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update of the docu which now describes the RRF option.

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suter_a
2016-01-22 16:16:29 +01:00
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# ChangeLog # ChangeLog
#--------------------------------------------------------------------- #---------------------------------------------------------------------
changes since 0.16.0
===================================
NEW 2016-01-22 update of the docu which now describes the RRF option.
changes since 0.15.0 changes since 0.15.0
=================================== ===================================
NEW 2016-01-22 add RRF fit option. At the same time, the version has been NEW 2016-01-22 add RRF fit option. At the same time, the version has been

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<div class="patternContent"><div class="foswikiTopic"> To be written...
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<p></p> <h1 id="BMWlibs_for_61musrfit_61"> BMWlibs for <code>musrfit</code> </h1> <ul>
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<h1><a name="BMWlibs_for_61musrfit_61"></a> BMWlibs for <code>musrfit</code> </h1> <ul>
<li> <a href="LibFitPofB.html"> <code>libFitPofB</code>: routines for calculating transverse-field muon-spin depolarization functions from various static field distributions in superconductors</a> <li> <a href="LibFitPofB.html"> <code>libFitPofB</code>: routines for calculating transverse-field muon-spin depolarization functions from various static field distributions in superconductors</a>
</li> <li> <a href="LibZFRelaxation.html"> <code>libZFRelaxation</code>: routines for calculating zero-field muon-spin depolarization functions from various static field distributions</a> </li> <li> <a href="LibZFRelaxation.html"> <code>libZFRelaxation</code>: routines for calculating zero-field muon-spin depolarization functions from various static field distributions</a>
</li></ul> </li></ul>
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-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://www.psi.ch/low-energy-muons/people" target="_top">AS</a> </div> -- <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> &amp; <a href="http://www.psi.ch/low-energy-muons/people">AS</a></div>
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<p></p> <div class="patternContent"><div class="foswikiTopic"> <h1 id="How_to_Cite_61musrfit_61_63"> How to Cite <code>musrfit</code>? </h1>
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Since quite some effort is going into the development and maintenance of the <code>musrfit</code> package, you should at least acknowledge it in your publication if you have used it to analyze your data. Even better of course is to cite it properly by the reference given beneath Since quite some effort is going into the development and maintenance of the <code>musrfit</code> package, you should at least acknowledge it in your publication if you have used it to analyze your data. Even better of course is to cite it properly by the reference given beneath
<p></p> <ul> <p></p> <ul>
<li> <a href="http://dx.doi.org/10.1016/j.phpro.2012.04.042" target="_top">A. Suter, B.M. Wojek, "Musrfit: A Free Platform-Independent Framework for &mu;SR Data Analysis", Physics Procedia 30, 69 (2012).</a> <li> <a href="http://dx.doi.org/10.1016/j.phpro.2012.04.042">A. Suter, B.M. Wojek, "Musrfit: A Free Platform-Independent Framework for &mu;SR Data Analysis", Physics Procedia 30, 69 (2012).</a>
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<h1 id="libFitPofB"> libFitPofB </h1>
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<h1><a name="libFitPofB"></a> libFitPofB </h1>
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
<li> <a href="LibFitPofB.html#libFitPofB"> libFitPofB </a> <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_1_Introduction"> 1 Introduction </a>
</li> <li> <a href="LibFitPofB.html#A_2_LE_45SR"> 2 LE-&mu;SR </a> <ul> </li> <li> <a href="LibFitPofB.html#A_2_LE_45SR"> 2 LE-&mu;SR </a> <ul>
@ -132,28 +137,28 @@ pre {
</li> <li> <a href="LibFitPofB.html#A_4_The_XML_startup_file"> 4 The XML startup file </a> </li> <li> <a href="LibFitPofB.html#A_4_The_XML_startup_file"> 4 The XML startup file </a>
</li></ul> </li></ul>
</div> </div>
<a name="IntroDuction"></a> <span id="IntroDuction"></span>
<h1><a name="A_1_Introduction"></a> 1 Introduction </h1> <h1 id="A_1_Introduction"> 1 Introduction </h1>
<p></p> <p></p>
<code>libFitPofB</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library generally implement calculations of one-dimensional static magnetic field distributions <img alt="P(B)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9cc0fd47eedada7247b14775bd308deb.png" title="PofB" /> which lead to muon-spin depolarization functions <code>libFitPofB</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library generally implement calculations of one-dimensional static magnetic field distributions <img alt="P(B)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9cc0fd47eedada7247b14775bd308deb.png" title="PofB" /> which lead to muon-spin depolarization functions
<p style="text-align:center"> <p style="text-align:center">
<img alt="\mathcal{P}(t) &#61; \int P(B)\cos\left(\gamma&#95;{\mu} B t + \varphi\right) \mathrm{d}B," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_70e57aa1afa7d337fa46f427b34feb54.png" title="PofT" /> <img alt="\mathcal{P}(t) &#61; \int P(B)\cos\left(\gamma&#95;{\mu} B t + \varphi\right) \mathrm{d}B," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_70e57aa1afa7d337fa46f427b34feb54.png" title="PofT" />
</p> </p>
where <img alt="\gamma&#95;{\mu} &#61; 2\pi\times 135.54~\mathrm{MHz/T}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9bb7e08c8e276a92650d89d6918b3769.png" title="gamma_mu" /> is the gyromagnetic ratio of the muon and <img alt="\varphi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_2339fd9b358ebe241da05c665668d48b.png" title="phi" /> is the initial phase of the muon spins with respect to the positron detector.<br> where <img alt="\gamma&#95;{\mu} &#61; 2\pi\times 135.54~\mathrm{MHz/T}" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_9bb7e08c8e276a92650d89d6918b3769.png" title="gamma_mu" /> is the gyromagnetic ratio of the muon and <img alt="\varphi" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_2339fd9b358ebe241da05c665668d48b.png" title="phi" /> is the initial phase of the muon spins with respect to the positron detector.<br>
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/" target="_top">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. 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> <p></p>
<hr /> <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 href="#XmlFile" class="foswikiCurrentTopicLink">below</a>.
<p></p> <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/" target="_top">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" target="_top">"wisdom handling"</a>). In case this feature shall be used, a valid wisdom file has to be specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>. <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> <p></p>
<strong><span class='foswikiBlackFG'>Remark 3:</span></strong> The model functions described in the following do generally not behave nicely in conjunction with <code>MINUIT</code> function minimizations (or maximizations). The analysis process at the moment in most cases involves some tedious <em>trial-and-error</em> procedure, where the displayed <code>MINUIT</code> information as always deserves attention. This is especially true if small effects should be analyzed (e.g. small diamagnetic shifts in superconductors). The parameter uncertainty in many cases has to be estimated independently. Due to these limitations, also the use of the fit option of <code><a href="Msr2Data.html">msr2data</a></code> cannot be advised. <strong><span class='foswikiBlackFG'>Remark 3:</span></strong> The model functions described in the following do generally not behave nicely in conjunction with <code>MINUIT</code> function minimizations (or maximizations). The analysis process at the moment in most cases involves some tedious <em>trial-and-error</em> procedure, where the displayed <code>MINUIT</code> information as always deserves attention. This is especially true if small effects should be analyzed (e.g. small diamagnetic shifts in superconductors). The parameter uncertainty in many cases has to be estimated independently. Due to these limitations, also the use of the fit option of <code><a href="Msr2Data.html">msr2data</a></code> cannot be advised.
<p></p> <p></p>
<strong><span class='foswikiBlackFG'>Remark 4:</span></strong> If these classes still prove useful and results obtained through them are part of scientific publications, <strong><span class='foswikiBlackFG'>Remark 4:</span></strong> If these classes still prove useful and results obtained through them are part of scientific publications,
an acknowledgement of the use of the library is appreciated. an acknowledgement of the use of the library is appreciated.
<p></p> <p></p>
<h1><a name="A_2_LE_45SR"></a> 2 LE-&mu;SR </h1> <h1 id="A_2_LE_45SR"> 2 LE-&mu;SR </h1>
<h2><a name="A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"></a> 2.1 One-dimensional London model for the Meissner state of isotropic superconductors </h2> <h2 id="A_2.1_One_45dimensional_London_model_for_the_Meissner_state_of_isotropic_superconductors"> 2.1 One-dimensional London model for the Meissner state of isotropic superconductors </h2>
<p></p> <p></p>
The models for analyzing LE-&mu;SR data assume the magnetic induction <img alt="B(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_532f98969690650ac4d127919a0eda38.png" title="BofZ" /> to vary only in the dimension parallel to the momentum of the incident muons. In such a case the magnetic field distribution is given by The models for analyzing LE-&mu;SR data assume the magnetic induction <img alt="B(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_532f98969690650ac4d127919a0eda38.png" title="BofZ" /> to vary only in the dimension parallel to the momentum of the incident muons. In such a case the magnetic field distribution is given by
<p style="text-align:center"> <p style="text-align:center">
@ -165,7 +170,7 @@ Assuming an array of <img alt="N" class="mmpImage" src="../pub/MUSR/LibFitPofB/_
<p style="text-align:center"> <p style="text-align:center">
<img alt="\frac{\partial^2}{\partial z^2}B&#95;i(z) &#61; \frac{1}{\lambda&#95;i^2}B&#95;i(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_dfd02951094e1cb98f48e3f6d4562f38.png" title="London-eq" /> <img alt="\frac{\partial^2}{\partial z^2}B&#95;i(z) &#61; \frac{1}{\lambda&#95;i^2}B&#95;i(z)" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_dfd02951094e1cb98f48e3f6d4562f38.png" title="London-eq" />
</p> </p>
for each layer <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" /> taking into account the boundary conditions<a name="FootNote1text"></a><span class='FootNoteTextLink' title='F. London, Superfluids: Macroscopic Theory of Superconductivity, Dover (1961), p. 34'><a href="#FootNote1note" class="foswikiCurrentTopicLink">(1)</a></span> for each layer <img alt="i" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c465118a8d86d5f25bba37cc1dcb38a0.png" title="i" /> taking into account the boundary conditions<a name="FootNote1text"></a><span class="FootNoteTextLink" title="F&#46; London&#44; Superfluids&#58; Macroscopic Theory of Superconductivity&#44; Dover &#40;1961&#41;&#44; p&#46; 34"><a class="foswikiCurrentTopicLink" href="#FootNote1note">(1)</a></span>
<p style="text-align:center"> <p style="text-align:center">
<img alt="B&#95;1(0) &#61; B&#95;N(d) &#61; \mu&#95;0H" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_432d7664e0756ded77e7423dd256c122.png" title="cond1" /> <img alt="B&#95;1(0) &#61; B&#95;N(d) &#61; \mu&#95;0H" class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_432d7664e0756ded77e7423dd256c122.png" title="cond1" />
</p> </p>
@ -184,19 +189,19 @@ userFcn libFitPofB TLondon1DHS 1 2 3 4 5
</dd></dl> </dd></dl>
The parameters are: <ol> The parameters are: <ol>
<li> phase (deg) <li> phase (deg)
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV) </li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
</li> <li> applied field (G) </li> <li> applied field (G)
</li> <li> thickness of the dead layer (nm) </li> <li> thickness of the dead layer (nm)
</li> <li> magnetic field penetration depth (nm) </li> <li> magnetic field penetration depth (nm)
</li></ol> </li></ol>
<p></p> <dl> <p></p> <dl>
<dt> Superconducting thin film (one layer) </dt><dd> <pre> <dt> Superconducting thin film (one layer) </dt><dd> <pre>
userFcn libFitPofB TLondon1D1L 1 2 3 4 5 6 &#91;a b] userFcn libFitPofB TLondon1D1L 1 2 3 4 5 6 &#91;a b&#93;
</pre> </pre>
</dd></dl> </dd></dl>
The mandatory parameters are: <ol> The mandatory parameters are: <ol>
<li> phase (deg) <li> phase (deg)
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV) </li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
</li> <li> applied field (G) </li> <li> applied field (G)
</li> <li> thickness of the dead layer (nm) </li> <li> thickness of the dead layer (nm)
</li> <li> thickness of the actually superconducting layer (nm) </li> <li> thickness of the actually superconducting layer (nm)
@ -204,17 +209,17 @@ The mandatory parameters are: <ol>
</li></ol> </li></ol>
<p></p> <p></p>
The optional parameters are: <ol> The optional parameters are: <ol>
<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the thin film contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1) <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the thin film contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1) </li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
</li></ol> </li></ol>
<p></p> <dl> <p></p> <dl>
<dt> Superconducting thin-film bilayer heterostructure </dt><dd> <pre> <dt> Superconducting thin-film bilayer heterostructure </dt><dd> <pre>
userFcn libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 &#91;a b c] userFcn libFitPofB TLondon1D2L 1 2 3 4 5 6 7 8 &#91;a b c&#93;
</pre> </pre>
</dd></dl> </dd></dl>
The mandatory parameters are: <ol> The mandatory parameters are: <ol>
<li> phase (deg) <li> phase (deg)
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV) </li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
</li> <li> applied field (G) </li> <li> applied field (G)
</li> <li> thickness of the dead layer (nm) </li> <li> thickness of the dead layer (nm)
</li> <li> thickness of the actually superconducting first layer (nm) </li> <li> thickness of the actually superconducting first layer (nm)
@ -224,18 +229,18 @@ The mandatory parameters are: <ol>
</li></ol> </li></ol>
<p></p> <p></p>
The optional parameters are: <ol> The optional parameters are: <ol>
<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1) <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1) </li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1) </li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
</li></ol> </li></ol>
<p></p> <dl> <p></p> <dl>
<dt> Superconducting thin-film trilayer heterostructure </dt><dd> <pre> <dt> Superconducting thin-film trilayer heterostructure </dt><dd> <pre>
userFcn libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 &#91;a b c d] userFcn libFitPofB TLondon1D3L 1 2 3 4 5 6 7 8 9 10 &#91;a b c d&#93;
</pre> </pre>
</dd></dl> </dd></dl>
The mandatory parameters are: <ol> The mandatory parameters are: <ol>
<li> phase (deg) <li> phase (deg)
</li> <li> muon implantation energy as specified in the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML startup file</a> (keV) </li> <li> muon implantation energy as specified in the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML startup file</a> (keV)
</li> <li> applied field (G) </li> <li> applied field (G)
</li> <li> thickness of the dead layer (nm) </li> <li> thickness of the dead layer (nm)
</li> <li> thickness of the actually superconducting first layer (nm) </li> <li> thickness of the actually superconducting first layer (nm)
@ -247,39 +252,39 @@ The mandatory parameters are: <ol>
</li></ol> </li></ol>
<p></p> <p></p>
The optional parameters are: <ol> The optional parameters are: <ol>
<li type="a"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1) <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>1</sub> of muons in the dead and first layer contributing to the signal (0 &le; <i>f</i><sub>1</sub> &le; 1)
</li> <li type="a"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1) </li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>2</sub> of muons in the second layer contributing to the signal (0 &le; <i>f</i><sub>2</sub> &le; 1)
</li> <li type="a"> fraction <i>f</i><sub>3</sub> of muons in the third layer contributing to the signal (0 &le; <i>f</i><sub>3</sub> &le; 1) </li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>3</sub> of muons in the third layer contributing to the signal (0 &le; <i>f</i><sub>3</sub> &le; 1)
</li> <li type="a"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1) </li> <li style="list-style-type:lower-alpha"> fraction <i>f</i><sub>s</sub> of muons in the substrate contributing to the signal (0 &le; <i>f</i><sub>s</sub> &le; 1)
</li></ol> </li></ol>
<p></p> <p></p>
<p></p> <p></p>
<p></p> <p></p>
Notes Notes
<p></p> <p></p>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text" class="foswikiCurrentTopicLink"> <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 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>
<p></p> <p></p>
<p></p> <p></p>
<p></p> <p></p>
<hr /> <hr />
<p></p> <p></p>
<h1><a name="A_3_Conventional_40bulk_41_SR"></a> 3 Conventional (bulk) &mu;SR </h1> <h1 id="A_3_Conventional_40bulk_41_SR"> 3 Conventional (bulk) &mu;SR </h1>
<h2><a name="A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"></a> 3.1 Field distributions in the mixed state of isotropic superconductors </h2> <h2 id="A_3.1_Field_distributions_in_the_mixed_state_of_isotropic_superconductors"> 3.1 Field distributions in the mixed state of isotropic superconductors </h2>
<p></p> <p></p>
When investigating superconductors in the mixed state by means of conventional &mu;SR a two-dimensional flux-line lattice is probed randomly by the muons. The spatial field distributions within such an ordered lattice are modeled using the Fourier series When investigating superconductors in the mixed state by means of conventional &mu;SR a two-dimensional flux-line lattice is probed randomly by the muons. The spatial field distributions within such an ordered lattice are modeled using the Fourier series
<p style="text-align:center"> <p style="text-align:center">
<img alt="B(\mathbf{r}) &#61; \langle B \rangle \sum\limits&#95;{\mathbf{K}}B&#95;{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r})," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c25933e91d56089992506f463d71de8f.png" title="spatialB" /> <img alt="B(\mathbf{r}) &#61; \langle B \rangle \sum\limits&#95;{\mathbf{K}}B&#95;{\mathbf{K}}\exp(-\imath\mathbf{K}\mathbf{r})," class="mmpImage" src="../pub/MUSR/LibFitPofB/_MathModePlugin_c25933e91d56089992506f463d71de8f.png" title="spatialB" />
</p> </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> 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.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568" target="_top">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.'><a href="#FootNote2note" class="foswikiCurrentTopicLink">(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> <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.M. Riseman <em>et al.</em>, <a href="http://dx.doi.org/10.1103/PhysRevB.52.10569" target="_top">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.'><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> 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. Yaouanc, P. Dalmas de R&eacute;otier and E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.55.11107" target="_top">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.'><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> 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></dl> </dd></dl>
Apart from the mentioned analytical models the <strong>numerical Ginzburg-Landau model</strong> <a name="FootNote5text"></a><span class='FootNoteTextLink' title='E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506" target="_top">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.'><a href="#FootNote5note" class="foswikiCurrentTopicLink">(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. 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> <p></p>
<span class='foswikiRedFG'>Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!</span> <span class='foswikiRedFG'>Concerning the applicability (e.g. field regions) of each of the mentioned models please refer to the original publications!</span>
<p></p> <p></p>
At the moment, the calculation of the field distribution has been implemented for triangular flux-line lattices. The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through the <a href="#XmlFile" class="foswikiCurrentTopicLink">XML file</a>.<br>The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl> At the moment, the calculation of the field distribution has been implemented for triangular flux-line lattices. The number of grid lines in which the inter-vortex distance is divided for the calculations to be specified through the <a class="foswikiCurrentTopicLink" href="#XmlFile">XML file</a>.<br>The muon-spin depolarization functions finally are calculated using the following lines in the THEORY block of a <code>musrfit</code> msr file: <dl>
<dt> 2D triangular vortex lattice, London model with Gaussian cutoff </dt><dd> <pre> <dt> 2D triangular vortex lattice, London model with Gaussian cutoff </dt><dd> <pre>
userFcn libFitPofB TBulkTriVortexLondon 1 2 3 4 userFcn libFitPofB TBulkTriVortexLondon 1 2 3 4
</pre> </pre>
@ -338,23 +343,23 @@ SAVE
<p></p> <p></p>
Notes Notes
<p></p> <p></p>
<a name="FootNote2note"></a><span class="FootNoteLabel"><a href="#FootNote2text" class="foswikiCurrentTopicLink"> <strong>2</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1007/BF00683568" target="_top">J. Low Temp. Phys. <strong>73</strong>, 355 (1988)</a>.</span> <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>
<p></p> <p></p>
<a name="FootNote3note"></a><span class="FootNoteLabel"><a href="#FootNote3text" class="foswikiCurrentTopicLink"> <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" target="_top">Phys. Rev. B <strong>52</strong>, 10569 (1995)</a>.</span> <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>
<p></p> <p></p>
<a name="FootNote4note"></a><span class="FootNoteLabel"><a href="#FootNote4text" class="foswikiCurrentTopicLink"> <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" target="_top">Phys. Rev. B <strong>55</strong>, 11107 (1997)</a>.</span> <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>
<p></p> <p></p>
<a name="FootNote5note"></a><span class="FootNoteLabel"><a href="#FootNote5text" class="foswikiCurrentTopicLink"> <strong>5</strong> </a></span>: <span class="FootNote">E.H. Brandt, <a href="http://dx.doi.org/10.1103/PhysRevB.68.054506" target="_top">Phys. Rev. B <strong>68</strong>, 054506 (2003)</a>.</span> <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>
<p></p> <p></p>
<p></p> <p></p>
<p></p> <p></p>
<hr /> <hr />
<p></p> <p></p>
<a name="XmlFile"></a> <span id="XmlFile"></span>
<h1><a name="A_4_The_XML_startup_file"></a> 4 The XML startup file </h1> <h1 id="A_4_The_XML_startup_file"> 4 The XML startup file </h1>
<code><b>BMW_startup.xml</b></code> is a configuration file located in the working directory. In this file some settings like the time and field resolution of the calculations as well as the present muon implantation profiles for a LE-&mu;SR analysis have to be defined. The following XML tags are allowed to define settings: <dl> <code><b>BMW_startup.xml</b></code> is a configuration file located in the working directory. In this file some settings like the time and field resolution of the calculations as well as the present muon implantation profiles for a LE-&mu;SR analysis have to be defined. The following XML tags are allowed to define settings: <dl>
<dt> &lt;debug&gt;ONE_OR_ZERO&lt;/debug&gt; </dt><dd> activate the debugging output of the settings read from the XML file by setting <strong>1</strong>, deactivate it with <strong>0</strong> <dt> &lt;debug&gt;ONE_OR_ZERO&lt;/debug&gt; </dt><dd> activate the debugging output of the settings read from the XML file by setting <strong>1</strong>, deactivate it with <strong>0</strong>
</dd> <dt> &lt;wisdom&gt;PATH_TO_FILE&lt;/wisdom&gt; </dt><dd> specify the <strong>PATH_TO_FILE</strong> to an <a href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom" target="_top">FFTW3 wisdom file</a> that should be used; if the <strong>PATH_TO_FILE</strong> is invalid, no FFTW3 wisdom will be used </dd> <dt> &lt;wisdom&gt;PATH_TO_FILE&lt;/wisdom&gt; </dt><dd> specify the <strong>PATH_TO_FILE</strong> to an <a href="http://fftw.org/fftw3_doc/Wisdom.html#Wisdom">FFTW3 wisdom file</a> that should be used; if the <strong>PATH_TO_FILE</strong> is invalid, no FFTW3 wisdom will be used
</dd> <dt> &lt;delta_t&gt;ResT&lt;/delta_t&gt; </dt><dd> set the time resolution <strong>ResT</strong> for the calculated depolarization function in <strong>microseconds</strong> </dd> <dt> &lt;delta_t&gt;ResT&lt;/delta_t&gt; </dt><dd> set the time resolution <strong>ResT</strong> for the calculated depolarization function in <strong>microseconds</strong>
</dd> <dt> &lt;delta_B&gt;ResB&lt;/delta_B&gt; </dt><dd> set the field resolution <strong>ResB</strong> for the calculated field distribution in <strong>Gauss</strong> </dd> <dt> &lt;delta_B&gt;ResB&lt;/delta_B&gt; </dt><dd> set the field resolution <strong>ResB</strong> for the calculated field distribution in <strong>Gauss</strong>
</dd> <dt> &lt;VortexLattice&gt;&lt;/VortexLattice&gt; </dt><dd> set the parameters used for the calculation of the spatial field distribution of a vortex lattice <dl> </dd> <dt> &lt;VortexLattice&gt;&lt;/VortexLattice&gt; </dt><dd> set the parameters used for the calculation of the spatial field distribution of a vortex lattice <dl>
@ -400,78 +405,29 @@ An example XML file looks as follows:
&#60;/BMW&#62; &#60;/BMW&#62;
</pre> </pre>
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-- <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> &amp; <a href="http://www.psi.ch/low-energy-muons/people" target="_top">AS</a> </div> -- <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> &amp; <a href="http://www.psi.ch/low-energy-muons/people">AS</a></div>
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<h1 id="libZFRelaxation"> libZFRelaxation </h1>
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<h1><a name="libZFRelaxation"></a> libZFRelaxation </h1>
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
<li> <a href="LibZFRelaxation.html#libZFRelaxation"> libZFRelaxation </a> <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_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> </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>
@ -128,8 +133,8 @@ pre {
</li> <li> <a href="LibZFRelaxation.html#A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4 Static Gaussian distributed fields with uniaxial anisotropy </a> </li> <li> <a href="LibZFRelaxation.html#A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4 Static Gaussian distributed fields with uniaxial anisotropy </a>
</li></ul> </li></ul>
</div> </div>
<a name="IntroDuction"></a> <span id="IntroDuction"></span>
<h1><a name="A_1_Introduction"></a> 1 Introduction </h1> <h1 id="A_1_Introduction"> 1 Introduction </h1>
<p></p> <p></p>
<code>libZFRelaxation</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library implement the calculation of some additional zero-field &mu;SR relaxation functions which are not built-in into <code>musrfit</code>. <code>libZFRelaxation</code> is a collection of <code>C++</code> classes using the <code><a href="MusrFit.html">musrfit</a></code> <code><a href="MusrFit.html#UserFunctions1">user-function interface</a></code> in order to facilitate the usage in conjunction with <code>musrfit</code>. The classes contained in this library implement the calculation of some additional zero-field &mu;SR relaxation functions which are not built-in into <code>musrfit</code>.
<p></p> <p></p>
@ -138,9 +143,9 @@ In the following the use of the implemented functions is shortly introduced&mdas
If these classes prove useful and results obtained through them are part of scientific publications, If these classes prove useful and results obtained through them are part of scientific publications,
an acknowledgement of the use of the library is appreciated. an acknowledgement of the use of the library is appreciated.
<p></p> <p></p>
<h1><a name="A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"></a> 2 Isotropic static Gaussian broadened randomly oriented internal fields </h1> <h1 id="A_2_Isotropic_static_Gaussian_broadened_randomly_oriented_internal_fields"> 2 Isotropic static Gaussian broadened randomly oriented internal fields </h1>
<p></p> <p></p>
E. I. Kornilov and V. Yu. Pomjakushin, Phys. Lett. A <b>153</b>, 364&#150;367 (1991), doi: <a href="http://dx.doi.org/10.1016/0375-9601(91)90959-C" target="_top">10.1016/0375-9601(91)90959-C</a> E. I. Kornilov and V. Yu. Pomjakushin, Phys. Lett. A <b>153</b>, 364&#150;367 (1991), doi: <a href="http://dx.doi.org/10.1016/0375-9601(91)90959-C">10.1016/0375-9601(91)90959-C</a>
<p></p> <p></p>
<p style="text-align:center"> <p style="text-align:center">
<img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-\frac{\sigma&#95;{\mathrm{L}}^2t^2}{2}\right)+\alpha\left(\cos\left(2\pi\nu t\right)-\frac{\sigma&#95;{\mathrm{T}}^2t}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-\frac{\sigma&#95;{\mathrm{T}}^2t^2}{2}\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_fca91646b118061038b53ada5563c17c.png" title="ZFMagGss" /> <img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-\frac{\sigma&#95;{\mathrm{L}}^2t^2}{2}\right)+\alpha\left(\cos\left(2\pi\nu t\right)-\frac{\sigma&#95;{\mathrm{T}}^2t}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-\frac{\sigma&#95;{\mathrm{T}}^2t^2}{2}\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_fca91646b118061038b53ada5563c17c.png" title="ZFMagGss" />
@ -156,9 +161,9 @@ The parameters are: <ol>
</li> <li> the "longitudinal depolarization rate" &sigma;<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article). </li> <li> the "longitudinal depolarization rate" &sigma;<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article).
</li></ol> </li></ol>
<p></p> <p></p>
<h1><a name="A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"></a> 3 Isotropic static Lorentzian broadened randomly oriented internal fields </h1> <h1 id="A_3_Isotropic_static_Lorentzian_broadened_randomly_oriented_internal_fields"> 3 Isotropic static Lorentzian broadened randomly oriented internal fields </h1>
<p></p> <p></p>
M. I. Larkin, Y. Fudamoto, I. M. Gat, A. Kinkhabwala, K. M. Kojima, G. M. Luke, J. Merrin, B. Nachumi, Y. J. Uemura, M. Azuma, T. Saito, and M. Takano, Physica B <b>289&#150;290</b>, 153&#150;156 (2000), doi: <a href="http://dx.doi.org/10.1016/S0921-4526(00)00337-9"" target="_top">10.1016/S0921-4526(00)00337-9</a> M. I. Larkin, Y. Fudamoto, I. M. Gat, A. Kinkhabwala, K. M. Kojima, G. M. Luke, J. Merrin, B. Nachumi, Y. J. Uemura, M. Azuma, T. Saito, and M. Takano, Physica B <b>289&#150;290</b>, 153&#150;156 (2000), doi: <a href="http://dx.doi.org/10.1016/S0921-4526(00)00337-9"">10.1016/S0921-4526(00)00337-9</a>
<p></p> <p></p>
<p style="text-align:center"> <p style="text-align:center">
<img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-a&#95;{\mathrm{L}}t\right) + \alpha\left(\cos\left(2\pi\nu t\right)-\frac{a&#95;{\mathrm{T}}}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-a&#95;{\mathrm{T}}t\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_975f948b57199037b2b8bfb5e986b6a9.png" title="ZFMagExp" /> <img alt="\mathcal{P}(t) &#61; \left(1-\alpha\right)\exp\left(-a&#95;{\mathrm{L}}t\right) + \alpha\left(\cos\left(2\pi\nu t\right)-\frac{a&#95;{\mathrm{T}}}{2\pi\nu}\sin\left(2\pi\nu t\right)\right)\exp\left(-a&#95;{\mathrm{T}}t\right)" class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_975f948b57199037b2b8bfb5e986b6a9.png" title="ZFMagExp" />
@ -174,9 +179,9 @@ The parameters are: <ol>
</li> <li> the "longitudinal depolarization rate" a<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article). </li> <li> the "longitudinal depolarization rate" a<sub>L</sub> (&mu;s<sup>-1</sup>) (= 0 in the article).
</li></ol> </li></ol>
<p></p> <p></p>
<h1><a name="A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"></a> 4 Static Gaussian distributed fields with uniaxial anisotropy </h1> <h1 id="A_4_Static_Gaussian_distributed_fields_with_uniaxial_anisotropy"> 4 Static Gaussian distributed fields with uniaxial anisotropy </h1>
<p></p> <p></p>
G. Solt, Hyperfine Interactions <b>96</b>, 167&#150;175 (1995), doi: <a href="http://dx.doi.org/10.1007/BF02066280" target="_top">10.1007/BF02066280</a> G. Solt, Hyperfine Interactions <b>96</b>, 167&#150;175 (1995), doi: <a href="http://dx.doi.org/10.1007/BF02066280">10.1007/BF02066280</a>
<p></p> <p></p>
<p style="text-align:center"> <p style="text-align:center">
<img alt="\mathcal{P}(t) &#61; \frac{1}{2}\sin^2\Theta + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;1\left(\epsilon\right) + \sin^2\Theta f&#95;2(\epsilon, \sigma&#95;1, t) + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;3\left(\epsilon, \sigma&#95;1, t\right)," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_4611c56f1556464dd8a6eaabbe070c05.png" title="UniaxialStatGssKT" /> <img alt="\mathcal{P}(t) &#61; \frac{1}{2}\sin^2\Theta + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;1\left(\epsilon\right) + \sin^2\Theta f&#95;2(\epsilon, \sigma&#95;1, t) + \left(\frac{3}{2}\cos^2\Theta-\frac{1}{2}\right)f&#95;3\left(\epsilon, \sigma&#95;1, t\right)," class="mmpImage" src="../pub/MUSR/LibZFRelaxation/_MathModePlugin_4611c56f1556464dd8a6eaabbe070c05.png" title="UniaxialStatGssKT" />
@ -205,78 +210,29 @@ The parameters are: <ol>
</li> <li> &Theta; (&deg;). </li> <li> &Theta; (&deg;).
</li></ol> </li></ol>
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<h1 id="A_61_61msr2data_61_61"> <code><b>msr2data</b></code> </h1>
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<h1><a name="A_61_61msr2data_61_61"></a> <code><b>msr2data</b></code> </h1>
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<li> <a href="Msr2Data.html#A_61_61msr2data_61_61"> msr2data </a> <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_1_Introduction"> 1 Introduction </a>
</li> <li> <a href="Msr2Data.html#A_2_Basic_Types_of_Usage"> 2 Basic Types of Usage </a> </li> <li> <a href="Msr2Data.html#A_2_Basic_Types_of_Usage"> 2 Basic Types of Usage </a>
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<a name="IntroDuction"></a> <span id="IntroDuction"></span>
<h1><a name="A_1_Introduction"></a> 1 Introduction </h1> <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 <a href="http://musr.org/xyfit/dbformat.html" target="_top">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/" target="_top">&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!'><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/" target="_top">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 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> is <a href="http://www.gnu.org/philosophy/free-sw.html" target="_top">free software</a> and licensed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html" target="_top">GNU GPL version 2</a> or any later version (at your option). <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> <p></p>
Before the usage of msr2data will be explained in greater detail first be aware of the following: Before the usage of msr2data will be explained in greater detail first be aware of the following:
<p></p> <p></p>
@ -149,14 +189,14 @@ Before the usage of msr2data will be explained in greater detail first be aware
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Notes Notes
<p></p> <p></p>
<a name="FootNote1note"></a><span class="FootNoteLabel"><a href="#FootNote1text" class="foswikiCurrentTopicLink"> <strong>1</strong> </a></span>: <span class="FootNote"> For an abridged description of this format see <a href="http://musr.org/xyfit/dbformat.html" target="_top">here</a>. The <strong>DB</strong> files produced by <code>msr2data</code> can be viewed for instance with <a href="http://musr.org/muview/" target="_top">&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="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>
<p></p> <p></p>
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<hr /> <hr />
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<a name="BasicTypesOfUsage"></a> <span id="BasicTypesOfUsage"></span>
<h1><a name="A_2_Basic_Types_of_Usage"></a> 2 Basic Types of Usage </h1> <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 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>
<dt> msr2data &lt;run&gt; &lt;extension&gt; [optional parameters] </dt><dd> A single run number. <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;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.
@ -165,20 +205,20 @@ Apart from numerous <a href="#OptionalParameters" class="foswikiCurrentTopicLink
</dd></dl> </dd></dl>
<p></p> <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: 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 href="#OptionalParameters" class="foswikiCurrentTopicLink">the -o option</a>) from <code><b>8472_tf_h13.msr</b></code>. <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 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 &#91;8472 8470] &#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> and <code><b>8470_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] &#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>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 &#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 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:
<a name="RunListStructure"></a> <span id="RunListStructure"></span>
<pre> <pre>
RUN VAR1 VAR2 VAR3 ... RUN VAR1 VAR2 VAR3 ...
8460 200 27.1 46.2 ... 8460 200 27.1 46.2 ...
8472 205 27.1 46.3 ... 8472 205 27.1 46.3 ...
8453 210 27.2 45.9 ... 8453 210 27.2 45.9 ...
<EFBFBD> <EFBFBD> <EFBFBD> <EFBFBD> · · · ·
<EFBFBD> <EFBFBD> <EFBFBD> <EFBFBD> · · · ·
<EFBFBD> <EFBFBD> <EFBFBD> <EFBFBD> · · · ·
</pre> </pre>
<span class='foswikiRedFG'>The first not commented and not empty line determines the parameter names and labels and has to be present!</span><br/> <span class='foswikiRedFG'>The first not commented and not empty line determines the parameter names and labels and has to be present!</span><br/>
It is allowed to add comments (with a preceding <strong>#</strong>) or empty lines to the run-list file. It is allowed to add comments (with a preceding <strong>#</strong>) or empty lines to the run-list file.
@ -187,14 +227,14 @@ 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> 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 href="#OptionalParameters" class="foswikiCurrentTopicLink">header and noheader options</a> as shall be seen later.
</li></ul> </li></ul>
<a name="NoExtension"></a> <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"> <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">
msr2data 8472 8460 &#34;&#34; msr2data 8472 8460 &#34;&#34;
</pre> </pre>
</li></ul> </li></ul>
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<a name="OptionalParameters"></a> <span id="OptionalParameters"></span>
<h1><a name="A_3_Optional_Parameters"></a> 3 Optional Parameters </h1> <h1 id="A_3_Optional_Parameters"> 3 Optional Parameters </h1>
As mentioned already above there are some optional parameters which change the behavior of <code>msr2data</code> and can be passed in any order. Here is a complete list: <dl> As mentioned already above there are some optional parameters which change the behavior of <code>msr2data</code> and can be passed in any order. Here is a complete list: <dl>
<dt> data </dt><dd> The output file format is changed to a simple column ASCII file (default output file name: <code><b>out.dat</b></code>). <dt> data </dt><dd> The output file format is changed to a simple column ASCII file (default output file name: <code><b>out.dat</b></code>).
</dd> <dt> new </dt><dd> An existing output file is deleted before new information is written to it. </dd> <dt> new </dt><dd> An existing output file is deleted before new information is written to it.
@ -215,7 +255,7 @@ msr2data 8400 8460 &#95;tf&#95;h13 -oABC.db fit-8472
</pre> </pre>
Using <code><b>8472_tf_h13.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8400_tf_h13.msr</b></code> through <code><b>8460_tf_h13.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits together with the <strong>DB</strong> header in the new file <code><b>ABC.db</b></code>. Additionally, some information about external parameters like the temperature will be passed to <code><b>ABC.db</b></code> if it is present in the data files. Using <code><b>8472_tf_h13.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8400_tf_h13.msr</b></code> through <code><b>8460_tf_h13.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits together with the <strong>DB</strong> header in the new file <code><b>ABC.db</b></code>. Additionally, some information about external parameters like the temperature will be passed to <code><b>ABC.db</b></code> if it is present in the data files.
<pre class="bash"> <pre class="bash">
msr2data &#91;8500 8502-8504 8507] &#95;zf fit-8472 noheader nosummary -o DEF.db msr2data &#91;8500 8502-8504 8507&#93; &#95;zf fit-8472 noheader nosummary -o DEF.db
</pre> </pre>
Using <code><b>8472_zf.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8500_zf.msr</b></code>, <code><b>8502_zf.msr</b></code>, <code><b>8503_zf.msr</b></code>, <code><b>8504_zf.msr</b></code> and <code><b>8507_zf.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits in the file <code><b>DEF.db</b></code> without writing the <strong>DB</strong> file header or attempting to read additional information from the data files. Using <code><b>8472_zf.msr</b></code> as first template, <code>msr2data</code> generates subsequent msr input files <code><b>8500_zf.msr</b></code>, <code><b>8502_zf.msr</b></code>, <code><b>8503_zf.msr</b></code>, <code><b>8504_zf.msr</b></code> and <code><b>8507_zf.msr</b></code>, calls <code>musrfit</code> to perform a fit of these files and collects the results of the fits in the file <code><b>DEF.db</b></code> without writing the <strong>DB</strong> file header or attempting to read additional information from the data files.
<pre class="bash"> <pre class="bash">
@ -231,12 +271,12 @@ msr2data 8472 8475 &#95;tf&#95;h13 msr-8471!
</pre> </pre>
Using <code><b>8471_tf_h13.msr</b></code> as template for <em>all</em> runs, <code>msr2data</code> generates the msr input files <code><b>8472_tf_h13.msr</b></code> through <code><b>8475_tf_h13.msr</b></code>. <span class='foswikiRedFG'>No fitting will be performed and no DB or ASCII output will be generated!</span> Using <code><b>8471_tf_h13.msr</b></code> as template for <em>all</em> runs, <code>msr2data</code> generates the msr input files <code><b>8472_tf_h13.msr</b></code> through <code><b>8475_tf_h13.msr</b></code>. <span class='foswikiRedFG'>No fitting will be performed and no DB or ASCII output will be generated!</span>
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<a name="TheGlobalMode"></a> <span id="TheGlobalMode"></span>
<h1><a name="A_4_The_Global_Mode"></a> 4 The Global Mode </h1> <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 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>.
<p></p> <p></p>
<a name="GlobalFileGeneration"></a> <span id="GlobalFileGeneration"></span>
<h2><a name="A_4.1_File_Generation"></a> 4.1 File Generation </h2> <h2 id="A_4.1_File_Generation"> 4.1 File Generation </h2>
The general idea of this mode is to generate a global msr file on the basis of a working single-run msr file. For this purpose a single-run template containing information about common and run-specific parameters should be created. These parameters are identified through their parameter names: <dl> The general idea of this mode is to generate a global msr file on the basis of a working single-run msr file. For this purpose a single-run template containing information about common and run-specific parameters should be created. These parameters are identified through their parameter names: <dl>
<dt> run-specific parameters </dt><dd> these parameters are tagged with the current run number in the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, at the end of the parameter name, e.g. for a 4-digit-formatted run number <strong>alpha0123</strong> if the run number was <strong>123</strong> or for a 8-digit-formatted run number <strong>alpha00123456</strong> if the run number was <strong>123456</strong>. <strong>X</strong> has to be at least 4. <dt> run-specific parameters </dt><dd> these parameters are tagged with the current run number in the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, at the end of the parameter name, e.g. for a 4-digit-formatted run number <strong>alpha0123</strong> if the run number was <strong>123</strong> or for a 8-digit-formatted run number <strong>alpha00123456</strong> if the run number was <strong>123456</strong>. <strong>X</strong> has to be at least 4.
</dd> <dt> common parameters </dt><dd> all parameters that are not run specific </dd> <dt> common parameters </dt><dd> all parameters that are not run specific
@ -281,19 +321,19 @@ During this reorganization all the affected parameter occurrences are changed ac
<p></p> <p></p>
<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> <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> <p></p>
<h2><a name="A_4.2_Parameter_Extraction"></a> 4.2 Parameter Extraction </h2> <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 href="#RunListStructure" class="foswikiCurrentTopicLink">run-list file</a>.
In order to reach this goal the global msr file has to obey certain rules: <ul> 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 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> <li> The RUN blocks have to be ordered according to the list of runs to be processed. </li> <li> The RUN blocks have to be ordered according to the list of runs to be processed.
</li></ul> </li></ul>
Following these rules&mdash;which is achieved most easily by generating the global msr file using <code>msr2data</code> as shown <a href="#GlobalFileGeneration" class="foswikiCurrentTopicLink">above</a>&mdash;the parameters can be extracted e.g. like <pre class="bash"> 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">
msr2data 8471 8470 &#95;example global data -o globalFit.dat msr2data 8471 8470 &#95;example global data -o globalFit.dat
</pre> </pre>
This will read in the file <code><b>8471+global_example.msr</b></code>, extract for each run all relevant parameters from the msr file as well as from the according data files (if available) and append all of them in columns to the ASCII file <code><b>globalFit.dat</b></code>. This will read in the file <code><b>8471+global_example.msr</b></code>, extract for each run all relevant parameters from the msr file as well as from the according data files (if available) and append all of them in columns to the ASCII file <code><b>globalFit.dat</b></code>.
<p></p> <p></p>
<a name="GlobalPlus"></a> <span id="GlobalPlus"></span>
<h2><a name="A_4.3_The_Extended_Global_Mode"></a> 4.3 The Extended Global Mode </h2> <h2 id="A_4.3_The_Extended_Global_Mode"> 4.3 The Extended Global Mode </h2>
If a new global input file is generated, it is also possible to do an automatic pre-analysis for each single run using the specified template first; afterwards the run-specific parameters of these single-run msr files are collected in the global msr file. In special cases this might be useful to obtain a better set of starting values for the parameters, however, in most cases it will not replace the "manual review" of the generated global input file. The option is activated by choosing the keyword <strong>global+</strong>. For example <pre class="bash"> If a new global input file is generated, it is also possible to do an automatic pre-analysis for each single run using the specified template first; afterwards the run-specific parameters of these single-run msr files are collected in the global msr file. In special cases this might be useful to obtain a better set of starting values for the parameters, however, in most cases it will not replace the "manual review" of the generated global input file. The option is activated by choosing the keyword <strong>global+</strong>. For example <pre class="bash">
msr2data 8471 8470 &#95;example global+ msr-8472 msr2data 8471 8470 &#95;example global+ msr-8472
</pre> </pre>
@ -305,8 +345,8 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
<p></p> <p></p>
<span class='foswikiRedFG'>Please be aware that the program in this mode always generates new single-run msr files and always calls <code>musrfit</code> for them. In case there are already single-run fits present, these cannot be used in conjunction with this option. The program on purpose behaves in this way in order to ensure the file integrity and correct parameter order within these files.</span> <span class='foswikiRedFG'>Please be aware that the program in this mode always generates new single-run msr files and always calls <code>musrfit</code> for them. In case there are already single-run fits present, these cannot be used in conjunction with this option. The program on purpose behaves in this way in order to ensure the file integrity and correct parameter order within these files.</span>
<p></p> <p></p>
<a name="KnownLimitations"></a> <span id="KnownLimitations"></span>
<h1><a name="A_5_Known_Limitations"></a> 5 Known Limitations </h1> <ul> <h1 id="A_5_Known_Limitations"> 5 Known Limitations </h1> <ul>
<li> The indexing run number of the msr file has to be at the begin of every filename. <li> The indexing run number of the msr file has to be at the begin of every filename.
</li> <li> Within the data file name the <strong>RUN#</strong> has the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, and has to be the rightmost number given in this format in the file name. <strong>X</strong> has to be at least 4. The highest treatable run number is 2<sup>32</sup>-1 = 4294967295. </li> <li> Within the data file name the <strong>RUN#</strong> has the format <strong>%0Xu</strong>, i.e. <strong>X</strong> digits with leading zeros, and has to be the rightmost number given in this format in the file name. <strong>X</strong> has to be at least 4. The highest treatable run number is 2<sup>32</sup>-1 = 4294967295.
</li> <li> In order to keep <code>msr2data</code> working properly the msr files should only contain <em><span class='foswikiRedFG'>one</span> STATISTIC block at the end of the file</em> and <i><span class='foswikiRedFG'>one</span> FITPARAMETER block right after the TITLE</i>&mdash;<code>musrfit</code> itself allows to have more creative msr files... </li> <li> In order to keep <code>msr2data</code> working properly the msr files should only contain <em><span class='foswikiRedFG'>one</span> STATISTIC block at the end of the file</em> and <i><span class='foswikiRedFG'>one</span> FITPARAMETER block right after the TITLE</i>&mdash;<code>musrfit</code> itself allows to have more creative msr files...
@ -314,11 +354,11 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
</li> <li> <code>msr2data</code> will write only up to <em>two successive</em> empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file, these are <em>not</em> copied! Actually, this measure is not a limitation but has been introduced to keep the msr files in a reasonable shape. </li> <li> <code>msr2data</code> will write only up to <em>two successive</em> empty lines in newly generated msr files. In case more subsequent empty lines are encountered in a template file, these are <em>not</em> copied! Actually, this measure is not a limitation but has been introduced to keep the msr files in a reasonable shape.
</li></ul> </li></ul>
<p></p> <p></p>
<a name="MusrGuiInterface"></a> <span id="MusrGuiInterface"></span>
<h1><a name="A_6_The_Graphical_User_Interface_Provided_by_61_61musrgui_61_61_47_61_61musredit_61_61"></a> 6 The Graphical User Interface Provided by <code><b>musrgui</b></code> / <code><b>musredit</b></code> </h1> <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> <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 src="../pub/MUSR/Msr2Data/msr2data-input-tabs.png" alt="msr2data-input-tabs.png" width='612' height='605' align="right" /> <dl> <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>
<dt> <span class='foswikiRedFG'>1&ndash;3</span> </dt><dd> Choose one of the <a href="#BasicTypesOfUsage" class="foswikiCurrentTopicLink">ways</a> to specify your list of runs. <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 href="#NoExtension" class="foswikiCurrentTopicLink">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'>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'>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.
@ -331,99 +371,63 @@ msr2data 8471 8470 -OneRunFit&#95;example -o OneRunFits.db
</dd> <dt> <span class='foswikiRedFG'>13</span> </dt><dd> If set, the <strong>-t</strong> option is passed to <code>msr2data</code>. </dd> <dt> <span class='foswikiRedFG'>13</span> </dt><dd> If set, the <strong>-t</strong> option is passed to <code>msr2data</code>.
</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'>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'>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 href="#TheGlobalMode" class="foswikiCurrentTopicLink">global mode</a>. </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 href="#GlobalPlus" class="foswikiCurrentTopicLink">extended global mode</a>.
</dd></dl> </dd></dl>
<p></p> <p></p>
<a name="BugTracking"></a> <span id="BugTracking"></span>
<h1><a name="A_7_Bugtracking"></a> 7 Bugtracking </h1> <h1 id="A_7_Bugtracking"> 7 Bugtracking </h1>
<p></p> <p></p>
For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues?status=new&amp;status=open" target="_top">Bitbucket Issues</a>, <a href="https://tracker.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter. For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues?status=new&amp;status=open">Bitbucket Issues</a>, <a href="https://tracker.psi.ch/jira/browse/MUSR">PSI Tracker</a> or send an e-mail to A. Suter.
<p></p> <p></p>
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</div></div><div id="patternTopBar"> <td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">20 Jul 2011 - 12:13</span> </td>
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<div id="patternTopBarContents"><table border="0" cellpadding="0" cellspacing="0" style="width:100%" summary=""> <td class="foswikiTableCol6 foswikiLastCol foswikiLast"> graphical interface to msr2data </td>
<tr><td valign="middle"><span id="foswikiLogo" class="foswikiImage"><a href="WebHome.html"><img src="../pub/Main/WebPreferences/psi_logo_150.gif" border="0" alt="Paul Scherrer Institut" style="border:none; margin: -8px 0 0 15px;" /></a></span></td> </tr>
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<p></p> <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 />
</td></tr></table> Topic revision: <span class='patternRevInfo'>16 Aug 2015, suter_a</span></div>
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<p></p> <div class="patternContent"><div class="foswikiTopic"> <h1 id="Acknowledgements_45_61_61musrfit_61_61"> Acknowledgements - <code><b>musrfit</b></code> </h1>
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<dt> Bastian M. Wojek </dt><dd> I am very much indebted to <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> for his rigorous testing of <code><a href="MusrFit.html">musrfit</a></code>, his many useful suggestions, contributions, and for the largest part of the <a href="WebHome.html" class="foswikiCurrentWebHomeLink">user manual of <code>musrfit</code></a> which makes it accessible to a broader audience! Many thanks Bastian! <dt> Bastian M. Wojek </dt><dd> I am very much indebted to <a href="http://www.fsf.org/register_form?referrer=8369">BMW</a> for his rigorous testing of <code><a href="MusrFit.html">musrfit</a></code>, his many useful suggestions, contributions, and for the largest part of the <a class="foswikiCurrentWebHomeLink" href="WebHome.html">user manual of <code>musrfit</code></a> which makes it accessible to a broader audience! Many thanks Bastian!
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<h1 id="A_61_61musredit_47_40musrgui_41_61_61"> <code><b>musredit / (musrgui)</b></code> </h1>
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<h1><a name="A_61_61musredit_47_40musrgui_41_61_61"></a> <code><b>musredit / (musrgui)</b></code> </h1>
<p></p>
<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
<li> <a href="MusrGui.html#A_61_61musredit_47_40musrgui_41_61_61"> musredit / (musrgui) </a> <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_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> </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>
@ -133,14 +173,14 @@ pre {
</li></ul> </li></ul>
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<p></p> <p></p>
<h1><a name="A_1_Introduction"></a> 1 Introduction </h1> <h1 id="A_1_Introduction"> 1 Introduction </h1>
<code>musredit</code> and <code>musrgui</code> are editors which also provide a graphical user interface to the programs contained in the <code><a href="MusrFit.html">musrfit</a></code> suite and are intended to help the user handle <code>musrfit</code> msr files. They are implemented in <code>C++</code> and use the <a href="http://qt.nokia.com/" target="_top">Qt</a> framework. Principally, <code>musrgui</code> and <code>musredit</code> are doing the same, but are based on different Qt versions. <code>musrgui</code> is based on Qt 3.x and will only be maintained on bug-fixing level since the Qt 3.x licensing is less straight forward than the Qt 4.x one. <code>musredit</code> is based on Qt 4.6 (or above) and this is the program which will be developed further.<br> <code>musredit</code> and <code>musrgui</code> are editors which also provide a graphical user interface to the programs contained in the <code><a href="MusrFit.html">musrfit</a></code> suite and are intended to help the user handle <code>musrfit</code> msr files. They are implemented in <code>C++</code> and use the <a href="http://qt.nokia.com/">Qt</a> framework. Principally, <code>musrgui</code> and <code>musredit</code> are doing the same, but are based on different Qt versions. <code>musrgui</code> is based on Qt 3.x and will only be maintained on bug-fixing level since the Qt 3.x licensing is less straight forward than the Qt 4.x one. <code>musredit</code> is based on Qt 4.6 (or above) and this is the program which will be developed further.<br>
On this documentation page only the features related to <code>musrfit</code> are described&mdash;the basic editor functions which should be self-explanatory are not. On this documentation page only the features related to <code>musrfit</code> are described&mdash;the basic editor functions which should be self-explanatory are not.
<strong><span class='foswikiRedFG'>Before going on using <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read the <a href="MusrFit.html">manual</a> of <code>musrfit</code> first!</span></strong> <strong><span class='foswikiRedFG'>Before going on using <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read the <a href="MusrFit.html">manual</a> of <code>musrfit</code> first!</span></strong>
<p></p> <p></p>
<h1><a name="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"></a> 2 Available Executables, Configuration Files and their Basic Usage </h1> <h1 id="A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2 Available Executables, Configuration Files and their Basic Usage </h1>
<a name="MusrEdit"></a> <span id="MusrEdit"></span>
<h2><a name="A_2.1_musredit_47_40musrgui_41"></a> 2.1 musredit / (musrgui) </h2> <h2 id="A_2.1_musredit_47_40musrgui_41"> 2.1 musredit / (musrgui) </h2>
<code>musredit</code> / <code>musrgui</code> are the editor executables. If called from within a shell they accept a few optional parameters: <dl> <code>musredit</code> / <code>musrgui</code> are the editor executables. If called from within a shell they accept a few optional parameters: <dl>
<dt> &lt;msr_files&gt; </dt><dd> file names of the msr files that should be opened in separate editor tabs on startup of <code>musrgui</code> / <code>musredit</code>. <dt> &lt;msr_files&gt; </dt><dd> file names of the msr files that should be opened in separate editor tabs on startup of <code>musrgui</code> / <code>musredit</code>.
</dd> <dt> --help </dt><dd> displays a small help notice in the shell explaining the basic usage of the program </dd> <dt> --help </dt><dd> displays a small help notice in the shell explaining the basic usage of the program
@ -149,8 +189,8 @@ On this documentation page only the features related to <code>musrfit</code> are
<p></p> <p></p>
If called without any parameters an empty editor window opens. If called without any parameters an empty editor window opens.
<p></p> <p></p>
<a name="MusreditStartupXml"></a> <span id="MusreditStartupXml"></span>
<h2><a name="A_2.2_musredit_startup.xml_47_musrgui_startup.xml"></a> 2.2 musredit_startup.xml / musrgui_startup.xml </h2> <h2 id="A_2.2_musredit_startup.xml_47_musrgui_startup.xml"> 2.2 musredit_startup.xml / musrgui_startup.xml </h2>
<code><b>musredit_startup.xml</b></code> / <code><b>musrgui_startup.xml</b></code> are configuration files located at the <code>musredit</code> / <code>musrgui</code> binary path. It is also possible to have another version of this file in the working directory which then will be used! <code><b>musredit_startup.xml</b></code> / <code><b>musrgui_startup.xml</b></code> are configuration files located at the <code>musredit</code> / <code>musrgui</code> binary path. It is also possible to have another version of this file in the working directory which then will be used!
<p></p> <p></p>
In this file the following XML tags are allowed to define settings and might proof useful for all users of <code>musredit</code> / <code>musrgui</code>: <dl> In this file the following XML tags are allowed to define settings and might proof useful for all users of <code>musredit</code> / <code>musrgui</code>: <dl>
@ -190,13 +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_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) <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></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 alt="LaTeX_logo.png" src="../pub/MUSR/MusrGui/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 src="../pub/MUSR/MusrGui/LaTeX_logo.png" alt="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> </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;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) <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;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;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 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;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;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> <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>
</dd></dl> </dd></dl>
@ -266,141 +306,94 @@ An example of the <code><b>musrgui_startup.xml</b></code> looks like:
&#60;/musrgui&#95;startup&#62; &#60;/musrgui&#95;startup&#62;
</pre> </pre>
<p></p> <p></p>
<a name="MusrfitFeatures"></a> <span id="MusrfitFeatures"></span>
<h1><a name="A_3_61_61musrfit_61_61_Features"></a> 3 <code><b>musrfit</b></code> Features </h1> <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. 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> <dl>
<dt> <img alt="musrasym.png" src="../pub/MUSR/MusrGui/musrasym.png" /> Asymmetry Default (Alt+a) </dt><dd> 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>.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrsinglehisto.png" src="../pub/MUSR/MusrGui/musrsinglehisto.png" /> Single-Histogram Default (Alt+h) </dt><dd> 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>.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrcalcchisq.png" src="../pub/MUSR/MusrGui/musrcalcchisq.png" /> Calculate Chisq (Alt+c) </dt><dd> <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>.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrfit.png" src="../pub/MUSR/MusrGui/musrfit.png" /> Fit (Alt+f) </dt><dd> <pre class="bash">musrfit &#60;msr&#95;file&#62; &#91;optional parameters]</pre> is called for the <strong>&lt;msr_file&gt;</strong> selected in the editor. The optional parameters may be chosen under <a href="#MusrPrefs" class="foswikiCurrentTopicLink">Preferences</a>. For further information refer to the <a href="MusrFit.html#MusrFit">manual</a> of <code>musrfit</code>.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrswap.png" src="../pub/MUSR/MusrGui/musrswap.png" /> Swap Msr &#8596; Mlog (Alt+s) </dt><dd> 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.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> Msr2data (Alt+m) </dt><dd> Opens a graphical interface to the <code>msr2data</code> program described in detail in its own <a href="Msr2Data.html#MusrGuiInterface">manual</a>.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> View (Alt+v) </dt><dd> <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>.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrt0.png" src="../pub/MUSR/MusrGui/musrt0.png" /> T0 (Alt+t) </dt><dd> <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>.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrFT.png" src="../pub/MUSR/MusrGui/musrFT.png" /> Raw Fourier </dt><dd> <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>.
</dd></dl>
<p></p> <p></p>
<a name="MusrPrefs"></a> <dl> $ <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>.
<dt> <img alt="musrprefs.png" src="../pub/MUSR/MusrGui/musrprefs.png" /> Preferences (Alt+p) </dt><dd> 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.
</dd></dl>
<p></p> <dl>
<dt> <img alt="musrdump.png" src="../pub/MUSR/MusrGui/musrdump.png" /> Dump Header </dt><dd> 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.
</dd></dl>
<p></p> <p></p>
<a name="EditorFeatures"></a> $ <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>.
<h1><a name="A_4_Editor_Features"></a> 4 Editor Features </h1> <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>.
<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>.
<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>.
<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>.
<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.
<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: 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 src="../pub/MUSR/MusrGui/musrgui-editor-v0.png" alt="musrgui editor features" width='415' height='566' align="right" /> <ul> <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>
<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> 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> <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> </li></ul>
<p></p> <p></p>
<a name="BugTracking"></a> <span id="BugTracking"></span>
<h1><a name="A_5_Bugtracking"></a> 5 Bugtracking </h1> <h1 id="A_5_Bugtracking"> 5 Bugtracking </h1>
<p></p> <p></p>
For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues" target="_top">Bitbucket Tracker</a>, <a href="https://tracker.psi.ch/jira/browse/MUSR/" target="_top">PSI Tracker</a> (PSI account needed) or send an e-mail to A. Suter. For reporting bugs or requesting new features and improvements please use the <a href="https://bitbucket.org/muonspin/musrfit/issues">Bitbucket Tracker</a>, <a href="https://tracker.psi.ch/jira/browse/MUSR/">PSI Tracker</a> (PSI account needed) or send an e-mail to A. Suter.
<p></p> <p></p>
-- <a href="http://www.psi.ch/low-energy-muons/people" target="_top">AS</a> &amp; <a href="http://www.fsf.org/register_form?referrer=8369" target="_top">BMW</a> </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></div>
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<div class="clear">&nbsp;</div> <td style="text-align:right" class="foswikiTableCol3 foswikiLast"> 37 K </td>
</div></div><div id="patternTopBar"> <td class="foswikiTableCol4 foswikiLast"> <span class="foswikiNoBreak">10 Apr 2009 - 14:53</span> </td>
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<div id="patternTopBarContents"><table border="0" cellpadding="0" cellspacing="0" style="width:100%" summary=""> <td class="foswikiTableCol6 foswikiLastCol foswikiLast"> musrgui options available upon right clicking a open msr-file </td>
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<h1 id="A_61_61MusrRoot_61_61"> <code><b>MusrRoot</b></code> </h1>
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<h1><a name="A_61_61MusrRoot_61_61"></a> <code><b>MusrRoot</b></code> </h1>
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<a name="foswikiTOC"></a><div class="foswikiToc"> <ul>
<li> <a href="MusrRoot.html#A_61_61MusrRoot_61_61"> MusrRoot </a> <li> <a href="MusrRoot.html#A_61_61MusrRoot_61_61"> MusrRoot </a>
</li> <li> <a href="MusrRoot.html#A_1_Introduction"> 1 Introduction </a> </li> <li> <a href="MusrRoot.html#A_1_Introduction"> 1 Introduction </a>
</li> <li> <a href="MusrRoot.html#A_2_Some_Basics_Concerning_61ROOT_61_Files"> 2 Some Basics Concerning ROOT Files </a> </li> <li> <a href="MusrRoot.html#A_2_Some_Basics_Concerning_61ROOT_61_Files"> 2 Some Basics Concerning ROOT Files </a>
@ -146,11 +186,11 @@ pre {
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<h1><a name="A_1_Introduction"></a> 1 Introduction </h1> <h1 id="A_1_Introduction"> 1 Introduction </h1>
Until 2011 different &#956;SR file formats were used within PSI. The bulk-&#956;SR instruments were writing their data in the <code>PSI-BIN</code> file format, which is a fixed binary format with rather stringent limitations. The LE-&#956;SR (LEM) instrument was using a <code>ROOT</code> (CERN) based file format which was tightly tailored to the special needs of the LEM instrument. This situation was unsatisfactorily and hence it was decided to move forward to a open file format called <code>MusrRoot</code> to be described in the following. Until 2011 different &#956;SR file formats were used within PSI. The bulk-&#956;SR instruments were writing their data in the <code>PSI-BIN</code> file format, which is a fixed binary format with rather stringent limitations. The LE-&#956;SR (LEM) instrument was using a <code>ROOT</code> (CERN) based file format which was tightly tailored to the special needs of the LEM instrument. This situation was unsatisfactorily and hence it was decided to move forward to a open file format called <code>MusrRoot</code> to be described in the following.
<p></p> <p></p>
<h1><a name="A_2_Some_Basics_Concerning_61ROOT_61_Files"></a> 2 Some Basics Concerning <code>ROOT</code> Files </h1> <h1 id="A_2_Some_Basics_Concerning_61ROOT_61_Files"> 2 Some Basics Concerning <code>ROOT</code> Files </h1>
The &#956;SR data acquisition systems at PSI are utilizing <code>MIDAS</code> (see <a href="http://midas.psi.ch/" target="_top">Midas Home Page</a> ). The <code>MIDAS</code> analyzer, which is responsible to build histograms, especially the &#956;SR decay histograms, makes it very easy to build <code>ROOT</code> (see <a href="http://root.cern.ch/" target="_top">ROOT/CERN home page</a> ) histogram objects (these are <code>TH1F</code> objects for &#956;SR decay histograms). <code>ROOT</code> is a C++ object-oriented data mining frame work. These histograms can be collected and saved in <code>ROOT</code> files (<code>TFile</code>). In order to ease the understanding of the upcoming definitions, a few <code>ROOT</code> related things shall be summaries here. For details concerning the <code>ROOT</code> frame work documentation please check <a href="http://root.cern.ch/drupal/content/users-guide" target="_top">ROOT/CERN Users Guide</a> and <a href="http://root.cern.ch/drupal/content/reference-guide" target="_top">ROOT/CERN Reference Guide</a> . The &#956;SR data acquisition systems at PSI are utilizing <code>MIDAS</code> (see <a href="http://midas.psi.ch/">Midas Home Page</a> ). The <code>MIDAS</code> analyzer, which is responsible to build histograms, especially the &#956;SR decay histograms, makes it very easy to build <code>ROOT</code> (see <a href="http://root.cern.ch/">ROOT/CERN home page</a> ) histogram objects (these are <code>TH1F</code> objects for &#956;SR decay histograms). <code>ROOT</code> is a C++ object-oriented data mining frame work. These histograms can be collected and saved in <code>ROOT</code> files (<code>TFile</code>). In order to ease the understanding of the upcoming definitions, a few <code>ROOT</code> related things shall be summaries here. For details concerning the <code>ROOT</code> frame work documentation please check <a href="http://root.cern.ch/drupal/content/users-guide">ROOT/CERN Users Guide</a> and <a href="http://root.cern.ch/drupal/content/reference-guide">ROOT/CERN Reference Guide</a> .
<p></p> <p></p>
<code>ROOT</code> files (<code>TFile</code>) are binary files which can hold any kind of objects. A <code>TFile</code> is organized similarly to a directory structure of an operating system. Within the <code>ROOT</code> framework, there is a <code>TFile</code> browser available which allows to inspect these files. This browser (<code>TBrowser</code>) will show all object saved in the <code>TFile</code> directly, if they derive from <code>TObject</code>. <code>ROOT</code> files (<code>TFile</code>) are binary files which can hold any kind of objects. A <code>TFile</code> is organized similarly to a directory structure of an operating system. Within the <code>ROOT</code> framework, there is a <code>TFile</code> browser available which allows to inspect these files. This browser (<code>TBrowser</code>) will show all object saved in the <code>TFile</code> directly, if they derive from <code>TObject</code>.
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@ -164,7 +204,7 @@ The <code>MusrRoot</code> file format to be described below is only using a smal
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Since all these objects are deriving form <code>TObject</code>, they will be directly accessible via the <code>TBrowser</code> -object. For instance, the &#956;-decay-histograms can be directly plotted, are even fitted, out of the box. Since all these objects are deriving form <code>TObject</code>, they will be directly accessible via the <code>TBrowser</code> -object. For instance, the &#956;-decay-histograms can be directly plotted, are even fitted, out of the box.
<p></p> <p></p>
<h1><a name="A_3_61MusrRoot_61_an_Extensible_Open_File_Format_for_SR"></a> 3 <code>MusrRoot</code> an Extensible Open File Format for &#956;SR </h1> <h1 id="A_3_61MusrRoot_61_an_Extensible_Open_File_Format_for_SR"> 3 <code>MusrRoot</code> an Extensible Open File Format for &#956;SR </h1>
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As mentioned before, <code>ROOT</code> files are open-file-format files meaning that they can contain more entries (and most probably will) than the ones specified in the following. The specified ones will be the mandatory ones for <em>all</em> instruments. Before defining all mandatory entries, the <code>MusrRoot</code> file structure shall be sketched. As mentioned before, <code>ROOT</code> files are open-file-format files meaning that they can contain more entries (and most probably will) than the ones specified in the following. The specified ones will be the mandatory ones for <em>all</em> instruments. Before defining all mandatory entries, the <code>MusrRoot</code> file structure shall be sketched.
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@ -194,7 +234,7 @@ RunHeader ---&#124;
</pre> </pre>
where <code>hDecay001</code>, etc. are <code>ROOT</code> histograms (to be more specific: <code>TH1F</code>), containing the &#956;SR decay histograms. There can be as many as needed, especially there is no limitation about their length. The histogram object names will be <code>hDecayXXX</code>, where <code>XXX</code> (leading zero <code>int</code>, <em>i.e.</em> <code>%03d</code> in C/C++ notation, starting with `1') is the histogram number. The title and name of the histogram (see description of the <code>TH1F</code> <code>ROOT</code> class) contains the label of the histogram, like `top', `forward', etc. How many of these histograms are present is accessible through the <code>RunInfo</code> folder in which the necessary header information are found (details see next sections). The folder <code>SCAnaModule</code> contains histograms of some of the slow-control parameters, as for instance the sample temperature versus time, the applied field versus time, etc. Again the label of the histogram will give more specific information about its content. where <code>hDecay001</code>, etc. are <code>ROOT</code> histograms (to be more specific: <code>TH1F</code>), containing the &#956;SR decay histograms. There can be as many as needed, especially there is no limitation about their length. The histogram object names will be <code>hDecayXXX</code>, where <code>XXX</code> (leading zero <code>int</code>, <em>i.e.</em> <code>%03d</code> in C/C++ notation, starting with `1') is the histogram number. The title and name of the histogram (see description of the <code>TH1F</code> <code>ROOT</code> class) contains the label of the histogram, like `top', `forward', etc. How many of these histograms are present is accessible through the <code>RunInfo</code> folder in which the necessary header information are found (details see next sections). The folder <code>SCAnaModule</code> contains histograms of some of the slow-control parameters, as for instance the sample temperature versus time, the applied field versus time, etc. Again the label of the histogram will give more specific information about its content.
<p></p> <p></p>
<h2><a name="A_3.1_Run_Information_Contained_in_61RunHeader_61"></a> 3.1 Run Information Contained in <code>RunHeader</code> </h2> <h2 id="A_3.1_Run_Information_Contained_in_61RunHeader_61"> 3.1 Run Information Contained in <code>RunHeader</code> </h2>
The <code>RunHeader</code> contains all needed meta-information to describe a &#956;SR-run. The list of the <em>minimal number of required</em> "folders" of the <code>RunHeader</code> is given in the following structure: The <code>RunHeader</code> contains all needed meta-information to describe a &#956;SR-run. The list of the <em>minimal number of required</em> "folders" of the <code>RunHeader</code> is given in the following structure:
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@ -206,40 +246,40 @@ RunHeader (TFolder) ---&#124;
&#124;- BeamlineInfo (TObjArray) &#124;- BeamlineInfo (TObjArray)
</pre> </pre>
<p></p> <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 href="#SampleEnvironmentInfoRequired" class="foswikiCurrentTopicLink">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 href="#BeamlineInfoRequired" class="foswikiCurrentTopicLink">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 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>).
<p></p> <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.). 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> <p></p>
<a name="RunInfo"></a> <span id="RunInfo"></span>
<h3><a name="A_3.1.1_61RunInfo_61_Overview"></a> 3.1.1 <code>RunInfo</code> Overview </h3> <h3 id="A_3.1.1_61RunInfo_61_Overview"> 3.1.1 <code>RunInfo</code> Overview </h3>
<p></p> <p></p>
<table class="foswikiTable" rules="none" border="1"> <table rules="none" border="1" class="foswikiTable">
<thead> <thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=1;up=0#sorted_table" title="Sort by this column">Name</a> </th> <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 align="center" class="foswikiTableCol1"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=1;up=0#sorted_table" title="Sort by this column">Internal Type</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 align="center" class="foswikiTableCol2 foswikiLastCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=1;up=0#sorted_table" title="Sort by this column">Comment</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>
</tr> </tr>
</thead> </thead>
<tbody> <tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Version </td> <td class="foswikiTableCol0 foswikiFirstCol"> Version </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> SVN version of <code>TMusrRunHeader</code> </td> <td class="foswikiTableCol2 foswikiLastCol"> SVN version of <code>TMusrRunHeader</code> </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Generic Validator URL </td> <td class="foswikiTableCol0 foswikiFirstCol"> Generic Validator URL </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td align="center" class="foswikiTableCol2 foswikiLastCol"> URL of the generic <code>MusrRoot</code> validation xsd-file. </td> <td style="text-align:center" class="foswikiTableCol2 foswikiLastCol"> URL of the generic <code>MusrRoot</code> validation xsd-file. </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Specific Validator URL </td> <td class="foswikiTableCol0 foswikiFirstCol"> Specific Validator URL </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td align="center" class="foswikiTableCol2 foswikiLastCol"> URL of the instrument specific validation xsd-file. </td> <td class="foswikiTableCol2 foswikiLastCol" style="text-align:center"> URL of the instrument specific validation xsd-file. </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Generator </td> <td class="foswikiTableCol0 foswikiFirstCol"> Generator </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> Program which wrote the <code>MusrRoot</code> file, </td> <td class="foswikiTableCol2 foswikiLastCol"> Program which wrote the <code>MusrRoot</code> file, </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -249,7 +289,7 @@ Before elaborating more on the required items within this structure, a few words
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> File Name </td> <td class="foswikiTableCol0 foswikiFirstCol"> File Name </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> File name of the <code>MusrRoot</code> file, </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -259,52 +299,52 @@ Before elaborating more on the required items within this structure, a few words
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Title </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Title </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Number </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Number </td>
<td 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"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Start Time </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Start Time </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> ISO 8601 date time </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Stop Time </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Stop Time </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> ISO 8601 date time </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Duration </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Duration </td>
<td align="center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td> <td class="foswikiTableCol1" style="text-align:center"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> run duration in sec </td> <td class="foswikiTableCol2 foswikiLastCol"> run duration in sec </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Laboratory </td> <td class="foswikiTableCol0 foswikiFirstCol"> Laboratory </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> PSI </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> PSI </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Instrument </td> <td class="foswikiTableCol0 foswikiFirstCol"> Instrument </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> GPS </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Beam Momentum </td> <td class="foswikiTableCol0 foswikiFirstCol"> Muon Beam Momentum </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 28.1 MeV/c </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Species </td> <td class="foswikiTableCol0 foswikiFirstCol"> Muon Species </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> positive, or negative muon </td> <td class="foswikiTableCol2 foswikiLastCol"> positive, or negative muon </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Source </td> <td class="foswikiTableCol0 foswikiFirstCol"> Muon Source </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> Target E - Low Energy Muons or </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -314,64 +354,64 @@ Before elaborating more on the required items within this structure, a few words
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Setup </td> <td class="foswikiTableCol0 foswikiFirstCol"> Setup </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Comment </td> <td class="foswikiTableCol0 foswikiFirstCol"> Comment </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Name </td> <td class="foswikiTableCol0 foswikiFirstCol"> Sample Name </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Temperature </td> <td class="foswikiTableCol0 foswikiFirstCol"> Sample Temperature </td>
<td 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> 3.21 +- 0.05 K; SP: 3.2; CF1 </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 3.21 +- 0.05 K; SP: 3.2; CF1 </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Magnetic Field </td> <td class="foswikiTableCol0 foswikiFirstCol"> Sample Magnetic Field </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 350.002 +- 0.005 G; SP: 350; WXY </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> No of Histos </td> <td class="foswikiTableCol0 foswikiFirstCol"> No of Histos </td>
<td 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"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Time Resolution </td> <td class="foswikiTableCol0 foswikiFirstCol"> Time Resolution </td>
<td align="center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 0.1953125 ns </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 0.1953125 ns </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> RedGreen Offsets </td> <td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> RedGreen Offsets </td>
<td align="center" class="foswikiTableCol1 foswikiLast"> <code>TIntVector</code> </td> <td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>TIntVector</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> <em>e.g.</em> 0; 20 </td> <td class="foswikiTableCol2 foswikiLastCol foswikiLast"> <em>e.g.</em> 0; 20 </td>
</tr> </tr>
</tbody></table> </tbody></table>
<p></p> <p></p>
These entries should be clear except for the <code>RedGreen Offsets</code> and the column "Internal Type" which shortly will be discussed before specifying the content of the other required folders. These entries should be clear except for the <code>RedGreen Offsets</code> and the column "Internal Type" which shortly will be discussed before specifying the content of the other required folders.
<p></p> <ol> <p></p> <ol>
<li type="i"> <code>RedGreen Offsets</code>: in case experiments are performed with external stimuli, there will be a collection of related histograms. For instance for electrical field experiments, there will be histograms for field on/off, doubling the number of needed histograms. In order to distinguish them easier in the data file, the <code>RedGreen Offsets</code> were introduced. One selection of histograms (assuming for the moment 8 detectors) will be numbered from 1 to 8 (lets say the field off ones). The other set of histograms (field on in this example) will then start with 21 through 28 (see table above). The same will be true for the detector information (see Sec. <a href="#DetectorInfoRequired" class="foswikiCurrentTopicLink"><code>DetectorInfo</code> Required</a>). The entry <code>No of Histos</code> will only give 8 for the given example, meaning that <span class='foswikiRedFG'>red</span>/<span class='foswikiGreenFG'>green</span> multiplication is defined rather via <code>RedGreen Offsets</code> than the number of histograms. <li style="list-style-type:lower-roman"> <code>RedGreen Offsets</code>: in case experiments are performed with external stimuli, there will be a collection of related histograms. For instance for electrical field experiments, there will be histograms for field on/off, doubling the number of needed histograms. In order to distinguish them easier in the data file, the <code>RedGreen Offsets</code> were introduced. One selection of histograms (assuming for the moment 8 detectors) will be numbered from 1 to 8 (lets say the field off ones). The other set of histograms (field on in this example) will then start with 21 through 28 (see table above). The same will be true for the detector information (see Sec. <a class="foswikiCurrentTopicLink" href="#DetectorInfoRequired"><code>DetectorInfo</code> Required</a>). The entry <code>No of Histos</code> will only give 8 for the given example, meaning that <span class='foswikiRedFG'>red</span>/<span class='foswikiGreenFG'>green</span> multiplication is defined rather via <code>RedGreen Offsets</code> than the number of histograms.
</li> <li type="i"> Internal Types: in order to ease the handling of the <code>MusrRoot</code> run header, a class <code>TMusrRunHeader</code> is available which deals with it. The "Internal Type" specified, corresponds to the internal representation in within this class. In the <code>MusrRoot</code> file these entries are all saved as browsable <code>ROOT</code> strings (<code>TObjString</code>). The only special type is <code>TMusrRunPhysicalQuantity</code> which is introduced to deal with physical quantities. They always can be represented in the following way: </li> <li style="list-style-type:lower-roman"> Internal Types: in order to ease the handling of the <code>MusrRoot</code> run header, a class <code>TMusrRunHeader</code> is available which deals with it. The "Internal Type" specified, corresponds to the internal representation in within this class. In the <code>MusrRoot</code> file these entries are all saved as browsable <code>ROOT</code> strings (<code>TObjString</code>). The only special type is <code>TMusrRunPhysicalQuantity</code> which is introduced to deal with physical quantities. They always can be represented in the following way:
</li></ol> </li></ol>
<pre> <pre>
&#60;property name&#62; &#60;value&#62; +- &#60;estimated error&#62; &#60;unit&#62;; SP: &#60;demand&#62;; &#60;description&#62; &#60;property name&#62; &#60;value&#62; +- &#60;estimated error&#62; &#60;unit&#62;; SP: &#60;demand&#62;; &#60;description&#62;
</pre> </pre>
Not all of these values are needed to be given and depending on which are given, the representation in the <code>MusrRoot</code> file will be different (handled by <code>TMusrRunHeader</code>). Examples are given in the comment column of the table above. For details see <a href="#TMusrRunPhysicalQuantity" class="foswikiCurrentTopicLink"><code>TMusrRunPhysicalQuantity</code> - Possible Representations</a>. Not all of these values are needed to be given and depending on which are given, the representation in the <code>MusrRoot</code> file will be different (handled by <code>TMusrRunHeader</code>). Examples are given in the comment column of the table above. For details see <a class="foswikiCurrentTopicLink" href="#TMusrRunPhysicalQuantity"><code>TMusrRunPhysicalQuantity</code> - Possible Representations</a>.
<p></p> <p></p>
A mock-up <code>TBrowser</code> print-out would look like the one shown in the following figure. You might notice, that at the end of each entry you find a " <code>-@X</code> ", where <code>X</code> is a number. This is an encoding of the internal type of the entry and is the price to be payed not using derived types. The next section will explain this in much more detail. A mock-up <code>TBrowser</code> print-out would look like the one shown in the following figure. You might notice, that at the end of each entry you find a " <code>-@X</code> ", where <code>X</code> is a number. This is an encoding of the internal type of the entry and is the price to be payed not using derived types. The next section will explain this in much more detail.
<p></p> <p></p>
<img src="../pub/MUSR/MusrRoot/RunInfo.png" alt="=TMusrRunHeader= mock up. The red shaded entries are of type =TMusrRunPhysicalQuantity="/> <img class='imagePlain imagePlain_none ' src='../pub/MUSR/MusrRoot/RunInfo.png' alt='TMusrRunHeader mock up. The red shaded entries are of type TMusrRunPhysicalQuantity' title='RunInfo.png' width='639' height='774' style='' />
<p></p> <p></p>
<code>TMusrRunHeader</code> mock up. The red shaded entries are of type <code>TMusrRunPhysicalQuantity</code> <code>TMusrRunHeader</code> mock up. The red shaded entries are of type <code>TMusrRunPhysicalQuantity</code>
<p></p> <p></p>
<a name="TMusrRunHeaderConcept"></a> <span id="TMusrRunHeaderConcept"></span>
<h1><a name="A_4_61TMusrRunHeader_61_Concept"></a> 4 <code>TMusrRunHeader</code> Concept </h1> <h1 id="A_4_61TMusrRunHeader_61_Concept"> 4 <code>TMusrRunHeader</code> Concept </h1>
The different &#956;SR instruments need different information to be written into the data file (next to the most important ones: the histograms). The above defined properties are the <em>minimal number of required</em> ones. There are different possible approaches to deal with it on the implementation level. The different &#956;SR instruments need different information to be written into the data file (next to the most important ones: the histograms). The above defined properties are the <em>minimal number of required</em> ones. There are different possible approaches to deal with it on the implementation level.
<p></p> <ul> <p></p> <ul>
<li> A base class dealing with <em>minimal required</em> standard is defined. Afterwards for each instrument a class is derived which is extending the base class to the needs of the instrument. <li> A base class dealing with <em>minimal required</em> standard is defined. Afterwards for each instrument a class is derived which is extending the base class to the needs of the instrument.
@ -391,10 +431,10 @@ Even though the first approach is very clean, it would mean a lot of maintenance
<p></p> <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 href="#ValidateMusrRoot" class="foswikiCurrentTopicLink">Validation</a> will discuss how to validate <code>MusrRoot</code> files.
<p></p> <p></p>
<h2><a name="A_4.1_User_Interface_for_61MusrRoot_61_Run_Header"></a> 4.1 User Interface for <code>MusrRoot</code> Run Header </h2> <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. 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.
<p></p> <p></p>
<h3><a name="A_4.1.1_Writing_a_61MusrRoot_61_Run_Header"></a> 4.1.1 Writing a <code>MusrRoot</code> Run Header </h3> <h3 id="A_4.1.1_Writing_a_61MusrRoot_61_Run_Header"> 4.1.1 Writing a <code>MusrRoot</code> Run Header </h3>
An example program <code>write_musrRoot_runHeader</code> which is writing a full run header is part of the <code>musrfit</code> package. Here I will concentrate just on the most essential parts. First one needs an instance of <code>TMusrRunHeader</code> An example program <code>write_musrRoot_runHeader</code> which is writing a full run header is part of the <code>musrfit</code> package. Here I will concentrate just on the most essential parts. First one needs an instance of <code>TMusrRunHeader</code>
<p></p> <p></p>
<pre class="cplusplus"> <pre class="cplusplus">
@ -423,7 +463,7 @@ prop.Set(&#34;CF3&#34;, MRH&#95;UNDEFINED, 3.27, 0.09, &#34;K&#34;, &#34;strange
header-&#62;Set(&#34;SampleEnvironmentInfo/CF3&#34;, prop); header-&#62;Set(&#34;SampleEnvironmentInfo/CF3&#34;, prop);
</pre> </pre>
<p></p> <p></p>
Here <code>TMusrRunPhysicalQuantity</code> objects are fed via the use of the overloaded set-method. For details see <a href="#TMusrRunPhysicalQuantity" class="foswikiCurrentTopicLink"><code>TMusrRunPhysicalQuantity</code> - Possible Representations</a>. Here <code>TMusrRunPhysicalQuantity</code> objects are fed via the use of the overloaded set-method. For details see <a class="foswikiCurrentTopicLink" href="#TMusrRunPhysicalQuantity"><code>TMusrRunPhysicalQuantity</code> - Possible Representations</a>.
<p></p> <p></p>
To set some property within "sub-sub-directories" it would like this: To set some property within "sub-sub-directories" it would like this:
<p></p> <p></p>
@ -451,7 +491,7 @@ if (header-&#62;FillFolder(runHeader)) {
f-&#62;Close(); f-&#62;Close();
</pre> </pre>
<p></p> <p></p>
<h3><a name="A_4.1.2_Reading_a_61MusrRoot_61_Run_Header"></a> 4.1.2 Reading a <code>MusrRoot</code> Run Header </h3> <h3 id="A_4.1.2_Reading_a_61MusrRoot_61_Run_Header"> 4.1.2 Reading a <code>MusrRoot</code> Run Header </h3>
The following code snippet shows how the extract the full run header from the <code>MusrRoot</code> file. The following code snippet shows how the extract the full run header from the <code>MusrRoot</code> file.
<p></p> <p></p>
<pre class="cplusplus"> <pre class="cplusplus">
@ -508,11 +548,11 @@ if (ok) {
} }
</pre> </pre>
<p></p> <p></p>
<a name="ValidateMusrRoot"></a> <span id="ValidateMusrRoot"></span>
<h2><a name="A_4.2_Validation_of_a_61MusrRoot_61_File"></a> 4.2 Validation of a <code>MusrRoot</code> File </h2> <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>: 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> <p></p>
<img src="../pub/MUSR/MusrRoot/MusrRootValidationScheme.png" height="700" title="MusrRoot validation scheme"/> <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='' />
<p></p> <p></p>
<code>MusrRoot</code> validation scheme <code>MusrRoot</code> validation scheme
<p></p> <p></p>
@ -526,46 +566,46 @@ In the following this validation scheme will be discussed as it is implemented i
<p></p> <p></p>
This validation scheme is useful for people which define instrument specific extensions of the base <code>MusrRoot</code>, as for instance the LEM instrument at PSI. It is also useful for people writing file converters in order to cross check if the generated file is valid. This validation scheme is useful for people which define instrument specific extensions of the base <code>MusrRoot</code>, as for instance the LEM instrument at PSI. It is also useful for people writing file converters in order to cross check if the generated file is valid.
<p></p> <p></p>
<a name="RunInfoRequired"></a> <span id="RunInfoRequired"></span>
<h1><a name="A_5_61RunInfo_61_Required"></a> 5 <code>RunInfo</code> Required </h1> <h1 id="A_5_61RunInfo_61_Required"> 5 <code>RunInfo</code> Required </h1>
<p></p> <p></p>
<table class="foswikiTable" rules="none" border="1"> <table class="foswikiTable" border="1" rules="none">
<thead> <thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=2;up=0#sorted_table" title="Sort by this column">Name</a> </th> <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 align="center" class="foswikiTableCol1"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=2;up=0#sorted_table" title="Sort by this column">Internal Type</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 align="center" class="foswikiTableCol2 foswikiLastCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=2;up=0#sorted_table" title="Sort by this column">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" title="Sort by this column" rel="nofollow">Comment</a> </th>
</tr> </tr>
</thead> </thead>
<tbody> <tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Version </td> <td class="foswikiTableCol0 foswikiFirstCol"> Version </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> SVN version of <code>TMusrRunHeader</code> </td> <td class="foswikiTableCol2 foswikiLastCol"> SVN version of <code>TMusrRunHeader</code> </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Generic Validator URL </td> <td class="foswikiTableCol0 foswikiFirstCol"> Generic Validator URL </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> URL of the generic <code>MusrRoot</code> validation xsd-file. </td> <td class="foswikiTableCol2 foswikiLastCol"> URL of the generic <code>MusrRoot</code> validation xsd-file. </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> &nbsp; </td> <td class="foswikiTableCol0 foswikiFirstCol"> &nbsp; </td>
<td class="foswikiTableCol1"> &nbsp; </td> <td class="foswikiTableCol1"> &nbsp; </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> <a href="http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd" target="_top">http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd</a> </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> <a href="http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd">http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd</a> </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Specific Validator URL </td> <td class="foswikiTableCol0 foswikiFirstCol"> Specific Validator URL </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> URL of the instrument specific validation xsd-file. </td> <td class="foswikiTableCol2 foswikiLastCol"> URL of the instrument specific validation xsd-file. </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> &nbsp; </td> <td class="foswikiTableCol0 foswikiFirstCol"> &nbsp; </td>
<td class="foswikiTableCol1"> &nbsp; </td> <td class="foswikiTableCol1"> &nbsp; </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> for LEM: <a href="http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd" target="_top">http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd</a> </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> for LEM: <a href="http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd">http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd</a> </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Generator </td> <td class="foswikiTableCol0 foswikiFirstCol"> Generator </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> Program which wrote the <code>MusrRoot</code> file, </td> <td class="foswikiTableCol2 foswikiLastCol"> Program which wrote the <code>MusrRoot</code> file, </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -575,7 +615,7 @@ This validation scheme is useful for people which define instrument specific ext
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> File Name </td> <td class="foswikiTableCol0 foswikiFirstCol"> File Name </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> File name of the <code>MusrRoot</code> file, </td> <td class="foswikiTableCol2 foswikiLastCol"> File name of the <code>MusrRoot</code> file, </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
@ -585,52 +625,52 @@ This validation scheme is useful for people which define instrument specific ext
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Title </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Title </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Number </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Number </td>
<td 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"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Start Time </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Start Time </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> ISO 8601 date time </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Stop Time </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Stop Time </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> ISO 8601 date time </td> <td class="foswikiTableCol2 foswikiLastCol"> ISO 8601 date time </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Run Duration </td> <td class="foswikiTableCol0 foswikiFirstCol"> Run Duration </td>
<td align="center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td> <td class="foswikiTableCol1" style="text-align:center"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> run duration in sec </td> <td class="foswikiTableCol2 foswikiLastCol"> run duration in sec </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Laboratory </td> <td class="foswikiTableCol0 foswikiFirstCol"> Laboratory </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> PSI </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> PSI </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Instrument </td> <td class="foswikiTableCol0 foswikiFirstCol"> Instrument </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> GPS </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> GPS </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Beam Momentum </td> <td class="foswikiTableCol0 foswikiFirstCol"> Muon Beam Momentum </td>
<td align="center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 28.1 MeV/c </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 28.1 MeV/c </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Species </td> <td class="foswikiTableCol0 foswikiFirstCol"> Muon Species </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> positive, or negative muon </td> <td class="foswikiTableCol2 foswikiLastCol"> positive, or negative muon </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Muon Source </td> <td class="foswikiTableCol0 foswikiFirstCol"> Muon Source </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> Target E - Low Energy Muons or </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> Target E - Low Energy Muons or </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
@ -640,48 +680,48 @@ This validation scheme is useful for people which define instrument specific ext
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Setup </td> <td class="foswikiTableCol0 foswikiFirstCol"> Setup </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Comment </td> <td class="foswikiTableCol0 foswikiFirstCol"> Comment </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Name </td> <td class="foswikiTableCol0 foswikiFirstCol"> Sample Name </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Temperature </td> <td class="foswikiTableCol0 foswikiFirstCol"> Sample Temperature </td>
<td 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> 3.21 +- 0.05 K; SP: 3.2; CF1 </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 3.21 +- 0.05 K; SP: 3.2; CF1 </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Sample Magnetic Field </td> <td class="foswikiTableCol0 foswikiFirstCol"> Sample Magnetic Field </td>
<td align="center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 350.002 +- 0.005 G; SP: 350; WXY </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 350.002 +- 0.005 G; SP: 350; WXY </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> No of Histos </td> <td class="foswikiTableCol0 foswikiFirstCol"> No of Histos </td>
<td 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"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Time Resolution </td> <td class="foswikiTableCol0 foswikiFirstCol"> Time Resolution </td>
<td align="center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TMusrRunPhysicalQuantity</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 0.1953125 ns </td> <td class="foswikiTableCol2 foswikiLastCol"> <em>e.g.</em> 0.1953125 ns </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> RedGreen Offsets </td> <td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> RedGreen Offsets </td>
<td 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> <td class="foswikiTableCol2 foswikiLastCol foswikiLast"> <em>e.g.</em> 0; 20 </td>
</tr> </tr>
</tbody></table> </tbody></table>
<p></p> <p></p>
<a name="DetectorInfoRequired"></a> <span id="DetectorInfoRequired"></span>
<h1><a name="A_6_61DetectorInfo_61_Required"></a> 6 <code>DetectorInfo</code> Required </h1> <h1 id="A_6_61DetectorInfo_61_Required"> 6 <code>DetectorInfo</code> Required </h1>
The <code>DetectorInfo</code> is organized in a sub-tree like The <code>DetectorInfo</code> is organized in a sub-tree like
<p></p> <p></p>
<pre> <pre>
@ -697,115 +737,115 @@ The numbering of the detectors has to correspond the its histogram, <em>e.g.</em
<p></p> <p></p>
<code>Detector&lt;XXX&gt;</code> has the elements <code>Detector&lt;XXX&gt;</code> has the elements
<p></p> <p></p>
<table class="foswikiTable" rules="none" border="1"> <table border="1" class="foswikiTable" rules="none">
<thead> <thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=3;up=0#sorted_table" title="Sort by this column">Name</a> </th> <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 align="center" class="foswikiTableCol1"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=3;up=0#sorted_table" title="Sort by this column">Internal Type</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 rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=3;up=0#sorted_table" title="Sort by this column">Comment</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>
</tr> </tr>
</thead> </thead>
<tbody> <tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Name </td> <td class="foswikiTableCol0 foswikiFirstCol"> Name </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> detector name, <em>e.g.</em> Left-NPP </td> <td class="foswikiTableCol2 foswikiLastCol"> detector name, <em>e.g.</em> Left-NPP </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Histo Number </td> <td class="foswikiTableCol0 foswikiFirstCol"> Histo Number </td>
<td align="center" class="foswikiTableCol1"> <code>Int_t</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <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> <td class="foswikiTableCol2 foswikiLastCol"> histogram number. This number corresponds to the histogram number in the <code>histos/DecayAnaModule</code> sub-tree. </td>
</tr> </tr>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Histo Length </td> <td class="foswikiTableCol0 foswikiFirstCol"> Histo Length </td>
<td align="center" class="foswikiTableCol1"> <code>Int_t</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <code>Int_t</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> length of the histogram </td> <td class="foswikiTableCol2 foswikiLastCol"> length of the histogram </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> Time Zero Bin </td> <td class="foswikiTableCol0 foswikiFirstCol"> Time Zero Bin </td>
<td align="center" class="foswikiTableCol1"> <code>Double_t</code> </td> <td style="text-align:center" class="foswikiTableCol1"> <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> <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>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> First Good Bin </td> <td class="foswikiTableCol0 foswikiFirstCol"> First Good Bin </td>
<td 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"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol"> &nbsp; </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> Last Good Bin </td> <td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> Last Good Bin </td>
<td align="center" class="foswikiTableCol1 foswikiLast"> <code>Int_t</code> </td> <td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>Int_t</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> &nbsp; </td> <td class="foswikiTableCol2 foswikiLastCol foswikiLast"> &nbsp; </td>
</tr> </tr>
</tbody></table> </tbody></table>
<p></p> <p></p>
<a name="SampleEnvironmentInfoRequired"></a> <span id="SampleEnvironmentInfoRequired"></span>
<h1><a name="A_7_61SampleEnvironmentInfo_61_Required"></a> 7 <code>SampleEnvironmentInfo</code> Required </h1> <h1 id="A_7_61SampleEnvironmentInfo_61_Required"> 7 <code>SampleEnvironmentInfo</code> Required </h1>
Here only a single entry is required, namely Here only a single entry is required, namely
<p></p> <p></p>
<table class="foswikiTable" rules="none" border="1"> <table rules="none" border="1" class="foswikiTable">
<thead> <thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=4;up=0#sorted_table" title="Sort by this column">Name</a> </th> <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 align="center" class="foswikiTableCol1"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=4;up=0#sorted_table" title="Sort by this column">Internal Type</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" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=4;up=0#sorted_table" title="Sort by this column">Comment</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>
</tr> </tr>
</thead> </thead>
<tbody> <tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> Cryo </td> <td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> Cryo </td>
<td align="center" class="foswikiTableCol1 foswikiLast"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> name of the used cryostat, <em>e.g.</em> Konti-2 </td> <td class="foswikiTableCol2 foswikiLastCol foswikiLast"> name of the used cryostat, <em>e.g.</em> Konti-2 </td>
</tr> </tr>
</tbody></table> </tbody></table>
<p></p> <p></p>
<a name="MagneticFieldEnvironmentInfoRequired"></a> <span id="MagneticFieldEnvironmentInfoRequired"></span>
<h1><a name="A_8_61MagneticFieldEnvironmentInfo_61_Required"></a> 8 <code>MagneticFieldEnvironmentInfo</code> Required </h1> <h1 id="A_8_61MagneticFieldEnvironmentInfo_61_Required"> 8 <code>MagneticFieldEnvironmentInfo</code> Required </h1>
<p></p> <p></p>
Here only a single entry is required, namely Here only a single entry is required, namely
<p></p> <p></p>
<table class="foswikiTable" rules="none" border="1"> <table class="foswikiTable" border="1" rules="none">
<thead> <thead>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=5;up=0#sorted_table" title="Sort by this column">Name</a> </th> <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 align="center" class="foswikiTableCol1"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=1;table=5;up=0#sorted_table" title="Sort by this column">Internal Type</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 rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=2;table=5;up=0#sorted_table" title="Sort by this column">Comment</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>
</tr> </tr>
</thead> </thead>
<tbody> <tbody>
<tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0"> <tr class="foswikiTableEven foswikiTableRowdataBgSorted0 foswikiTableRowdataBg0">
<td class="foswikiTableCol0 foswikiFirstCol"> Magnet Name </td> <td class="foswikiTableCol0 foswikiFirstCol"> Magnet Name </td>
<td align="center" class="foswikiTableCol1"> <code>TString</code> </td> <td class="foswikiTableCol1" style="text-align:center"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol"> name of the used magnet, <em>e.g.</em> WEW. </td> <td class="foswikiTableCol2 foswikiLastCol"> name of the used magnet, <em>e.g.</em> WEW. </td>
</tr> </tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1"> <tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> &nbsp; </td> <td class="foswikiTableCol0 foswikiFirstCol foswikiLast"> &nbsp; </td>
<td class="foswikiTableCol1 foswikiLast"> &nbsp; </td> <td class="foswikiTableCol1 foswikiLast"> &nbsp; </td>
<td align="right" class="foswikiTableCol2 foswikiLastCol foswikiLast"> In case of ZF measurements, there might be an entry like <code>ZF</code>. </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>
</tr> </tr>
</tbody></table> </tbody></table>
<p></p> <p></p>
<a name="BeamlineInfoRequired"></a> <span id="BeamlineInfoRequired"></span>
<h1><a name="A_9_61BeamlineInfo_61_Required"></a> 9 <code>BeamlineInfo</code> Required </h1> <h1 id="A_9_61BeamlineInfo_61_Required"> 9 <code>BeamlineInfo</code> Required </h1>
<p></p> <p></p>
Here only a single entry is required, namely Here only a single entry is required, namely
<p></p> <p></p>
<table class="foswikiTable" rules="none" border="1"> <table rules="none" class="foswikiTable" border="1">
<thead> <thead>
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<th class="foswikiTableCol0 foswikiFirstCol"> <a rel="nofollow" href="https://intranet.psi.ch/MUSR/MusrRoot?cover=print;sortcol=0;table=6;up=0#sorted_table" title="Sort by this column">Name</a> </th> <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>
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<td align="center" class="foswikiTableCol1 foswikiLast"> <code>TString</code> </td> <td style="text-align:center" class="foswikiTableCol1 foswikiLast"> <code>TString</code> </td>
<td class="foswikiTableCol2 foswikiLastCol foswikiLast"> name of the beamline, <em>e.g.</em> <code>piM3.2</code>. </td> <td class="foswikiTableCol2 foswikiLastCol foswikiLast"> name of the beamline, <em>e.g.</em> <code>piM3.2</code>. </td>
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<p></p> <p></p>
<h1><a name="A_10_Exhaustive_61MusrRoot_61_Tree_Including_Everything_Required"></a> 10 Exhaustive <code>MusrRoot</code> Tree Including Everything <em>Required</em> </h1> <h1 id="A_10_Exhaustive_61MusrRoot_61_Tree_Including_Everything_Required"> 10 Exhaustive <code>MusrRoot</code> Tree Including Everything <em>Required</em> </h1>
Here it is assumed that there are <em>hypothetical</em> <span class='foswikiRedFG'>red</span> / <span class='foswikiGreenFG'>green</span> data with electric field on/off and light on/off, and hence 4 data sets per detector, and 8 detectors of the instrument: <code>left/forward, top/forward, right/forward, bottom/forward, left/backward, top/backward, right/backward, bottom/backward</code>. To show the whole tree structure, it will be splitted in the representation afterwards, but keep in mind: this will be all part of a single <code>MusrRoot</code> file. I will add comments in the tree structure by the symbol <code>#</code>. Lets start with the &#956;SR data histograms: Here it is assumed that there are <em>hypothetical</em> <span class='foswikiRedFG'>red</span> / <span class='foswikiGreenFG'>green</span> data with electric field on/off and light on/off, and hence 4 data sets per detector, and 8 detectors of the instrument: <code>left/forward, top/forward, right/forward, bottom/forward, left/backward, top/backward, right/backward, bottom/backward</code>. To show the whole tree structure, it will be splitted in the representation afterwards, but keep in mind: this will be all part of a single <code>MusrRoot</code> file. I will add comments in the tree structure by the symbol <code>#</code>. Lets start with the &#956;SR data histograms:
<p></p> <p></p>
<pre> <pre>
@ -861,7 +901,7 @@ Next the whole <code>RunHeader</code>. Here the information will be grouped in d
<p></p> <p></p>
<pre> <pre>
RunInfo: RunInfo:
000 - Version: $Id: TMusrRunHeader.cpp 5092 2012-03-13 07:47:00Z nemu $ -&#64;0 000 - Version: &#36;Id: TMusrRunHeader.cpp 5092 2012-03-13 07:47:00Z nemu &#36; -&#64;0
001 - Generic Validator URL: http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd -&#64;0 001 - Generic Validator URL: http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRoot.xsd -&#64;0
002 - Specific Validator URL: http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd -&#64;0 002 - Specific Validator URL: http://lmu.web.psi.ch/facilities/software/MusrRoot/Validation/MusrRootLEM.xsd -&#64;0
003 - Generator: nemu&#95;analyzer -&#64;0 003 - Generator: nemu&#95;analyzer -&#64;0
@ -940,8 +980,8 @@ RunSummary:
<p></p> <p></p>
Comment: the last sub-tree <code>RunSummary</code> is not following <code>TMusrRunHeader</code> rule <code>&lt;number&gt; - &lt;label&gt;: &lt;value&gt; -@&lt;type&gt;</code>. It is added in the instrument analyzer directly by other means than the <code>TMusrRunHeader::Set</code> -method. This is no problem! Since <code>RunSummary</code> is not part of the <em>required</em> <code>MusrRoot</code> -file. One is quite free in adding any <code>ROOT</code> based information here. Comment: the last sub-tree <code>RunSummary</code> is not following <code>TMusrRunHeader</code> rule <code>&lt;number&gt; - &lt;label&gt;: &lt;value&gt; -@&lt;type&gt;</code>. It is added in the instrument analyzer directly by other means than the <code>TMusrRunHeader::Set</code> -method. This is no problem! Since <code>RunSummary</code> is not part of the <em>required</em> <code>MusrRoot</code> -file. One is quite free in adding any <code>ROOT</code> based information here.
<p></p> <p></p>
<a name="TMusrRunPhysicalQuantity"></a> <span id="TMusrRunPhysicalQuantity"></span>
<h1><a name="A_11_61TMusrRunPhysicalQuantity_61_45_Possible_Representations"></a> 11 <code>TMusrRunPhysicalQuantity</code> - Possible Representations </h1> <h1 id="A_11_61TMusrRunPhysicalQuantity_61_45_Possible_Representations"> 11 <code>TMusrRunPhysicalQuantity</code> - Possible Representations </h1>
A physical property can be described as A physical property can be described as
<p></p> <p></p>
<pre> <pre>
@ -953,7 +993,7 @@ where <code>&lt;property name&gt;</code> is the name of the quantity, <em>e.g.</
Note, not all of these quantities are always needed. The list of handled combination are given hereafter together with the C++ code snipped how to set it. It is assumed that <code>TMusrRunPhysicalQuantity prop;</code> is somewhere defined. Note, not all of these quantities are always needed. The list of handled combination are given hereafter together with the C++ code snipped how to set it. It is assumed that <code>TMusrRunPhysicalQuantity prop;</code> is somewhere defined.
<p></p> <p></p>
<pre> <pre>
&#60;property name&#62;: &#60;value&#62; &#60;unit&#62; &#91;; &#60;description&#62;] &#60;property name&#62;: &#60;value&#62; &#60;unit&#62; &#91;; &#60;description&#62;&#93;
</pre> </pre>
<p></p> <p></p>
Code snippet: Code snippet:
@ -976,7 +1016,7 @@ The number on front of the token (<em>e.g.</em> <code>011</code> in front of <co
<hr /> <hr />
<p></p> <p></p>
<pre> <pre>
&#60;property name&#62;: &#60;val&#62; +- &#60;err&#62; &#60;unit&#62;&#91;; &#60;description&#62;] &#60;property name&#62;: &#60;val&#62; +- &#60;err&#62; &#60;unit&#62;&#91;; &#60;description&#62;&#93;
</pre> </pre>
<p></p> <p></p>
Code snippet: Code snippet:
@ -993,7 +1033,7 @@ Result in the <code>RunHeader/SampleEnvironmentInfo</code>:
<hr /> <hr />
<p></p> <p></p>
<pre> <pre>
&#60;property name&#62;: &#60;val&#62; &#60;unit&#62;; SP: &#60;demand&#62;&#91;; &#60;description&#62;] &#60;property name&#62;: &#60;val&#62; &#60;unit&#62;; SP: &#60;demand&#62;&#91;; &#60;description&#62;&#93;
</pre> </pre>
<p></p> <p></p>
Code snippet: Code snippet:
@ -1028,90 +1068,63 @@ Result in the <code>RunHeader/SampleEnvironmentInfo</code>:
017 - Sample Magnetic Field: 350.002 +- 0.005 G; SP: 350.0; WXY -&#64;3 017 - Sample Magnetic Field: 350.002 +- 0.005 G; SP: 350.0; WXY -&#64;3
</pre> </pre>
<p></p> <p></p>
-- <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a> - 29 March 2012 </div> -- <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a> - 29 March 2012</div>
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<p></p> <div class="patternContent"><div class="foswikiTopic"> <h1 id="Quickstart_for_61_61WKM_61_61_users"> Quickstart for <code><b>WKM</b></code> users </h1>
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</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="Quickstart_for_61_61WKM_61_61_users"></a> Quickstart for <code><b>WKM</b></code> users </h1>
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<li> <a href="QuickStart.html#Quickstart_for_61_61WKM_61_61_users"> Quickstart for WKM users </a> <ul> <li> <a href="QuickStart.html#Quickstart_for_61_61WKM_61_61_users"> Quickstart for WKM users </a> <ul>
<li> <a href="QuickStart.html#Introduction"> Introduction </a> <li> <a href="QuickStart.html#Introduction"> Introduction </a>
</li> <li> <a href="QuickStart.html#Differences_between_61WKM_61_and_61musrfit_61_msr_files"> Differences between WKM and musrfit msr files </a> </li> <li> <a href="QuickStart.html#Differences_between_61WKM_61_and_61musrfit_61_msr_files"> Differences between WKM and musrfit msr files </a>
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</li></ul> </li></ul>
</li></ul> </li></ul>
</div> </div>
<h2><a name="Introduction"></a> Introduction </h2> <h2 id="Introduction"> Introduction </h2>
<p></p> <p></p>
<code>musrfit</code> is a program suite for analyzing &mu;SR data. It is implemented in <code>C++/<a href="http://root.cern.ch/" target="_top">ROOT</a></code> and uses the <a href="http://www.cern.ch/minuit/" target="_top">MINUIT2</a> libraries developed at <a href="http://www.cern.ch/" target="_top">CERN</a> for fitting data. <code>musrfit</code> is a program suite for analyzing &mu;SR data. It is implemented in <code>C++/<a href="http://root.cern.ch/">ROOT</a></code> and uses the <a href="http://www.cern.ch/minuit/">MINUIT2</a> libraries developed at <a href="http://www.cern.ch/">CERN</a> for fitting data.
Installation instructions for Linux, MS Windows, and Mac OS X can be found <a href="MusrFitSetup.html">here</a>. The full user manual is available <a href="MusrFit.html">here</a>.<br> Installation instructions for Linux, MS Windows, and Mac OS X can be found <a href="MusrFitSetup.html">here</a>. The full user manual is available <a href="MusrFit.html">here</a>.<br>
In principle the programs can be used in the same fashion as <code>WKM</code> (<code>wkmfit, wkmview</code>). In principle the programs can be used in the same fashion as <code>WKM</code> (<code>wkmfit, wkmview</code>).
E.g., for fitting data as defined in the input file <code><b>8472.msr</b></code> one types:<pre>musrfit 8472.msr</pre> for plotting data and the corresponding E.g., for fitting data as defined in the input file <code><b>8472.msr</b></code> one types:<pre>musrfit 8472.msr</pre> for plotting data and the corresponding
fit one calls:<pre>musrview 8472.msr</pre> fit one calls:<pre>musrview 8472.msr</pre>
Additionally, there are editors called <code><a href="MusrGui.html">musrgui/musredit</a></code> available which can do everything the <code>emacs</code> plug-in for <code>WKM</code> is capable of and even more. <strong><span class='foswikiRedFG'>However, before going to use only <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read at least this "Quickstart" since there are a few differences between the programs as well as new features which are partially described in the following.</span></strong> Additionally, there are editors called <code><a href="MusrGui.html">musrgui/musredit</a></code> available which can do everything the <code>emacs</code> plug-in for <code>WKM</code> is capable of and even more. <strong><span class='foswikiRedFG'>However, before going to use only <code>musrgui</code> / <code>musredit</code> it is strongly recommended to read at least this "Quickstart" since there are a few differences between the programs as well as new features which are partially described in the following.</span></strong>
<p></p> <p></p>
<h2><a name="Differences_between_61WKM_61_and_61musrfit_61_msr_files"></a> Differences between <code>WKM</code> and <code>musrfit</code> msr files </h2> <h2 id="Differences_between_61WKM_61_and_61musrfit_61_msr_files"> Differences between <code>WKM</code> and <code>musrfit</code> msr files </h2>
<p></p> <p></p>
The msr file format of <code>WKM</code> has some weaknesses and has therefore been extended for the use with <code>musrfit</code>. Existing <code>WKM</code> files can be converted using the <a href="MusrFit.html#Msr2Msr">small utility</a> <code>msr2msr</code>. The changes are: <ul> The msr file format of <code>WKM</code> has some weaknesses and has therefore been extended for the use with <code>musrfit</code>. Existing <code>WKM</code> files can be converted using the <a href="MusrFit.html#Msr2Msr">small utility</a> <code>msr2msr</code>. The changes are: <ul>
<li> The <code>musrfit</code> msr and mlog files contain an additional column in the FITPARAMETER block for the representation of positive uncertainties if <code>MINOS</code> was called during fitting. In that case the <strong>Step</strong> column holds the negative uncertainties. If there has not been performed an error analysis using <code>MINOS</code>, the symmetric error can be found in the <strong>Step</strong> column, whereas the <strong>Pos_Error</strong> column contains only <strong>none</strong> entries. The beginning of the FITPARAMETER block then might look like this <pre> <li> The <code>musrfit</code> msr and mlog files contain an additional column in the FITPARAMETER block for the representation of positive uncertainties if <code>MINOS</code> was called during fitting. In that case the <strong>Step</strong> column holds the negative uncertainties. If there has not been performed an error analysis using <code>MINOS</code>, the symmetric error can be found in the <strong>Step</strong> column, whereas the <strong>Pos_Error</strong> column contains only <strong>none</strong> entries. The beginning of the FITPARAMETER block then might look like this <pre>
@ -172,7 +174,7 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP (name beamline institute dat
</li> <li> The commands <strong>SET BATCH</strong> and <strong>END RETURN</strong> may be omitted in the COMMANDS block. </li> <li> The commands <strong>SET BATCH</strong> and <strong>END RETURN</strong> may be omitted in the COMMANDS block.
</li></ul> </li></ul>
<p></p> <p></p>
<h2><a name="Selected_new_features_in_61musrfit_61"></a> Selected new features in <code>musrfit</code> </h2> <ul> <h2 id="Selected_new_features_in_61musrfit_61"> Selected new features in <code>musrfit</code> </h2> <ul>
<li> If single-histogram fits are done, the normalization and background constants are given either "per nanosecond" or "per rebinned bin". The nanosecond normalization allows to change the binning without the need of re-doing the fit to the data. <li> If single-histogram fits are done, the normalization and background constants are given either "per nanosecond" or "per rebinned bin". The nanosecond normalization allows to change the binning without the need of re-doing the fit to the data.
</li> <li> The use of functions in the RUN block is now possible for the normalization parameter, e.g. for the definition of an &alpha; parameter in simultaneous single-histogram fits of two histograms. </li> <li> The use of functions in the RUN block is now possible for the normalization parameter, e.g. for the definition of an &alpha; parameter in simultaneous single-histogram fits of two histograms.
</li> <li> Apart from the default &chi;<sup>2</sup> minimization, when doing single-histogram fits (fit type <strong>0</strong>) in <code>musrfit</code> there is also the possibility to do a log-likelihood maximization instead. For switching, just put <strong>MAX_LIKELIHOOD</strong> in the COMMANDS block. </li> <li> Apart from the default &chi;<sup>2</sup> minimization, when doing single-histogram fits (fit type <strong>0</strong>) in <code>musrfit</code> there is also the possibility to do a log-likelihood maximization instead. For switching, just put <strong>MAX_LIKELIHOOD</strong> in the COMMANDS block.
@ -202,7 +204,7 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP (name beamline institute dat
<li> <strong>gamma_mu</strong> = &gamma;<sub>&mu;</sub>/2&pi; = 0.0135538817 MHz/G <li> <strong>gamma_mu</strong> = &gamma;<sub>&mu;</sub>/2&pi; = 0.0135538817 MHz/G
</li> <li> <strong>pi</strong> = &pi; = 3.14159265358979323846 </li> <li> <strong>pi</strong> = &pi; = 3.14159265358979323846
</li></ul> </li></ul>
</li> <li> As theory function also the so called skewed Gaussian can be chosen. The properties of this function are summarized in <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf" target="_top">a memo</a> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/pdf.png" width="16" height="16" alt="pdf" /></span>. The function is called in the THEORY block as follows: <pre> </li> <li> As theory function also the so called skewed Gaussian can be chosen. The properties of this function are summarized in <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf">a memo</a> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/pdf.png' width='16' height='16' alt='pdf' /></span>. The function is called in the THEORY block as follows: <pre>
skewedGss 1 2 3 4 (phase frequency rate&#95;m rate&#95;p) skewedGss 1 2 3 4 (phase frequency rate&#95;m rate&#95;p)
</pre> </pre>
</li> <li> After fitting it is possible to keep the <code>MINUIT2</code> output including the correlation matrix of the parameters. Calling <code>musrfit</code> with the <strong>--keep-mn2-ouput</strong> or <strong>-k</strong> option will provide you an ASCII and a ROOT file with the complete output, e.g. <pre>musrfit 8472.msr --keep-mn2-ouput</pre> generates <code><b>8472-mn2.output</b></code> and <code><b>8472-mn2.root</b></code> (and of course <code><b>8472.mlog</b></code>). </li> <li> After fitting it is possible to keep the <code>MINUIT2</code> output including the correlation matrix of the parameters. Calling <code>musrfit</code> with the <strong>--keep-mn2-ouput</strong> or <strong>-k</strong> option will provide you an ASCII and a ROOT file with the complete output, e.g. <pre>musrfit 8472.msr --keep-mn2-ouput</pre> generates <code><b>8472-mn2.output</b></code> and <code><b>8472-mn2.root</b></code> (and of course <code><b>8472.mlog</b></code>).
@ -260,78 +262,29 @@ RUN 2008/lem08&#95;his&#95;8472 MUE4 PSI ROOT-NPP (name beamline institute dat
</pre> In the above example <code>musrfit</code> reads the data from the file <code><b>superconductor-data.db</b></code>; the <i>x</i> and <i>y</i> data are specified by the <strong>DB</strong> parameter names <code><b>range</b></code> and <code><b>field</b></code>. An alternative specification of the <i>x</i> and <i>y</i> data by the parameter number in the <strong>DB</strong> file is also possible! </pre> In the above example <code>musrfit</code> reads the data from the file <code><b>superconductor-data.db</b></code>; the <i>x</i> and <i>y</i> data are specified by the <strong>DB</strong> parameter names <code><b>range</b></code> and <code><b>field</b></code>. An alternative specification of the <i>x</i> and <i>y</i> data by the parameter number in the <strong>DB</strong> file is also possible!
</li></ul> </li></ul>
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<p></p> <div class="patternContent"><div class="foswikiTopic"> <h1 id="A_61_61musrfit_61_61_Single_45Histogram_45Fit_Tutorial"> <code><b>musrfit</b></code> Single-Histogram-Fit Tutorial </h1>
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</div><div class="patternContent"><div class="foswikiTopic"><h1><a name="A_61_61musrfit_61_61_Single_45Histogram_45Fit_Tutorial"></a> <code><b>musrfit</b></code> Single-Histogram-Fit Tutorial </h1>
<p></p> <p></p>
The &mu;SR-data-analysis process using <code>musrfit</code> is based on so-called <code>msr</code> files. These files contain all information needed for the analysis such as names of the data files, a theory function, fit and plot parameters, and so on. It is the idea of this page to explain the basic use of an <code>msr</code> file and the different programs of the <code>musrfit</code> suite using the example of a single-histogram fit to time-differential transverse-field &mu;SR data. For a complete description of all options please refer to the <a href="MusrFit.html">manual</a>. The &mu;SR-data-analysis process using <code>musrfit</code> is based on so-called <code>msr</code> files. These files contain all information needed for the analysis such as names of the data files, a theory function, fit and plot parameters, and so on. It is the idea of this page to explain the basic use of an <code>msr</code> file and the different programs of the <code>musrfit</code> suite using the example of a single-histogram fit to time-differential transverse-field &mu;SR data. For a complete description of all options please refer to the <a href="MusrFit.html">manual</a>.
<p></p> <p></p>
The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html" target="_top">GPS spectrometer</a> at <a href="http://www.psi.ch/" target="_top">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50&#176; up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110. The example deals with a diamagnetic sample that has been measured in an applied field of approximately 150 G in the <a href="http://lmu.web.psi.ch/facilities/gps/gps.html">GPS spectrometer</a> at <a href="http://www.psi.ch/">PSI</a> using the "transverse geometry". In this geometry the muon spin is rotated about 50&#176; up and the field is applied parallel to the muon momentum. Hence, the relevant positron counters (to detect the spin precession) are placed above (histogram 3), below (histogram 4) and right of (histogram 5) the sample. The run numbers start from 3110.
<p></p> <p></p>
To analyze these data (in a simple way) one starts out from the <code>msr</code> file <strong>3110_tutorial.msr</strong> provided together with the source-code distribution in the sub-directory <strong>doc/examples/</strong>. This ASCII file can be edited using any text editor. For convenience the editors <code>musredit</code>/<code>musrgui</code> are provided which offer some <code>msr</code>-file-specific functionalities and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is open within <code>musredit</code>. To analyze these data (in a simple way) one starts out from the <code>msr</code> file <strong>3110_tutorial.msr</strong> provided together with the source-code distribution in the sub-directory <strong>doc/examples/</strong>. This ASCII file can be edited using any text editor. For convenience the editors <code>musredit</code>/<code>musrgui</code> are provided which offer some <code>msr</code>-file-specific functionalities and additionally serve as front ends to the underlying programs. In the following it is assumed that the file is open within <code>musredit</code>.
<p></p> <p></p>
<h1><a name="A_1_The_61msr_61_file"></a> 1 The <code>msr</code> file </h1> <h1 id="A_1_The_61msr_61_file"> 1 The <code>msr</code> file </h1>
<p></p> <p></p>
The <code>msr</code> file itself is divided into different blocks&mdash;a full description of the format can be found <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">here</a>. The <code>msr</code> file itself is divided into different blocks&mdash;a full description of the format can be found <a href="MusrFit.html#DescriptionOfTheMsrFileFormat">here</a>.
In the file <strong>3110_tutorial.msr</strong> these blocks are successively: <ul> In the file <strong>3110_tutorial.msr</strong> these blocks are successively: <ul>
@ -232,129 +269,138 @@ STATISTIC --- 2011-07-09 10:58:44
</pre> This block is the last block of a <code>msr</code> file. It contains some information on the fit: the date and time as well as the absolute and normalized values of &#967;<sup>2</sup> and the number of degrees of freedom in the fit.<br> These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged! </pre> This block is the last block of a <code>msr</code> file. It contains some information on the fit: the date and time as well as the absolute and normalized values of &#967;<sup>2</sup> and the number of degrees of freedom in the fit.<br> These information only have a meaning if the fitting procedure has been executed at least once and the fit has converged!
</li></ul> </li></ul>
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<h1><a name="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"></a> 2 Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1> <h1 id="A_2_Determine_t0_and_the_data_range_using_61musrt0_61"> 2 Determine <i>t</i><sub>0</sub> and the data range using <code>musrt0</code> </h1>
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 /> 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 src="../pub/MUSR/TutorialSingleHisto/musrt0-1.png" alt="musrt0-1" align="center" /><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 /> 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 src="../pub/MUSR/TutorialSingleHisto/musrt0-2.png" alt="musrt0-2" width='708' height='529' align="center" /><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 />
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. 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>. A full description of <code>musrt0</code> can be found <a href="MusrFit.html#MusrT0">here</a>.
<p></p> <p></p>
<h1><a name="A_3_Fit_the_model_to_the_data_using_61musrfit_61"></a> 3 Fit the model to the data using <code>musrfit</code> </h1> <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 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> 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>
<p></p> <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. 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> <p></p>
<h1><a name="A_4_View_the_data_and_the_fit_using_61musrview_61"></a> 4 View the data and the fit using <code>musrview</code> </h1> <h1 id="A_4_View_the_data_and_the_fit_using_61musrview_61"> 4 View the data and the fit using <code>musrview</code> </h1>
The data and the corresponding fit can be visualized by choosing <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> in <code>musredit</code> or calling from a terminal <pre>musrview 3110&#95;tutorial.msr</pre> This creates the windows according to the given PLOT blocks in the <code>msr</code> file:<br /> The data and the corresponding fit can be visualized by choosing <img alt="musrview.png" src="../pub/MUSR/MusrGui/musrview.png" /> in <code>musredit</code> or calling from a terminal <pre>musrview 3110&#95;tutorial.msr</pre> This creates the windows according to the given PLOT blocks in the <code>msr</code> file:<br />
<img src="../pub/MUSR/TutorialSingleHisto/musrview-1.png" alt="musrview-1" align="center" /><br /> <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-1.png' alt='musrview-1' title='musrview-1.png' width='808' height='629' style='' /><br />
<img src="../pub/MUSR/TutorialSingleHisto/musrview-2.png" alt="musrview-2" align="center" /><br /> <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-2.png' alt='musrview-2' title='musrview-2.png' width='808' height='629' style='' /><br />
The basic features of <code>musrview</code> can be found in the Musrfit menu. They include: <ul> The basic features of <code>musrview</code> can be found in the Musrfit menu. They include: <ul>
<li> export the shown data and the model to an ASCII file with comma-separated values <li> export the shown data and the model to an ASCII file with comma-separated values
</li> <li> presenting the difference between the shown data and the model (keyboard shortcut: <strong>d</strong>) </li> <li> presenting the difference between the shown data and the model (keyboard shortcut: <strong>d</strong>)
</li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br /> <img src="../pub/MUSR/TutorialSingleHisto/musrview-3.png" alt="musrview-3" align="center" /><br /> </li> <li> calculate and show the Fourier transform of the shown data (keyboard shortcut: <strong>f</strong>), e.g. for the asymmetry of the "Up" and "Down" detectors:<br /> <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/musrview-3.png' alt='musrview-3' title='musrview-3.png' width='808' height='629' style='' /><br />
</li></ul> </li></ul>
<p></p> <p></p>
<h1><a name="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"></a> 5 Process multiple <code>msr</code> files using <code>msr2data</code> </h1> <h1 id="A_5_Process_multiple_61msr_61_files_using_61msr2data_61"> 5 Process multiple <code>msr</code> files using <code>msr2data</code> </h1>
This short introduction is concluded by calling attention to the program <code><a href="Msr2Data.html">msr2data</a></code>. As the name indicates the main purpose of this program is to extract the FITPARAMETER-block information from multiple <code>msr</code> files with the same structure and to summarize them in a single ASCII file (either in TRIUMF DB format or simple columns). However, as described in detail in the <code><a href="Msr2Data.html">manual</a></code>, it is not only possible to collect data from <code>msr</code> files but also to create new <code>msr</code> files from a template and to process these files using <code>musrfit</code> on the fly.<br> This short introduction is concluded by calling attention to the program <code><a href="Msr2Data.html">msr2data</a></code>. As the name indicates the main purpose of this program is to extract the FITPARAMETER-block information from multiple <code>msr</code> files with the same structure and to summarize them in a single ASCII file (either in TRIUMF DB format or simple columns). However, as described in detail in the <code><a href="Msr2Data.html">manual</a></code>, it is not only possible to collect data from <code>msr</code> files but also to create new <code>msr</code> files from a template and to process these files using <code>musrfit</code> on the fly.<br>
Assuming the successive runs <strong>3111</strong> through <strong>3114</strong> can be analyzed using the same model introduced above for run <strong>3110</strong> (e.g. in the case one has done measurements at different temperatures) one can use the file <strong>3110_tutorial.msr</strong> as template, generate the files <strong>3111_tutorial.msr</strong> through <strong>3114_tutorial.msr</strong> with the corresponding updates in the RUN blocks, call for each one <code>musrfit</code> and finally summarize the FITPARAMETER-block information of all processed files in an ASCII output file <strong>tutorial-T-dependence.dat</strong> (simple columns). If further information on the temperature or the applied field is available in the data files these will be included as well in the resulting ASCII file.<br> Assuming the successive runs <strong>3111</strong> through <strong>3114</strong> can be analyzed using the same model introduced above for run <strong>3110</strong> (e.g. in the case one has done measurements at different temperatures) one can use the file <strong>3110_tutorial.msr</strong> as template, generate the files <strong>3111_tutorial.msr</strong> through <strong>3114_tutorial.msr</strong> with the corresponding updates in the RUN blocks, call for each one <code>musrfit</code> and finally summarize the FITPARAMETER-block information of all processed files in an ASCII output file <strong>tutorial-T-dependence.dat</strong> (simple columns). If further information on the temperature or the applied field is available in the data files these will be included as well in the resulting ASCII file.<br>
From the terminal this would be done as follows:<pre> From the terminal this would be done as follows:<pre>
msr2data 3110 3114 &#95;tutorial fit-3110 -o tutorial-T-dependence.dat data msr2data 3110 3114 &#95;tutorial fit-3110 -o tutorial-T-dependence.dat data
</pre> </pre>
To achieve the same in <code>musredit</code> one selects <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> and fills the form accordingly:<br /> To achieve the same in <code>musredit</code> one selects <img alt="musrmsr2data.png" src="../pub/MUSR/MusrGui/musrmsr2data.png" /> and fills the form accordingly:<br />
<img src="../pub/MUSR/TutorialSingleHisto/msr2data.png" alt="msr2data" align="center" /> <img class='imagePlain imagePlain_center ' src='../pub/MUSR/TutorialSingleHisto/msr2data.png' alt='msr2data' title='msr2data.png' width='612' height='605' style='' />
<p></p> <p></p>
<h1><a name="A_6_Further_reading"></a> 6 Further reading </h1> <h1 id="A_6_Further_reading"> 6 Further reading </h1>
This page only summarizes the very basic features and options of the programs contained in the <code>musrfit</code> suite. For a complete description please refer to the manuals of <ul> This page only summarizes the very basic features and options of the programs contained in the <code>musrfit</code> suite. For a complete description please refer to the manuals of <ul>
<li> <code><a href="MusrFit.html">musrfit</a></code> (including <code><a href="MusrFit.html#MusrFit">musrfit</a></code>, <code><a href="MusrFit.html#MusrView">musrview</a></code>, <code><a href="MusrFit.html#MusrT0">musrt0</a></code> and the full description of the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat"><code>msr</code>-file format</a>) <li> <code><a href="MusrFit.html">musrfit</a></code> (including <code><a href="MusrFit.html#MusrFit">musrfit</a></code>, <code><a href="MusrFit.html#MusrView">musrview</a></code>, <code><a href="MusrFit.html#MusrT0">musrt0</a></code> and the full description of the <a href="MusrFit.html#DescriptionOfTheMsrFileFormat"><code>msr</code>-file format</a>)
</li> <li> <code><a href="MusrGui.html">musredit</a></code> </li> <li> <code><a href="MusrGui.html">musredit</a></code>
</li> <li> <code><a href="Msr2Data.html">msr2data</a></code>. </li> <li> <code><a href="Msr2Data.html">msr2data</a></code>.
</li></ul> </li></ul>
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<div class="patternContent"><div class="foswikiTopic"> <h1 id="Welcome_to_the_MUSR_web"> Welcome to the MUSR web </h1>
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<p></p> <h2 id="Documentation_of_the_SR_data_analysis_suite_61musrfit_61"> Documentation of the &#956;SR data analysis suite <code>musrfit</code> </h2> <ul>
<li> <a href="CiteMusrFit.html">How to cite <code>musrfit</code>? <img class='smily' src='../pub/Main/SmiliesPluginPSI_/yes.gif' alt='yes' title='yes' /> </a>
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<h2><a name="Documentation_of_the_SR_data_analysis_suite_61musrfit_61"></a> Documentation of the &#956;SR data analysis suite <code>musrfit</code> </h2> <ul>
<li> <a href="CiteMusrFit.html">How to cite <code>musrfit</code>? <img src="../pub/Main/SmiliesPluginPSI/yes.gif" alt="yes" title="yes" border="0" /> </a>
</li> <li> <a href="TutorialSingleHisto.html">Single-histogram-fit tutorial for <code>musrfit</code> introducing the basic features of the programs and <code>msr</code> files</a> </li> <li> <a href="TutorialSingleHisto.html">Single-histogram-fit tutorial for <code>musrfit</code> introducing the basic features of the programs and <code>msr</code> files</a>
</li> <li> <a href="MusrFit.html">User manual of the &#956;SR data analysis software <code>musrfit</code> </a> </li> <li> <a href="MusrFit.html">User manual of the &#956;SR data analysis software <code>musrfit</code> </a>
</li> <li> <a href="MusrFitSetup.html">Setting up <code>musrfit</code> on Different Platforms</a> </li> <li> <a href="MusrFitSetup.html">Setting up <code>musrfit</code> on Different Platforms</a>
@ -136,78 +138,29 @@ pre {
</li> <li> <a href="MusrFitAcknowledgements.html">Acknowledgements</a> </li> <li> <a href="MusrFitAcknowledgements.html">Acknowledgements</a>
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</div>
<p></p> <p></p>
<p></p> <p></p>
<b>PSI Webs</b> <ul>
<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebHome">Main</a>
</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/psi.png" width="16" height="16" alt="psi" /></span> <a href="https://intranet.psi.ch/Main/WebList">weitere Webs</a>
</li></ul>
<hr />
<b>System Webs</b> <ul>
<li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/Sandbox/WebHome">Sandbox</a>
</li> <li> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/foswiki.png" width="16" height="16" alt="foswiki" /></span> <a href="https://intranet.psi.ch/System/WebHome">Documentation</a>
</li></ul>
<hr /> <ul>
<li> <a href="https://intranet.psi.ch/MUSR/WebCreateNewTopic?parent=WebHome" target="_top"><span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/newtopic.png" width="16" height="16" alt="newtopic" /></span> Create New Topic</a>
</li> <li> <a href="WebTopicList.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/index.png" width="16" height="16" alt="index" /></span> Show All Topics</a>
</li> <li> <a href="WebSearch.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/searchtopic.png" width="16" height="16" alt="searchtopic" /></span> Search in Topics</a>
</li> <li> <a href="https://intranet.psi.ch/search/#?fq=%20-web_search:Applications%26fq%3D%7B!tag%3Dweb%20q.op%3DOR%7Dweb:(MUSR)&amp;sort=date%20desc"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/changes.png" width="16" height="16" alt="changes" /></span> Recent Changes</a>
</li> <li> <a href="WebNotify.html"> <span class="foswikiIcon"><img src="../pub/System/DocumentGraphics/notify.png" width="16" height="16" alt="notify" /></span> Define Notifications</a>
</li></ul>
<p></p>
</div></div>
</div> </div>
<div class="clear">&nbsp;</div> <div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>WebHome <br />
</div></div><div id="patternTopBar"> Topic revision: <span class='patternRevInfo'>19 Jan 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
<div id="patternTopBarContentsWrapper">
<div id="patternTopBarContents"><table border="0" cellpadding="0" cellspacing="0" style="width:100%" summary="">
<tr><td valign="middle"><span id="foswikiLogo" class="foswikiImage"><a href="WebHome.html"><img src="../pub/Main/WebPreferences/psi_logo_150.gif" border="0" alt="Paul Scherrer Institut" style="border:none; margin: -8px 0 0 15px;" /></a></span></td>
<td align="right" valign="top" class="patternMetaMenu" id="psimetanav">
<p></p> <ul>
<p></p>
</td></tr></table>
</div><!--/patternTopBarContents-->
</div><!--/patternTopBarContentsWrapper-->
</div><!-- /patternTopBar--><div id="patternBottomBar"><div id="patternBottomBarContents"><div id="patternWebBottomBar">Ideas, requests, problems regarding <a href="https://intranet.psi.ch/Main/WebHome">PSI Wiki</a>? <a href="mailto&#58;psi&#46;intranet&#64;psi&#46;ch&#63;subject&#61;PSI&#32;Wiki&#37;20Feedback&#37;20on&#37;20MUSR&#46;WebHome">Send feedback</a></div></div></div>
</div> </div>
</div> </div>
</div> </div>
</div></body> </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>
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<p></p> <p></p>
<p></p> <!-- Piwik -->
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2
doc/html/user/pub/System/PatternSkin/print.css
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@ -1 +1 @@
body{margin:0;padding:0;}#patternScreen, #patternPageShadow, #patternPage, #patternOuter{margin:0;padding:0;top:0;border:none;float:none;}#patternMain{width:100%;float:none;display:inline;overflow:visible;}#patternSideBar{display:none;}#patternWrapper{height:1%;}#patternTopBar, #patternClearHeaderCenter, #patternClearHeaderLeft, #patternClearHeaderRight, #patternTopBarContentsOuter{display:none;}.patternTopicAction, .patternToolBar, .patternToolBarBottom, .patternHomePath img, .patternHomePathTitle, .foswikiActionFormStepSign{display:none;}#patternMainContents{margin:0;padding:1em 2em;}#patternBottomBar{border:none;}.patternTopicFooter{margin:1em 0 0 0;}#attachmentsshow, #attachmentshide{display:none;}pre, html>body pre{overflow:visible !important;}h1, h2, h3, h4, h5, h6{page-break-after:avoid;page-break-inside:avoid;}img{page-break-inside:avoid;page-break-after:avoid;}blockquote, table, pre{page-break-inside:avoid;}ul, ol, dl{page-break-before:avoid;}.commentPlugin{display:none;}.twistyTrigger{display:none;}.editTableEditImageButton{display:none;}html body{background-color:#fff;}h2, h3, h4, h5, h6{background-color:transparent;}#patternBottomBar{background-color:transparent;}pre, code, tt{color:#5b4221;}.foswikiTable th{border-style:solid;border-width:0 0 1px 1px;border-color:#ccc;color:#000;}.foswikiTable th a:link, .foswikiTable th a:visited, .foswikiTable th a font, .foswikiAttachments .foswikiTable th a:link, .foswikiAttachments .foswikiTable th a:visited, .foswikiAttachments .foswikiTable th a font{color:#000;text-decoration:none;}:visited, .foswikiTopic a:visited{color:#06c;background-color:transparent;}.foswikiAttachments, .patternContent .foswikiAttachments, .foswikiForm, .patternContent .foswikiForm{background-color:#fff;}.patternRevInfo, .foswikiGrayText{color:#666;}.patternRevInfo a:link, .patternRevInfo a:visited .foswikiGrayText a:link, .foswikiGrayText a:visited{color:#666;}@media print{body{margin:0;padding:0;}#patternScreen, #patternPageShadow, #patternPage, #patternOuter{margin:0;padding:0;top:0;border:none;float:none;}#patternMain{width:100%;float:none;display:inline;overflow:visible;}#patternSideBar{display:none;}#patternWrapper{height:1%;}#patternTopBar, #patternClearHeaderCenter, #patternClearHeaderLeft, #patternClearHeaderRight, #patternTopBarContentsOuter{display:none;}.patternTopicAction, .patternToolBar, .patternToolBarBottom, .patternHomePath img, .patternHomePathTitle, .foswikiActionFormStepSign{display:none;}#patternMainContents{margin:0;padding:1em 2em;}#patternBottomBar{border:none;}.patternTopicFooter{margin:1em 0 0 0;}#attachmentsshow, #attachmentshide{display:none;}pre, html>body pre{overflow:visible !important;}h1, h2, h3, h4, h5, h6{page-break-after:avoid;page-break-inside:avoid;}img{page-break-inside:avoid;page-break-after:avoid;}blockquote, table, pre{page-break-inside:avoid;}ul, ol, dl{page-break-before:avoid;}.commentPlugin{display:none;}.twistyTrigger{display:none;}.editTableEditImageButton{display:none;}html body{background-color:#fff;}h2, h3, h4, h5, h6{background-color:transparent;}#patternBottomBar{background-color:transparent;}pre, code, tt{color:#5b4221;}.foswikiTable th{border-style:solid;border-width:0 0 1px 1px;border-color:#ccc;color:#000;}.foswikiTable th a:link, .foswikiTable th a:visited, .foswikiTable th a font, .foswikiAttachments .foswikiTable th a:link, .foswikiAttachments .foswikiTable th a:visited, .foswikiAttachments .foswikiTable th a font{color:#000;text-decoration:none;}:visited, .foswikiTopic a:visited{color:#06c;background-color:transparent;}.foswikiAttachments, .patternContent .foswikiAttachments, .foswikiForm, .patternContent .foswikiForm{background-color:#fff;}.patternRevInfo, .foswikiGrayText{color:#666;}.patternRevInfo a:link, .patternRevInfo a:visited .foswikiGrayText a:link, .foswikiGrayText a:visited{color:#666;}} #peopleIcon {display: none;} #tooltip {display: none;} .ecpHeading img {display: none;} .foswikiTopicInfo { border-bottom: 0; } #patternBottomBar, .patternTopicActions, .foswikiFormSteps { display:none; } .foswikiTopicInfo {margin-top: 50px;} .foswikiTopicInfo h1 a {text-decoration:none;} h1 a:visited { color: #D1400E; }html{overflow:visible} body{margin:0;padding:0}#patternScreen,#patternPageShadow,#patternPage,.patternViewPage #patternOuter{margin:0;padding:0;top:0;border:0;float:none}#patternMain{width:auto;float:none;display:inline;overflow:visible}#patternSideBar{display:none}#patternWrapper{height:1%}#patternTopBarButtons,#patternTopBar,#patternClearHeaderCenter,#patternClearHeaderLeft,#patternClearHeaderRight,#patternTopBarContentsOuter{display:none}.patternTop,.patternTopicAction,.patternTopicActions,.patternToolBar,.patternToolBarBottom,.patternHomePath img,.patternHomePathTitle,.foswikiContentFooter+.foswikiFormSteps,.foswikiActionFormStepSign{display:none}#patternMainContents{margin:0;padding:1em 2em}#patternBottomBar{display:none}.patternTopicFooter{margin:1em 0 0 0}#attachmentsshow,#attachmentshide{display:none}pre,html>body pre{overflow:visible!important}h1,h2,h3,h4,h5,h6{page-break-after:avoid;page-break-inside:avoid}img{page-break-inside:avoid;page-break-after:avoid}blockquote,table,pre{page-break-inside:avoid}ul,ol,dl{page-break-before:avoid}.commentPlugin{display:none}.twistyTrigger{display:none}.editTableEditImageButton{display:none}html body{background-color:#fff}h2,h3,h4,h5,h6{background-color:transparent}#patternBottomBar{background-color:transparent}pre,code,tt{color:#5b4221}.foswikiTable th{border-style:solid;border-width:0 0 1px 1px;border-color:#ccc;color:#000}.foswikiTable th a:link,.foswikiTable th a:visited,.foswikiTable th a font,.foswikiAttachments .foswikiTable th a:link,.foswikiAttachments .foswikiTable th a:visited,.foswikiAttachments .foswikiTable th a font{color:#000;text-decoration:none}:visited,.foswikiTopic a:visited{color:#06c;background-color:transparent}.foswikiAttachments,.patternContent .foswikiAttachments,.foswikiForm,.patternContent .foswikiForm{background-color:#fff}.patternRevInfo,.foswikiGrayText{color:#666}.patternRevInfo a:link,.patternRevInfo a:visited .foswikiGrayText a:link,.foswikiGrayText a:visited{color:#666}@media print{body{margin:0;padding:0}#patternScreen,#patternPageShadow,#patternPage,#patternOuter{margin:0;padding:0;top:0;border:0;float:none}#patternMain{width:100%;float:none;display:inline;overflow:visible}#patternSideBar{display:none}#patternWrapper{height:1%}#patternTopBar,#patternClearHeaderCenter,#patternClearHeaderLeft,#patternClearHeaderRight,#patternTopBarContentsOuter{display:none}.patternTopicAction,.patternToolBar,.patternToolBarBottom,.patternHomePath img,.patternHomePathTitle,.foswikiActionFormStepSign{display:none}#patternMainContents{margin:0;padding:1em 2em}#patternBottomBar{border:0}.patternTopicFooter{margin:1em 0 0 0}#attachmentsshow,#attachmentshide{display:none}pre,html>body pre{overflow:visible!important}h1,h2,h3,h4,h5,h6{page-break-after:avoid;page-break-inside:avoid}img{page-break-inside:avoid;page-break-after:avoid}blockquote,table,pre{page-break-inside:avoid}ul,ol,dl{page-break-before:avoid}.commentPlugin{display:none}.twistyTrigger{display:none}.editTableEditImageButton{display:none}html body{background-color:#fff}h2,h3,h4,h5,h6{background-color:transparent}#patternBottomBar{background-color:transparent}pre,code,tt{color:#5b4221}.foswikiTable th{border-style:solid;border-width:0 0 1px 1px;border-color:#ccc;color:#000}.foswikiTable th a:link,.foswikiTable th a:visited,.foswikiTable th a font,.foswikiAttachments .foswikiTable th a:link,.foswikiAttachments .foswikiTable th a:visited,.foswikiAttachments .foswikiTable th a font{color:#000;text-decoration:none}:visited,.foswikiTopic a:visited{color:#06c;background-color:transparent}.foswikiAttachments,.patternContent .foswikiAttachments,.foswikiForm,.patternContent .foswikiForm{background-color:#fff}.patternRevInfo,.foswikiGrayText{color:#666}.patternRevInfo a:link,.patternRevInfo a:visited .foswikiGrayText a:link,.foswikiGrayText a:visited{color:#666}html,body{height:auto}#patternFloatWrap{float:none}}

795
doc/html/user/pub/System/PatternSkinTheme2009/colors.css
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13
doc/html/user/pub/System/PatternSkinTheme2009/column_left.css
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@ -1,12 +1 @@
/* #patternOuter{margin-left:16em}#patternSideBar{width:16em;margin-left:-16em}
places the side bar at the left
depends on global settings in layout.css
*/
#patternOuter {
margin-left:16em;
}
#patternSideBar {
width:16em;
margin-left:-16em;
}

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doc/html/user/pub/System/PatternSkinTheme2009/style.css
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46
doc/html/user/pub/System/PatternSkinTheme2009/variant_twiki.css
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@ -1,45 +1 @@
/* #patternScreen{padding:0}#patternPage{border:0}#patternBottomBarContents,#patternTopBarContents{padding-right:2em;padding-left:1em}#patternMainContents{padding-right:2em;padding-left:2em}#patternSideBarContents,#patternMainContents{padding-top:1em}#patternBottomBarContents{padding-top:1em}#patternTopBarContents{background-image:url(TWiki_header.gif);background-repeat:no-repeat;background-color:#fff}#patternTopBar,#patternTopBarContents{height:64px;overflow:hidden}
Compatible skin for TWiki-like installations
Overrides global settings in layout.css, style.css and colors.css
*/
/* outer 'frame' */
#patternScreen {
padding:0;
}
#patternPage {
border:none;
}
/* paddings of main content elements */
#patternBottomBarContents,
#patternTopBarContents {
padding-right:2em;
padding-left:1em;
}
#patternMainContents {
padding-right:2em;
padding-left:2em;
}
#patternSideBarContents,
#patternMainContents {
padding-top:1em;
}
#patternBottomBarContents {
padding-top:1em;
}
/* top bar */
#patternTopBarContents {
background-image:url(TWiki_header.gif);
background-repeat:no-repeat;
background-color:#fff;
}
#patternTopBar,
#patternClearHeaderCenter,
#patternClearHeaderLeft,
#patternClearHeaderRight,
#patternTopBarContents {
height:64px;
overflow:hidden;
}

19
doc/html/user/pub/System/PsiSkin/psistyle.css
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@ -99,7 +99,8 @@ blockquote.psi {
/* DMS Icon */ /* DMS Icon */
.patternContent a[href^="http:"] { .patternContent a[href^="http:"],
.patternContent a[href^="https:"] {
background-image: url(../DocumentGraphics/external.gif); background-image: url(../DocumentGraphics/external.gif);
background-position: right center; background-position: right center;
background-repeat: no-repeat; background-repeat: no-repeat;
@ -107,11 +108,14 @@ blockquote.psi {
} }
.patternContent a[href^="http:"]:hover, .patternContent a[href^="http:"]:hover,
.patternContent a[href^="http:"]:visited:hover { .patternContent a[href^="http:"]:visited:hover,
.patternContent a[href^="https:"]:hover,
.patternContent a[href^="https:"]:visited:hover {
background-image: url(../DocumentGraphics/external-hover.gif); background-image: url(../DocumentGraphics/external-hover.gif);
} }
.patternContent a[href^="http:"]:visited { .patternContent a[href^="http:"]:visited,
.patternContent a[href^="https:"]:visited {
background-image: url(../DocumentGraphics/external-visited.gif); background-image: url(../DocumentGraphics/external-visited.gif);
} }
@ -128,14 +132,17 @@ blockquote.psi {
padding-right: 0px; padding-right: 0px;
} }
.patternContent a[href^="http://i.psi.ch"] { .patternContent a[href^="http://i.psi.ch"],
.patternContent a[href^="https://intranet.psi.ch"] {
background: transparent; background: transparent;
padding-right: 0px; padding-right: 0px;
background-repeat: no-repeat; background-repeat: no-repeat;
background-image: none; background-image: none;
} }
.patternContent a[href^="http://i.psi.ch"]:hover, .patternContent a[href^="http://i.psi.ch"]:hover,
.patternContent a[href^="http://i.psi.ch"]:visited:hover { .patternContent a[href^="http://i.psi.ch"]:visited:hover,
.patternContent a[href^="https://intranet.psi.ch"]:hover,
.patternContent a[href^="https://intranet.psi.ch"]:visited:hover {
background-image: none; background-image: none;
background-color: #0055B5; background-color: #0055B5;
} }
@ -175,7 +182,7 @@ caption {
:lang(de) { quotes:"\201E" "\201C" "\201A" "\2018"; } :lang(de) { quotes:"\201E" "\201C" "\201A" "\2018"; }
:lang(en) { quotes:"\201C" "\201D" "\2018" "\2019"; } :lang(en) { quotes:"\201C" "\201D" "\2018" "\2019"; }
:lang(fr) { quotes:"\00AB\A0" "\A0\00BB" "\2039\A0" "\A0\203A"; } :lang(fr) { quotes:"\00AB" "\00BB" "\2039" "\203A"; }
q:before { content:open-quote; color:#000000; } q:before { content:open-quote; color:#000000; }
q:after { content:close-quote; color:#000000; } q:after { content:close-quote; color:#000000; }

2
doc/html/user/pub/System/SkinTemplates/base.css
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