequence (without <code>NeXus</code> support) might then look like<a name="FootNote1text"></a><span class="FootNoteTextLink" title="In case the normal user has no write permissions to the &#38;&#35;36&#59;ROOTSYS and the installation path the &#34;make install&#34; commands have to be executed as superuser&#46;"><a href="#FootNote1note" class="foswikiCurrentTopicLink">(3)</a></span>:
When the <strong>configure</strong> script has been called successfully everything is ready for building the <code>musrfit</code> libraries and executables. A standard installation sequence (without <code>NeXus</code> support) might then look like<a name="FootNote1text"></a><span class="FootNoteTextLink" title="In case the normal user has no write permissions to the &#38;&#35;36&#59;ROOTSYS and the installation path the &#34;make install&#34; commands have to be executed as superuser&#46;"><a class="foswikiCurrentTopicLink" href="#FootNote1note">(3)</a></span>:
<pre class="bash">
&#36; cd &#36;HOME/Apps/musrfit
&#36; sh autogen.sh
@ -376,7 +376,7 @@ If <code>musrgui</code> has been installed, just open one of the <strong>test-&#
<p></p>
Notes
<p></p>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="MusrFitSetup.html#FootNote1text"> <strong>3</strong> </a></span>: <span class="FootNote">In case the normal user has no write permissions to the &#36;ROOTSYS and the installation path the "make install" commands have to be executed as superuser.</span>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text"><b>3</b></a></span>: <span class="FootNote">In case the normal user has no write permissions to the &#36;ROOTSYS and the installation path the "make install" commands have to be executed as superuser.</span>
<p></p>
<p></p>
<p></p>
@ -596,7 +596,7 @@ file:///Users/username/dports
</li></ol>
<hr />
Then the <code>MacPorts</code> system should be set up and can be used to install additional software.<br>
The installation of the software mentioned <a href="#ReqSw" class="foswikiCurrentTopicLink">above</a> is then done in the terminal:
The installation of the software mentioned <a class="foswikiCurrentTopicLink" href="#ReqSw">above</a> is then done in the terminal:
<pre class="bash">
&#36; sudo port -v install pkgconfig autoconf automake libtool fftw-3 fftw-3-single gsl boost libxml2 qt4-mac
</pre>
@ -604,7 +604,7 @@ With <code><b>qt4-mac</b></code>, <code>musredit</code> will be installed. If it
<p></p>
<h3 id="A_5.1.2_Installation_of_61_61NeXus_61_61_requirements_40optional_41"> 5.1.2 Installation of <code><b>NeXus</b></code> requirements (optional) </h3>
<p></p>
<span class='foswikiRedFG'>Only if</span> <code>musrfit</code> should support reading data files in the <code>NeXus</code> format the further <a href="#ReqSwNeXus" class="foswikiCurrentTopicLink">required</a> packages are set up:
<span class='foswikiRedFG'>Only if</span> <code>musrfit</code> should support reading data files in the <code>NeXus</code> format the further <a class="foswikiCurrentTopicLink" href="#ReqSwNeXus">required</a> packages are set up:
<pre class="bash">
&#36; sudo port -v install jpeg6b hdf4 hdf5
</pre>
@ -625,7 +625,7 @@ Unfortunately, the <code>minixml</code> and <code>NeXus</code> libraries have to
</pre>
<p></p>
<h3 id="A_5.1.3_61_61ROOT_61_61"> 5.1.3 <code><b>ROOT</b></code> </h3>
The best way to get <code>ROOT</code> exactly the way needed for <code>musrfit</code> is to install it from source. Before describing it, please make sure that you have installed all required packages listed under <a href="#ReqSw" class="foswikiCurrentTopicLink">Requested Software</a> (e.g. fftw, gsl, etc).
The best way to get <code>ROOT</code> exactly the way needed for <code>musrfit</code> is to install it from source. Before describing it, please make sure that you have installed all required packages listed under <a class="foswikiCurrentTopicLink" href="#ReqSw">Requested Software</a> (e.g. fftw, gsl, etc).
<p></p>
For the following it is assumed that <code>ROOT</code> shall be installed under <code>$HOME/Apps</code>. If you want to install it somewhere else, just systematically replace the related terms of the following description. For the following list of commands the '$' will be given, the command prompt. Do <strong>not</strong> enter it! Also some comments will be added starting with a '#' which can be omitted. They are only there to explain what is going on.
<pre class="bash">
@ -884,9 +884,9 @@ alias mgui&#61;&#39;/Applications/musrgui.app/Contents/MacOS/musrgui&#39;
<p></p>
Notes
<p></p>
<a name="FootNote2note"></a><span class="FootNoteLabel"><a class="foswikiCurrentWebHomeLink" href="MusrFitSetup.html#FootNote2text"> <strong>2</strong> </a></span>: <span class="FootNote"> When using <code>GCC</code> &#8805; 4.2 please make sure that the environment variables <strong>USE_PARALLEL_MINUIT2</strong> and <strong>USE_OPENMP</strong> are <em>not</em> set! Otherwise <code>MINUIT2</code> will be compiled with parallelization support and cannot be used together with <code>musrfit</code> afterwards since the <code>musrfit</code> code is <em>not</em> fully thread-safe! When compiled with <code>GCC</code> &#8805; 4.2 <code>musrfit</code> itself will parallelize the &chi;<sup>2</sup> calculation.</span>
<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text"><b>2</b></a></span>: <span class="FootNote"> When using <code>GCC</code> &#8805; 4.2 please make sure that the environment variables <strong>USE_PARALLEL_MINUIT2</strong> and <strong>USE_OPENMP</strong> are <em>not</em> set! Otherwise <code>MINUIT2</code> will be compiled with parallelization support and cannot be used together with <code>musrfit</code> afterwards since the <code>musrfit</code> code is <em>not</em> fully thread-safe! When compiled with <code>GCC</code> &#8805; 4.2 <code>musrfit</code> itself will parallelize the &chi;<sup>2</sup> calculation.</span>
<p></p>
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="MusrFitSetup.html#FootNote3text" class="foswikiCurrentWebHomeLink"> <strong>4</strong> </a></span>: <span class="FootNote">In the case <code><b>qt3-mac</b></code> has not been installed, there will be no <strong>musrgui.app</strong> but only the executable <strong>musrgui</strong> which will be placed in the directory <strong>$ROOTSYS/bin</strong> and has to be called from the terminal.</span>
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text"><b>4</b></a></span>: <span class="FootNote">In the case <code><b>qt3-mac</b></code> has not been installed, there will be no <strong>musrgui.app</strong> but only the executable <strong>musrgui</strong> which will be placed in the directory <strong>$ROOTSYS/bin</strong> and has to be called from the terminal.</span>
<p></p>
<p></p>
<p></p>
@ -904,12 +904,12 @@ If <code>musrgui</code> has been installed, just open one of the <strong>test-&#
<p></p>
<p></p>
</div>
<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFitSetup <br />
<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFitSetup <br />
Topic revision: <span class='patternRevInfo'>23 Nov 2015, suter_a</span></div>
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</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:andre.lichtsteiner@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.MusrFitSetup'>Send feedback</a></div></div></div>
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.MusrFitSetup'>Send feedback</a></div></div></div>
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@ -923,6 +923,6 @@ Topic revision: <span class='patternRevInfo'>23 Nov 2015, suter_a</span></div>
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@ -1,6 +1,6 @@
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@ -14,11 +14,13 @@
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<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
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<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><style class='head TABLEPLUGIN_default' type="text/css" media="all">
<base /><!--[if IE]></base><![endif]--><link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
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<style class='head TABLEPLUGIN_default' type="text/css" media="all">
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body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
body .foswikiTable td {border-style:solid none; vertical-align:top}
@ -32,12 +34,10 @@ body .foswikiTable tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-col
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<style class='head TABLEPLUGIN_specific' type="text/css" media="all">
body .foswikiTable#tableMusrGui1 td {vertical-align:middle; vertical-align:top}
body .foswikiTable#tableMusrGui1 td.foswikiTableCol0 {text-align:left}
@ -138,16 +138,16 @@ body .foswikiTable#tableMusrGui1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {
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@ -160,7 +160,7 @@ body .foswikiTable#tableMusrGui1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {
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<h1 id="A_61_61musredit_47_40musrgui_41_61_61"> <code><b>musredit / (musrgui)</b></code> </h1>
<p></p>
<div id="foswikiTOC" class="foswikiToc"> <ul>
<div class="foswikiToc" id="foswikiTOC"> <ul>
<li> <a href="MusrGui.html#A_61_61musredit_47_40musrgui_41_61_61"> musredit / (musrgui) </a>
</li> <li> <a href="MusrGui.html#A_1_Introduction"> 1 Introduction </a>
</li> <li> <a href="MusrGui.html#A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2 Available Executables, Configuration Files and their Basic Usage </a> <ul>
@ -197,7 +197,7 @@ In this file the following XML tags are allowed to define settings and might pro
<dt> &lt;general&gt;&lt;/general&gt; </dt><dd> set the default paths to executables and files in this environment <dl>
<dt> &lt;exec_path&gt;PATH_TO_EXEC&lt;/exec_path&gt; </dt><dd> set the path <strong>PATH_TO_EXEC</strong> where the executables <code>musrfit</code>, <code>musrview</code>, <code>musrt0</code>, etc. can be found (inside the &lt;general&gt; environment)
</dd> <dt> &lt;default_save_path&gt;SAV_PATH&lt;/default_save_path&gt; </dt><dd> specify the path <strong>SAV_PATH</strong> where <code>musrgui</code> / <code>musredit</code> point by default when opening and saving msr files (inside the &lt;general&gt; environment)
</dd> <dt> &lt;msr_default_file_path&gt;MSR_DEF_PATH&lt;/msr_default_file_path&gt; </dt><dd> set the path <strong>MSR_DEF_PATH</strong> where the <a href="#MusrfitFeatures" class="foswikiCurrentTopicLink">default msr files provided by</a> <code>musrgui</code> are stored (inside the &lt;general&gt; environment)
</dd> <dt> &lt;msr_default_file_path&gt;MSR_DEF_PATH&lt;/msr_default_file_path&gt; </dt><dd> set the path <strong>MSR_DEF_PATH</strong> where the <a class="foswikiCurrentTopicLink" href="#MusrfitFeatures">default msr files provided by</a> <code>musrgui</code> are stored (inside the &lt;general&gt; environment)
</dd> <dt> &lt;title_from_data_file&gt;y/n&lt;/title_from_data_file&gt; </dt><dd> specify if <code>musrfit</code> should be called with the <a href="MusrFit.html#MusrFit">-t option</a> by default (inside the &lt;general&gt; environment)
</dd> <dt> &lt;enable_musrt0&gt;y/n&lt;/enable_musrt0&gt; </dt><dd> specify if <code><a href="MusrFit.html#MusrT0">musrt0</a></code> can be called from within <code>musrgui</code> / <code>musredit</code> (inside the &lt;general&gt; environment)
</dd></dl>
@ -230,13 +230,13 @@ Additionally, there are some settings defined in this XML file which should be o
<dt> &lt;help_section&gt;&lt;/help_section&gt; </dt><dd> define various help messages in this environment <dl>
<dt> &lt;help_main&gt;HELP TEXT&lt;/help_main&gt; </dt><dd> set the main help message <strong>HELP TEXT</strong> here (inside a &lt;help_section&gt; environment)
</dd></dl>
</dd> <dt> &lt;func_pixmap_path&gt;PIX_PATH&lt;/func_pixmap_path&gt; </dt><dd> set the path <strong>PIX_PATH</strong> to <img src="../pub/MUSR/MusrGui/LaTeX_logo.png" alt="LaTeX_logo.png" /> pixmaps visualizing the various supported theory functions
</dd> <dt> &lt;func_pixmap_path&gt;PIX_PATH&lt;/func_pixmap_path&gt; </dt><dd> set the path <strong>PIX_PATH</strong> to <img alt="LaTeX_logo.png" src="../pub/MUSR/MusrGui/LaTeX_logo.png" /> pixmaps visualizing the various supported theory functions
</dd> <dt> &lt;theory_functions&gt;&lt;/theory_functions&gt; </dt><dd> define the functions for a msr file's THEORY block <a href="MusrFit.html#TheoryTable">according to the correct syntax</a> in this environment <dl>
<dt> &lt;func&gt;&lt;/func&gt; </dt><dd> specify a function here (inside a &lt;theory_functions&gt; environment) <dl>
<dt> &lt;name&gt;NAME&lt;/name&gt; </dt><dd> the <strong>NAME</strong> of the function in the msr file (inside a &lt;func&gt; environment)
</dd> <dt> &lt;comment&gt;COMMENT&lt;/comment&gt; </dt><dd> description of the used parameters (inside a &lt;func&gt; environment)
</dd> <dt> &lt;label&gt;LABEL&lt;/label&gt; </dt><dd> <strong>LABEL</strong> of the function in the <code>musrgui</code> / <code>musredit</code> menu (inside a &lt;func&gt; environment)
</dd> <dt> &lt;pixmap&gt;PIXMAP&lt;/pixmap&gt; </dt><dd> <img src="../pub/MUSR/MusrGui/LaTeX_logo.png" alt="LaTeX_logo.png" /> picture used to describe the function and stored in the <strong>PIX_PATH</strong> (inside a &lt;func&gt; environment)
</dd> <dt> &lt;pixmap&gt;PIXMAP&lt;/pixmap&gt; </dt><dd> <img alt="LaTeX_logo.png" src="../pub/MUSR/MusrGui/LaTeX_logo.png" /> picture used to describe the function and stored in the <strong>PIX_PATH</strong> (inside a &lt;func&gt; environment)
</dd> <dt> &lt;params&gt;N&lt;/params&gt; </dt><dd> number of parameters <strong>N</strong> used by the function (inside a &lt;func&gt; environment)
</dd></dl>
</dd></dl>
@ -310,33 +310,33 @@ An example of the <code><b>musrgui_startup.xml</b></code> looks like:
<h1 id="A_3_61_61musrfit_61_61_Features"> 3 <code><b>musrfit</b></code> Features </h1>
The features of <code>musrfit</code> which can be accessed by the graphical front ends <code>musrgui</code> / <code>musredit</code> are described in the following. All functions can either be called by choosing them from the MusrFit menu, by clicking the respective button in the MusrFit bar, or by using a keyboard shortcut.
<p></p>
$ <img src="../pub/MUSR/MusrGui/musrasym.png" alt="musrasym.png" /> Asymmetry Default (Alt+a): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>2</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/2007/lem07_his_8472.root</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>2007/lem07_his_8472</b></code> and the file format either <strong>ROOT-NPP</strong> or <strong>ROOT-PPC</strong>.
$ <img alt="musrasym.png" src="../pub/MUSR/MusrGui/musrasym.png" /> Asymmetry Default (Alt+a): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>2</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/2007/lem07_his_8472.root</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>2007/lem07_his_8472</b></code> and the file format either <strong>ROOT-NPP</strong> or <strong>ROOT-PPC</strong>.
<p></p>
$ <img src="../pub/MUSR/MusrGui/musrsinglehisto.png" alt="musrsinglehisto.png" /> Single-Histogram Default (Alt+h): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>0</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/d2007/deltat_pta_gps_8472.bin</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>d2007/deltat_pta_gps_8472</b></code> and the file format <strong>PSI-BIN</strong>.
$ <img alt="musrsinglehisto.png" src="../pub/MUSR/MusrGui/musrsinglehisto.png" /> Single-Histogram Default (Alt+h): Generate a full msr file suitable for the <a href="MusrFit.html#FitTypes">fit type</a> <strong>0</strong> of <code>musrfit</code> from defaults. Calling this function opens a window where the relative path and file name to a data file as well as the file format that should be used have to be specified. For instance if the data file <code><b>/path-to-datadir/d2007/deltat_pta_gps_8472.bin</b></code> should be used and <code><b>/path-to-datadir</b></code> is on the path where <code>musrfit</code> <a href="MusrFit.html#PathToDataFiles">looks for data files</a> then the file name would be <code><b>d2007/deltat_pta_gps_8472</b></code> and the file format <strong>PSI-BIN</strong>.
<p></p>
$ <img alt="musrcalcchisq.png" src="../pub/MUSR/MusrGui/musrcalcchisq.png" /> Calculate Chisq (Alt+c): <pre class="bash">musrfit &#60;msr&#95;file&#62; --chisq-only</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
<p></p>
$ <img src="../pub/MUSR/MusrGui/musrfit.png" alt="musrfit.png" /> Fit (Alt+f): <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters&#93;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a class="foswikiCurrentTopicLink" href="#MusrPrefs">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
$ <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> Fit (Alt+f): <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters&#93;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a class="foswikiCurrentTopicLink" href="#MusrPrefs">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
<p></p>
$ <img alt="musrswap.png" src="../pub/MUSR/MusrGui/musrswap.png" /> Swap Msr &#8596; Mlog (Alt+s): Swap the msr and mlog files. E.g., for a file called <code><b>8472_zf.msr</b></code>, this is copied to <code><b>8472_zf.mlog</b></code> and vice versa.
<p></p>
$ <img src="../pub/MUSR/MusrGui/musrmsr2data.png" alt="musrmsr2data.png" /> Msr2data (Alt+m): Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
$ <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> Msr2data (Alt+m): Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
<p></p>
$ <img src="../pub/MUSR/MusrGui/musrview.png" alt="musrview.png" /> View (Alt+v): <pre class="bash">musrview &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrView">manual</a> of <code>musrfit</code>.
$ <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> View (Alt+v): <pre class="bash">musrview &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrView">manual</a> of <code>musrfit</code>.
<p></p>
$ <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> T0 (Alt+t): <pre class="bash">musrt0 &#60;msr&#95;file&#62;</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. For further information refer to the <a href="MusrFit.html#MusrT0">manual</a> of <code>musrfit</code>.
<p></p>
$ <img src="../pub/MUSR/MusrGui/musrFT.png" alt="musrFT.png" /> Raw Fourier: <code>musrFT &lt;with-many-options&gt;</code> is called. For a proper documentation of it, check the <a href="MusrFit.html#MusrFT">manual</a> of <code>musrFT</code>.
$ <img alt="musrFT.png" src="../pub/MUSR/MusrGui/musrFT.png" /> Raw Fourier: <code>musrFT &lt;with-many-options&gt;</code> is called. For a proper documentation of it, check the <a href="MusrFit.html#MusrFT">manual</a> of <code>musrFT</code>.
<p></p>
<span id="MusrPrefs"></span>
$ <img src="../pub/MUSR/MusrGui/musrprefs.png" alt="musrprefs.png" /> Preferences (Alt+p): Opens a window in which the optional parameters that should be passed to <code>musrfit</code> can be chosen. These options are <code><b>--keep-mn2-output</b></code>, <code><b>--dump ascii</b></code>, <code><b>--dump root</b></code>, and <code><b>--title-from-data-file</b></code>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>. Additionally, the access to <code>musrt0</code> can be enabled temporarily.
$ <img alt="musrprefs.png" src="../pub/MUSR/MusrGui/musrprefs.png" /> Preferences (Alt+p): Opens a window in which the optional parameters that should be passed to <code>musrfit</code> can be chosen. These options are <code><b>--keep-mn2-output</b></code>, <code><b>--dump ascii</b></code>, <code><b>--dump root</b></code>, and <code><b>--title-from-data-file</b></code>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>. Additionally, the access to <code>musrt0</code> can be enabled temporarily.
<p></p>
$ <img alt="musrdump.png" src="../pub/MUSR/MusrGui/musrdump.png" /> Dump Header: Opens a file dialog which allows to select a &mu;SR data file. When this file can be read, the run header info is dumped into a dialog window. Essentially this calls <code><b>dump_header</b></code> internally.
<p></p>
<span id="EditorFeatures"></span>
<h1 id="A_4_Editor_Features"> 4 Editor Features </h1>
Besides the functions described above and which are mostly interfacing <code>musrfit/msr2data</code> the editors of <code>musrgui</code> / <code>musredit</code> offer various functions for manipulating especially <code>musrfit</code> msr files:
<img class='imagePlain imagePlain_right ' src='../pub/MUSR/MusrGui/igp_6000206c604d890d5466ca71a2eda191_musrgui-editor-v0.png' alt='musrgui editor features' title='musrgui-editor-v0.png' width='415' height='566' style='' /> <ul>
<img class='imagePlain imagePlain_right ' src='../pub/MUSR/MusrGui/igp_4e5811420d6b5b31cac70e88b8477a14_musrgui-editor-v0.png' alt='musrgui editor features' title='musrgui-editor-v0.png' width='415' height='566' style='' /> <ul>
<li> Upon right-clicking an open msr file a menu as shown to the right is displayed which offers the addition of any valid msr file block or theory function. In case a simple theory function is chosen, the function will be inserted into the THEORY block using the <a href="MusrFit.html#TheoryTable">correct syntax</a>. If one chooses to add a whole block to the file a dialog opens in which the necessary information for each block as described in the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">manual</a> of <code>musrfit</code> can be supplied. <span class='foswikiBlueFG'>This feature is available only in <code>musrgui</code>. In <code>musredit</code> the respective functions can be accessed through the <em>Edit</em> menu.</span>
</li> <li> In order to comment or uncomment lines in a msr file select the according lines and apply <strong>Edit &rarr; (Un)Comment</strong> or use the keyboard shortcut <strong>Ctrl+(Shift)+m</strong>.
</li></ul>
@ -350,17 +350,17 @@ For reporting bugs or requesting new features and improvements please use the <a
<p></p>
<p></p>
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<th class="foswikiTableCol3"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=3;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Size</a> </th>
<th class="foswikiTableCol4"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=4;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Date</a> </th>
<th class="foswikiTableCol5"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=5;table=1;up=0#sorted_table">Who</a> </th>
<th class="foswikiTableCol6 foswikiLastCol"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=6;table=1;up=0#sorted_table">Comment</a> </th>
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<th class="foswikiTableCol6 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrGui?cover=print;sortcol=6;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
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@ -368,19 +368,19 @@ For reporting bugs or requesting new features and improvements please use the <a
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrgui-editor-v0.png' /></span><span class="foswikiHidden">png</span> </td>
<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/MusrGui/musrgui-editor-v0.png">musrgui-editor-v0.png</a> </td>
<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/MusrGui?filename=musrgui-editor-v0.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
<td style="text-align:right" class="foswikiTableCol3 foswikiLast"> 37 K </td>
<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 37 K </td>
<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">10 Apr 2009 - 14:53</span> </td>
<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> musrgui options available upon right clicking a open msr-file </td>
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<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a href="WebHome.html" class="foswikiCurrentWebHomeLink">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrGui <br />
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@ -394,6 +394,6 @@ Topic revision: <span class='patternRevInfo'>19 Feb 2015, suter_a</span></div>
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body .foswikiTable {border-width:1px}
body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
body .foswikiTable td {border-style:solid none; vertical-align:top}
@ -52,10 +50,12 @@ body .foswikiTable#tableMusrRoot7 th.foswikiSortedCol {background-color:#eeeeee}
body .foswikiTable#tableMusrRoot7 tr.foswikiTableRowdataBg0 td {background-color:#ffffff}
body .foswikiTable#tableMusrRoot7 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f5f5f5}
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@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -135,19 +135,19 @@ body .foswikiTable#tableMusrRoot7 tr.foswikiTableRowdataBg0 td.foswikiSortedCol
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<body class="foswikiNoJs patternViewPage patternPrintPage">
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@ -246,35 +246,35 @@ RunHeader (TFolder) ---&#124;
&#124;- BeamlineInfo (TObjArray)
</pre>
<p></p>
In brackets the object type is given. <code>RunInfo</code> contains most information relevant for the user and will be itemized Sec. <a href="#RunInfo" class="foswikiCurrentTopicLink">RunInfo Overview</a> and <a href="#RunInfoRequired" class="foswikiCurrentTopicLink">RunInfo Required</a>. <code>DetectorInfo</code> contains detector specific information, like detector name, time zero bin, etc. (details in Sec. <a href="#DetectorInfoRequired" class="foswikiCurrentTopicLink">DetectorInfo Required</a>). <code>SampleEnvironmentInfo</code> (details in Sec. <a class="foswikiCurrentTopicLink" href="#SampleEnvironmentInfoRequired">SampleEnvironmentInfo Required</a>), and <code>MagneticFieldEnvironmentInfo</code> (details in Sec. <a href="#MagneticFieldEnvironmentInfoRequired" class="foswikiCurrentTopicLink">MagneticFieldEnvironmentInfo Required</a>) store additional, more detailed information concerning the sample environment. <code>BeamlineInfo</code> stores beamline relevant information (details in Sec. <a class="foswikiCurrentTopicLink" href="#BeamlineInfoRequired">BeamlineInfo Required</a>).
In brackets the object type is given. <code>RunInfo</code> contains most information relevant for the user and will be itemized Sec. <a class="foswikiCurrentTopicLink" href="#RunInfo">RunInfo Overview</a> and <a class="foswikiCurrentTopicLink" href="#RunInfoRequired">RunInfo Required</a>. <code>DetectorInfo</code> contains detector specific information, like detector name, time zero bin, etc. (details in Sec. <a class="foswikiCurrentTopicLink" href="#DetectorInfoRequired">DetectorInfo Required</a>). <code>SampleEnvironmentInfo</code> (details in Sec. <a class="foswikiCurrentTopicLink" href="#SampleEnvironmentInfoRequired">SampleEnvironmentInfo Required</a>), and <code>MagneticFieldEnvironmentInfo</code> (details in Sec. <a class="foswikiCurrentTopicLink" href="#MagneticFieldEnvironmentInfoRequired">MagneticFieldEnvironmentInfo Required</a>) store additional, more detailed information concerning the sample environment. <code>BeamlineInfo</code> stores beamline relevant information (details in Sec. <a class="foswikiCurrentTopicLink" href="#BeamlineInfoRequired">BeamlineInfo Required</a>).
<p></p>
Before elaborating more on the required items within this structure, a few words on the <code>ROOT</code> types used here: <code>RunHeader</code> is a <code>TFolder</code> object. All the "sub-directory" entries are of type <code>TObjArray</code> and collect items of type <code>TObjString</code> or other <code>TObjArray</code> (<em>i.e.</em> sub-directories and sub-sub-directories, etc.).
<p></p>
<span id="RunInfo"></span>
<h3 id="A_3.1.1_61RunInfo_61_Overview"> 3.1.1 <code>RunInfo</code> Overview </h3>
<p></p>
<table rules="none" border="1" class="foswikiTable">
<table border="1" class="foswikiTable" rules="none">
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=1;up=0#sorted_table" title="Sort by this column" rel="nofollow">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=1;up=0#sorted_table">Internal Type</a> </th>
<th style="text-align:center" class="foswikiTableCol2 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=1;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
</tr>
</thead>
<tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Version </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> SVN version of <code>TMusrRunHeader</code> </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Generic Validator URL </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td style="text-align:center" class="foswikiTableCol2 foswikiLastCol"> URL of the generic <code>MusrRoot</code> validation xsd-file. </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol" style="text-align:center"> URL of the generic <code>MusrRoot</code> validation xsd-file. </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Specific Validator URL </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol" style="text-align:center"> URL of the instrument specific validation xsd-file. </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -299,7 +299,7 @@ Before elaborating more on the required items within this structure, a few words
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Title </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -324,7 +324,7 @@ Before elaborating more on the required items within this structure, a few words
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Laboratory </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> PSI </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -354,7 +354,7 @@ Before elaborating more on the required items within this structure, a few words
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Setup </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -364,7 +364,7 @@ Before elaborating more on the required items within this structure, a few words
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Name </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -384,12 +384,12 @@ Before elaborating more on the required items within this structure, a few words
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Time Resolution </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 0.1953125 ns </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> RedGreen Offsets </td>
<td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>TIntVector</code> </td>
<td class="foswikiTableCol1 foswikiLast" style="text-align:center"> <code>TIntVector</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> <em>e.g.</em> 0; 20 </td>
</tr>
</tbody></table>
@ -423,13 +423,13 @@ Even though the first approach is very clean, it would mean a lot of maintenance
<li> Strings, represented by <code>TString</code>
</li> <li> Integers, represented by <code>Int_t</code>
</li> <li> Floating point numbers, represented by <code>Double_t</code>
</li> <li> Physical quantities, represented by <a href="#TMusrRunPhysicalQuantity" class="foswikiCurrentTopicLink"><code>TMusrRunPhysicalQuantity</code> - Possible Representations</a>
</li> <li> Physical quantities, represented by <a class="foswikiCurrentTopicLink" href="#TMusrRunPhysicalQuantity"><code>TMusrRunPhysicalQuantity</code> - Possible Representations</a>
</li> <li> Collection of strings, represented by <code>TStringVector</code>
</li> <li> Collection of integers, represented by <code>TIntVector</code>
</li> <li> Collection of floating point numbers, represented by <code>TDoubleVector</code>
</li></ol>
<p></p>
These properties can be collected by themselves in form of vectors. This way any needed information can be written into the <code>ROOT</code> file. The class <code>TMusrRunHeader</code> is implementing this run header concept. In following section code snippets will be discussed, showing how this is used on level of the <code>MIDAS</code> analyzer, <code>musrfit</code> reader routine, and <code>any2many</code> conversion routines. The section <a href="#ValidateMusrRoot" class="foswikiCurrentTopicLink">Validation</a> will discuss how to validate <code>MusrRoot</code> files.
These properties can be collected by themselves in form of vectors. This way any needed information can be written into the <code>ROOT</code> file. The class <code>TMusrRunHeader</code> is implementing this run header concept. In following section code snippets will be discussed, showing how this is used on level of the <code>MIDAS</code> analyzer, <code>musrfit</code> reader routine, and <code>any2many</code> conversion routines. The section <a class="foswikiCurrentTopicLink" href="#ValidateMusrRoot">Validation</a> will discuss how to validate <code>MusrRoot</code> files.
<p></p>
<h2 id="A_4.1_User_Interface_for_61MusrRoot_61_Run_Header"> 4.1 User Interface for <code>MusrRoot</code> Run Header </h2>
There are two things needed to deal with the <code>MusrRoot</code> run header, namely writing it and reading it. I will start with the writing as will be done in the <code>MIDAS</code> analyzer.
@ -450,7 +450,7 @@ header-&#62;Set(&#34;RunInfo/Run Title&#34;, &#34;here comes the run title&#34;)
header-&#62;Set(&#34;RunInfo/Run Number&#34;, 2871);
</pre>
<p></p>
Adding information is done via the multiple overloaded <code>Set(&lt;pathName&gt;,&lt;value&gt;)</code> method. Here <code>&lt;pathName&gt;</code> is a string representing the "path" like representation in the <code>MusrRoot</code> file structure, followed by the "value" to be set, <em>e.g.</em> "=File Name=". <code>&lt;value&gt;</code> can be any of the types listed at the beginning of Sec. <a href="#TMusrRunHeaderConcept" class="foswikiCurrentTopicLink"><code>TMusrRunHeader</code> Concept</a>. Here a few examples how to set <code>TMusrRunPhysicalQuantity</code>.
Adding information is done via the multiple overloaded <code>Set(&lt;pathName&gt;,&lt;value&gt;)</code> method. Here <code>&lt;pathName&gt;</code> is a string representing the "path" like representation in the <code>MusrRoot</code> file structure, followed by the "value" to be set, <em>e.g.</em> "=File Name=". <code>&lt;value&gt;</code> can be any of the types listed at the beginning of Sec. <a class="foswikiCurrentTopicLink" href="#TMusrRunHeaderConcept"><code>TMusrRunHeader</code> Concept</a>. Here a few examples how to set <code>TMusrRunPhysicalQuantity</code>.
<p></p>
<pre class="cplusplus">
prop.Set(&#34;Sample Temperature&#34;, 3.2, 3.21, 0.05, &#34;K&#34;, &#34;CF1&#34;);
@ -552,7 +552,7 @@ if (ok) {
<h2 id="A_4.2_Validation_of_a_61MusrRoot_61_File"> 4.2 Validation of a <code>MusrRoot</code> File </h2>
Since <code>MusrRoot</code> is an open and extensible file format a mechanism is needed to validate that a given file is indeed holding the <em>minimum of required</em> entries. To check this the following scheme is implemented in the program <code>musrRootValidation</code>:
<p></p>
<img class='imagePlain imagePlain_none ' src='../pub/MUSR/MusrRoot/igp_83c77f15ea1749504415a3ddb97bfa42_MusrRootValidationScheme.png' alt='MusrRootValidationScheme.png' title='MusrRoot validation scheme' width='495' height='700' style='' />
<img class='imagePlain imagePlain_none ' src='../pub/MUSR/MusrRoot/igp_f8f224022828dc9d95784de27d20b709_MusrRootValidationScheme.png' alt='MusrRootValidationScheme.png' title='MusrRoot validation scheme' width='495' height='700' style='' />
<p></p>
<code>MusrRoot</code> validation scheme
<p></p>
@ -569,23 +569,23 @@ This validation scheme is useful for people which define instrument specific ext
<span id="RunInfoRequired"></span>
<h1 id="A_5_61RunInfo_61_Required"> 5 <code>RunInfo</code> Required </h1>
<p></p>
<table class="foswikiTable" border="1" rules="none">
<table border="1" class="foswikiTable" rules="none">
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=2;up=0#sorted_table">Name</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=2;up=0#sorted_table" rel="nofollow" title="Sort by this column">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=2;up=0#sorted_table" rel="nofollow" title="Sort by this column">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=2;up=0#sorted_table" title="Sort by this column" rel="nofollow">Comment</a> </th>
<th class="foswikiTableCol2 foswikiLastCol" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=2;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
</tr>
</thead>
<tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Version </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> SVN version of <code>TMusrRunHeader</code> </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Generic Validator URL </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> URL of the generic <code>MusrRoot</code> validation xsd-file. </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -595,7 +595,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Specific Validator URL </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> URL of the instrument specific validation xsd-file. </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -615,7 +615,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> File Name </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> File name of the <code>MusrRoot</code> file, </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -625,7 +625,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Title </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -640,7 +640,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Stop Time </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> ISO 8601 date time </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -650,17 +650,17 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Laboratory </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> PSI </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Instrument </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> GPS </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Beam Momentum </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 28.1 MeV/c </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -670,7 +670,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Source </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> Target E - Low Energy Muons or </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -680,7 +680,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Setup </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -700,7 +700,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Magnetic Field </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 350.002 +- 0.005 G; SP: 350; WXY </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -710,7 +710,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Time Resolution </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 0.1953125 ns </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -740,30 +740,30 @@ The numbering of the detectors has to correspond the its histogram, <em>e.g.</em
<table border="1" class="foswikiTable" rules="none">
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=3;up=0#sorted_table">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=3;up=0#sorted_table">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=3;up=0#sorted_table" title="Sort by this column" rel="nofollow">Comment</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=3;up=0#sorted_table" rel="nofollow" title="Sort by this column">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=3;up=0#sorted_table" rel="nofollow" title="Sort by this column">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=3;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
</tr>
</thead>
<tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Name </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> detector name, <em>e.g.</em> Left-NPP </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Histo Number </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>Int_t</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>Int_t</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> histogram number. This number corresponds to the histogram number in the <code>histos/DecayAnaModule</code> sub-tree. </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Histo Length </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>Int_t</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>Int_t</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> length of the histogram </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Time Zero Bin </td>
<td style="text-align:center" class="foswikiTableCol1"> <code>Double_t</code> </td>
<td class="foswikiTableCol1" style="text-align:center"> <code>Double_t</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> The type is <code>Double_t</code> since for the high-field spectrometer at PSI an <code>Int_t</code> representation would be not good enough. </td>
</tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -773,7 +773,7 @@ The numbering of the detectors has to correspond the its histogram, <em>e.g.</em
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> Last Good Bin </td>
<td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>Int_t</code> </td>
<td class="foswikiTableCol1 foswikiLast" style="text-align:center"> <code>Int_t</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> &nbsp; </td>
</tr>
</tbody></table>
@ -782,18 +782,18 @@ The numbering of the detectors has to correspond the its histogram, <em>e.g.</em
<h1 id="A_7_61SampleEnvironmentInfo_61_Required"> 7 <code>SampleEnvironmentInfo</code> Required </h1>
Here only a single entry is required, namely
<p></p>
<table rules="none" border="1" class="foswikiTable">
<table border="1" class="foswikiTable" rules="none">
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=4;up=0#sorted_table">Name</a> </th>
<th style="text-align:center" class="foswikiTableCol1"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=4;up=0#sorted_table">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=4;up=0#sorted_table">Comment</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=4;up=0#sorted_table" rel="nofollow" title="Sort by this column">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=4;up=0#sorted_table" rel="nofollow" title="Sort by this column">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=4;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
</tr>
</thead>
<tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> Cryo </td>
<td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>TString</code> </td>
<td class="foswikiTableCol1 foswikiLast" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> name of the used cryostat, <em>e.g.</em> Konti-2 </td>
</tr>
</tbody></table>
@ -803,12 +803,12 @@ Here only a single entry is required, namely
<p></p>
Here only a single entry is required, namely
<p></p>
<table class="foswikiTable" border="1" rules="none">
<table border="1" class="foswikiTable" rules="none">
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=5;up=0#sorted_table">Name</a> </th>
<th style="text-align:center" class="foswikiTableCol1"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=5;up=0#sorted_table">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=5;up=0#sorted_table">Comment</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=5;up=0#sorted_table" rel="nofollow" title="Sort by this column">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=5;up=0#sorted_table" rel="nofollow" title="Sort by this column">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=5;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
</tr>
</thead>
<tbody>
@ -820,7 +820,7 @@ Here only a single entry is required, namely
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> &nbsp; </td>
<td class="foswikiTableCol1 foswikiLast"> &nbsp; </td>
<td style="text-align:right" class="foswikiTableCol2 foswikiLastCol foswikiLast"> In case of ZF measurements, there might be an entry like <code>ZF</code>. </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast" style="text-align:right"> In case of ZF measurements, there might be an entry like <code>ZF</code>. </td>
</tr>
</tbody></table>
<p></p>
@ -829,18 +829,18 @@ Here only a single entry is required, namely
<p></p>
Here only a single entry is required, namely
<p></p>
<table rules="none" class="foswikiTable" border="1">
<table border="1" class="foswikiTable" rules="none">
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=6;up=0#sorted_table">Name</a> </th>
<th style="text-align:center" class="foswikiTableCol1"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=6;up=0#sorted_table" rel="nofollow" title="Sort by this column">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=6;up=0#sorted_table">Comment</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=6;up=0#sorted_table" rel="nofollow" title="Sort by this column">Name</a> </th>
<th class="foswikiTableCol1" style="text-align:center"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=6;up=0#sorted_table" rel="nofollow" title="Sort by this column">Internal Type</a> </th>
<th class="foswikiTableCol2 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=6;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
</tr>
</thead>
<tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> Name </td>
<td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>TString</code> </td>
<td class="foswikiTableCol1 foswikiLast" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> name of the beamline, <em>e.g.</em> <code>piM3.2</code>. </td>
</tr>
</tbody></table>
@ -1073,15 +1073,15 @@ Result in the <code>RunHeader/SampleEnvironmentInfo</code>:
<p></p>
<br class="imageClear" clear="all"/><div class="foswikiAttachments">
<div class="twistyPlugin foswikiMakeVisible"><span id="topicattachmentslist1show" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleopen.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>2</span></span></a></span><span id="topicattachmentslist1hide" style="display:none" class="twistyRememberSetting twistyTrigger foswikiUnvisited twistyInited"><a class="patternTwistyButton" href="#"><img src="../pub/System/DocumentGraphics/toggleclose.png" border="0" alt="" /><span class="foswikiLinkLabel foswikiUnvisited">Attachments <span class='foswikiSmall foswikiGrayText'>2</span></span></a></span></div><div class="twistyPlugin"><div id="topicattachmentslist1toggle" style="" class="twistyRememberSetting twistyContent twistyInited">
<table border="1" class="foswikiTable" rules="none" summary="Topic attachments" id="tableMusrRoot7"><caption>Topic attachments</caption>
<table border="1" class="foswikiTable" id="tableMusrRoot7" rules="none" summary="Topic attachments"><caption>Topic attachments</caption>
<thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=7;up=0#sorted_table">I</a> </th>
<th class="foswikiTableCol1"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=7;up=0#sorted_table">Attachment</a> </th>
<th class="foswikiTableCol2"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=7;up=0#sorted_table">Action</a> </th>
<th class="foswikiTableCol3"> <a title="Sort by this column" rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=3;table=7;up=0#sorted_table">Size</a> </th>
<th class="foswikiTableCol4"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=4;table=7;up=0#sorted_table" title="Sort by this column" rel="nofollow">Date</a> </th>
<th class="foswikiTableCol5"> <a rel="nofollow" title="Sort by this column" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=5;table=7;up=0#sorted_table">Who</a> </th>
<th class="foswikiTableCol0 foswikiFirstCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=7;up=0#sorted_table" rel="nofollow" title="Sort by this column">I</a> </th>
<th class="foswikiTableCol1"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=7;up=0#sorted_table" rel="nofollow" title="Sort by this column">Attachment</a> </th>
<th class="foswikiTableCol2"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=7;up=0#sorted_table" rel="nofollow" title="Sort by this column">Action</a> </th>
<th class="foswikiTableCol3"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=3;table=7;up=0#sorted_table" rel="nofollow" title="Sort by this column">Size</a> </th>
<th class="foswikiTableCol4"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=4;table=7;up=0#sorted_table" rel="nofollow" title="Sort by this column">Date</a> </th>
<th class="foswikiTableCol5"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=5;table=7;up=0#sorted_table" rel="nofollow" title="Sort by this column">Who</a> </th>
<th class="foswikiTableCol6 foswikiLastCol"> <a href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=6;table=7;up=0#sorted_table" rel="nofollow" title="Sort by this column">Comment</a> </th>
</tr>
</thead>
@ -1090,7 +1090,7 @@ Result in the <code>RunHeader/SampleEnvironmentInfo</code>:
<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='MusrRootValidationScheme.png' /></span><span class="foswikiHidden">png</span> </td>
<td class="foswikiTableCol1"> <a href="../pub/MUSR/MusrRoot/MusrRootValidationScheme.png">MusrRootValidationScheme.png</a> </td>
<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/MusrRoot?filename=MusrRootValidationScheme.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
<td style="text-align:right" class="foswikiTableCol3"> 96 K </td>
<td class="foswikiTableCol3" style="text-align:right"> 96 K </td>
<td class="foswikiTableCol4"> <span class="foswikiNoBreak">29 Mar 2012 - 11:15</span> </td>
<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
@ -1099,7 +1099,7 @@ Result in the <code>RunHeader/SampleEnvironmentInfo</code>:
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='RunInfo.png' /></span><span class="foswikiHidden">png</span> </td>
<td class="foswikiTableCol1 foswikiLast"> <a href="../pub/MUSR/MusrRoot/RunInfo.png">RunInfo.png</a> </td>
<td class="foswikiTableCol2 foswikiLast"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/MusrRoot?filename=RunInfo.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
<td style="text-align:right" class="foswikiTableCol3 foswikiLast"> 53 K </td>
<td class="foswikiTableCol3 foswikiLast" style="text-align:right"> 53 K </td>
<td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">27 Mar 2012 - 16:09</span> </td>
<td class="foswikiTableCol5 foswikiLast"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
<td class="foswikiTableCol6 foswikiLastCol foswikiLast"> &nbsp; </td>
@ -1111,7 +1111,7 @@ Topic revision: <span class='patternRevInfo'>29 Mar 2012, suter_a</span></div>
</div>
</div>
</div>
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:andre.lichtsteiner@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.MusrRoot'>Send feedback</a></div></div></div>
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.MusrRoot'>Send feedback</a></div></div></div>
</div>
</div>
</div>
@ -1125,6 +1125,6 @@ Topic revision: <span class='patternRevInfo'>29 Mar 2012, suter_a</span></div>
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@ -271,7 +271,7 @@ Topic revision: <span class='patternRevInfo'>10 Jul 2011, wojek</span></div>
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@ -33,6 +34,9 @@ body .foswikiTable tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-col
body .foswikiTable tr.foswikiTableRowdataBg1 td {background-color:#f7f7f6}
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@ -51,11 +55,7 @@ body .foswikiTable#tableTutorialSingleHisto1 th.foswikiSortedCol {background-col
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@ -138,13 +138,13 @@ body .foswikiTable#tableTutorialSingleHisto1 tr.foswikiTableRowdataBg0 td.foswik
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@ -273,12 +273,12 @@ STATISTIC --- 2011-07-09 10:58:44
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&#95;tutorial.msr</pre> opens an interactive window plotting the data of the first RUN block:<br />
<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 />
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 />
<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 />
<img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/igp_9c0f9b31d4414f37be0d3d171836fe63_musrt0-2.png' alt='musrt0-2' title='musrt0-2.png' width='688' height='529' style='' /><br />
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.
A full description of <code>musrt0</code> can be found <a href="MusrFit.html#MusrT0">here</a>.
<p></p>
<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>
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&#95;tutorial.msr</pre>
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&#95;tutorial.msr</pre>
<p></p>
After the fitting procedure has finished the <code>msr</code> file is updated and contains the newly determined values of the fit parameters.
<p></p>
@ -312,15 +312,15 @@ This page only summarizes the very basic features and options of the programs co
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<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
@ -366,7 +366,7 @@ This page only summarizes the very basic features and options of the programs co
<td class="foswikiTableCol0 foswikiFirstCol"> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/png.png' width='16' height='16' alt='musrview-2.png' /></span><span class="foswikiHidden">png</span> </td>
<td class="foswikiTableCol1"> <a href="../pub/MUSR/TutorialSingleHisto/musrview-2.png">musrview-2.png</a> </td>
<td class="foswikiTableCol2"> <a href="https://intranet.psi.ch/wiki/bin/attach/MUSR/TutorialSingleHisto?filename=musrview-2.png;revInfo=1" title="change, update, previous revisions, move, delete..." rel="nofollow">manage</a> </td>
<td style="text-align:right" class="foswikiTableCol3"> 36 K </td>
<td class="foswikiTableCol3" style="text-align:right"> 36 K </td>
<td class="foswikiTableCol4"> <span class="foswikiNoBreak">09 Jul 2011 - 15:48</span> </td>
<td class="foswikiTableCol5"> <a href="https://intranet.psi.ch/Main/UnknownUser">UnknownUser</a> </td>
<td class="foswikiTableCol6 foswikiLastCol"> &nbsp; </td>
@ -387,7 +387,7 @@ Topic revision: <span class='patternRevInfo'>02 Sep 2011, wojek</span></div>
</div>
</div>
</div>
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:andre.lichtsteiner@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.TutorialSingleHisto'>Send feedback</a></div></div></div>
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.TutorialSingleHisto'>Send feedback</a></div></div></div>
</div>
</div>
</div>
@ -401,6 +401,6 @@ Topic revision: <span class='patternRevInfo'>02 Sep 2011, wojek</span></div>
</body>
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<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Tue, 26 Apr 2016 06:39:04 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
</html>

24
doc/html/user/MUSR/WebHome.html
View File

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 22 Jan 2016 15:12:54 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Tue, 26 Apr 2016 06:39:38 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1453475525" type="application/x-wiki" title="edit WebHome" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1461652732" type="application/x-wiki" title="edit WebHome" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<base /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -104,12 +104,12 @@
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiPref-->
<!--JavascriptFiles/foswikiForm-->
<!--PatternSkin/pattern-->
<!--JQUERYPLUGIN::COMMENT--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
<body class="foswikiNoJs patternViewPage patternPrintPage">
<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@ -138,16 +138,16 @@
</li> <li> <a href="MusrFitAcknowledgements.html">Acknowledgements</a>
</li></ul>
<p></p>
-- <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369">BMW</a>) - last update January 19, 2016</div>
-- <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369">BMW</a>) - last update April 26, 2016</div>
<p></p>
<p></p>
</div>
<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>WebHome <br />
Topic revision: <span class='patternRevInfo'>19 Jan 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
Topic revision: <span class='patternRevInfo'>26 Apr 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
</div>
</div>
</div>
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:andre.lichtsteiner@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.WebHome'>Send feedback</a></div></div></div>
</div><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar"><span class="foswikiRight"> <a href="http://foswiki.org/"><img src="../pub/System/ProjectLogos/foswiki-badge.png" alt="This site is powered by Foswiki" title="This site is powered by Foswiki" /></a></span>Copyright &copy; by the contributing authors. All material on this collaboration platform is the property of the contributing authors. <br /> Ideas, requests, problems regarding PSI Wiki? <a href='mailto:thomas.buecklers@psi.ch?subject=PSI Wiki %20Feedback%20on%20MUSR.WebHome'>Send feedback</a></div></div></div>
</div>
</div>
</div>
@ -161,6 +161,6 @@ Topic revision: <span class='patternRevInfo'>19 Jan 2016, <a href="https://intr
</body>
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