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@@ -133,6 +134,8 @@ pre {
</li> <li> <a href="MusrFit.html#A_2.4_musrparam"> 2.4 musrparam </a>
</li> <li> <a href="MusrFit.html#A_2.5_musrfit_startup.xml"> 2.5 musrfit_startup.xml </a>
</li> <li> <a href="MusrFit.html#A_2.6_msr2msr"> 2.6 msr2msr </a>
</li> <li> <a href="MusrFit.html#A_2.7_any2many"> 2.7 any2many </a>
</li> <li> <a href="MusrFit.html#A_2.8_nexus_dump"> 2.8 nexus_dump </a>
</li></ul>
</li> <li> <a href="MusrFit.html#A_3_Auxiliary_Programs"> 3 Auxiliary Programs </a>
</li> <li> <a href="MusrFit.html#A_4_Description_of_the_msr_File_Format"> 4 Description of the msr File Format </a> <ul>
@@ -346,6 +349,56 @@ A typical example then looks like:
<pre class="bash">msr2msr 8472-WKM.msr 8472-musrfit.msr</pre>
If the input file has already the <code>musrfit</code> msr file structure, the output file will be just a copy of the input file.
<p></p>
<a name="Any2Many"></a>
<h2><a name="A_2.7_any2many"></a> 2.7 any2many </h2>
<code>any2many</code> is a muSR data file converter. Currently different facilities (PSI, TRIUMF, ISIS, J-PARC) are saving their muSR data files in different formats, or even worse some instruments are using other muSR data formats than others. The aim of <code>any2many</code> is that these files can be converted into each other. Of course only a subset of header information can be converted.
<p></p>
Currently <code>any2many</code> can convert the following muSR data file formats: <ul>
<li> <strong>input formats:</strong> <code>PSI-BIN</code> (PSI bulk), <code>ROOT</code> (PSI LEM), <code>MUD</code> (TRIUMF), <code>NeXus IDF1</code> and <code>NeXus IDF2</code> (ISIS), PSI-MDU (PSI bulk <em>internal only</em>), <code>WKM</code> (outdated ascii file format).
</li> <li> <strong>output formats:</strong> <code>PSI-BIN</code>, <code>ROOT</code>, <code>MUD</code>, <code>NeXus1-HDF4</code>, <code>NeXus1-HDF5</code>, <code>NeXus1-XML</code>, <code>NeXus2-HDF4</code>, <code>NeXus2-HDF5</code>, <code>NeXus2-XML</code>, <code>WKM</code>, <code>ASCII</code>
</li></ul>
<p></p>
Since the goal was to create a very flexible converter tool, it has ample of options which will listed below, followed by many examples showing how to use it. The options: <dl>
<dt> -f &lt;filenameList-input&gt; </dt><dd> where <code>&lt;filenameList-input&gt;</code> is a space separated list of file names (not starting with a '-'), e.g. <code>2010/lem10_his_0111.root 2010/lem10_his_0113.root</code>.
</dd> <dt> -o &lt;outputFileName&gt; </dt><dd> this option allows to given an output-file-name for the converted file. This option <em>only</em> makes sense if <code>&lt;filenameList-input&gt;</code> is a single input-file-name!
</dd> <dt> -r &lt;runList-input&gt; </dt><dd> where <code>&lt;runList-input&gt;</code> is a list of run numbers separated by spaces of the form: <code>&lt;run1&gt; &lt;run2&gt; &lt;run3&gt;</code> etc., or a sequence of runs <code>&lt;runStart&gt;-&lt;runEnd&gt;</code>, e.g. <code>111-123</code>. This option cannot be combined with <code>-f</code> and vice versa.
</dd> <dt> -t &lt;in-template&gt; &lt;out-template&gt; </dt><dd> where <code>&lt;in-/out-template&gt;</code> are templates to generate real file names from run numbers. The following template tags can be used: <code>[yy]</code> for year, and <code>[rrrr]</code> for the run number. If the run number tag is used, the number of <code>'r'</code> will give the number of digits used with leading zeros, e.g. <code>[rrrrrr]</code> and run <code>123</code> will result in <code>000123</code>. Similarly <code>[yyyy]</code> will result in something like <code>1999</code>, whereas <code>[yy]</code> into something like <code>99</code>. For more details best check the examples below.
</dd> <dt> -c &lt;in-Format&gt; &lt;out-Format&gt; </dt><dd> this is used to tell <code>any2many</code> what is the input-file-format and into which output-file-format the data shall be converted. The possible input-/output-file-formats are listed above.
</dd> <dt> -p &lt;output-path&gt; </dt><dd> where <code>&lt;output-path&gt;</code> is the output path for the converted files. If no <code>&lt;output-path&gt;</code> is given, the current directory will be used, unless the option <code>-s</code> is used.
</dd> <dt> -y &lt;year&gt; </dt><dd> here a <code>&lt;year&gt;</code> in the form <code>yy</code> or <code>yyyy</code> can be given. If this is the case, any automatic file name generation which needs a year will use this given one.
</dd> <dt> -s </dt><dd> with this option the output data file will be sent to the stdout. It is intended to be used together with web applications.
</dd> <dt> -rebin &lt;n&gt; </dt><dd> where <code>&lt;n&gt;</code> is the number of bins to be packed/rebinned.
</dd> <dt> -z [g|b] &lt;compressed&gt; </dt><dd> where <code>&lt;compressed&gt;</code> is the output file name (without extension) of the compressed data collection, and <code>'g'</code> will result in <code>.tar.gz</code>, and <code>'b'</code> in <code>.tar.bz2</code> files.
</dd> <dt> --help </dt><dd> displays a help notice in the shell explaining the basic usage of the program.
</dd> <dt> --version </dt><dd> shows the current <code>SVN</code> version of <code>any2many</code>.
</dd></dl>
<p></p>
If the template option <code>'-t'</code> is absent, the output file name will be generated according to the input data file name (not possible with <code>&lt;runList-input&gt;</code>), and the output data format.
<p></p>
Here now a couple of examples which should help to understand the switches.
<p></p>
<pre class="bash">any2many -f 2010/lem10&#95;his&#95;0123.root -c ROOT ASCII -rebin 25</pre>
Will take the LEM ROOT file <code>'2010/lem10_his_0123.root'</code> rebin it by 25 and convert it to ASCII. The output file name will be <code>lem10_his_0123.ascii</code>, and the file will be saved in the current directory. The data in <code>lem10_his_0123.ascii</code> are written in columns.
<p></p>
<pre class="bash">any2many -f 2010/lem10&#95;his&#95;0123.root -c ROOT NEXUS2-HDF5 -o 2010/lem10&#95;his&#95;0123&#95;v2.nxs</pre>
Will take the LEM ROOT file <code>'2010/lem10_his_0123.root'</code> and convert it to <a href="https://intranet.psi.ch/wiki/bin/edit/MUSR/NeXus?topicparent=MUSR.MusrFit" rel="nofollow" title="Create this topic" class="newlink">NeXus</a> IDF V2. The output file name will be <code>lem10_his_0123_v2.nxs</code>, and will be saved in the current directory.
<p></p>
<pre class="bash">any2many -r 123 137 -c PSI-BIN MUD -t d&#91;yyyy]/deltat&#95;tdc&#95;gps&#95;&#91;rrrr].bin &#91;rrrrrr].msr -y 2001</pre>
Will take the run 123 and 137, will generate the input file names: <code>d2001/deltat_tdc_gps_0123.bin</code> and <code>d2001/deltat_tdc_gps_0137.bin</code>, read these files, and convert them to the output files with names <code>000123.msr</code> and <code>000137.msr</code>, respectively.
<p></p>
<pre class="bash">any2many -r 100-117 -c PSI-MDU ASCII -t d&#91;yyyy]/deltat&#95;tdc&#95;alc&#95;&#91;rrrr].mdu &#91;rrr].ascii -y 2011 -s</pre>
Will take the runs 100 through 117 and convert the <code>PSI-MDU</code> input files to <code>ASCII</code> output and instead of saving them into a file, they will be spit to the standard output.
<p></p>
<pre class="bash">any2many -r 100-117 -c NEXUS ROOT -t d&#91;yyyy]/psi&#95;gps&#95;&#91;rrrr].NXS psi&#95;&#91;yyyy]&#95;gps&#95;&#91;rrrr].root -z b psi&#95;gps&#95;run&#95;100to117</pre>
Will take the runs 100 through 117 and convert the <code>NeXus</code> input files to <code>ROOT</code> output. Afterwards these new files will be collected in a compressed archive <code>psi_gps_run_100to117.tar.bz2</code>.
<p></p>
<pre class="bash">any2many -f 2010/lem10&#95;his&#95;0123.root 2010/lem10&#95;his&#95;0012.root -c ROOT ROOT -rebin 25</pre>
Will read the two files <code>'2010/lem10_his_0123.root'</code> and <code>'2010/lem10_his_0012.root'</code>, rebin them with 25 and export them as <code>LEM ROOT</code> files with adding <code>rebin25</code> to the name, e.g. <code>2010/lem10_his_0123_rebin25.root</code>.
<p></p>
<a name="NexusDump"></a>
<h2><a name="A_2.8_nexus_dump"></a> 2.8 nexus_dump </h2>
<code>nexus_dump</code> is a little program which tries to read a <code>NeXus</code> file and send the relevant information (required header info, start of the histos, etc.) to the standard output.
<p></p>
<a name="AuxiliaryPrograms"></a>
<h1><a name="A_3_Auxiliary_Programs"></a> 3 Auxiliary Programs </h1>
Additionally to the programs mentioned above editor front ends called <code><a href="MusrGui.html">musrgui/musredit</a></code> and another tool named <code><a href="Msr2Data.html">msr2data</a></code> are available. The purpose of <code>msr2data</code> is to process multiple msr files with the same parameters and to summarize the fitting results either in a <strong>DB</strong> or a <strong>column ASCII</strong> file. Also, new msr files can be generated from a template. For details refer to its <a href="Msr2Data.html">manual</a>.
@@ -796,8 +849,9 @@ etc.
<p></p>
<a name="ForwardHisto"></a> <dl>
<dt> forward (fit type 0) </dt><dd> Number of the histogram in the data file to be processed. If histograms shall be grouped, all the numbers which shall be grouped. Examples: <pre>
forward 3 # no grouping, take histogram number 3
forward 1 2 # group histogram number 1 and 2
forward 3 # no grouping, take histogram number 3
forward 1 2 # group histogram number 1 and 2
forward 1-10 12 # group histograms with numbers from 1 to 10 and additionally histogram 12
</pre>
</dd></dl>
<p></p> <dl>
@@ -808,6 +862,9 @@ etc.
# build forward/backward asymmetry with groupings 1+2+3 and 7+8+9
forward 1 2 3
backward 7 8 9
# build forward/backward asymmetry with groupings 1+2+3 and 7+8+9 (alternative notation)
forward 1-3
backward 7-9
</pre>
</dd></dl>
<p></p> <dl>
@@ -1335,12 +1392,58 @@ A technical description of the musrfit framework can be found <a href="http://lm
<p></p>
For reporting bugs or requesting new features and improvements please use the <a href="https://tracker.intranet.psi.ch/jira/browse/MUSR" target="_top">PSI Tracker</a> or send an e-mail to A. Suter.
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