LMU/musrfit
LMU/musrfit
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Merged muonspin/musrfit into master

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This commit is contained in:
Zaher Salman 2016-12-19 17:15:13 +01:00
commit 65e73041fa
49 changed files with 1783 additions and 648 deletions
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17
ChangeLog
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@ -2,8 +2,23 @@
# ChangeLog
#---------------------------------------------------------------------
changes since 0.18.0
===================================
changes since 0.17.0
===================================
NEW 2016-12-18 for maxLH it is now possible to get the per-run-block maxLH,
and the expected maxLH.
NEW 2016-12-18 musrview allows no to show directly the Fourier transform,
and the averaged data/Fourier transform.
NEW 2016-12-18 added a first full version of an automatic phase correction
for the real part of the Fourier transform. It is based on
the algorithm published in JMR 158, 164 (2002).
NEW 2016-12-18 a couple of improvements in dump_header: (i) it is not
only searching in the current directory, but also in all
default paths defined in musrfit_startup.xml. (ii) it is
now possible also to give only run numbers instead of the
full file name.
NEW 2016-08-24 in musrview it is now possible to enable/disable a
crosshair cursor by pressing 'c'.
NEW 2016-04-28 updated licence info in musredit and added paramList
@ -13,6 +28,8 @@ NEW 2016-04-28 msr2data gets a new option: paramList which allows to
of msr-files.
NEW 2016-04-22 Added the theory function muMinusExpTF for mu minus fits
NEW 2016-02-23 It is now possible to export the averaged data/Fourier
CHANGED 2016-12-18 updated the docu.
CHANGED 2016-12-18 a couple of little improvements in musredit.
CHANGED 2016-08-10 drop NeXus support for Version < 4.4
CHANGED 2016-04-26 start-/endTimeBin are now class members. This reduces
the number of recalculations.

4
configure.ac
View File

@ -1,7 +1,7 @@
AC_REVISION([m4_esyscmd_s([git describe --always])])
AC_PREREQ(2.63)
AC_INIT([musrfit],[0.17.0],[andreas.suter@psi.ch])
AC_INIT([musrfit],[0.18.0],[andreas.suter@psi.ch])
AC_CONFIG_AUX_DIR(admin)
AC_CANONICAL_HOST
#AC_MSG_RESULT([${host} ${host_cpu} ${host_vendor} ${host_os}])
@ -35,7 +35,7 @@ dnl -----------------------------------------------
#release versioning
MUSR_MAJOR_VERSION=0
MUSR_MINOR_VERSION=17
MUSR_MINOR_VERSION=18
MUSR_MICRO_VERSION=0
#release versioning

12
doc/html/user/MUSR/BmwLibs.html
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@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
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<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/BmwLibs?t=1472103697" type="application/x-wiki" title="edit BmwLibs" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/BmwLibs?t=1481904045" type="application/x-wiki" title="edit BmwLibs" />
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<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<base /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -149,6 +149,6 @@ Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
</body>
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</html>

12
doc/html/user/MUSR/CiteMusrFit.html
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@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/CiteMusrFit?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:42:18 GMT -->
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<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/CiteMusrFit?t=1472103697" type="application/x-wiki" title="edit CiteMusrFit" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/CiteMusrFit?t=1481904044" type="application/x-wiki" title="edit CiteMusrFit" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
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<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
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<base /><!--[if IE]></base><![endif]--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -147,6 +147,6 @@ Topic revision: <span class='patternRevInfo'>19 Jun 2012, suter_a</span></div>
</body>
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18
doc/html/user/MUSR/LibFitPofB.html
View File

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/LibFitPofB?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:42:18 GMT -->
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<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibFitPofB?t=1472103697" type="application/x-wiki" title="edit LibFitPofB" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibFitPofB?t=1481904045" type="application/x-wiki" title="edit LibFitPofB" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
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<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -101,18 +101,18 @@
<!--<![endif]-->
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<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::METADATA-->
<!--JQUERYPLUGIN::CHILI-->
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<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
<body class="foswikiNoJs patternViewPage patternPrintPage">
<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@ -428,6 +428,6 @@ Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
</body>
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22
doc/html/user/MUSR/LibZFRelaxation.html
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@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
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<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibZFRelaxation?t=1472103694" type="application/x-wiki" title="edit LibZFRelaxation" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/LibZFRelaxation?t=1481904042" type="application/x-wiki" title="edit LibZFRelaxation" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
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<base /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -102,17 +102,17 @@
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<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::METADATA-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiPref-->
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<!--JQUERYPLUGIN::CHILI-->
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<body class="foswikiNoJs patternViewPage patternPrintPage">
<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@ -233,6 +233,6 @@ Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
</body>
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26
doc/html/user/MUSR/Msr2Data.html
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@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/Msr2Data?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:42:18 GMT -->
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@ -14,11 +14,12 @@
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<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/Msr2Data?t=1472103697" type="application/x-wiki" title="edit Msr2Data" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/Msr2Data?t=1481904045" type="application/x-wiki" title="edit Msr2Data" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
<base /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<style class='head TABLEPLUGIN_default' type="text/css" media="all">
body .foswikiTable {border-width:1px}
body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
@ -33,7 +34,6 @@ body .foswikiTable tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-col
body .foswikiTable tr.foswikiTableRowdataBg1 td {background-color:#f7f7f6}
body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-color:#f0f0ee}
</style><!--TABLEPLUGIN_default-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<style class='head TABLEPLUGIN_specific' type="text/css" media="all">
body .foswikiTable#tableMsr2Data1 td {vertical-align:middle; vertical-align:top}
body .foswikiTable#tableMsr2Data1 td.foswikiTableCol0 {text-align:left}
@ -52,10 +52,10 @@ body .foswikiTable#tableMsr2Data1 th.foswikiSortedCol {background-color:#eeeeee}
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@ -146,7 +146,7 @@ body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-col
</li> <li> <a href="MusrFit.html#A_2_Available_Executables_44_Configuration_Files_and_their_Basic_Usage"> 2 Available Executables, Configuration Files and their Basic Usage </a> <ul>
<li> <a href="MusrFit.html#A_2.1_musrfit"> 2.1 musrfit </a>
</li> <li> <a href="MusrFit.html#A_2.2_musrview"> 2.2 musrview </a>
</li> <li> <a href="MusrFit.html#A_2.3_musrFT"> 2.3 musrFT <img src="../pub/System/DocumentGraphics/new.png" alt="NEW" title="NEW" width="30" height="16" /> </a>
</li> <li> <a href="MusrFit.html#A_2.3_musrFT"> 2.3 musrFT </a>
</li> <li> <a href="MusrFit.html#A_2.4_musrt0"> 2.4 musrt0 </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>
@ -199,10 +199,12 @@ body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-col
If called from within a shell it accepts several parameters: <dl>
<dt> &lt;msr_file&gt; </dt><dd> filename of the msr input file defining all the details needed for performing a fit to a specified set of data&mdash;the only mandatory parameter
</dd> <dt> -k, --keep-mn2-output </dt><dd> selects the option for keeping the output of <code>MINUIT2</code> including the correlation coefficients between different parameters and renaming the files <code><b>MINUIT2.OUTPUT</b></code> and <code><b>MINUIT2.root</b></code> to <code><b>&lt;msr_file_without_extension&gt;-mn2.output</b></code> and <code><b>&lt;msr_file_without_extension&gt;-mn2.root</b></code>, repectively, e.g. <strong>&lt;msr_file&gt;</strong> = <code><b>8472.msr</b></code> &rarr; <code><b>8472-mn2.output</b></code> , <code><b>8472-mn2.root</b></code>
</dd> <dt> -c, --chisq-only </dt><dd> Instead of fitting the model, <code>musrfit</code> calculates &#967;<sup>2</sup> only once and sends the result to the standard output if called with this option. This might be useful for the adjustment of the initial values of the fit parameters.
</dd> <dt> -c, --chisq-only </dt><dd> Instead of fitting the model, <code>musrfit</code> calculates &#967;<sup>2</sup> or max. log-likelihood, maxLH, only once and sends the result to the standard output if called with this option. This is e.g. useful for the adjustment of the initial values of the fit parameters.
</dd> <dt> -t, --title-from-data-file </dt><dd> If this option is given <code>musrfit</code> will replace the title in the <strong>&lt;msr_file&gt;</strong> by the run title in the data file of the first run appearing in a RUN block. In case there is no run title in the data file no substitution is done.
</dd> <dt> -e, --estimateN0 </dt><dd> estimate N0 for single histogram fits.
</dd> <dt> -p, --per-run-block-chisq </dt><dd> will write per run block chisq/maxLH into the msr-file.
</dd> <dt> --dump &lt;type&gt; </dt><dd> is writing a data file with the fit data and the theory; <strong>&lt;type&gt;</strong> can be <strong>ascii</strong> (data in columns) or <strong>root</strong> (data in <code>ROOT</code> histograms)
</dd> <dt> --timeout &lt;timeout_tag&gt; </dt><dd> overwrites the predefined timeout of 3600 sec. &lt;timeout_tag&gt;&lt;=0 means the timeout facility is not enabled. &lt;timeout_tag&gt; &gt; 0, e.g. <code>nn</code> will set the timeout to <code>nn</code> (sec). If during a fit this timeout is reached, <code>musrfit</code> will terminate. This is used to prevent orphan musrfit process to jam the system.
</dd> <dt> --timeout &lt;timeout_tag&gt; </dt><dd> overwrites the predefined timeout of 3600 sec. &lt;timeout_tag&gt;&lt;=0 means the timeout facility is not enabled. &lt;timeout_tag&gt; &gt; 0, e.g. <code>nn</code> will set the timeout to <code>nn</code> (sec). If during a fit this timeout is reached, <code>musrfit</code> will terminate. This is used to prevent orphan musrfit processes to jam the system.
</dd> <dt> --help </dt><dd> displays a small help notice in the shell explaining the basic usage of the program
</dd> <dt> --version </dt><dd> prints the version number of <code>musrfit</code>
</dd></dl>
@ -211,14 +213,21 @@ If called with a msr input file, e.g.
<pre class="bash">musrfit 8472.msr</pre>
the fit described in the input file will be executed and the results will be written to a mlog output file&mdash;in the example <code><b>8472.mlog</b></code>. When the fitting has terminated the msr file and the mlog file are swapped, so that the resultant parameter values can be found in the msr file and the mlog file contains a copy of the input file. The format of the mlog file is the same as that of the msr file. For a detailed description of the msr file format refer to <a class="foswikiCurrentTopicLink" href="#DescriptionOfTheMsrFileFormat">the corresponding section</a>.
<p></p>
Another example:
<pre class="bash">musrfit -c -e 8472&#95;tf&#95;histo.msr</pre>
This will calculate the chisq/maxLH of the run <code><b>8472</b></code> after estimating the N0.
<p></p>
<span id="MusrView"></span>
<h2 id="A_2.2_musrview"> 2.2 musrview </h2>
<code>musrview</code> is an interactive graphical user interface for the presentation of the analyzed data and the corresponding fits. If called from within a shell it accepts the following parameters: <dl>
<dt> &lt;msr_file&gt; </dt><dd> name of the msr input or output file to be displayed&mdash;this parameter is mandatory
</dd> <dt> --&lt;graphic_format_extension&gt; </dt><dd> will produce a graphics output file without starting a <code>ROOT</code> session. The filename is based on the name of the <strong>&lt;msr_file&gt;</strong>, e.g. <code><b>8472.msr</b></code> &rarr; <code><b>8472_0.png</b></code> <br> Supported values for <strong>&lt;graphic_format_extension&gt;</strong> are <strong>eps</strong>, <strong>pdf</strong>, <strong>gif</strong>, <strong>jpg</strong>, <strong>png</strong>, <strong>svg</strong>, <strong>xpm</strong>, <strong>root</strong>
</dd> <dt> --timeout &lt;timeout&gt; </dt><dd> &lt;timeout&gt; given in seconds after which <code>musrview</code> terminates. If &lt;timeout&gt; &lt;= 0, no timeout will take place. Default for &lt;timeout&gt; is 0.
</dd> <dt> --help </dt><dd> displays a small help notice in the shell explaining the basic usage of the program
</dd> <dt> --version </dt><dd> prints the version number of <code>musrview</code>
</dd> <dt> -f, --fourier </dt><dd> will directly present the Fourier transform of the &lt;msr_file&gt; with Fourier options as defined in the &lt;msr_file&gt;.
</dd> <dt> -a, --avg </dt><dd> will directly present the averaged data/Fourier of the &lt;msr_file&gt;.
</dd> <dt> --&lt;graphic_format_extension&gt; </dt><dd> will produce a graphics output file without starting a <code>ROOT</code> session. The filename is based on the name of the <strong>&lt;msr_file&gt;</strong>, e.g. <code><b>8472.msr</b></code> &rarr; <code><b>8472_0.png</b></code> <br> Supported values for <strong>&lt;graphic_format_extension&gt;</strong> are <strong>eps</strong>, <strong>pdf</strong>, <strong>gif</strong>, <strong>jpg</strong>, <strong>png</strong>, <strong>svg</strong>, <strong>xpm</strong>, <strong>root</strong>
</dd> <dt> --ascii </dt><dd> will generate an ascii dump of the data and theory as plotted.
</dd> <dt> --timeout &lt;timeout&gt; </dt><dd> &lt;timeout&gt; given in seconds after which <code>musrview</code> terminates. If &lt;timeout&gt; &lt;= 0, no timeout will take place. Default for &lt;timeout&gt; is 0.
</dd></dl>
<p></p>
If called with a msr file and the <strong>--&lt;graphic_format_extension&gt;</strong> option, e.g.
@ -230,6 +239,10 @@ If called only with a msr file, e.g.
a <code>ROOT</code> canvas is drawn; it contains all experimental data and fits specified in the PLOT block of the msr file.
For a description of the various plotting types refer to <a class="foswikiCurrentTopicLink" href="#DescriptionOfTheMsrFileFormat">the corresponding section</a>.
<p></p>
Example:
<pre class="bash">musrview 8472&#95;tf&#95;histo.msr -f -a</pre>
will show the averaged Fourier transform of the data of run <code>8472</code>.
<p></p>
Within the drawn canvas all standard actions applicable to <code>ROOT</code> canvases might be performed.
In the menu bar the <strong>Musrfit</strong> menu can be found. From there some <code>musrfit</code>-specific actions might be taken: <dl>
<dt> Fourier </dt><dd> performs the Fourier transformation of the selected data and shows the result
@ -248,7 +261,7 @@ Additionally, some functions can be accessed using key-shortcuts: <dl>
</dd></dl>
<p></p>
<span id="MusrFT"></span>
<h2 id="A_2.3_musrFT"> 2.3 musrFT <img src="../pub/System/DocumentGraphics/new.png" alt="NEW" title="NEW" width="30" height="16" /> </h2>
<h2 id="A_2.3_musrFT"> 2.3 musrFT </h2>
<code>musrFT</code> is an interactive graphical user interface for the presentation of Fourier transforms of raw &#956;SR histograms. It's purpose is to get a quick overview for high TF-field data, as found e.g. at the HAL-9500 instrument at PSI. It Fourier transforms the raw histogram data, i.e. N(t) rather than A(t), and hence shows the lifetime contribution of the muon. This is no problem for large enough fields, but will be a severe problem at very low fields. <code>musrFT</code> is still in its early stage and should be considered a <strong>beta-version</strong>.
<p></p>
If called from within a shell it accepts the following parameters: <dl>
@ -296,6 +309,7 @@ Additionally, some functions can be accessed using key-shortcuts: <dl>
</dd> <dt> a </dt><dd> toggle between average of the presented data and single Fourier histos, e.g. the averaged Fourier power spectra of various detectors.
</dd> <dt> d </dt><dd> toggle between average per data set and single Fourier histos, e.g. the averaged Fourier power spectra of various detectors for the different data sets given.
</dd> <dt> u </dt><dd> reset the plotting range to the area given in the msr-file or the form the command line ("unzoom")
</dd> <dt> c </dt><dd> toggles between normal and crosshair cursor
</dd></dl>
<p></p>
<span id="MusrT0"></span>
@ -447,6 +461,26 @@ Will read the two files <code>'2010/lem10_his_0123.root'</code> and <code>'2010/
<span id="DumpHeader"></span>
<h2 id="A_2.8_dump_header"> 2.8 dump_header </h2>
<code>dump_header</code> is a little program which tries to read a &#956;SR data file and sends the relevant information (required header info, start of the histos, etc.) to the standard output. Currently the following &#956;SR data file formats are supported: <code>MusrROOT</code>, <code>ROOT</code> (old LEM format), <code>PSI-BIN</code>, <code>PSI-MDU</code>, <code>NeXus</code> (IDF1 and IDF2), <code>MUD</code>, and <code>WKM</code>.
<p></p> <dl>
<dt> -rn, --runNo &lt;runNo&gt; </dt><dd> run number of the header to be dumped.
</dd> <dt> -fn, --fileName &lt;fileName&gt; </dt><dd> muSR data file name.
</dd> <dt> -ff, --fileFormat &lt;fileFormat&gt; </dt><dd> where &lt;fileFormat&gt; is one of the above listed ones.
</dd> <dt> -y, --year &lt;year&gt; </dt><dd> &lt;year&gt; has to be a 4 digit value, e.g. 2005, if provided it is used to generate the file name for the given &lt;runNo&gt;, otherwise the current year is used. If a file name is given, this option has no effect.
</dd> <dt> -s, --summary </dt><dd> this option is used for LE-muSR data sets only. It will, additionally to the header information, print the summary file content.
</dd> <dt> --psi-bulk &lt;opt&gt; </dt><dd> where &lt;opt&gt; consists of two items: (i) <code>pta</code> or <code>tdc</code>, (ii) the instrument name, i.e. <code>gps</code>, <code>ltf</code>, <code>dolly</code>, <code>gpd</code>, or <code>hifi</code>. This is needed in combination with the file formats <code>PSI-BIN</code> and <code>PSI-MDU</code> when providing a run number.
</dd> <dt> -h, --help </dt><dd> will show a short help.
</dd> <dt> -v, --version </dt><dd> will print the current version.
</dd></dl>
<p></p>
Examples:
<pre class="bash">dump&#95;header -fn tdc&#95;hifi&#95;2015&#95;00123.mdu -y 2015</pre>
will dump the header information for the run <code>123</code> of the <code>HAL-9500</code> instrument of the year <code>2015</code>.
<p></p>
<pre class="bash">dump&#95;header -rn 123 -ff PSI-MDU --psi-bulk tdc hifi -y 2015</pre>
the same as the previous example, except that the file name is constructed via the number and the additionally provided information.
<p></p>
<pre class="bash">dump&#95;header -rn 3456 -s</pre>
Will dump the <code>LEM</code> header information of run <code>3456</code> including the content of the run summary file.
<p></p>
<span id="AuxiliaryPrograms"></span>
<h1 id="A_3_Auxiliary_Programs"> 3 Auxiliary Programs </h1>
@ -672,7 +706,7 @@ The THEORY block is used to define the fit function. There is a set of predefine
<td class="foswikiTableCol1"> skg </td>
<td class="foswikiTableCol2"> <img alt="\varphi\,(^{\circ})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_61136f20673ad20f955c43e43b8cec9d.png" />, <img alt="\nu\,(\mathrm{MHz})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7188605a647615e4fb92cc89274b22a0.png" />, <img alt="\sigma&#95;{-}\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_bd5c765027d46aa1433dda03f540c17e.png" />, <img alt="\sigma&#95;{+}\,(\mu\text{s}^{-1})" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_82adbab00b6a057f04037b44746e33eb.png" /> </td>
<td class="foswikiTableCol3"> <img alt="\frac{\sigma&#95;{-}}{\sigma&#95;{+}+\sigma&#95;{-}}\exp\left&#91;-\frac{\sigma&#95;{-}^2t^2}{2}\right]\left\lbrace\cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)+\sin\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\mathrm{Erfi}\left(\frac{\sigma&#95;{-}t}{\sqrt{2}}\right)\right\rbrace+ \frac{\sigma&#95;{+}}{\sigma&#95;{+}+\sigma&#95;{-}}\exp\left&#91;-\frac{\sigma&#95;{+}^2t^2}{2}\right]\left\lbrace\cos\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)-\sin\left(2\pi\nu t+\frac{\pi\varphi}{180}\right)\mathrm{Erfi}\left(\frac{\sigma&#95;{+}t}{\sqrt{2}}\right)\right\rbrace" class="mmpImage" src="../pub/MUSR/MusrFit/_MathModePlugin_7f4cd42199fbf712ad5a86f9d94bd698.png" /> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a href="http://nemu.web.psi.ch/doc/LEM_Memo/skewedGaussian/skewedGaussian.pdf">memo</a> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/pdf.png' width='16' height='16' alt='pdf' /></span> </td>
<td class="foswikiTableCol4 foswikiLastCol"> <a href="http://lmu.web.psi.ch/musrfit/memos/skewedGaussian.pdf">memo</a> <span class='foswikiIcon'><img src='../pub/System/DocumentGraphics/pdf.png' width='16' height='16' alt='pdf' /></span> </td>
</tr>
<tr class="foswikiTableOdd foswikiTableRowdataBgSorted1 foswikiTableRowdataBg1">
<td class="foswikiTableCol0 foswikiFirstCol"> staticNKZF </td>
@ -1228,7 +1262,7 @@ The Fourier transform is done and the results are plotted within <code>musrview<
</dd> <dt> phase </dt><dd> The phase of the Fourier transform is plotted.
</dd></dl>
</dd> <dt> phase </dt><dd> The initial phase of the input data is given here in degrees. Optionally the phase parameter from the FITPARAMETER block can be given, e.g. <code><b>par3</b></code>, which would take the value of parameter number 3.
</dd> <dt> range_for_phase_correction </dt><dd> An interval within which the initial phase should be optimized automatically can be specified here. The interval is given by its start and end values in degrees.
</dd> <dt> range_for_phase_correction </dt><dd> An interval in Fourier space given in units as define with the 'units' tag, or the tag 'all' in which case the range given under 'range' will be used. The given interval will be used for an automatic phasing of the real Fourier transform. This will allow to add real Fourier spectra coherently.
</dd> <dt> range </dt><dd> The plotting range is set here. The interval is specified through its start and end points given in the units set after the <strong>units</strong> tag.
</dd></dl>
<p></p>
@ -1240,7 +1274,7 @@ Altogether, a possible FOURIER block might look like that:
apodization NONE
plot real&#95;and&#95;imag
phase 22.6 # par3
#range&#95;for&#95;phase&#95;correction 10.0 40.0
range&#95;for&#95;phase&#95;correction all
range 0.0 17.03
</pre>
<p></p>
@ -1679,7 +1713,7 @@ For reporting bugs or requesting new features and improvements please use the <a
<p></p>
</div>
<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFit <br />
Topic revision: <span class='patternRevInfo'>24 Aug 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
Topic revision: <span class='patternRevInfo'>16 Dec 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
</div>
</div>
</div>
@ -1697,6 +1731,6 @@ Topic revision: <span class='patternRevInfo'>24 Aug 2016, <a href="https://intr
</body>
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16
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View File

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitAcknowledgements?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:53 GMT -->
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<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitAcknowledgements?t=1472103696" type="application/x-wiki" title="edit MusrFitAcknowledgements" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitAcknowledgements?t=1481904044" type="application/x-wiki" title="edit MusrFitAcknowledgements" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<base /><!--[if IE]></base><![endif]--><link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -101,9 +101,9 @@
<!--<![endif]-->
<!--JQUERYPLUGIN-->
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::MIGRATE-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiPref-->
<!--JavascriptFiles/foswikiForm-->
@ -145,6 +145,6 @@ Topic revision: <span class='patternRevInfo'>03 Jul 2015, suter_a</span></div>
</body>
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</html>

34
doc/html/user/MUSR/MusrFitSetup.html
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@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/MusrFitSetup?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:53 GMT -->
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<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,12 +14,12 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitSetup?t=1472103696" type="application/x-wiki" title="edit MusrFitSetup" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrFitSetup?t=1481904043" type="application/x-wiki" title="edit MusrFitSetup" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<base /><!--[if IE]></base><![endif]--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@ -101,18 +101,18 @@
<!--<![endif]-->
<!--JQUERYPLUGIN-->
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::METADATA-->
<!--JQUERYPLUGIN::CHILI-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiForm-->
<!--JavascriptFiles/foswikiPref-->
<!--JQUERYPLUGIN::METADATA-->
<!--PatternSkin/pattern-->
<!--JQUERYPLUGIN::CHILI--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JQUERYPLUGIN::COMMENT-->
<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
<body class="foswikiNoJs patternViewPage patternPrintPage">
<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@ -312,7 +312,7 @@ When all required software has been set up it can be proceeded with the <code>mu
or
<pre class="bash">
&#36; cd &#36;HOME/Apps
&#36; git clone git://gitorious.psi.ch/nemu/musrfit.git
&#36; git clone git://gitlab.psi.ch/nemu/musrfit.git
</pre>
<p></p>
<strong>Note:</strong> musrfit has moved from svn to git. In case you still have an <em>old</em> svn version of musrfit, it is advised to remove it first. For svn users: for a smooth transition from svn to git, please check the following link:
@ -502,7 +502,7 @@ First, the most recent source code should be downloaded. First, the most recent
or
<pre class="bash">
&#36; cd
&#36; git clone git://gitorious.psi.ch/nemu/musrfit.git
&#36; git clone git://gitlab.psi.ch/nemu/musrfit.git
</pre>
<p></p>
<strong>Note:</strong> musrfit has moved from svn to git. In case you still have an <em>old</em> svn version of musrfit, it is advised to remove it first. For svn users: for a smooth transition from svn to git, please check the following link:
@ -840,7 +840,7 @@ First, the most recent source code should be downloaded. First, the most recent
or
<pre class="bash">
&#36; cd ~/Apps
&#36; git clone git://gitorious.psi.ch/nemu/musrfit.git
&#36; git clone git://gitlab.psi.ch/nemu/musrfit.git
</pre>
<p></p>
<p></p>
@ -940,7 +940,7 @@ If <code>musrgui</code> has been installed, just open one of the <strong>test-&#
<p></p>
</div>
<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span><a class="foswikiCurrentWebHomeLink" href="WebHome.html">WebHome</a> &gt; <a href="MusrFit.html">MusrFit</a><span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>MusrFitSetup <br />
Topic revision: <span class='patternRevInfo'>10 Aug 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
Topic revision: <span class='patternRevInfo'>25 Aug 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
</div>
</div>
</div>
@ -958,6 +958,6 @@ Topic revision: <span class='patternRevInfo'>10 Aug 2016, <a href="https://intr
</body>
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20
doc/html/user/MUSR/MusrGui.html
View File

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:50 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/MusrGui?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:59 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrGui?t=1472103695" type="application/x-wiki" title="edit MusrGui" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrGui?t=1481904043" type="application/x-wiki" title="edit MusrGui" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
<base /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<style class='head TABLEPLUGIN_default' type="text/css" media="all">
body .foswikiTable {border-width:1px}
body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
@ -54,7 +54,7 @@ body .foswikiTable#tableMusrGui1 th.foswikiSortedCol {background-color:#eeeeee}
body .foswikiTable#tableMusrGui1 tr.foswikiTableRowdataBg0 td {background-color:#ffffff}
body .foswikiTable#tableMusrGui1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f5f5f5}
</style><!--TABLEPLUGIN_specific-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@ -138,16 +138,16 @@ body .foswikiTable#tableMusrGui1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiPref-->
<!--JQUERYPLUGIN::TWISTY-->
<!--JavascriptFiles/foswikiForm-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--PatternSkin/pattern-->
<!--JQUERYPLUGIN::METADATA-->
<!--JQUERYPLUGIN::CHILI-->
<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JQUERYPLUGIN::TWISTY-->
<!--JQUERYPLUGIN::COMMENT--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
<body class="foswikiNoJs patternViewPage patternPrintPage">
<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@ -394,6 +394,6 @@ Topic revision: <span class='patternRevInfo'>19 Feb 2015, suter_a</span></div>
</body>
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</html>

26
doc/html/user/MUSR/MusrRoot.html
View File

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/MusrRoot?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:38 GMT -->
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<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,12 +14,11 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrRoot?t=1472103693" type="application/x-wiki" title="edit MusrRoot" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/MusrRoot?t=1481904041" type="application/x-wiki" title="edit MusrRoot" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<base /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
<style class='head TABLEPLUGIN_default' type="text/css" media="all">
body .foswikiTable {border-width:1px}
body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
@ -52,10 +51,11 @@ body .foswikiTable#tableMusrRoot7 th.foswikiSortedCol {background-color:#eeeeee}
body .foswikiTable#tableMusrRoot7 tr.foswikiTableRowdataBg0 td {background-color:#ffffff}
body .foswikiTable#tableMusrRoot7 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f5f5f5}
</style><!--TABLEPLUGIN_specific-->
<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
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<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -136,16 +136,16 @@ body .foswikiTable#tableMusrRoot7 tr.foswikiTableRowdataBg0 td.foswikiSortedCol
<!--<![endif]-->
<!--JQUERYPLUGIN-->
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiForm-->
<!--JavascriptFiles/foswikiPref-->
<!--JavascriptFiles/foswikiForm-->
<!--PatternSkin/pattern-->
<!--JQUERYPLUGIN::METADATA-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JQUERYPLUGIN::TWISTY-->
<!--JQUERYPLUGIN::METADATA-->
<!--PatternSkin/pattern-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JQUERYPLUGIN::CHILI--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
@ -1125,6 +1125,6 @@ Topic revision: <span class='patternRevInfo'>29 Mar 2012, suter_a</span></div>
</body>
<!-- Mirrored from intranet.psi.ch/MUSR/MusrRoot?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:43 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/MusrRoot?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:51 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
</html>

20
doc/html/user/MUSR/QuickStart.html
View File

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:49 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:58 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1472103695" type="application/x-wiki" title="edit QuickStart" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/QuickStart?t=1481904043" type="application/x-wiki" title="edit QuickStart" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<base /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -105,11 +105,11 @@
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiPref-->
<!--JavascriptFiles/foswikiForm-->
<!--PatternSkin/pattern-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JQUERYPLUGIN::COMMENT--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<!--JavascriptFiles/foswikiPref-->
<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
<body class="foswikiNoJs patternViewPage patternPrintPage">
<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@ -285,6 +285,6 @@ Topic revision: <span class='patternRevInfo'>10 Jul 2011, wojek</span></div>
</body>
<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:50 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/QuickStart?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:59 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
</html>

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

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:46 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:55 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,13 +14,11 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/TutorialSingleHisto?t=1472103694" type="application/x-wiki" title="edit TutorialSingleHisto" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/TutorialSingleHisto?t=1481904042" type="application/x-wiki" title="edit TutorialSingleHisto" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<style class='head TABLEPLUGIN_default' type="text/css" media="all">
<base /><!--[if IE]></base><![endif]--><style class='head TABLEPLUGIN_default' type="text/css" media="all">
body .foswikiTable {border-width:1px}
body .foswikiTable .tableSortIcon img {padding-left:.3em; vertical-align:text-bottom}
body .foswikiTable td {border-style:solid none; vertical-align:top}
@ -34,6 +32,8 @@ body .foswikiTable tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-col
body .foswikiTable tr.foswikiTableRowdataBg1 td {background-color:#f7f7f6}
body .foswikiTable tr.foswikiTableRowdataBg1 td.foswikiSortedCol {background-color:#f0f0ee}
</style><!--TABLEPLUGIN_default-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<style class='head TABLEPLUGIN_specific' type="text/css" media="all">
body .foswikiTable#tableTutorialSingleHisto1 td {vertical-align:middle; vertical-align:top}
body .foswikiTable#tableTutorialSingleHisto1 td.foswikiTableCol0 {text-align:left}
@ -52,10 +52,10 @@ body .foswikiTable#tableTutorialSingleHisto1 th.foswikiSortedCol {background-col
body .foswikiTable#tableTutorialSingleHisto1 tr.foswikiTableRowdataBg0 td {background-color:#ffffff}
body .foswikiTable#tableTutorialSingleHisto1 tr.foswikiTableRowdataBg0 td.foswikiSortedCol {background-color:#f5f5f5}
</style><!--TABLEPLUGIN_specific-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref-->
<link class='head IMAGEPLUGIN' rel="stylesheet" href="../pub/System/ImagePlugin/style.css" type="text/css" media="all" /><!--IMAGEPLUGIN-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head JQUERYPLUGIN::TWISTY' rel='stylesheet' href='../pub/System/TwistyPlugin/twisty327a.css?version=1.6.0' type='text/css' media='all' /><!--JQUERYPLUGIN::TWISTY: requires= missing ids: JavascriptFiles/foswikiPref--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -136,14 +136,14 @@ body .foswikiTable#tableTutorialSingleHisto1 tr.foswikiTableRowdataBg0 td.foswik
<!--<![endif]-->
<!--JQUERYPLUGIN-->
<!--JQUERYPLUGIN::MIGRATE-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::LIVEQUERY-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiPref-->
<!--JQUERYPLUGIN::TWISTY-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JavascriptFiles/foswikiForm-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
<body class="foswikiNoJs patternViewPage patternPrintPage">
@ -401,6 +401,6 @@ Topic revision: <span class='patternRevInfo'>02 Sep 2011, wojek</span></div>
</body>
<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:41:49 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/TutorialSingleHisto?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:00:58 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
</html>

22
doc/html/user/MUSR/WebHome.html
View File

@ -1,6 +1,6 @@
<!DOCTYPE html><html lang="en">
<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:42:26 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:33 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
<head>
<link rel="stylesheet" href="../pub/System/HeadlinesPlugin/style.css" type="text/css" media="all" />
@ -14,14 +14,14 @@
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent" />
<link rel="icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="shortcut icon" href="../pub/Main/WebPreferences/favicon.ico" type="image/x-icon" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1472103697" type="application/x-wiki" title="edit WebHome" />
<link rel="alternate" href="https://intranet.psi.ch/wiki/bin/edit/MUSR/WebHome?t=1481904045" type="application/x-wiki" title="edit WebHome" />
<meta name="TEXT_NUM_TOPICS" content="Number of topics:" />
<meta name="TEXT_MODIFY_SEARCH" content="Modify search" />
<meta name="robots" content="noindex" /><link rel="alternate" type="application/rss+xml" title="RSS Feed" href="WebRsshtml.html" />
<base /><!--[if IE]></base><![endif]--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<base /><!--[if IE]></base><![endif]--><link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head SMILIESPLUGIN' rel='stylesheet' href='../pub/System/SmiliesPlugin/smilies.css' type='text/css' media='all' /><!--SMILIESPLUGIN-->
<link class='head CLASSIFICATIONPLUGIN::CSS' rel="stylesheet" href="../pub/System/ClassificationPlugin/styles.css" media="all" /><!--CLASSIFICATIONPLUGIN::CSS-->
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<link class='head JQUERYPLUGIN::COMMENT' rel='stylesheet' href='../pub/System/CommentPlugin/commentf5b6.css?version=3.0' type='text/css' media='all' /><!--JQUERYPLUGIN::COMMENT-->
<link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS--><link rel='stylesheet' href='../pub/System/SkinTemplates/base.css' media='all' type='text/css' />
<style type="text/css" media="all">
@import url('../pub/System/PatternSkinTheme/layout.css');
@import url('../pub/System/PatternSkinTheme2009/style.css');
@ -106,10 +106,10 @@
<!--JQUERYPLUGIN::FOSWIKI-->
<!--JavascriptFiles/foswikiString-->
<!--JavascriptFiles/foswikiPref-->
<!--JavascriptFiles/foswikiForm-->
<!--PatternSkin/pattern-->
<!--JQUERYPLUGIN::FOSWIKI::PREFERENCES-->
<!--JQUERYPLUGIN::COMMENT--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
<!--JQUERYPLUGIN::COMMENT-->
<!--JavascriptFiles/foswikiForm-->
<!--PatternSkin/pattern--><link class='head FOOTNOTEPLUGIN_LINKCSS' rel="stylesheet" href="../pub/System/FootNotePlugin/styles.css" type="text/css" media="all" /><!--FOOTNOTEPLUGIN_LINKCSS-->
</head>
<body class="foswikiNoJs patternViewPage patternPrintPage">
<span id="PageTop"></span><div class="foswikiPage"><div id="patternScreen">
@ -138,12 +138,12 @@
</li> <li> <a href="MusrFitAcknowledgements.html">Acknowledgements</a>
</li></ul>
<p></p>
-- <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369">BMW</a>) - last update August 24, 2016</div>
-- <a href="http://www.psi.ch/low-energy-muons/people">AS</a> &amp; (<a href="http://www.fsf.org/register_form?referrer=8369">BMW</a>) - last update Dec 15, 2016</div>
<p></p>
<p></p>
</div>
<div class="patternInfo">This topic: MUSR<span class='foswikiSeparator'>&nbsp;&gt;&nbsp;</span>WebHome <br />
Topic revision: <span class='patternRevInfo'>24 Aug 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
Topic revision: <span class='patternRevInfo'>15 Dec 2016, <a href="https://intranet.psi.ch/Main/AndreasSuter">AndreasSuter</a></span></div>
</div>
</div>
</div>
@ -161,6 +161,6 @@ Topic revision: <span class='patternRevInfo'>24 Aug 2016, <a href="https://intr
</body>
<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Thu, 25 Aug 2016 05:42:27 GMT -->
<!-- Mirrored from intranet.psi.ch/MUSR/WebHome?cover=print by HTTrack Website Copier/3.x [XR&CO'2010], Fri, 16 Dec 2016 16:01:34 GMT -->
<!-- Added by HTTrack --><meta http-equiv="content-type" content="text/html;charset=utf-8"><!-- /Added by HTTrack -->
</html>

104
src/classes/PFitter.cpp
View File

@ -1564,64 +1564,66 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
}
// handle expected chisq if applicable
if (fUseChi2) {
fParams = *(fRunInfo->GetMsrParamList()); // get the update parameters back
fParams = *(fRunInfo->GetMsrParamList()); // get the update parameters back
// calculate expected chisq
std::vector<Double_t> param;
Double_t totalExpectedChisq = 0.0;
std::vector<Double_t> expectedChisqPerHisto;
std::vector<UInt_t> ndfPerHisto;
// calculate expected chisq
std::vector<Double_t> param;
Double_t totalExpectedChisq = 0.0;
std::vector<Double_t> expectedChisqPerHisto;
std::vector<UInt_t> ndfPerHisto;
for (UInt_t i=0; i<fParams.size(); i++)
param.push_back(fParams[i].fValue);
for (UInt_t i=0; i<fParams.size(); i++)
param.push_back(fParams[i].fValue);
fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerHisto);
// CalcExpectedChiSquare handles both, chisq and mlh
fFitterFcn->CalcExpectedChiSquare(param, totalExpectedChisq, expectedChisqPerHisto);
// calculate chisq per run
std::vector<Double_t> chisqPerHisto;
for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
// calculate chisq per run
std::vector<Double_t> chisqPerHisto;
for (UInt_t i=0; i<fRunInfo->GetMsrRunList()->size(); i++) {
if (fUseChi2)
chisqPerHisto.push_back(fRunListCollection->GetSingleRunChisq(param, i));
}
if (totalExpectedChisq != 0.0) { // i.e. applicable for single histogram fits only
// get the ndf's of the histos
UInt_t ndf_histo;
for (UInt_t i=0; i<expectedChisqPerHisto.size(); i++) {
ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
ndfPerHisto.push_back(ndf_histo);
}
// feed the msr-file handler
PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
if (statistics) {
statistics->fMinPerHisto = chisqPerHisto;
statistics->fMinExpected = totalExpectedChisq;
statistics->fMinExpectedPerHisto = expectedChisqPerHisto;
statistics->fNdfPerHisto = ndfPerHisto;
}
} else if (chisqPerHisto.size() > 1) { // in case expected chisq is not applicable like for asymmetry fits
UInt_t ndf_histo = 0;
for (UInt_t i=0; i<chisqPerHisto.size(); i++) {
ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
ndfPerHisto.push_back(ndf_histo);
}
// feed the msr-file handler
PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
if (statistics) {
statistics->fMinPerHisto = chisqPerHisto;
statistics->fNdfPerHisto = ndfPerHisto;
}
}
// clean up
param.clear();
expectedChisqPerHisto.clear();
ndfPerHisto.clear();
chisqPerHisto.clear();
else
chisqPerHisto.push_back(fRunListCollection->GetSingleRunMaximumLikelihood(param, i));
}
if (totalExpectedChisq != 0.0) { // i.e. applicable for single histogram fits only
// get the ndf's of the histos
UInt_t ndf_histo;
for (UInt_t i=0; i<expectedChisqPerHisto.size(); i++) {
ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
ndfPerHisto.push_back(ndf_histo);
}
// feed the msr-file handler
PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
if (statistics) {
statistics->fMinPerHisto = chisqPerHisto;
statistics->fMinExpected = totalExpectedChisq;
statistics->fMinExpectedPerHisto = expectedChisqPerHisto;
statistics->fNdfPerHisto = ndfPerHisto;
}
} else if (chisqPerHisto.size() > 1) { // in case expected chisq is not applicable like for asymmetry fits
UInt_t ndf_histo = 0;
for (UInt_t i=0; i<chisqPerHisto.size(); i++) {
ndf_histo = fFitterFcn->GetNoOfFittedBins(i) - fRunInfo->GetNoOfFitParameters(i);
ndfPerHisto.push_back(ndf_histo);
}
// feed the msr-file handler
PMsrStatisticStructure *statistics = fRunInfo->GetMsrStatistic();
if (statistics) {
statistics->fMinPerHisto = chisqPerHisto;
statistics->fNdfPerHisto = ndfPerHisto;
}
}
// clean up
param.clear();
expectedChisqPerHisto.clear();
ndfPerHisto.clear();
chisqPerHisto.clear();
cout << ">> PFitter::ExecuteSave(): will write minuit2 output file ..." << endl;
ofstream fout;

11
src/classes/PFitterFcn.cpp
View File

@ -110,15 +110,20 @@ void PFitterFcn::CalcExpectedChiSquare(const std::vector<Double_t> &par, Double_
totalExpectedChisq = 0.0;
expectedChisqPerRun.clear();
// only do something for chisq
Double_t value = 0.0;
if (fUseChi2) {
Double_t value = 0.0;
// single histo
for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
value = fRunListCollection->GetSingleHistoChisqExpected(par, i); // calculate the expected chisq for single histo run block 'i'
expectedChisqPerRun.push_back(value);
totalExpectedChisq += value;
}
} else { // log max. likelihood
// single histo
for (UInt_t i=0; i<fRunListCollection->GetNoOfSingleHisto(); i++) {
value = fRunListCollection->GetSingleHistoMaximumLikelihoodExpected(par, i); // calculate the expected mlh for single histo run block 'i'
expectedChisqPerRun.push_back(value);
totalExpectedChisq += value;
}
}
}

332
src/classes/PFourier.cpp
View File

@ -37,7 +37,9 @@ using namespace std;
#include "TF1.h"
#include "TAxis.h"
//#include "TFile.h"
#include "Minuit2/FunctionMinimum.h"
#include "Minuit2/MnUserParameters.h"
#include "Minuit2/MnMinimize.h"
#include "PMusr.h"
#include "PFourier.h"
@ -45,6 +47,227 @@ using namespace std;
#define PI 3.14159265358979312
#define PI_HALF 1.57079632679489656
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// PFTPhaseCorrection
//--------------------------------------------------------------------------
// Constructor
//--------------------------------------------------------------------------
/**
*
*/
PFTPhaseCorrection::PFTPhaseCorrection(const Int_t minBin, const Int_t maxBin) :
fMinBin(minBin), fMaxBin(maxBin)
{
Init();
}
//--------------------------------------------------------------------------
// Constructor
//--------------------------------------------------------------------------
/**
*
*/
PFTPhaseCorrection::PFTPhaseCorrection(vector<Double_t> &reFT, vector<Double_t> &imFT, const Int_t minBin, const Int_t maxBin) :
fReal(reFT), fImag(imFT), fMinBin(minBin), fMaxBin(maxBin)
{
Init();
if (fMinBin == -1)
fMinBin = 0;
if (fMaxBin == -1)
fMaxBin = fReal.size();
if (fMaxBin > fReal.size())
fMaxBin = fReal.size();
fRealPh.resize(fReal.size());
fImagPh.resize(fReal.size());
}
//--------------------------------------------------------------------------
// Minimize (public)
//--------------------------------------------------------------------------
/**
*
*/
void PFTPhaseCorrection::Minimize()
{
// create Minuit2 parameters
ROOT::Minuit2::MnUserParameters upar;
upar.Add("c0", fPh_c0, 2.0);
upar.Add("c1", fPh_c1, 2.0);
// create minimizer
ROOT::Minuit2::MnMinimize mn_min(*this, upar);
// minimize
ROOT::Minuit2::FunctionMinimum min = mn_min();
if (min.IsValid()) {
fPh_c0 = min.UserState().Value("c0");
fPh_c1 = min.UserState().Value("c1");
fMin = min.Fval();
} else {
fMin = -1.0;
fValid = false;
cout << endl << ">> **WARNING** minimize failed to find a minimum for the real FT phase correction ..." << endl;
return;
}
}
//--------------------------------------------------------------------------
// GetPhaseCorrectionParam (public)
//--------------------------------------------------------------------------
/**
*
*/
Double_t PFTPhaseCorrection::GetPhaseCorrectionParam(UInt_t idx)
{
Double_t result=0.0;
if (idx == 0)
result = fPh_c0;
else if (idx == 1)
result = fPh_c1;
else
cerr << ">> **ERROR** requested phase correction parameter with index=" << idx << " does not exist!" << endl;
return result;
}
//--------------------------------------------------------------------------
// GetMinimum (public)
//--------------------------------------------------------------------------
/**
*
*/
Double_t PFTPhaseCorrection::GetMinimum()
{
if (!fValid) {
cerr << ">> **ERROR** requested minimum is invalid!" << endl;
return -1.0;
}
return fMin;
}
//--------------------------------------------------------------------------
// Init (private)
//--------------------------------------------------------------------------
/**
*
*/
void PFTPhaseCorrection::Init()
{
fValid = true;
fPh_c0 = 0.0;
fPh_c1 = 0.0;
fGamma = 1.0;
fMin = -1.0;
}
//--------------------------------------------------------------------------
// CalcPhasedFT (private)
//--------------------------------------------------------------------------
/**
*
*/
void PFTPhaseCorrection::CalcPhasedFT() const
{
Double_t phi=0.0;
Double_t w=0.0;
for (UInt_t i=0; i<fRealPh.size(); i++) {
w = (Double_t)i / (Double_t)fReal.size();
phi = fPh_c0 + fPh_c1 * w;
fRealPh[i] = fReal[i]*cos(phi) - fImag[i]*sin(phi);
fImagPh[i] = fReal[i]*sin(phi) + fImag[i]*cos(phi);
}
}
//--------------------------------------------------------------------------
// CalcRealPhFTDerivative (private)
//--------------------------------------------------------------------------
/**
*
*/
void PFTPhaseCorrection::CalcRealPhFTDerivative() const
{
fRealPhD.resize(fRealPh.size());
fRealPhD[0] = 1.0;
fRealPhD[fRealPh.size()-1] = 1.0;
for (UInt_t i=1; i<fRealPh.size()-1; i++)
fRealPhD[i] = fRealPh[i+1]-fRealPh[i];
}
//--------------------------------------------------------------------------
// Penalty (private)
//--------------------------------------------------------------------------
/**
*
*/
Double_t PFTPhaseCorrection::Penalty() const
{
Double_t penalty = 0.0;
for (UInt_t i=fMinBin; i<fMaxBin; i++) {
if (fRealPh[i] < 0.0)
penalty += fRealPh[i]*fRealPh[i];
}
return fGamma*penalty;
}
//--------------------------------------------------------------------------
// Entropy (private)
//--------------------------------------------------------------------------
/**
*
*/
Double_t PFTPhaseCorrection::Entropy() const
{
Double_t norm = 0.0;
for (UInt_t i=fMinBin; i<fMaxBin; i++)
norm += fabs(fRealPhD[i]);
Double_t entropy = 0.0;
Double_t dval = 0.0, hh = 0.0;
for (UInt_t i=fMinBin; i<fMaxBin; i++) {
dval = fabs(fRealPhD[i]);
if (dval > 1.0e-15) {
hh = dval / norm;
entropy -= hh * log(hh);
}
}
return entropy;
}
//--------------------------------------------------------------------------
// operator() (private)
//--------------------------------------------------------------------------
/**
*
*/
double PFTPhaseCorrection::operator()(const vector<double> &par) const
{
// par : [0]: c0, [1]: c1
fPh_c0 = par[0];
fPh_c1 = par[1];
CalcPhasedFT();
CalcRealPhFTDerivative();
return Entropy()+Penalty();
}
//++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
// PFourier
//--------------------------------------------------------------------------
// Constructor
//--------------------------------------------------------------------------
@ -73,6 +296,7 @@ PFourier::PFourier(TH1F *data, Int_t unitTag, Double_t startTime, Double_t endTi
fValid = true;
fIn = 0;
fOut = 0;
//as fPhCorrectedReFT = 0;
fApodization = F_APODIZATION_NONE;
@ -160,6 +384,8 @@ PFourier::~PFourier()
fftw_free(fIn);
if (fOut)
fftw_free(fOut);
//as if (fPhCorrectedReFT)
//as delete fPhCorrectedReFT;
}
//--------------------------------------------------------------------------
@ -259,104 +485,100 @@ TH1F* PFourier::GetRealFourier(const Double_t scale)
}
//--------------------------------------------------------------------------
// GetPhaseOptRealFourier (public)
// GetPhaseOptRealFourier (public, static)
//--------------------------------------------------------------------------
/**
* <p>returns the phase corrected real Fourier transform. The correction angle is
* past back as well.
* <p>Currently it simply does the following thing: (i) rotate the complex Fourier
* transform through all angles in 1/2° steps, i.e.
* \f$ f_{\rm rot} = (f_{\rm real} + i f_{\rm imag}) \exp(- \alpha)\f$,
* hence \f$ f_{\rm rot} = f_{\rm real} \cos(\alpha) + f_{\rm imag} \sin(\alpha)\f$.
* (ii) search the maximum of \f$ sum_{\alpha} {\cal R}\{f_{\rm rot}\}\f$ for all
* \f$\alpha\f$. From this one gets \f$\alpha_{\rm opt}\f$. (iii) The 'optimal'
* real Fourier transform is \f$f_{\rm opt} = (f_{\rm real} + i f_{\rm imag})
* \exp(- \alpha_{\rm opt})\f$.
* <p>returns the phase corrected real Fourier transform.
*
* \return the TH1F histo of the phase 'optimzed' real Fourier transform.
*
* \param phase return value of the optimal phase
* \param re real part Fourier histogram
* \param im imaginary part Fourier histogram
* \param phase return value of the optimal phase dispersion phase[0]+phase[1]*i/N
* \param scale normalisation factor
* \param min minimal freq / field from which to optimise. Given in the choosen unit.
* \param max maximal freq / field up to which to optimise. Given in the choosen unit.
*/
TH1F* PFourier::GetPhaseOptRealFourier(Double_t &phase, const Double_t scale, const Double_t min, const Double_t max)
TH1F* PFourier::GetPhaseOptRealFourier(const TH1F *re, const TH1F *im, vector<Double_t> &phase,
const Double_t scale, const Double_t min, const Double_t max)
{
UInt_t noOfFourierBins = 0;
if (fNoOfBins % 2 == 0)
noOfFourierBins = fNoOfBins/2;
else
noOfFourierBins = (fNoOfBins+1)/2;
if ((re == 0) || (im == 0))
return 0;
UInt_t minBin = 0;
UInt_t maxBin = noOfFourierBins;
phase.resize(2); // c0, c1
TAxis *axis = re->GetXaxis();
Int_t minBin = 1;
Int_t maxBin = axis->GetNbins();
Int_t noOfBins = axis->GetNbins();
Double_t res = axis->GetBinWidth(1);
// check if minimum frequency is given. If yes, get the proper minBin
if (min != -1.0) {
minBin = (UInt_t)(min/fResolution);
minBin = axis->FindFixBin(min);
if ((minBin == 0) || (minBin > maxBin)) {
minBin = 1;
cerr << "**WARNING** minimum frequency/field out of range. Will adopted it." << endl;
}
}
// check if maximum frequency is given. If yes, get the proper maxBin
if (max != -1.0) {
maxBin = (UInt_t)(max/fResolution);
if (maxBin >= noOfFourierBins) {
maxBin = noOfFourierBins;
maxBin = axis->FindFixBin(max);
if ((maxBin == 0) || (maxBin > axis->GetNbins())) {
maxBin = axis->GetNbins();
cerr << "**WARNING** maximum frequency/field out of range. Will adopted it." << endl;
}
}
// copy the real/imag Fourier from min to max
vector<Double_t> realF, imagF;
for (UInt_t i=minBin; i<=maxBin; i++) {
realF.push_back(fOut[i][0]);
imagF.push_back(fOut[i][1]);
for (Int_t i=minBin; i<=maxBin; i++) {
realF.push_back(re->GetBinContent(i));
imagF.push_back(im->GetBinContent(i));
}
// rotate trough real/imag Fourier through 360° with a 1/2° resolution and keep the integral
Double_t rotRealIntegral[720];
Double_t sum = 0.0;
Double_t da = 8.72664625997164774e-03; // pi / 360
for (UInt_t i=0; i<720; i++) {
sum = 0.0;
for (UInt_t j=0; j<realF.size(); j++) {
sum += realF[j]*cos(da*i) + imagF[j]*sin(da*i);
}
rotRealIntegral[i] = sum;
// optimize real FT phase
PFTPhaseCorrection *phCorrectedReFT = new PFTPhaseCorrection(realF, imagF);
if (phCorrectedReFT == 0) {
cerr << endl << "**SEVERE ERROR** couldn't invoke PFTPhaseCorrection object." << endl;
return 0;
}
// find the maximum in rotRealIntegral
Double_t maxRot = 0.0;
UInt_t maxRotBin = 0;
for (UInt_t i=0; i<720; i++) {
if (maxRot < rotRealIntegral[i]) {
maxRot = rotRealIntegral[i];
maxRotBin = i;
}
phCorrectedReFT->Minimize();
if (!phCorrectedReFT->IsValid()) {
cerr << endl << "**ERROR** could not find a valid phase correction minimum." << endl;
return 0;
}
// keep the optimal phase
phase = maxRotBin*da;
phase[0] = phCorrectedReFT->GetPhaseCorrectionParam(0);
phase[1] = phCorrectedReFT->GetPhaseCorrectionParam(1);
// clean up
if (phCorrectedReFT) {
delete phCorrectedReFT;
phCorrectedReFT = 0;
}
realF.clear();
imagF.clear();
// invoke the real phase optimised histo to be filled. Caller is the owner!
Char_t name[256];
Char_t title[256];
snprintf(name, sizeof(name), "%s_Fourier_PhOptRe", fData->GetName());
snprintf(title, sizeof(title), "%s_Fourier_PhOptRe", fData->GetTitle());
snprintf(name, sizeof(name), "%s_Fourier_PhOptRe", re->GetName());
snprintf(title, sizeof(title), "%s_Fourier_PhOptRe", re->GetTitle());
TH1F *realPhaseOptFourier = new TH1F(name, title, noOfFourierBins, -fResolution/2.0, (Double_t)(noOfFourierBins-1)*fResolution+fResolution/2.0);
TH1F *realPhaseOptFourier = new TH1F(name, title, noOfBins, -res/2.0, (Double_t)(noOfBins-1)*res+res/2.0);
if (realPhaseOptFourier == 0) {
fValid = false;
cerr << endl << "**SEVERE ERROR** couldn't allocate memory for the real part of the Fourier transform." << endl;
return 0;
}
// fill realFourier vector
for (UInt_t i=0; i<noOfFourierBins; i++) {
realPhaseOptFourier->SetBinContent(i+1, scale*(fOut[i][0]*cos(phase) + fOut[i][1]*sin(phase)));
Double_t ph;
for (Int_t i=0; i<noOfBins; i++) {
ph = phase[0] + phase[1] * (Double_t)((Int_t)i-(Int_t)minBin) / (Double_t)(maxBin-minBin);
realPhaseOptFourier->SetBinContent(i+1, scale*(re->GetBinContent(i+1)*cos(ph) - im->GetBinContent(i+1)*sin(ph)));
realPhaseOptFourier->SetBinError(i+1, 0.0);
}

270
src/classes/PFourierCanvas.cpp
View File

@ -341,6 +341,16 @@ void PFourierCanvas::HandleCmdKey(Int_t event, Int_t x, Int_t y, TObject *select
CleanupAverage();
PlotFourier();
}
} else if (x == 'c') {
Int_t state = fFourierPad->GetCrosshair();
if (state == 0) {
fMainCanvas->ToggleEventStatus();
fFourierPad->SetCrosshair(2);
} else {
fMainCanvas->ToggleEventStatus();
fFourierPad->SetCrosshair(0);
}
fMainCanvas->Update();
} else if (x == '+') { // increment phase (Fourier real/imag)
IncrementFourierPhase();
} else if (x == '-') { // decrement phase (Fourier real/imag)
@ -366,32 +376,62 @@ void PFourierCanvas::HandleMenuPopup(Int_t id)
fPopupFourier->UnCheckEntries();
fPopupFourier->CheckEntry(P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_REAL);
fCurrentPlotView = FOURIER_PLOT_REAL;
PlotFourier();
if (!fAveragedView) {
PlotFourier();
} else {
HandleAverage();
PlotAverage();
}
} else if (id == P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_IMAG) {
fPopupFourier->UnCheckEntries();
fPopupFourier->CheckEntry(P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_IMAG);
fCurrentPlotView = FOURIER_PLOT_IMAG;
PlotFourier();
if (!fAveragedView) {
PlotFourier();
} else {
HandleAverage();
PlotAverage();
}
} else if (id == P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_REAL_AND_IMAG) {
fPopupFourier->UnCheckEntries();
fPopupFourier->CheckEntry(P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_REAL_AND_IMAG);
fCurrentPlotView = P_MENU_ID_FOURIER_REAL_AND_IMAG;
PlotFourier();
if (!fAveragedView) {
PlotFourier();
} else {
HandleAverage();
PlotAverage();
}
} else if (id == P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PWR) {
fPopupFourier->UnCheckEntries();
fPopupFourier->CheckEntry(P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PWR);
fCurrentPlotView = FOURIER_PLOT_POWER;
PlotFourier();
if (!fAveragedView) {
PlotFourier();
} else {
HandleAverage();
PlotAverage();
}
} else if (id == P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PHASE) {
fPopupFourier->UnCheckEntries();
fPopupFourier->CheckEntry(P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PHASE);
fCurrentPlotView = FOURIER_PLOT_PHASE;
PlotFourier();
if (!fAveragedView) {
PlotFourier();
} else {
HandleAverage();
PlotAverage();
}
} else if (id == P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PHASE_OPT_REAL) {
fPopupFourier->UnCheckEntries();
fPopupFourier->CheckEntry(P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PHASE_OPT_REAL);
fCurrentPlotView = FOURIER_PLOT_PHASE_OPT_REAL;
PlotFourier();
if (!fAveragedView) {
PlotFourier();
} else {
HandleAverage();
PlotAverage();
}
} else if (id == P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PHASE_PLUS) {
IncrementFourierPhase();
} else if (id == P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_PHASE_MINUS) {
@ -624,6 +664,12 @@ void PFourierCanvas::ExportData(const Char_t *pathFileName)
xMinBin = fFourierHistos[0].dataFourierIm->GetXaxis()->GetFirst();
xMaxBin = fFourierHistos[0].dataFourierIm->GetXaxis()->GetLast();
break;
case FOURIER_PLOT_REAL_AND_IMAG:
xAxis = fFourierHistos[0].dataFourierRe->GetXaxis()->GetTitle();
yAxis = TString("Real+Imag");
xMinBin = fFourierHistos[0].dataFourierRe->GetXaxis()->GetFirst();
xMaxBin = fFourierHistos[0].dataFourierRe->GetXaxis()->GetLast();
break;
case FOURIER_PLOT_POWER:
xAxis = fFourierHistos[0].dataFourierPwr->GetXaxis()->GetTitle();
yAxis = TString("Power");
@ -703,42 +749,46 @@ void PFourierCanvas::ExportData(const Char_t *pathFileName)
for (UInt_t j=0; j<fFourierHistos.size()-1; j++) {
switch (fCurrentPlotView) {
case FOURIER_PLOT_REAL:
fout << fFourierHistos[j].dataFourierRe->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierRe->GetBinContent(i) << ", ";
break;
fout << fFourierHistos[j].dataFourierRe->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierRe->GetBinContent(i) << ", ";
break;
case FOURIER_PLOT_IMAG:
fout << fFourierHistos[j].dataFourierIm->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierIm->GetBinContent(i) << ", ";
break;
fout << fFourierHistos[j].dataFourierIm->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierIm->GetBinContent(i) << ", ";
break;
case FOURIER_PLOT_REAL_AND_IMAG:
break;
case FOURIER_PLOT_POWER:
fout << fFourierHistos[j].dataFourierPwr->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierPwr->GetBinContent(i) << ", ";
break;
fout << fFourierHistos[j].dataFourierPwr->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierPwr->GetBinContent(i) << ", ";
break;
case FOURIER_PLOT_PHASE:
fout << fFourierHistos[j].dataFourierPhase->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierPhase->GetBinContent(i) << ", ";
break;
fout << fFourierHistos[j].dataFourierPhase->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierPhase->GetBinContent(i) << ", ";
break;
case FOURIER_PLOT_PHASE_OPT_REAL:
fout << fFourierHistos[j].dataFourierPhaseOptReal->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierPhaseOptReal->GetBinContent(i) << ", ";
break;
fout << fFourierHistos[j].dataFourierPhaseOptReal->GetBinCenter(i) << ", " << fFourierHistos[j].dataFourierPhaseOptReal->GetBinContent(i) << ", ";
break;
default:
break;
break;
}
}
switch (fCurrentPlotView) {
case FOURIER_PLOT_REAL:
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierRe->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierRe->GetBinContent(i) << endl;
break;
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierRe->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierRe->GetBinContent(i) << endl;
break;
case FOURIER_PLOT_IMAG:
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierIm->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierIm->GetBinContent(i) << endl;
break;
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierIm->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierIm->GetBinContent(i) << endl;
break;
case FOURIER_PLOT_REAL_AND_IMAG:
break;
case FOURIER_PLOT_POWER:
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierPwr->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierPwr->GetBinContent(i) << endl;
break;
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierPwr->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierPwr->GetBinContent(i) << endl;
break;
case FOURIER_PLOT_PHASE:
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierPhase->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierPhase->GetBinContent(i) << endl;
break;
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierPhase->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierPhase->GetBinContent(i) << endl;
break;
case FOURIER_PLOT_PHASE_OPT_REAL:
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierPhaseOptReal->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierPhaseOptReal->GetBinContent(i) << endl;
break;
fout << fFourierHistos[fFourierHistos.size()-1].dataFourierPhaseOptReal->GetBinCenter(i) << ", " << fFourierHistos[fFourierHistos.size()-1].dataFourierPhaseOptReal->GetBinContent(i) << endl;
break;
default:
break;
break;
}
}
}
@ -804,8 +854,10 @@ void PFourierCanvas::InitFourierDataSets()
fFourierHistos[i].dataFourierIm = fFourier[i]->GetImaginaryFourier();
fFourierHistos[i].dataFourierPwr = fFourier[i]->GetPowerFourier();
fFourierHistos[i].dataFourierPhase = fFourier[i]->GetPhaseFourier();
fFourierHistos[i].dataFourierPhaseOptReal = fFourier[i]->GetPhaseOptRealFourier(fFourierHistos[i].optPhase, 1.0, fInitialXRange[0], fInitialXRange[1]);
cout << "debug> histo[" << i << "]: opt. phase = " << fFourierHistos[i].optPhase * 180.0 / TMath::Pi() << "°" << endl;
if (fCurrentPlotView == FOURIER_PLOT_PHASE_OPT_REAL) {
fFourierHistos[i].dataFourierPhaseOptReal = fFourier[i]->GetPhaseOptRealFourier(fFourierHistos[i].dataFourierRe,
fFourierHistos[i].dataFourierIm, fFourierHistos[i].optPhase, 1.0, fInitialXRange[0], fInitialXRange[1]);
}
}
// rescale histo to abs(maximum) == 1
@ -870,17 +922,19 @@ void PFourierCanvas::InitFourierDataSets()
}
}
// phase opt real
for (UInt_t i=0; i<fFourierHistos.size(); i++) {
for (Int_t j=start; j<=end; j++) {
dval = fFourierHistos[i].dataFourierPhaseOptReal->GetBinContent(j);
if (fabs(dval) > max)
max = dval;
if (fCurrentPlotView == FOURIER_PLOT_PHASE_OPT_REAL) {
// phase opt real
for (UInt_t i=0; i<fFourierHistos.size(); i++) {
for (Int_t j=start; j<=end; j++) {
dval = fFourierHistos[i].dataFourierPhaseOptReal->GetBinContent(j);
if (fabs(dval) > max)
max = dval;
}
}
}
for (UInt_t i=0; i<fFourierHistos.size(); i++) {
for (Int_t j=1; j<fFourierHistos[i].dataFourierPhaseOptReal->GetNbinsX(); j++) {
fFourierHistos[i].dataFourierPhaseOptReal->SetBinContent(j, fFourierHistos[i].dataFourierPhaseOptReal->GetBinContent(j)/fabs(max));
for (UInt_t i=0; i<fFourierHistos.size(); i++) {
for (Int_t j=1; j<fFourierHistos[i].dataFourierPhaseOptReal->GetNbinsX(); j++) {
fFourierHistos[i].dataFourierPhaseOptReal->SetBinContent(j, fFourierHistos[i].dataFourierPhaseOptReal->GetBinContent(j)/fabs(max));
}
}
}
@ -894,8 +948,10 @@ void PFourierCanvas::InitFourierDataSets()
fFourierHistos[i].dataFourierPwr->SetLineColor(fColorList[i]);
fFourierHistos[i].dataFourierPhase->SetMarkerColor(fColorList[i]);
fFourierHistos[i].dataFourierPhase->SetLineColor(fColorList[i]);
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerColor(fColorList[i]);
fFourierHistos[i].dataFourierPhaseOptReal->SetLineColor(fColorList[i]);
if (fCurrentPlotView == FOURIER_PLOT_PHASE_OPT_REAL) {
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerColor(fColorList[i]);
fFourierHistos[i].dataFourierPhaseOptReal->SetLineColor(fColorList[i]);
}
}
// set the marker symbol and size
@ -908,8 +964,10 @@ void PFourierCanvas::InitFourierDataSets()
fFourierHistos[i].dataFourierPwr->SetMarkerSize(0.7);
fFourierHistos[i].dataFourierPhase->SetMarkerStyle(fMarkerList[i]);
fFourierHistos[i].dataFourierPhase->SetMarkerSize(0.7);
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerStyle(fMarkerList[i]);
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerSize(0.7);
if (fCurrentPlotView == FOURIER_PLOT_PHASE_OPT_REAL) {
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerStyle(fMarkerList[i]);
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerSize(0.7);
}
}
// initialize average histos
@ -1107,6 +1165,10 @@ void PFourierCanvas::HandleAverage()
TString name("");
Double_t dval=0.0;
Bool_t phaseOptRealPresent = false;
if (fFourierHistos[0].dataFourierPhaseOptReal != 0)
phaseOptRealPresent = true;
// check if ALL data shall be averaged
if (fAveragedView) {
fFourierAverage.resize(1);
@ -1132,10 +1194,12 @@ void PFourierCanvas::HandleAverage()
fFourierHistos[0].dataFourierPhase->GetXaxis()->GetXmin(),
fFourierHistos[0].dataFourierPhase->GetXaxis()->GetXmax());
name = TString(fFourierHistos[0].dataFourierPhaseOptReal->GetTitle()) + "_avg";
fFourierAverage[0].dataFourierPhaseOptReal = new TH1F(name, name, fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmin(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmax());
if (phaseOptRealPresent) {
name = TString(fFourierHistos[0].dataFourierPhaseOptReal->GetTitle()) + "_avg";
fFourierAverage[0].dataFourierPhaseOptReal = new TH1F(name, name, fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmin(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmax());
}
// real average
for (Int_t j=0; j<fFourierHistos[0].dataFourierRe->GetNbinsX(); j++) {
@ -1197,20 +1261,22 @@ void PFourierCanvas::HandleAverage()
fFourierAverage[0].dataFourierPhase->SetMarkerSize(0.8);
fFourierAverage[0].dataFourierPhase->SetMarkerStyle(22);
// phase optimised real average
for (Int_t j=0; j<fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(); j++) {
dval = 0.0;
for (UInt_t i=0; i<fFourierHistos.size(); i++) {
if (j < fFourierHistos[i].dataFourierPhaseOptReal->GetNbinsX())
dval += GetInterpolatedValue(fFourierHistos[i].dataFourierPhaseOptReal, fFourierHistos[0].dataFourierPhaseOptReal->GetBinCenter(j));
if (phaseOptRealPresent) {
// phase optimised real average
for (Int_t j=0; j<fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(); j++) {
dval = 0.0;
for (UInt_t i=0; i<fFourierHistos.size(); i++) {
if (j < fFourierHistos[i].dataFourierPhaseOptReal->GetNbinsX())
dval += GetInterpolatedValue(fFourierHistos[i].dataFourierPhaseOptReal, fFourierHistos[0].dataFourierPhaseOptReal->GetBinCenter(j));
}
fFourierAverage[0].dataFourierPhaseOptReal->SetBinContent(j, dval/fFourierHistos.size());
}
fFourierAverage[0].dataFourierPhaseOptReal->SetBinContent(j, dval/fFourierHistos.size());
// set marker color, line color, maker size, marker type
fFourierAverage[0].dataFourierPhaseOptReal->SetMarkerColor(kBlack);
fFourierAverage[0].dataFourierPhaseOptReal->SetLineColor(kBlack);
fFourierAverage[0].dataFourierPhaseOptReal->SetMarkerSize(0.8);
fFourierAverage[0].dataFourierPhaseOptReal->SetMarkerStyle(22);
}
// set marker color, line color, maker size, marker type
fFourierAverage[0].dataFourierPhaseOptReal->SetMarkerColor(kBlack);
fFourierAverage[0].dataFourierPhaseOptReal->SetLineColor(kBlack);
fFourierAverage[0].dataFourierPhaseOptReal->SetMarkerSize(0.8);
fFourierAverage[0].dataFourierPhaseOptReal->SetMarkerStyle(22);
}
// check if per data set shall be averaged
@ -1274,10 +1340,12 @@ void PFourierCanvas::HandleAverage()
fFourierHistos[0].dataFourierPhase->GetXaxis()->GetXmin(),
fFourierHistos[0].dataFourierPhase->GetXaxis()->GetXmax());
name = TString(fFourierHistos[start].dataFourierPhaseOptReal->GetTitle()) + "_avg";
fFourierAverage[i].dataFourierPhaseOptReal = new TH1F(name, name, fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmin(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmax());
if (phaseOptRealPresent) {
name = TString(fFourierHistos[start].dataFourierPhaseOptReal->GetTitle()) + "_avg";
fFourierAverage[i].dataFourierPhaseOptReal = new TH1F(name, name, fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmin(),
fFourierHistos[0].dataFourierPhaseOptReal->GetXaxis()->GetXmax());
}
// real average
for (Int_t j=0; j<fFourierHistos[0].dataFourierRe->GetNbinsX(); j++) {
@ -1339,24 +1407,61 @@ void PFourierCanvas::HandleAverage()
fFourierAverage[i].dataFourierPhase->SetMarkerSize(0.8);
fFourierAverage[i].dataFourierPhase->SetMarkerStyle(22); // closed up triangle
// phase optimised real average
for (Int_t j=0; j<fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(); j++) {
dval = 0.0;
for (Int_t k=start; k<=end; k++) {
if (j < fFourierHistos[k].dataFourierPhaseOptReal->GetNbinsX())
dval += GetInterpolatedValue(fFourierHistos[k].dataFourierPhaseOptReal, fFourierHistos[0].dataFourierPhaseOptReal->GetBinCenter(j));
if (phaseOptRealPresent) {
// phase optimised real average
for (Int_t j=0; j<fFourierHistos[0].dataFourierPhaseOptReal->GetNbinsX(); j++) {
dval = 0.0;
for (Int_t k=start; k<=end; k++) {
if (j < fFourierHistos[k].dataFourierPhaseOptReal->GetNbinsX())
dval += GetInterpolatedValue(fFourierHistos[k].dataFourierPhaseOptReal, fFourierHistos[0].dataFourierPhaseOptReal->GetBinCenter(j));
}
fFourierAverage[i].dataFourierPhaseOptReal->SetBinContent(j, dval/(end-start+1));
}
fFourierAverage[i].dataFourierPhaseOptReal->SetBinContent(j, dval/(end-start+1));
// set marker color, line color, maker size, marker type
fFourierAverage[i].dataFourierPhaseOptReal->SetMarkerColor(fColorList[i]);
fFourierAverage[i].dataFourierPhaseOptReal->SetLineColor(fColorList[i]);
fFourierAverage[i].dataFourierPhaseOptReal->SetMarkerSize(0.8);
fFourierAverage[i].dataFourierPhaseOptReal->SetMarkerStyle(22); // closed up triangle
}
// set marker color, line color, maker size, marker type
fFourierAverage[i].dataFourierPhaseOptReal->SetMarkerColor(fColorList[i]);
fFourierAverage[i].dataFourierPhaseOptReal->SetLineColor(fColorList[i]);
fFourierAverage[i].dataFourierPhaseOptReal->SetMarkerSize(0.8);
fFourierAverage[i].dataFourierPhaseOptReal->SetMarkerStyle(22); // closed up triangle
}
}
}
//--------------------------------------------------------------------------
// CalcPhaseOptReal (private)
//--------------------------------------------------------------------------
/**
* <p>calculate the phase opt. real FT
*/
void PFourierCanvas::CalcPhaseOptReal()
{
Int_t start = fFourierHistos[0].dataFourierRe->FindFixBin(fInitialXRange[0]);
Int_t end = fFourierHistos[0].dataFourierRe->FindFixBin(fInitialXRange[1]);
Double_t dval=0.0, max=0.0;
for (UInt_t i=0; i<fFourierHistos.size(); i++) {
fFourierHistos[i].dataFourierPhaseOptReal = fFourier[i]->GetPhaseOptRealFourier(fFourierHistos[i].dataFourierRe,
fFourierHistos[i].dataFourierIm, fFourierHistos[i].optPhase, 1.0, fInitialXRange[0], fInitialXRange[1]);
// normalize it
max = 0.0;
for (Int_t j=start; j<=end; j++) {
dval = fFourierHistos[i].dataFourierPhaseOptReal->GetBinContent(j);
if (fabs(dval) > max)
max = dval;
}
for (Int_t j=1; j<fFourierHistos[i].dataFourierPhaseOptReal->GetNbinsX(); j++) {
fFourierHistos[i].dataFourierPhaseOptReal->SetBinContent(j, fFourierHistos[i].dataFourierPhaseOptReal->GetBinContent(j)/fabs(max));
}
// set the marker and line color
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerColor(fColorList[i]);
fFourierHistos[i].dataFourierPhaseOptReal->SetLineColor(fColorList[i]);
// set the marker symbol and size
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerStyle(fMarkerList[i]);
fFourierHistos[i].dataFourierPhaseOptReal->SetMarkerSize(0.7);
}
}
//--------------------------------------------------------------------------
// PlotFourier (private)
//--------------------------------------------------------------------------
@ -1365,6 +1470,14 @@ void PFourierCanvas::HandleAverage()
*/
void PFourierCanvas::PlotFourier()
{
// check if phase opt real Fourier spectra already exists if requested,
// and if not calculate them first
if (fCurrentPlotView == FOURIER_PLOT_PHASE_OPT_REAL) {
if (fFourierHistos[0].dataFourierPhaseOptReal == 0) { // not yet calculated
CalcPhaseOptReal();
}
}
fFourierPad->cd();
Double_t xmin=0, xmax=0;
@ -1660,6 +1773,11 @@ void PFourierCanvas::PlotAverage()
fFourierAverage[0].dataFourierPhase->Draw("p");
break;
case FOURIER_PLOT_PHASE_OPT_REAL:
if (fFourierHistos[0].dataFourierPhaseOptReal == 0) {
cout << "debug> need to calculate phase opt. average first ..." << endl;
CalcPhaseOptReal();
HandleAverage();
}
fFourierAverage[0].dataFourierPhaseOptReal->GetXaxis()->SetRangeUser(xmin, xmax);
ymin = GetMinimum(fFourierAverage[0].dataFourierPhaseOptReal, xmin, xmax);
ymax = GetMaximum(fFourierAverage[0].dataFourierPhaseOptReal, xmin, xmax);

379
src/classes/PMsrHandler.cpp
View File

@ -825,13 +825,7 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
fout << left << "lifetime";
fout << fRuns[runNo].GetLifetimeParamNo() << endl;
} else if (sstr.BeginsWith("lifetimecorrection")) {
/* obsolate, hence do nothing here
if ((fRuns[runNo].IsLifetimeCorrected()) &&
((fRuns[runNo].GetFitType() == MSR_FITTYPE_SINGLE_HISTO) ||
(fGlobal.GetFitType() == MSR_FITTYPE_SINGLE_HISTO))) {
fout << "lifetimecorrection" << endl;
}
*/
// obsolate, hence do nothing here
} else if (sstr.BeginsWith("map")) {
fout << "map ";
for (UInt_t j=0; j<fRuns[runNo].GetMap()->size(); j++) {
@ -1113,8 +1107,10 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
fout << "POWER";
} else if (fFourier.fPlotTag == FOURIER_PLOT_PHASE) {
fout << "PHASE";
} else if (fFourier.fPlotTag == FOURIER_PLOT_PHASE_OPT_REAL) {
fout << "PHASE_OPT_REAL";
}
fout << " # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE";
fout << " # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL";
fout << endl;
} else if (sstr.BeginsWith("phase")) {
if (fFourier.fPhaseParamNo > 0) {
@ -1213,38 +1209,38 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
if (fStatistic.fValid) { // valid fit result
if (fStatistic.fChisq) {
str.Form(" chisq = %.1lf, NDF = %d, chisq/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
} else {
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
}
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
if (fStatistic.fChisq) {
str.Form(" expected chisq = %.1lf, NDF = %d, expected chisq/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
} else {
str.Form(" expected maxLH = %.1lf, NDF = %d, expected maxLH/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << endl << str.Data() << endl;
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
str.Form(" expected chisq = %.1lf, NDF = %d, expected chisq/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << endl << str.Data() << endl;
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
if (fStatistic.fChisq) {
str.Form(" run block %d: (NDF/red.chisq/red.chisq_e) = (%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
} else {
str.Form(" run block %d: (NDF/red.maxLH/red.maxLH_e) = (%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
}
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
@ -1254,11 +1250,23 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
cout << str.Data() << endl;
}
}
} else { // maxLH
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
if (fStatistic.fChisq) {
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
} else {
str.Form(" run block %d: (NDF/maxLH.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
}
}
} else {
fout << "*** FIT DID NOT CONVERGE ***" << endl;
@ -1270,38 +1278,38 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
if (fStatistic.fValid) { // valid fit result
if (fStatistic.fChisq) { // chisq
str.Form(" chisq = %.1lf, NDF = %d, chisq/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
} else {
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
}
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
if (fStatistic.fChisq) { // chisq
str.Form(" expected chisq = %.1lf, NDF = %d, expected chisq/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
} else {
str.Form(" expected maxLH = %.1lf, NDF = %d, expected maxLH/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
if (fStatistic.fChisq) { // chisq
str.Form(" run block %d: (NDF/red.chisq/red.chisq_e) = (%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
} else {
str.Form(" run block %d: (NDF/red.maxLH/red.maxLH_e) = (%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
}
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
@ -1311,11 +1319,23 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
cout << str.Data() << endl;
}
}
} else { // max. log. liklihood
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
if (fStatistic.fChisq) { // chisq
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
} else {
str.Form(" run block %d: (NDF/red.maxLH) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
}
}
} else {
fout << "*** FIT DID NOT CONVERGE ***" << endl;
@ -1326,7 +1346,7 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
if (str.Length() > 0) {
sstr = str;
sstr.Remove(TString::kLeading, ' ');
if (!sstr.BeginsWith("expected chisq") && !sstr.BeginsWith("run block"))
if (!sstr.BeginsWith("expected chisq") && !sstr.BeginsWith("expected maxLH") && !sstr.BeginsWith("run block"))
fout << str.Data() << endl;
} else { // only write endl if not eof is reached. This is preventing growing msr-files, i.e. more and more empty lines at the end of the file
if (!fin.eof())
@ -1349,38 +1369,38 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
if (fStatistic.fValid) { // valid fit result
if (fStatistic.fChisq) {
str.Form(" chisq = %.1lf, NDF = %d, chisq/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
} else {
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
}
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
if (fStatistic.fChisq) {
str.Form(" expected chisq = %.1lf, NDF = %d, expected chisq/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
} else {
str.Form(" expected maxLH = %.1lf, NDF = %d, expected maxLH/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
if (fStatistic.fChisq) {
str.Form(" run block %d: (NDF/red.chisq/red.chisq_e) = (%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
} else {
str.Form(" run block %d: (NDF/red.maxLH/red.maxLH_e) = (%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
}
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
@ -1390,13 +1410,23 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
cout << str.Data() << endl;
}
}
} else { // maxLH
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
if (fStatistic.fChisq) {
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
} else {
str.Form(" run block %d: (NDF/red.maxLH) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
// check if per run block maxLH needs to be written
if (messages)
cout << str.Data() << endl;
}
}
} else {
fout << "*** FIT DID NOT CONVERGE ***" << endl;
@ -1414,38 +1444,38 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
if (fStatistic.fValid) { // valid fit result
if (fStatistic.fChisq) { // chisq
str.Form(" chisq = %.1lf, NDF = %d, chisq/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
} else {
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
}
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
// check if expected chisq needs to be written
if (fStatistic.fMinExpected != 0.0) {
if (fStatistic.fChisq) { // chisq
str.Form(" expected chisq = %.1lf, NDF = %d, expected chisq/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
} else {
str.Form(" expected maxLH = %.1lf, NDF = %d, expected maxLH/NDF = %lf",
fStatistic.fMinExpected, fStatistic.fNdf, fStatistic.fMinExpected/fStatistic.fNdf);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
for (UInt_t i=0; i<fStatistic.fMinExpectedPerHisto.size(); i++) {
if (fStatistic.fNdfPerHisto[i] > 0) {
if (fStatistic.fChisq) { // chisq
str.Form(" run block %d: (NDF/red.chisq/red.chisq_e) =(%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
} else {
str.Form(" run block %d: (NDF/red.maxLH/red.maxLH_e) =(%d/%lf/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i], fStatistic.fMinExpectedPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
}
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
@ -1455,11 +1485,23 @@ Int_t PMsrHandler::WriteMsrLogFile(const Bool_t messages)
cout << str.Data() << endl;
}
}
} else { // max. log. liklihood
str.Form(" maxLH = %.1lf, NDF = %d, maxLH/NDF = %lf", fStatistic.fMin, fStatistic.fNdf, fStatistic.fMin / fStatistic.fNdf);
fout << str.Data() << endl;
if (messages)
cout << endl << str.Data() << endl;
} else if (fStatistic.fNdfPerHisto.size() > 1) { // check if per run chisq needs to be written
for (UInt_t i=0; i<fStatistic.fNdfPerHisto.size(); i++) {
if (fStatistic.fChisq) { // chisq
str.Form(" run block %d: (NDF/red.chisq) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
} else {
str.Form(" run block %d: (NDF/red.maxLH) = (%d/%lf)",
i+1, fStatistic.fNdfPerHisto[i], fStatistic.fMinPerHisto[i]/fStatistic.fNdfPerHisto[i]);
}
if (fStartupOptions) {
if (fStartupOptions->writeExpectedChisq)
fout << str.Data() << endl;
}
if (messages)
cout << str.Data() << endl;
}
}
} else {
fout << "*** FIT DID NOT CONVERGE (4) ***" << endl;
@ -2146,8 +2188,10 @@ Int_t PMsrHandler::WriteMsrFile(const Char_t *filename, map<UInt_t, TString> *co
fout << "POWER";
} else if (fFourier.fPlotTag == FOURIER_PLOT_PHASE) {
fout << "PHASE";
} else if (fFourier.fPlotTag == FOURIER_PLOT_PHASE_OPT_REAL) {
fout << "PHASE_OPT_REAL";
}
fout << " # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE";
fout << " # REAL, IMAG, REAL_AND_IMAG, POWER, PHASE, PHASE_OPT_REAL";
fout << endl;
}
@ -3844,7 +3888,7 @@ Bool_t PMsrHandler::HandleFourierEntry(PMsrLines &lines)
TObjArray *tokens = 0;
TObjString *ostr = 0;
TString str;
TString str, pcStr=TString("");
Int_t ival;
@ -3951,6 +3995,8 @@ Bool_t PMsrHandler::HandleFourierEntry(PMsrLines &lines)
fourier.fPlotTag = FOURIER_PLOT_POWER;
} else if (!str.CompareTo("phase", TString::kIgnoreCase)) {
fourier.fPlotTag = FOURIER_PLOT_PHASE;
} else if (!str.CompareTo("phase_opt_real", TString::kIgnoreCase)) {
fourier.fPlotTag = FOURIER_PLOT_PHASE_OPT_REAL;
} else { // unrecognized plot tag
error = true;
continue;
@ -3993,21 +4039,10 @@ Bool_t PMsrHandler::HandleFourierEntry(PMsrLines &lines)
}
}
} else if (iter->fLine.BeginsWith("range_for_phase_correction", TString::kIgnoreCase)) {
if (tokens->GetEntries() < 3) { // range values are missing
error = true;
continue;
} else {
for (UInt_t i=0; i<2; i++) {
ostr = dynamic_cast<TObjString*>(tokens->At(i+1));
str = ostr->GetString();
if (str.IsFloat()) {
fourier.fRangeForPhaseCorrection[i] = str.Atof();
} else {
error = true;
continue;
}
}
}
// keep the string. It can only be handled at the very end of the FOURIER block evaluation
// since it needs potentially the range input and there is no guaranty this is already
// available at this point.
pcStr = iter->fLine;
} else if (iter->fLine.BeginsWith("range", TString::kIgnoreCase)) { // fourier plot range
if (tokens->GetEntries() < 3) { // plot range values are missing
error = true;
@ -4045,6 +4080,45 @@ Bool_t PMsrHandler::HandleFourierEntry(PMsrLines &lines)
tokens = 0;
}
// handle range_for_phase_correction if present
if ((pcStr.Length() != 0) && !error) {
// tokenize line
tokens = pcStr.Tokenize(" \t");
switch (tokens->GetEntries()) {
case 2:
ostr = dynamic_cast<TObjString*>(tokens->At(1));
str = ostr->GetString();
if (!str.CompareTo("all", TString::kIgnoreCase)) {
fourier.fRangeForPhaseCorrection[0] = fourier.fPlotRange[0];
fourier.fRangeForPhaseCorrection[1] = fourier.fPlotRange[1];
} else {
error = true;
}
break;
case 3:
for (UInt_t i=0; i<2; i++) {
ostr = dynamic_cast<TObjString*>(tokens->At(i+1));
str = ostr->GetString();
if (str.IsFloat()) {
fourier.fRangeForPhaseCorrection[i] = str.Atof();
} else {
error = true;
}
}
break;
default:
error = true;
break;
}
// clean up
if (tokens) {
delete tokens;
tokens = 0;
}
}
if (error) {
cerr << endl << ">> PMsrHandler::HandleFourierEntry: **ERROR** in line " << iter->fLineNo << ":";
cerr << endl;
@ -4059,9 +4133,9 @@ Bool_t PMsrHandler::HandleFourierEntry(PMsrLines &lines)
cerr << endl << ">> 0 <= n <= 20 are allowed values";
cerr << endl << ">> [dc-corrected true | false]";
cerr << endl << ">> [apodization none | weak | medium | strong]";
cerr << endl << ">> [plot real | imag | real_and_imag | power | phase]";
cerr << endl << ">> [plot real | imag | real_and_imag | power | phase | phase_opt_real]";
cerr << endl << ">> [phase value]";
cerr << endl << ">> [range_for_phase_correction min max]";
cerr << endl << ">> [range_for_phase_correction min max | all]";
cerr << endl << ">> [range min max]";
cerr << endl;
} else { // save last run found
@ -4641,7 +4715,8 @@ Bool_t PMsrHandler::HandleStatisticEntry(PMsrLines &lines)
if (tstr.Length() > 0) {
if (!tstr.BeginsWith("#") && !tstr.BeginsWith("STATISTIC") && !tstr.BeginsWith("chisq") &&
!tstr.BeginsWith("maxLH") && !tstr.BeginsWith("*** FIT DID NOT CONVERGE ***") &&
!tstr.BeginsWith("expected chisq") && !tstr.BeginsWith("run block")) {
!tstr.BeginsWith("expected chisq") && !tstr.BeginsWith("expected maxLH") &&
!tstr.BeginsWith("run block")) {
cerr << endl << ">> PMsrHandler::HandleStatisticEntry: **SYNTAX ERROR** in line " << lines[i].fLineNo;
cerr << endl << ">> '" << lines[i].fLine.Data() << "'";
cerr << endl << ">> not a valid STATISTIC block line";
@ -6025,6 +6100,7 @@ Bool_t PMsrHandler::EstimateN0()
/**
* <p>returns alpha to estimate N0
*/
/*as
Double_t PMsrHandler::GetAlphaEstimateN0()
{
if (fStartupOptions == 0)
@ -6032,6 +6108,7 @@ Double_t PMsrHandler::GetAlphaEstimateN0()
return fStartupOptions->alphaEstimateN0;
}
*/
//--------------------------------------------------------------------------
// NeededPrecision (private)

93
src/classes/PRunListCollection.cpp
View File

@ -355,7 +355,7 @@ Double_t PRunListCollection::GetSingleHistoChisqExpected(const std::vector<Doubl
}
Int_t type = fMsrInfo->GetMsrRunList()->at(idx).GetFitType();
if (type == -1) { // i.e. not forun in the RUN block, try the GLOBAL block
if (type == -1) { // i.e. not found in the RUN block, try the GLOBAL block
type = fMsrInfo->GetMsrGlobal()->GetFitType();
}
@ -583,6 +583,97 @@ Double_t PRunListCollection::GetNonMusrMaximumLikelihood(const std::vector<Doubl
return mlh;
}
//--------------------------------------------------------------------------
// GetSingleHistoMaximumLikelihoodExpected (public)
//--------------------------------------------------------------------------
/**
* <p>Calculates expected mlh of the single histogram with run block index idx of a msr-file.
*
* <b>return:</b>
* - expected mlh of for a single histogram
*
* \param par fit parameter vector
* \param idx run block index
*/
Double_t PRunListCollection::GetSingleHistoMaximumLikelihoodExpected(const std::vector<Double_t>& par, const UInt_t idx) const
{
Double_t expected_mlh = 0.0;
if (idx > fMsrInfo->GetMsrRunList()->size()) {
cerr << ">> PRunListCollection::GetSingleHistoMaximumLikelihoodExpected() **ERROR** idx=" << idx << " is out of range [0.." << fMsrInfo->GetMsrRunList()->size() << "[" << endl << endl;
return expected_mlh;
}
Int_t type = fMsrInfo->GetMsrRunList()->at(idx).GetFitType();
if (type == -1) { // i.e. not found in the RUN block, try the GLOBAL block
type = fMsrInfo->GetMsrGlobal()->GetFitType();
}
// count how many entries of this fit-type are present up to idx
UInt_t subIdx = 0;
for (UInt_t i=0; i<idx; i++) {
if (fMsrInfo->GetMsrRunList()->at(i).GetFitType() == type)
subIdx++;
}
// return the mlh of the single run
switch (type) {
case PRUN_SINGLE_HISTO:
expected_mlh = fRunSingleHistoList[subIdx]->CalcMaxLikelihoodExpected(par);
break;
default:
break;
}
return expected_mlh;
}
//--------------------------------------------------------------------------
// GetSingleRunMaximumLikelihood (public)
//--------------------------------------------------------------------------
/**
* <p>Calculates mlh of a single run-block entry of the msr-file.
*
* <b>return:</b>
* - mlh of single run-block entry with index idx
*
* \param par fit parameter vector
* \param idx run block index
*/
Double_t PRunListCollection::GetSingleRunMaximumLikelihood(const std::vector<Double_t>& par, const UInt_t idx) const
{
Double_t mlh = 0.0;
if (idx > fMsrInfo->GetMsrRunList()->size()) {
cerr << ">> PRunListCollection::GetSingleRunMaximumLikelihood() **ERROR** idx=" << idx << " is out of range [0.." << fMsrInfo->GetMsrRunList()->size() << "[" << endl << endl;
return mlh;
}
Int_t subIdx = 0;
Int_t type = fMsrInfo->GetMsrRunList()->at(idx).GetFitType();
if (type == -1) { // i.e. not found in the RUN block, try the GLOBAL block
type = fMsrInfo->GetMsrGlobal()->GetFitType();
subIdx = idx;
} else { // found in the RUN block
// count how many entries of this fit-type are present up to idx
for (UInt_t i=0; i<idx; i++) {
if (fMsrInfo->GetMsrRunList()->at(i).GetFitType() == type)
subIdx++;
}
}
// return the mlh of the single run
switch (type) {
case PRUN_SINGLE_HISTO:
mlh = fRunSingleHistoList[subIdx]->CalcMaxLikelihood(par);
break;
default:
break;
}
return mlh;
}
//--------------------------------------------------------------------------
// GetNoOfBinsFitted (public)
//--------------------------------------------------------------------------

100
src/classes/PRunSingleHisto.cpp
View File

@ -393,6 +393,103 @@ Double_t PRunSingleHisto::CalcMaxLikelihood(const std::vector<Double_t>& par)
return 2.0*mllh;
}
//--------------------------------------------------------------------------
// CalcMaxLikelihoodExpected (public)
//--------------------------------------------------------------------------
/**
* <p>Calculate expected log maximum-likelihood.
*
* <b>return:</b>
* - log maximum-likelihood value
*
* \param par parameter vector iterated by minuit2
*/
Double_t PRunSingleHisto::CalcMaxLikelihoodExpected(const std::vector<Double_t>& par)
{
Double_t mllh = 0.0; // maximum log likelihood assuming poisson distribution for the single bin
Double_t N0;
// check if norm is a parameter or a function
if (fRunInfo->GetNormParamNo() < MSR_PARAM_FUN_OFFSET) { // norm is a parameter
N0 = par[fRunInfo->GetNormParamNo()-1];
} else { // norm is a function
// get function number
UInt_t funNo = fRunInfo->GetNormParamNo()-MSR_PARAM_FUN_OFFSET;
// evaluate function
N0 = fMsrInfo->EvalFunc(funNo, *fRunInfo->GetMap(), par);
}
// get tau
Double_t tau;
if (fRunInfo->GetLifetimeParamNo() != -1)
tau = par[fRunInfo->GetLifetimeParamNo()-1];
else
tau = PMUON_LIFETIME;
// get background
Double_t bkg;
if (fRunInfo->GetBkgFitParamNo() == -1) { // bkg not fitted
if (fRunInfo->GetBkgFix(0) == PMUSR_UNDEFINED) { // no fixed background given (background interval)
bkg = fBackground;
} else { // fixed bkg given
bkg = fRunInfo->GetBkgFix(0);
}
} else { // bkg fitted
bkg = par[fRunInfo->GetBkgFitParamNo()-1];
}
// calculate functions
for (Int_t i=0; i<fMsrInfo->GetNoOfFuncs(); i++) {
Int_t funcNo = fMsrInfo->GetFuncNo(i);
fFuncValues[i] = fMsrInfo->EvalFunc(funcNo, *fRunInfo->GetMap(), par);
}
// calculate maximum log likelihood
Double_t theo;
Double_t data;
Double_t time(1.0);
Int_t i;
// norm is needed since there is no simple scaling like in chisq case to get the correct Max.Log.Likelihood value when normlizing N(t) to 1/ns
Double_t normalizer = 1.0;
if (fScaleN0AndBkg)
normalizer = fPacking * (fTimeResolution * 1.0e3);
// Calculate the theory function once to ensure one function evaluation for the current set of parameters.
// This is needed for the LF and user functions where some non-thread-save calculations only need to be calculated once
// for a given set of parameters---which should be done outside of the parallelized loop.
// For all other functions it means a tiny and acceptable overhead.
time = fTheory->Func(time, par, fFuncValues);
#ifdef HAVE_GOMP
Int_t chunk = (fEndTimeBin - fStartTimeBin)/omp_get_num_procs();
if (chunk < 10)
chunk = 10;
#pragma omp parallel for default(shared) private(i,time,theo,data) schedule(dynamic,chunk) reduction(-:mllh)
#endif
for (i=fStartTimeBin; i<fEndTimeBin; ++i) {
time = fData.GetDataTimeStart() + (Double_t)i*fData.GetDataTimeStep();
// calculate theory for the given parameter set
theo = N0*TMath::Exp(-time/tau)*(1.0+fTheory->Func(time, par, fFuncValues))+bkg;
theo *= normalizer;
data = normalizer*fData.GetValue()->at(i);
if (theo <= 0.0) {
cerr << ">> PRunSingleHisto::CalcMaxLikelihood: **WARNING** NEGATIVE theory!!" << endl;
continue;
}
if (data > 1.0e-9) { // is this correct?? needs to be checked. See G-test
mllh += data*log(data/theo);
}
}
return 2.0*mllh;
}
//--------------------------------------------------------------------------
// CalcTheory (public)
//--------------------------------------------------------------------------
@ -1571,7 +1668,6 @@ void PRunSingleHisto::EstimateN0()
Double_t tau = PMUON_LIFETIME;
UInt_t t0 = (UInt_t)round(fT0s[0]);
Double_t alpha = fMsrInfo->GetAlphaEstimateN0();
Double_t dval = 0.0;
Double_t nom = 0.0;
Double_t denom = 0.0;
@ -1580,14 +1676,12 @@ void PRunSingleHisto::EstimateN0()
// calc nominator
for (UInt_t i=t0; i<fForward.size(); i++) {
xx = exp(-dt*(Double_t)(i-t0)/tau);
xx += alpha;
nom += xx;
}
// calc denominator
for (UInt_t i=t0; i<fForward.size(); i++) {
xx = exp(-dt*(Double_t)(i-t0)/tau);
xx += alpha;
dval = fForward[i];
if (dval > 0)
denom += xx*xx/dval;

25
src/classes/PStartupHandler.cpp
View File

@ -178,10 +178,6 @@ void PStartupHandler::OnStartDocument()
fFourierDefaults.fPlotRange[0] = -1.0;
fFourierDefaults.fPlotRange[1] = -1.0;
fFourierDefaults.fPhaseIncrement = 1.0;
fStartupOptions.writeExpectedChisq = false;
fStartupOptions.estimateN0 = true;
fStartupOptions.alphaEstimateN0 = 0.0;
}
//--------------------------------------------------------------------------
@ -210,12 +206,6 @@ void PStartupHandler::OnStartElement(const Char_t *str, const TList *attributes)
{
if (!strcmp(str, "data_path")) {
fKey = eDataPath;
} else if (!strcmp(str, "write_per_run_block_chisq")) {
fKey = eWritePerRunBlockChisq;
} else if (!strcmp(str, "estimate_n0")) {
fKey = eEstimateN0;
} else if (!strcmp(str, "alpha_estimate_n0")) {
fKey = eAlphaEstimateN0;
} else if (!strcmp(str, "marker")) {
fKey = eMarker;
} else if (!strcmp(str, "color")) {
@ -270,21 +260,6 @@ void PStartupHandler::OnCharacters(const Char_t *str)
// add str to the path list
fDataPathList.push_back(str);
break;
case eWritePerRunBlockChisq:
tstr = TString(str);
if (tstr.BeginsWith("y") || tstr.BeginsWith("Y"))
fStartupOptions.writeExpectedChisq = true;
break;
case eEstimateN0:
tstr = TString(str);
if (tstr.BeginsWith("n") || tstr.BeginsWith("N"))
fStartupOptions.estimateN0 = false;
break;
case eAlphaEstimateN0:
tstr = TString(str);
if (tstr.IsFloat())
fStartupOptions.alphaEstimateN0 = tstr.Atof();
break;
case eMarker:
// check that str is a number
tstr = TString(str);

417
src/dump_header.cpp
View File

@ -31,12 +31,16 @@
#include "config.h"
#endif
#include <unistd.h>
#include <cerrno>
#include <cctype>
#include <cstring>
#include <ctime>
#include <cassert>
#include <iostream>
#include <fstream>
#include <sstream>
#include <string>
#include <vector>
@ -46,6 +50,7 @@ using namespace std;
#include <TFile.h>
#include "git-revision.h"
#include "PStartupHandler.h"
#include "TMusrRunHeader.h"
#include "TLemRunHeader.h"
#include "MuSR_td_PSI_bin.h"
@ -64,16 +69,29 @@ using namespace std;
*/
void dump_header_syntax()
{
cout << endl << "usage: dump_header <fileName> [--file_format <fileFormat>] | --help | --version";
cout << endl << " Dumps the header information of a given muSR data file onto the standard output.";
cout << endl << " If no <fileFormat> is given, it will try to fiddle out what <fileFormat> it might be.";
cout << endl << "usage: dump_header [-rn <runNo> | -fn <fileName>] [-ff, --fileFormat <fileFormat>]";
cout << endl << " [-y, --year <year>] [-s, --summary] [--psi-bulk <opt>] |";
cout << endl << " --help | --version";
cout << endl;
cout << endl << " <fileName>: muSR data file name.";
cout << endl << " --file_format <fileFormat>: where <fileFormat> can be:";
cout << endl << " Dumps the header information of a given muSR data file onto the standard output.";
cout << endl << " If no <fileFormat> info is povided, it will try to guess what <fileFormat> it might be.";
cout << endl << " For <runNo> guessing of the file format is not possible. The default assumption here is 'MusrRoot'.";
cout << endl;
cout << endl << " -rn, --runNo <runNo> : run number of the header to be dumped.";
cout << endl << " -fn, --fileName <fileName> : muSR data file name.";
cout << endl << " -ff, --fileFormat <fileFormat> : where <fileFormat> can be:";
cout << endl << " MusrRoot, NeXus, ROOT (old LEM), PSI-BIN, PSI-MDU, MUD, WKM";
cout << endl << " NeXus is only supported if enabled.";
cout << endl << " --help, -h : will show this help";
cout << endl << " --version, -v : will show the current version.";
cout << endl << " -y, --year <year> : <year> has to be 4 digit, e.g. 2005, if provided it is used to";
cout << endl << " generate the file name for the given <runNo>, otherwise the current";
cout << endl << " year is used. If a file name is given, this option has no effect.";
cout << endl << " -s, --summary : this option is used for LE-uSR data sets only. It will, additionally";
cout << endl << " to the header information, print the summary file content.";
cout << endl << " --psi-bulk <opt> : where <opt> consists of two items: (i) pta or tdc, ";
cout << endl << " (ii) gps | ltf | dolly | gpd | hifi. This is needed in combination with";
cout << endl << " the file formats PSI-BIN and PSI-MDU.";
cout << endl << " -h, --help : will show this help";
cout << endl << " -v, --version : will show the current version.";
cout << endl << endl;
}
@ -81,7 +99,7 @@ void dump_header_syntax()
/**
*
*/
int dump_header_root(const string fileName, const string fileFormat)
int dump_header_root(const string fileName, const string fileFormat, const bool summary)
{
TFile f(fileName.c_str());
if (f.IsZombie()) {
@ -178,6 +196,27 @@ int dump_header_root(const string fileName, const string fileFormat)
delete header;
}
// summary as well?
if (summary && (fileType == DH_MUSR_ROOT)) {
TObjArray *runSum=0;
runSum = (TObjArray*)folder->FindObject("RunSummary");
if (!runSum) { // something is wrong!!
cerr << endl << "**ERROR** Couldn't obtain RunSummary " << fileName << endl;
f.Close();
return 1;
}
cout << "++++++++++++++++++++" << endl;
cout << " Run Summary" << endl;
cout << "++++++++++++++++++++" << endl;
TObjString *tstr;
TString str;
for (Int_t i=0; i<runSum->GetEntries(); i++) {
tstr = (TObjString*)runSum->At(i);
str = tstr->String();
cout << str;
}
}
f.Close();
return 0;
@ -562,7 +601,145 @@ int dump_header_wkm(const string fileName, const string fileFormat)
//------------------------------------------------------------------------
/**
*
* @brief is_number
* @param s
* @return
*/
bool dump_is_number(const char *s)
{
int i=0;
if (s == 0) // make sure it is not a null pointer
return false;
while (isdigit(s[i]))
i++;
if (s[i] == '\0')
return true;
else
return false;
}
//------------------------------------------------------------------------
/**
* @brief dump_current_year
* @return
*/
int dump_current_year()
{
time_t rawtime;
struct tm * timeinfo;
char buffer[32];
time (&rawtime);
timeinfo = localtime(&rawtime);
strftime(buffer, 32, "%Y", timeinfo);
return atoi(buffer);
}
//------------------------------------------------------------------------
/**
* @brief dump_create_fln
* @param runNo
* @param year
* @param fileFormat
* @return
*/
string dump_create_fln(string runNo, string year, string fileFormat, bool pta, string instrument)
{
string result = "??";
int yearShort=0;
int iRunNo=0;
if (fileFormat.empty())
fileFormat = "MusrRoot";
// make sure that a 'legal' file format has been found
if (!boost::iequals(fileFormat, "MusrRoot") &&
!boost::iequals(fileFormat, "NeXus") &&
!boost::iequals(fileFormat, "ROOT") &&
!boost::iequals(fileFormat, "PSI-BIN") &&
!boost::iequals(fileFormat, "PSI-MDU") &&
!boost::iequals(fileFormat, "MDU") &&
!boost::iequals(fileFormat, "WKM")) {
return result;
}
// if year is an empty string get the current year
int yy=-1;
stringstream ss;
if (year.empty()) {
yy = dump_current_year();
ss << yy;
year = ss.str();
}
yy = atoi(year.c_str());
if (yy > 2000)
yearShort = yy - 2000;
else
yearShort = yy - 1900;
iRunNo = atoi(runNo.c_str());
char fln[64];
char ptatdc[8];
if (pta)
strcpy(ptatdc, "pta");
else
strcpy(ptatdc, "tdc");
if (boost::iequals(fileFormat, "MusrRoot") || boost::iequals(fileFormat, "ROOT")) {
snprintf(fln, sizeof(fln), "lem%02d_his_%04d.root", yearShort, iRunNo);
} else if (boost::iequals(fileFormat, "NeXus")) {
snprintf(fln, sizeof(fln), "%s.nxs", runNo.c_str());
} else if (boost::iequals(fileFormat, "PSI-BIN")) {
snprintf(fln, sizeof(fln), "deltat_%s_%s_%04d.bin", ptatdc, instrument.c_str(), iRunNo);
} else if (boost::iequals(fileFormat, "PSI-MDU")) {
snprintf(fln, sizeof(fln), "%s_%s_%s_%05d.mdu", ptatdc, instrument.c_str(), year.c_str(), iRunNo);
} else if (boost::iequals(fileFormat, "MUD")) {
snprintf(fln, sizeof(fln), "%06d.msr", iRunNo);
} else if (boost::iequals(fileFormat, "WKM")) {
}
result = fln;
return result;
}
//------------------------------------------------------------------------
/**
* @brief dump_file_exists
* @param pathName
* @return
*/
bool dump_file_exists(const string pathName)
{
bool exists = true;
int res = access(pathName.c_str(), R_OK);
if (res < 0) {
if (errno == ENOENT) {
// file does not exist
exists = false;
} else if (errno == EACCES) {
// file exists but is not readable
exists = false;
} else {
// FAIL
exists = false;
}
}
return exists;
}
//------------------------------------------------------------------------
/**
* @brief main
* @param argc
* @param argv
* @return
*/
int main(int argc, char *argv[])
{
@ -571,9 +748,14 @@ int main(int argc, char *argv[])
return 0;
}
string runNo("");
string fileName("");
string fileFormat("");
int count=0;
string year("");
bool pta(false);
string instrument("");
bool summary(false);
for (int i=1; i<argc; i++) {
if (!strcmp(argv[i], "--help") || !strcmp(argv[i], "-h")) {
dump_header_syntax();
@ -585,9 +767,40 @@ int main(int argc, char *argv[])
cout << endl << "dump_header: git-rev: " << GIT_REVISION << endl << endl;
#endif
return 0;
} else if (!strcmp(argv[i], "--file_format")) {
} else if (!strcmp(argv[i], "-rn") || !strcmp(argv[i], "--runNo")) {
if (i+1 >= argc) {
cout << endl << "**ERROR** found '--file_format' without <fileFormat>!" << endl;
cerr << endl << "**ERROR** found -rn, --runNo without <runNo>!" << endl;
dump_header_syntax();
return 1;
}
// make sure there is only one 'legal' run number
int count = 1;
while (dump_is_number(argv[i+count]) && (i+count < argc))
count++;
// make sure there is one and only one run number given
if (count == 1) {
cerr << endl << "**ERROR** found -rn, --runNo without <runNo>, or the provided <runNo> ('" << argv[i+1] << "') is not a number!" << endl;
dump_header_syntax();
return 1;
}
if (count > 2) {
cerr << endl << "**ERROR** found -rn, --runNo with more than one <runNo>! This is not yet supported." << endl;
dump_header_syntax();
return 1;
}
runNo = argv[i+1];
i++;
} else if (!strcmp(argv[i], "-fn") || !strcmp(argv[i], "--fileName")) {
if (i+1 >= argc) {
cerr << endl << "**ERROR** found -fn, --fileName without <fileName>!" << endl;
dump_header_syntax();
return 1;
}
fileName = argv[i+1];
i++;
} else if (!strcmp(argv[i], "--fileFormat") || !strcmp(argv[i], "-ff")) {
if (i+1 >= argc) {
cerr << endl << "**ERROR** found -ff, --fileFormat without <fileFormat>!" << endl;
dump_header_syntax();
return 1;
}
@ -595,27 +808,169 @@ int main(int argc, char *argv[])
if (!boost::iequals(ff, "MusrRoot") && !boost::iequals(ff, "NeXus") && !boost::iequals(ff, "ROOT") &&
!boost::iequals(ff, "PSI-BIN") && !boost::iequals(ff, "PSI-MDU") && !boost::iequals(ff, "MUD") &&
!boost::iequals(ff, "WKM")) { // none of the listed found
cout << endl << "**ERROR** found unsupported muSR file data format: " << argv[i+1] << endl;
cerr << endl << "**ERROR** found unsupported muSR file data format: " << argv[i+1] << endl;
dump_header_syntax();
return 1;
}
fileFormat = argv[i+1];
i++;
} else if (!strcmp(argv[i], "-y") || !strcmp(argv[i], "--year")) {
if (i+1 >= argc) {
cerr << endl << "**ERROR** found -y, --year without <year>!" << endl;
dump_header_syntax();
return 1;
}
if (!dump_is_number(argv[i+1])) {
cerr << endl << "**ERROR** found -y, --year with sensless <year> '" << argv[i+1] << "'!" << endl;
dump_header_syntax();
return 1;
}
int yy = strtod(argv[i+1], (char**)0);
if ((yy < 1950) || (yy > dump_current_year())) {
cerr << endl << "**ERROR** found -y, --year with <year> '" << yy << "'!";
cerr << endl << " Well, cannot handle files in the pre-muSR time nor in the future." << endl;
dump_header_syntax();
return 1;
}
year = argv[i+1];
i++;
} else if (!strcmp(argv[i], "-s") || !strcmp(argv[i], "--summary")) {
summary = true;
} else if (!strcmp(argv[i], "--psi-bulk")) {
if (i+2 >= argc) {
cerr << endl << "**ERROR** found --psi-bulk with insufficient input!" << endl;
dump_header_syntax();
return 1;
}
if (!strcmp(argv[i+1], "pta"))
pta = true;
else if (!strcmp(argv[i+1], "tdc"))
pta = false;
else {
cerr << endl << "**ERROR** found --psi-bulk with 1st argument '" << argv[i+1] << "'! Allowed is 'pta' or 'tdc'." << endl;
dump_header_syntax();
return 1;
}
if (strcmp(argv[i+2], "gps") && strcmp(argv[i+2], "ltf") && strcmp(argv[i+2], "dolly") &&
strcmp(argv[i+2], "gpd") && strcmp(argv[i+2], "hifi")) {
cerr << endl << "**ERROR** found --psi-bulk with 2nd argument '" << argv[i+1] << "'! This is an unkown instrument." << endl;
dump_header_syntax();
return 1;
}
instrument = argv[i+2];
i += 2;
} else {
count++;
fileName = argv[i];
cerr << endl << "**ERROR** found unkown option '" << argv[i] << "'." << endl;
dump_header_syntax();
return 1;
}
}
// check if more then one file name was given
if (count != 1) {
cout << endl << "**ERROR** (only) a single file name is needed!" << endl;
dump_header_syntax();
// if year is not provided, take the current one
if (year.empty()) {
stringstream ss;
ss << dump_current_year();
year = ss.str();
}
if ((runNo.length() != 0) && (fileName.length() != 0)) {
cerr << endl << "**ERROR** currently only either runNo or fileName can be handled, not both simultanously." << endl;
return 1;
}
// invoke the startup handler in order to get the default search paths to the data files
// read startup file
char startup_path_name[128];
TSAXParser *saxParser = new TSAXParser();
PStartupHandler *startupHandler = new PStartupHandler();
if (!startupHandler->StartupFileFound()) {
cerr << endl << ">> musrfit **WARNING** couldn't find " << startupHandler->GetStartupFilePath().Data();
cerr << endl;
// clean up
if (saxParser) {
delete saxParser;
saxParser = 0;
}
if (startupHandler) {
delete startupHandler;
startupHandler = 0;
}
} else {
strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
saxParser->ConnectToHandler("PStartupHandler", startupHandler);
//status = saxParser->ParseFile(startup_path_name);
// parsing the file as above seems to lead to problems in certain environments;
// use the parseXmlFile function instead (see PStartupHandler.cpp for the definition)
int status = parseXmlFile(saxParser, startup_path_name);
// check for parse errors
if (status) { // error
cerr << endl << ">> musrfit **WARNING** Reading/parsing musrfit_startup.xml failed.";
cerr << endl;
// clean up
if (saxParser) {
delete saxParser;
saxParser = 0;
}
if (startupHandler) {
delete startupHandler;
startupHandler = 0;
}
}
}
// runNo given, hence try to create the necessary file name based on the provided information
if (runNo != "") {
string str = dump_create_fln(runNo, year, fileFormat, pta, instrument);
if (str == "??") {
cerr << endl << "**ERROR** couldn't get a proper file name." << endl;
return 1;
}
fileName = str;
}
bool found_fln = false;
// 1st check if the file name is found in the current directory
string pathFln("");
pathFln = "./" + fileName;
if (dump_file_exists(pathFln))
found_fln = true;
// 2nd check if file name is found in any default search paths if not already found in the current directory
if (!found_fln) {
PStringVector pathList = startupHandler->GetDataPathList();
for (unsigned int i=0; i<pathList.size(); i++) {
if (boost::iequals(fileFormat, "MusrRoot") || boost::iequals(fileFormat, "ROOT") ||
boost::iequals(fileFormat, "WKM")) {
pathFln = pathList[i] + "/" + year + "/" + fileName;
} else {
if (pta)
pathFln = pathList[i] + "/d" + year + "/pta/" + fileName;
else
pathFln = pathList[i] + "/d" + year + "/tdc/" + fileName;
}
if (dump_file_exists(pathFln)) {
found_fln = true;
break;
}
}
}
if (!found_fln) {
cerr << "**ERROR** couldn't find any appropriate file." << endl;
// cleanup
if (saxParser) {
delete saxParser;
saxParser = 0;
}
if (startupHandler) {
delete startupHandler;
startupHandler = 0;
}
return 1;
}
// if file format is not given explicitly try to guess it based on the file name extension
if (fileFormat == "") {
if ((fileFormat == "") && (fileName != "")) {
string fln(fileName);
boost::to_lower(fln);
if (fln.find(".root") != string::npos)
@ -624,6 +979,8 @@ int main(int argc, char *argv[])
fileFormat = "NeXus";
else if (fln.find(".bin") != string::npos)
fileFormat = "PSI-BIN";
else if (fln.find(".mdu") != string::npos)
fileFormat = "PSI-MDU";
else if (fln.find(".msr") != string::npos)
fileFormat = "MUD";
else if ((fln.find(".nemu") != string::npos) || (fln.find(".wkm") != string::npos))
@ -640,19 +997,29 @@ int main(int argc, char *argv[])
boost::to_lower(fileFormat);
if (boost::iequals(fileFormat, "MusrRoot") || boost::iequals(fileFormat, "ROOT")) {
dump_header_root(fileName, fileFormat);
dump_header_root(pathFln, fileFormat, summary);
} else if (boost::iequals(fileFormat, "NeXus")) {
#ifdef PNEXUS_ENABLED
dump_header_nexus(fileName);
dump_header_nexus(pathFln);
#else
cout << endl << "Sorry, NeXus is not enabled, hence I cannot help you." << endl;
#endif
} else if (boost::iequals(fileFormat, "PSI-BIN") || boost::iequals(fileFormat, "PSI-MDU")) {
dump_header_psi_bin(fileName, fileFormat);
dump_header_psi_bin(pathFln, fileFormat);
} else if (boost::iequals(fileFormat, "MUD")) {
dump_header_mud(fileName, fileFormat);
dump_header_mud(pathFln, fileFormat);
} else if (boost::iequals(fileFormat, "WKM")) {
dump_header_wkm(fileName, fileFormat);
dump_header_wkm(pathFln, fileFormat);
}
// cleanup
if (saxParser) {
delete saxParser;
saxParser = 0;
}
if (startupHandler) {
delete startupHandler;
startupHandler = 0;
}
return 0;

58
src/include/PFourier.h
View File

@ -30,8 +30,13 @@
#ifndef _PFOURIER_H_
#define _PFOURIER_H_
#include <vector>
using namespace std;
#include "fftw3.h"
#include "Minuit2/FCNBase.h"
#include "PMusr.h"
#define F_APODIZATION_NONE 1
@ -39,6 +44,52 @@
#define F_APODIZATION_MEDIUM 3
#define F_APODIZATION_STRONG 4
/**
* Re Fourier phase correction
*/
class PFTPhaseCorrection : public ROOT::Minuit2::FCNBase
{
public:
PFTPhaseCorrection(const Int_t minBin=-1, const Int_t maxBin=-1);
PFTPhaseCorrection(vector<Double_t> &reFT, vector<Double_t> &imFT, const Int_t minBin=-1, const Int_t maxBin=-1);
virtual ~PFTPhaseCorrection() {}
virtual Bool_t IsValid() { return fValid; }
virtual void Minimize();
virtual void SetGamma(const Double_t gamma) { fGamma = gamma; }
virtual void SetPh(const Double_t c0, const Double_t c1) { fPh_c0 = c0; fPh_c1 = c1; CalcPhasedFT(); CalcRealPhFTDerivative(); }
virtual Double_t GetGamma() { return fGamma; }
virtual Double_t GetPhaseCorrectionParam(UInt_t idx);
virtual Double_t GetMinimum();
private:
Bool_t fValid;
vector<Double_t> fReal; /// original real Fourier data set
vector<Double_t> fImag; /// original imag Fourier data set
mutable vector<Double_t> fRealPh; /// phased real Fourier data set
mutable vector<Double_t> fImagPh; /// phased imag Fourier data set
mutable vector<Double_t> fRealPhD; /// 1st derivative of fRealPh
Double_t fMinBin; /// minimum bin from Fourier range to be used for the phase correction estimate
Double_t fMaxBin; /// maximum bin from Fourier range to be used for the phase correction estimate
mutable Double_t fPh_c0; /// constant part of the phase dispersion used for the phase correction
mutable Double_t fPh_c1; /// linear part of the phase dispersion used for the phase correction
Double_t fGamma; /// gamma parameter to balance between entropy and penalty
Double_t fMin; /// keeps the minimum of the entropy/penalty minimization
virtual void Init();
virtual void CalcPhasedFT() const;
virtual void CalcRealPhFTDerivative() const;
virtual Double_t Penalty() const;
virtual Double_t Entropy() const;
virtual Double_t Up() const { return 1.0; }
virtual Double_t operator()(const vector<Double_t>&) const;
};
/**
* muSR Fourier class.
*/
@ -57,11 +108,14 @@ class PFourier
virtual Double_t GetResolution() { return fResolution; }
virtual Double_t GetMaxFreq();
virtual TH1F* GetRealFourier(const Double_t scale = 1.0);
virtual TH1F* GetPhaseOptRealFourier(Double_t &phase, const Double_t scale = 1.0, const Double_t min = -1.0, const Double_t max = -1.0);
//as virtual TH1F* GetPhaseOptRealFourier(vector<Double_t> &phase, const Double_t scale = 1.0, const Double_t min = -1.0, const Double_t max = -1.0);
virtual TH1F* GetImaginaryFourier(const Double_t scale = 1.0);
virtual TH1F* GetPowerFourier(const Double_t scale = 1.0);
virtual TH1F* GetPhaseFourier(const Double_t scale = 1.0);
static TH1F* GetPhaseOptRealFourier(const TH1F *re, const TH1F *im, vector<Double_t> &phase,
const Double_t scale = 1.0, const Double_t min = -1.0, const Double_t max = -1.0);
virtual Bool_t IsValid() { return fValid; }
private:
@ -85,6 +139,8 @@ class PFourier
fftw_complex *fIn; ///< real part of the Fourier transform
fftw_complex *fOut; ///< imaginary part of the Fourier transform
//as PFTPhaseCorrection *fPhCorrectedReFT;
virtual void PrepareFFTwInputData(UInt_t apodizationTag);
virtual void ApodizeData(Int_t apodizationTag);
};

3
src/include/PFourierCanvas.h
View File

@ -71,7 +71,7 @@ typedef struct {
TH1F *dataFourierPwr; ///< power spectrum of the Fourier transform of the data histogram
TH1F *dataFourierPhase; ///< phase spectrum of the Fourier transform of the data histogram
TH1F *dataFourierPhaseOptReal; ///< phase otpimized real Fourier transform of the data histogram
Double_t optPhase; ///< optimal phase which maximizes the real Fourier
vector<Double_t> optPhase; ///< optimal phase which maximizes the real Fourier
} PFourierCanvasDataSet;
//------------------------------------------------------------------------
@ -159,6 +159,7 @@ class PFourierCanvas : public TObject, public TQObject
virtual void InitFourierCanvas(const Char_t* title, Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh);
virtual void CleanupAverage();
virtual void HandleAverage();
virtual void CalcPhaseOptReal();
virtual void PlotFourier();
virtual void PlotFourierPhaseValue();

2
src/include/PMsrHandler.h
View File

@ -107,7 +107,7 @@ class PMsrHandler
virtual void GetGroupingString(Int_t runNo, TString detector, TString &groupingStr);
virtual Bool_t EstimateN0();
virtual Double_t GetAlphaEstimateN0();
//as virtual Double_t GetAlphaEstimateN0();
private:
Bool_t fFourierOnly; ///< flag indicating if Fourier transform only is wished. If yes, some part of the msr-file blocks are not needed.

3
src/include/PMusr.h
View File

@ -815,12 +815,11 @@ typedef struct {
//-------------------------------------------------------------
/**
* <p>Holds the informations for the any2many converter program
* <p>Holds the informations
*/
typedef struct {
Bool_t writeExpectedChisq; ///< if set to true, expected chisq per block will be written
Bool_t estimateN0; ///< if set to true, for single histogram fits N0 will be estimated
Double_t alphaEstimateN0; ///< relates the Bkg to N0, i.e. Bkg = alpha*N0
} PStartupOptions;
//-------------------------------------------------------------

38
src/include/PMusrCanvas.h
View File

@ -55,12 +55,13 @@
#define XTHEO 0.75
// Current Plot Views
#define PV_DATA 1
#define PV_FOURIER_REAL 2
#define PV_FOURIER_IMAG 3
#define PV_FOURIER_REAL_AND_IMAG 4
#define PV_FOURIER_PWR 5
#define PV_FOURIER_PHASE 6
#define PV_DATA 1
#define PV_FOURIER_REAL 2
#define PV_FOURIER_IMAG 3
#define PV_FOURIER_REAL_AND_IMAG 4
#define PV_FOURIER_PWR 5
#define PV_FOURIER_PHASE 6
#define PV_FOURIER_PHASE_OPT_REAL 7
// Canvas menu id's
#define P_MENU_ID_DATA 10001
@ -71,13 +72,14 @@
#define P_MENU_PLOT_OFFSET 1000
#define P_MENU_ID_FOURIER_REAL 100
#define P_MENU_ID_FOURIER_IMAG 101
#define P_MENU_ID_FOURIER_REAL_AND_IMAG 102
#define P_MENU_ID_FOURIER_PWR 103
#define P_MENU_ID_FOURIER_PHASE 104
#define P_MENU_ID_FOURIER_PHASE_PLUS 105
#define P_MENU_ID_FOURIER_PHASE_MINUS 106
#define P_MENU_ID_FOURIER_REAL 100
#define P_MENU_ID_FOURIER_IMAG 101
#define P_MENU_ID_FOURIER_REAL_AND_IMAG 102
#define P_MENU_ID_FOURIER_PWR 103
#define P_MENU_ID_FOURIER_PHASE 104
#define P_MENU_ID_FOURIER_PHASE_OPT_REAL 105
#define P_MENU_ID_FOURIER_PHASE_PLUS 106
#define P_MENU_ID_FOURIER_PHASE_MINUS 107
//------------------------------------------------------------------------
/**
@ -122,16 +124,19 @@ typedef struct {
TH1F *dataFourierIm; ///< imaginary part of the Fourier transform of the data histogram
TH1F *dataFourierPwr; ///< power spectrum of the Fourier transform of the data histogram
TH1F *dataFourierPhase; ///< phase spectrum of the Fourier transform of the data histogram
TH1F *dataFourierPhaseOptReal; ///< phase optimized real part spectrum Fourier transform of the data histogram
TH1F *theory; ///< theory histogram belonging to the data histogram
TH1F *theoryFourierRe; ///< real part of the Fourier transform of the theory histogram
TH1F *theoryFourierIm; ///< imaginary part of the Fourier transform of the theory histogram
TH1F *theoryFourierPwr; ///< power spectrum of the Fourier transform of the theory histogram
TH1F *theoryFourierPhase; ///< phase spectrum of the Fourier transform of the theory histogram
TH1F *theoryFourierPhaseOptReal; ///< phase optimized real part spectrum Fourier transform of the theory histogram
TH1F *diff; ///< difference histogram, i.e. data-theory
TH1F *diffFourierRe; ///< real part of the Fourier transform of the diff histogram
TH1F *diffFourierIm; ///< imaginary part of the Fourier transform of the diff histogram
TH1F *diffFourierPwr; ///< power spectrum of the Fourier transform of the diff histogram
TH1F *diffFourierPhase; ///< phase spectrum of the Fourier transform of the diff histogram
TH1F *diffFourierPhaseOptReal; ///< phase optimized real part spectrum Fourier transform of the diff histogram
PMusrCanvasPlotRange *dataRange; ///< keep the msr-file plot data range
UInt_t diffFourierTag; ///< 0=not relevant, 1=d-f (Fourier of difference time spectra), 2=f-d (difference of Fourier spectra)
} PMusrCanvasDataSet;
@ -201,12 +206,12 @@ class PMusrCanvas : public TObject, public TQObject
PMusrCanvas();
PMusrCanvas(const Int_t number, const Char_t* title,
Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh, const Bool_t batch,
const Bool_t fourier=false);
const Bool_t fourier=false, const Bool_t avg=false);
PMusrCanvas(const Int_t number, const Char_t* title,
Int_t wtopx, Int_t wtopy, Int_t ww, Int_t wh,
PMsrFourierStructure fourierDefault,
const PIntVector markerList, const PIntVector colorList, const Bool_t batch,
const Bool_t fourier=false);
const Bool_t fourier=false, const Bool_t avg=false);
virtual ~PMusrCanvas();
virtual Bool_t IsValid() { return fValid; }
@ -231,6 +236,7 @@ class PMusrCanvas : public TObject, public TQObject
private:
Bool_t fStartWithFourier; ///< flag if true, the Fourier transform will be presented bypassing the time domain representation
Bool_t fStartWithAvg; ///< flag if true, the averaged data/Fourier will be presented
Int_t fTimeout; ///< timeout after which the Done signal should be emited. If timeout <= 0, no timeout is taking place
Bool_t fScaleN0AndBkg; ///< true=N0 and background is scaled to (1/ns), otherwise (1/bin) for the single histogram case
Bool_t fBatchMode; ///< musrview in ROOT batch mode
@ -302,12 +308,12 @@ class PMusrCanvas : public TObject, public TQObject
virtual void HandleDifferenceFourier();
virtual void HandleFourierDifference();
virtual void HandleAverage();
virtual Double_t FindOptimalFourierPhase();
virtual void CleanupDifference();
virtual void CleanupFourier();
virtual void CleanupFourierDifference();
virtual void CleanupAverage();
virtual void CalcPhaseOptReFT();
virtual Double_t CalculateDiff(const Double_t x, const Double_t y, TH1F *theo);
virtual Double_t CalculateDiff(const Double_t x, const Double_t y, TGraphErrors *theo);
virtual Int_t FindBin(const Double_t x, TGraphErrors *graph);

3
src/include/PRunListCollection.h
View File

@ -76,6 +76,9 @@ class PRunListCollection
virtual Double_t GetMuMinusMaximumLikelihood(const std::vector<Double_t>& par) const;
virtual Double_t GetNonMusrMaximumLikelihood(const std::vector<Double_t>& par) const;
virtual Double_t GetSingleHistoMaximumLikelihoodExpected(const std::vector<Double_t>& par, const UInt_t idx) const;
virtual Double_t GetSingleRunMaximumLikelihood(const std::vector<Double_t>& par, const UInt_t idx) const;
virtual UInt_t GetNoOfBinsFitted(const UInt_t idx) const;
virtual UInt_t GetTotalNoOfBinsFitted() const;

1
src/include/PRunSingleHisto.h
View File

@ -45,6 +45,7 @@ class PRunSingleHisto : public PRunBase
virtual Double_t CalcChiSquare(const std::vector<Double_t>& par);
virtual Double_t CalcChiSquareExpected(const std::vector<Double_t>& par);
virtual Double_t CalcMaxLikelihood(const std::vector<Double_t>& par);
virtual Double_t CalcMaxLikelihoodExpected(const std::vector<Double_t>& par);
virtual void CalcTheory();
virtual UInt_t GetNoOfFitBins();

9
src/include/PStartupHandler.h
View File

@ -73,17 +73,15 @@ class PStartupHandler : public TObject, public TQObject
virtual void CheckLists();
virtual PStartupOptions* GetStartupOptions() { return &fStartupOptions; } ///< returns the startup options
virtual PMsrFourierStructure GetFourierDefaults() { return fFourierDefaults; } ///< returns the Fourier defaults
virtual const PStringVector GetDataPathList() const { return fDataPathList; } ///< returns the search data path list
virtual const PIntVector GetMarkerList() const { return fMarkerList; } ///< returns the marker list
virtual const PIntVector GetColorList() const { return fColorList; } ///< returns the color list
virtual void SetStartupOptions(const PStartupOptions opt) { fStartupOptions = opt; }
private:
enum EKeyWords {eEmpty, eComment, eDataPath, eOptions, eWritePerRunBlockChisq, eEstimateN0, eAlphaEstimateN0,
eFourierSettings, eUnits, eFourierPower, eApodization, ePlot, ePhase, ePhaseIncrement,
enum EKeyWords {eEmpty, eComment, eDataPath, eOptions,
eFourierSettings, eUnits, eFourierPower,
eApodization, ePlot, ePhase, ePhaseIncrement,
eRootSettings, eMarkerList, eMarker,
eColorList, eColor};
EKeyWords fKey; ///< xml filter key
@ -94,7 +92,6 @@ class PStartupHandler : public TObject, public TQObject
PStringVector fDataPathList; ///< search data path list
PIntVector fMarkerList; ///< marker list
PIntVector fColorList; ///< color list
PStartupOptions fStartupOptions; ///< collects all startup options which will be requested by PMsrFileHandler
Bool_t StartupFileExists(Char_t *fln);

8
src/musrFT.cpp
View File

@ -713,7 +713,7 @@ Int_t musrFT_dumpData(TString fln, vector<PFourier*> &fourierData, Double_t star
musrFT_cleanup(hRe);
for (UInt_t i=1; i<fourierData.size(); i++) {
hRe = fourierData[i]->GetRealFourier();
if (hRe->GetNbinsX()-1 < minSize)
if (hRe->GetNbinsX()-1 < (Int_t)minSize)
minSize = hRe->GetNbinsX()-1;
musrFT_cleanup(hRe);
}
@ -721,7 +721,7 @@ Int_t musrFT_dumpData(TString fln, vector<PFourier*> &fourierData, Double_t star
for (UInt_t i=0; i<fourierData.size(); i++) {
hRe = fourierData[i]->GetRealFourier();
hIm = fourierData[i]->GetImaginaryFourier();
for (Int_t j=1; j<minSize; j++) {
for (Int_t j=1; j<(Int_t)minSize; j++) {
dval = hRe->GetBinCenter(j);
if ((dval >= start) && (dval <= end)) {
freq.push_back(dval);
@ -1020,7 +1020,6 @@ Int_t main(Int_t argc, Char_t *argv[])
PStartupOptions startup_options;
startup_options.writeExpectedChisq = false;
startup_options.estimateN0 = true;
startup_options.alphaEstimateN0 = 0.0;
TSAXParser *saxParser = new TSAXParser();
PStartupHandler *startupHandler = new PStartupHandler();
if (!startupHandler->StartupFileFound()) {
@ -1057,7 +1056,6 @@ Int_t main(Int_t argc, Char_t *argv[])
}
}
}
startupHandler->SetStartupOptions(startup_options);
// defines the raw time-domain data vector
PPrepFourier data(startupParam.packing, startupParam.bkg_range, startupParam.bkg);
@ -1066,7 +1064,7 @@ Int_t main(Int_t argc, Char_t *argv[])
vector<PMsrHandler*> msrHandler;
msrHandler.resize(startupParam.msrFln.size());
for (UInt_t i=0; i<startupParam.msrFln.size(); i++) {
msrHandler[i] = new PMsrHandler(startupParam.msrFln[i].Data(), startupHandler->GetStartupOptions(), true);
msrHandler[i] = new PMsrHandler(startupParam.msrFln[i].Data(), &startup_options, true);
status = msrHandler[i]->ReadMsrFile();
if (status != PMUSR_SUCCESS) {
switch (status) {

16
src/musredit/PAdmin.cpp
View File

@ -87,6 +87,8 @@ bool PAdminXMLParser::startElement( const QString&, const QString&,
fKeyWord = eTitleFromDataFile;
} else if (qName == "musrview_show_fourier") {
fKeyWord = eMusrviewShowFourier;
} else if (qName == "musrview_show_avg") {
fKeyWord = eMusrviewShowAvg;
} else if (qName == "enable_musrt0") {
fKeyWord = eEnableMusrT0;
} else if (qName == "keep_minuit2_output") {
@ -251,6 +253,13 @@ bool PAdminXMLParser::characters(const QString& str)
flag = false;
fAdmin->setMusrviewShowFourierFlag(flag);
break;
case eMusrviewShowAvg:
if (str == "y")
flag = true;
else
flag = false;
fAdmin->setMusrviewShowAvgFlag(flag);
break;
case eEnableMusrT0:
if (str == "y")
flag = true;
@ -614,6 +623,7 @@ PAdmin::PAdmin() : QObject()
fFileFormat = QString("");
fMusrviewShowFourier = false;
fMusrviewShowAvg = false;
fTitleFromDataFile = false;
fEnableMusrT0 = false;
@ -837,6 +847,12 @@ int PAdmin::savePrefs(QString pref_fln)
else
data[i] = " <musrview_show_fourier>n</musrview_show_fourier>";
}
if (data[i].contains("<musrview_show_avg>") && data[i].contains("</musrview_show_avg>")) {
if (fMusrviewShowAvg)
data[i] = " <musrview_show_avg>y</musrview_show_avg>";
else
data[i] = " <musrview_show_avg>n</musrview_show_avg>";
}
if (data[i].contains("<enable_musrt0>") && data[i].contains("</enable_musrt0>")) {
if (fEnableMusrT0)
data[i] = " <enable_musrt0>y</enable_musrt0>";

6
src/musredit/PAdmin.h
View File

@ -69,7 +69,8 @@ class PAdminXMLParser : public QXmlDefaultHandler
private:
enum EAdminKeyWords {eEmpty, eTimeout, eKeepMinuit2Output, eDumpAscii, eDumpRoot,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0, eMusrviewShowFourier, eEnableMusrT0,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0,
eMusrviewShowFourier, eMusrviewShowAvg, eEnableMusrT0,
eFontName, eFontSize, eExecPath, eDefaultSavePath,
eRecentFile, eBeamline, eInstitute, eFileFormat, eLifetimeCorrection, eMsrDefaultFilePath,
eTheoFuncPixmapPath, eFunc, eFuncName, eFuncComment, eFuncLabel,
@ -119,6 +120,7 @@ class PAdmin : public QObject
QString getDefaultSavePath() { return fDefaultSavePath; }
bool getTitleFromDataFileFlag() { return fTitleFromDataFile; }
bool getMusrviewShowFourierFlag() { return fMusrviewShowFourier; }
bool getMusrviewShowAvgFlag() { return fMusrviewShowAvg; }
bool getEnableMusrT0Flag() { return fEnableMusrT0; }
bool getKeepMinuit2OutputFlag() { return fKeepMinuit2Output; }
bool getDumpAsciiFlag() { return fDumpAscii; }
@ -142,6 +144,7 @@ class PAdmin : public QObject
void setTimeout(const int ival) { fTimeout = ival; }
void setTitleFromDataFileFlag(const bool flag) { fTitleFromDataFile = flag; }
void setMusrviewShowFourierFlag(const bool flag) { fMusrviewShowFourier = flag; }
void setMusrviewShowAvgFlag(const bool flag) { fMusrviewShowAvg = flag; }
void setEnableMusrT0Flag(const bool flag) { fEnableMusrT0 = flag; }
void setKeepMinuit2OutputFlag(const bool flag) { fKeepMinuit2Output = flag; }
void setDumpAsciiFlag(const bool flag) { fDumpAscii = flag; }
@ -185,6 +188,7 @@ class PAdmin : public QObject
QVector<QString> fRecentFile; ///< keep vector of recent path-file names
bool fMusrviewShowFourier; ///< flag indicating if musrview should show at startup data (=false) or Fourier of data (=true).
bool fMusrviewShowAvg; ///< flag indicating if musrview should show at startup averaged (=true) or original (=false) data/Fourier.
bool fKeepMinuit2Output; ///< flag indicating if the Minuit2 output shall be kept (default: no)
bool fDumpAscii; ///< flag indicating if musrfit shall make an ascii-dump file (for debugging purposes, default: no).
bool fDumpRoot; ///< flag indicating if musrfit shall make an root-dump file (for debugging purposes, default: no).

1
src/musredit/PPrefsDialog.cpp
View File

@ -62,6 +62,7 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
fPerRunBlockChisq_checkBox->setChecked(fAdmin->getChisqPerRunBlockFlag());
fEstimateN0_checkBox->setChecked(fAdmin->getEstimateN0Flag());
fFourier_checkBox->setChecked(fAdmin->getMusrviewShowFourierFlag());
fAvg_checkBox->setChecked(fAdmin->getMusrviewShowAvgFlag());
fTimeout_lineEdit->setText(QString("%1").arg(fAdmin->getTimeout()));
fTimeout_lineEdit->setValidator(new QIntValidator(fTimeout_lineEdit));

1
src/musredit/PPrefsDialog.h
View File

@ -47,6 +47,7 @@ class PPrefsDialog : public QDialog, private Ui::PPrefsDialog
PPrefsDialog(PAdmin *admin);
bool getMusrviewShowFourierFlag() { return fFourier_checkBox->isChecked(); }
bool getMusrviewShowAvgFlag() { return fAvg_checkBox->isChecked(); }
bool getKeepMinuit2OutputFlag() { return fKeepMn2Output_checkBox->isChecked(); }
bool getTitleFromDataFileFlag() { return fTitleFromData_checkBox->isChecked(); }
bool getEnableMusrT0Flag() { return fEnableMusrT0_checkBox->isChecked(); }

20
src/musredit/PTextEdit.cpp
View File

@ -1699,6 +1699,12 @@ void PTextEdit::musrCalcChisq()
if ( !currentEditor() )
return;
int result = 0;
if (fAdmin->getEstimateN0Flag())
result = QMessageBox::question(this, "Estimate N0 active",
"Do you wish a chisq/mlh evaluation with an automatic N0 estimate?",
QMessageBox::Yes, QMessageBox::No);
QString tabLabel = fTabWidget->tabText(fTabWidget->currentIndex());
if (tabLabel == "noname") {
QMessageBox::critical(this, "**ERROR**", "For a fit a real msr-file is needed.");
@ -1716,8 +1722,8 @@ void PTextEdit::musrCalcChisq()
cmd.append(str);
cmd.append(QFileInfo(*fFilenames.find( currentEditor())).fileName() );
cmd.append("--chisq-only");
cmd.append("--estimateN0");
cmd.append("no");
if (fAdmin->getEstimateN0Flag() && (result == QMessageBox::Yes))
cmd.append("--estimateN0");
PFitOutputHandler fitOutputHandler(QFileInfo(*fFilenames.find( currentEditor() )).absolutePath(), cmd);
fitOutputHandler.setModal(true);
fitOutputHandler.exec();
@ -1770,19 +1776,11 @@ void PTextEdit::musrFit()
// check estimate N0 flag
if (fAdmin->getEstimateN0Flag()) {
cmd.append("--estimateN0");
cmd.append("yes");
} else {
cmd.append("--estimateN0");
cmd.append("no");
}
// check per-run-block-chisq flag
if (fAdmin->getChisqPerRunBlockFlag()) {
cmd.append("--per-run-block-chisq");
cmd.append("yes");
} else {
cmd.append("--per-run-block-chisq");
cmd.append("no");
}
// add timeout
@ -2203,6 +2201,8 @@ void PTextEdit::musrView()
cmd += str + "\" --timeout " + numStr;
if (fAdmin->getMusrviewShowFourierFlag())
cmd += " -f ";
if (fAdmin->getMusrviewShowAvgFlag())
cmd += " -a ";
cmd += " &";
int status=system(cmd.toLatin1());

15
src/musredit/forms/PPrefsDialog.ui
View File

@ -33,7 +33,7 @@
<item>
<widget class="QTabWidget" name="fTabWidget">
<property name="currentIndex">
<number>0</number>
<number>2</number>
</property>
<widget class="QWidget" name="fGeneral_tab">
<attribute name="title">
@ -175,6 +175,19 @@
<string>start with Fourier</string>
</property>
</widget>
<widget class="QCheckBox" name="fAvg_checkBox">
<property name="geometry">
<rect>
<x>10</x>
<y>40</y>
<width>261</width>
<height>22</height>
</rect>
</property>
<property name="text">
<string>start with averaged data/Fourier</string>
</property>
</widget>
</widget>
<widget class="QWidget" name="fMusrt0_tab">
<attribute name="title">

45
src/musredit_qt5/PAdmin.cpp
View File

@ -37,6 +37,8 @@ using namespace std;
#include <QTextStream>
#include <QVector>
#include <QProcessEnvironment>
#include "PAdmin.h"
//--------------------------------------------------------------------------
@ -87,6 +89,8 @@ bool PAdminXMLParser::startElement( const QString&, const QString&,
fKeyWord = eTitleFromDataFile;
} else if (qName == "musrview_show_fourier") {
fKeyWord = eMusrviewShowFourier;
} else if (qName == "musrview_show_avg") {
fKeyWord = eMusrviewShowAvg;
} else if (qName == "enable_musrt0") {
fKeyWord = eEnableMusrT0;
} else if (qName == "keep_minuit2_output") {
@ -234,7 +238,7 @@ bool PAdminXMLParser::characters(const QString& str)
case eExecPath:
fAdmin->setExecPath(QString(str.toLatin1()).trimmed());
break;
case eDefaultSavePath:
case eDefaultSavePath:
fAdmin->setDefaultSavePath(QString(str.toLatin1()).trimmed());
break;
case eTitleFromDataFile:
@ -251,6 +255,13 @@ bool PAdminXMLParser::characters(const QString& str)
flag = false;
fAdmin->setMusrviewShowFourierFlag(flag);
break;
case eMusrviewShowAvg:
if (str == "y")
flag = true;
else
flag = false;
fAdmin->setMusrviewShowAvgFlag(flag);
break;
case eEnableMusrT0:
if (str == "y")
flag = true;
@ -477,7 +488,7 @@ bool PAdminXMLParser::endDocument()
str = expandPath(fAdmin->getDefaultSavePath());
if (!str.isEmpty())
fAdmin->setDefaultSavePath(str);
}
}
if (fAdmin->getMsrDefaultFilePath().indexOf('$') >= 0) {
str = expandPath(fAdmin->getMsrDefaultFilePath());
@ -567,13 +578,21 @@ QString PAdminXMLParser::expandPath(const QString &str)
QString msg;
QString newStr="";
QProcessEnvironment procEnv = QProcessEnvironment::systemEnvironment();
QStringList list = str.split("/");
for ( QStringList::Iterator it = list.begin(); it != list.end(); ++it ) {
token = *it;
if (token.contains("$")) {
token.remove('$');
path = std::getenv(token.toLatin1());
if (!procEnv.contains(token)) {
msg = QString("Couldn't find '%1'. Some things might not work properly").arg(token);
QMessageBox::warning(0, "**WARNING**", msg, QMessageBox::Ok, QMessageBox::NoButton);
newStr = "";
break;
}
path = procEnv.value(token, "");
if (path.isEmpty()) {
msg = QString("Couldn't expand '%1'. Some things might not work properly").arg(token);
QMessageBox::warning(0, "**WARNING**", msg, QMessageBox::Ok, QMessageBox::NoButton);
@ -614,6 +633,7 @@ PAdmin::PAdmin() : QObject()
fFileFormat = QString("");
fMusrviewShowFourier = false;
fMusrviewShowAvg = false;
fTitleFromDataFile = false;
fEnableMusrT0 = false;
@ -646,17 +666,18 @@ PAdmin::PAdmin() : QObject()
QString path = QString("./");
QString fln = QString("musredit_startup.xml");
QString pathFln = path + fln;
QProcessEnvironment procEnv = QProcessEnvironment::systemEnvironment();
if (!QFile::exists(pathFln)) {
// 2nd: check $HOME/.musrfit/musredit/musredit_startup.xml
path = std::getenv("HOME");
path = procEnv.value("HOME", "");
pathFln = path + "/.musrfit/musredit/" + fln;
if (!QFile::exists(pathFln)) {
// 3rd: check $MUSRFITPATH/musredit_startup.xml
path = std::getenv("MUSRFITPATH");
path = procEnv.value("MUSRFITPATH", "");
pathFln = path + "/" + fln;
if (!QFile::exists(pathFln)) {
// 4th: check $ROOTSYS/bin/musredit_startup.xml
path = std::getenv("ROOTSYS");
path = procEnv.value("ROOTSYS", "");
pathFln = path + "/bin/" + fln;
}
}
@ -837,12 +858,24 @@ int PAdmin::savePrefs(QString pref_fln)
else
data[i] = " <musrview_show_fourier>n</musrview_show_fourier>";
}
if (data[i].contains("<musrview_show_avg>") && data[i].contains("</musrview_show_avg>")) {
if (fMusrviewShowAvg)
data[i] = " <musrview_show_avg>y</musrview_show_avg>";
else
data[i] = " <musrview_show_avg>n</musrview_show_avg>";
}
if (data[i].contains("<enable_musrt0>") && data[i].contains("</enable_musrt0>")) {
if (fEnableMusrT0)
data[i] = " <enable_musrt0>y</enable_musrt0>";
else
data[i] = " <enable_musrt0>n</enable_musrt0>";
}
if (data[i].contains("<font_name>") && data[i].contains("</font_name>")) {
data[i] = QString(" <font_name>%1</font_name>").arg(fFontName);
}
if (data[i].contains("<font_size>") && data[i].contains("</font_size>")) {
data[i] = QString(" <font_size>%1</font_size>").arg(fFontSize);
}
}
// write prefs

6
src/musredit_qt5/PAdmin.h
View File

@ -69,7 +69,8 @@ class PAdminXMLParser : public QXmlDefaultHandler
private:
enum EAdminKeyWords {eEmpty, eTimeout, eKeepMinuit2Output, eDumpAscii, eDumpRoot,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0, eMusrviewShowFourier, eEnableMusrT0,
eTitleFromDataFile, eChisqPreRunBlock, eEstimateN0,
eMusrviewShowFourier, eMusrviewShowAvg, eEnableMusrT0,
eFontName, eFontSize, eExecPath, eDefaultSavePath,
eRecentFile, eBeamline, eInstitute, eFileFormat, eLifetimeCorrection, eMsrDefaultFilePath,
eTheoFuncPixmapPath, eFunc, eFuncName, eFuncComment, eFuncLabel,
@ -119,6 +120,7 @@ class PAdmin : public QObject
QString getDefaultSavePath() { return fDefaultSavePath; }
bool getTitleFromDataFileFlag() { return fTitleFromDataFile; }
bool getMusrviewShowFourierFlag() { return fMusrviewShowFourier; }
bool getMusrviewShowAvgFlag() { return fMusrviewShowAvg; }
bool getEnableMusrT0Flag() { return fEnableMusrT0; }
bool getKeepMinuit2OutputFlag() { return fKeepMinuit2Output; }
bool getDumpAsciiFlag() { return fDumpAscii; }
@ -142,6 +144,7 @@ class PAdmin : public QObject
void setTimeout(const int ival) { fTimeout = ival; }
void setTitleFromDataFileFlag(const bool flag) { fTitleFromDataFile = flag; }
void setMusrviewShowFourierFlag(const bool flag) { fMusrviewShowFourier = flag; }
void setMusrviewShowAvgFlag(const bool flag) { fMusrviewShowAvg = flag; }
void setEnableMusrT0Flag(const bool flag) { fEnableMusrT0 = flag; }
void setKeepMinuit2OutputFlag(const bool flag) { fKeepMinuit2Output = flag; }
void setDumpAsciiFlag(const bool flag) { fDumpAscii = flag; }
@ -185,6 +188,7 @@ class PAdmin : public QObject
QVector<QString> fRecentFile; ///< keep vector of recent path-file names
bool fMusrviewShowFourier; ///< flag indicating if musrview should show at startup data (=false) or Fourier of data (=true).
bool fMusrviewShowAvg; ///< flag indicating if musrview should show at startup averaged (=true) or original (=false) data/Fourier.
bool fKeepMinuit2Output; ///< flag indicating if the Minuit2 output shall be kept (default: no)
bool fDumpAscii; ///< flag indicating if musrfit shall make an ascii-dump file (for debugging purposes, default: no).
bool fDumpRoot; ///< flag indicating if musrfit shall make an root-dump file (for debugging purposes, default: no).

4
src/musredit_qt5/PFitOutputHandler.cpp
View File

@ -62,6 +62,10 @@ PFitOutputHandler::PFitOutputHandler(QString workingDirectory, QVector<QString>
// QProcess related code
fProc = new QProcess( this );
// make sure that the system environment variables are properly set
QProcessEnvironment env = QProcessEnvironment::systemEnvironment();
env.insert("LD_LIBRARY_PATH", env.value("ROOTSYS") + "/lib:" + env.value("LD_LIBRARY_PATH"));
fProc->setProcessEnvironment(env);
fProc->setWorkingDirectory(workingDirectory);
// Set up the command and arguments.

1
src/musredit_qt5/PPrefsDialog.cpp
View File

@ -62,6 +62,7 @@ PPrefsDialog::PPrefsDialog(PAdmin *admin) : fAdmin(admin)
fPerRunBlockChisq_checkBox->setChecked(fAdmin->getChisqPerRunBlockFlag());
fEstimateN0_checkBox->setChecked(fAdmin->getEstimateN0Flag());
fFourier_checkBox->setChecked(fAdmin->getMusrviewShowFourierFlag());
fAvg_checkBox->setChecked(fAdmin->getMusrviewShowAvgFlag());
fTimeout_lineEdit->setText(QString("%1").arg(fAdmin->getTimeout()));
fTimeout_lineEdit->setValidator(new QIntValidator(fTimeout_lineEdit));

1
src/musredit_qt5/PPrefsDialog.h
View File

@ -47,6 +47,7 @@ class PPrefsDialog : public QDialog, private Ui::PPrefsDialog
PPrefsDialog(PAdmin *admin);
bool getMusrviewShowFourierFlag() { return fFourier_checkBox->isChecked(); }
bool getMusrviewShowAvgFlag() { return fAvg_checkBox->isChecked(); }
bool getKeepMinuit2OutputFlag() { return fKeepMn2Output_checkBox->isChecked(); }
bool getTitleFromDataFileFlag() { return fTitleFromData_checkBox->isChecked(); }
bool getEnableMusrT0Flag() { return fEnableMusrT0_checkBox->isChecked(); }

36
src/musredit_qt5/PTextEdit.cpp
View File

@ -848,6 +848,13 @@ void PTextEdit::fileOpen()
++it;
}
// in case there is a 1st empty tab "noname", remove it
if (fTabWidget->tabText(0) == "noname") { // has to be the first, otherwise do nothing
fFileSystemWatcher->removePath("noname");
delete fTabWidget->widget(0);
}
}
//----------------------------------------------------------------------------------------------------
@ -879,6 +886,13 @@ void PTextEdit::fileOpenRecent()
else
fileReload();
}
// in case there is a 1st empty tab "noname", remove it
if (fTabWidget->tabText(0) == "noname") { // has to be the first, otherwise do nothing
fFileSystemWatcher->removePath("noname");
delete fTabWidget->widget(0);
}
}
//----------------------------------------------------------------------------------------------------
@ -1699,6 +1713,11 @@ void PTextEdit::musrCalcChisq()
if ( !currentEditor() )
return;
int result = 0;
if (fAdmin->getEstimateN0Flag())
result = QMessageBox::question(this, "Estimate N0 active",
"Do you wish a chisq/mlh evaluation with an automatic N0 estimate?");
QString tabLabel = fTabWidget->tabText(fTabWidget->currentIndex());
if (tabLabel == "noname") {
QMessageBox::critical(this, "**ERROR**", "For a fit a real msr-file is needed.");
@ -1716,8 +1735,8 @@ void PTextEdit::musrCalcChisq()
cmd.append(str);
cmd.append(QFileInfo(*fFilenames.find( currentEditor())).fileName() );
cmd.append("--chisq-only");
cmd.append("--estimateN0");
cmd.append("no");
if (fAdmin->getEstimateN0Flag() && (result == QMessageBox::Yes))
cmd.append("--estimateN0");
PFitOutputHandler fitOutputHandler(QFileInfo(*fFilenames.find( currentEditor() )).absolutePath(), cmd);
fitOutputHandler.setModal(true);
fitOutputHandler.exec();
@ -1770,19 +1789,11 @@ void PTextEdit::musrFit()
// check estimate N0 flag
if (fAdmin->getEstimateN0Flag()) {
cmd.append("--estimateN0");
cmd.append("yes");
} else {
cmd.append("--estimateN0");
cmd.append("no");
}
// check per-run-block-chisq flag
if (fAdmin->getChisqPerRunBlockFlag()) {
cmd.append("--per-run-block-chisq");
cmd.append("yes");
} else {
cmd.append("--per-run-block-chisq");
cmd.append("no");
}
// add timeout
@ -2205,6 +2216,10 @@ void PTextEdit::musrView()
if (fAdmin->getMusrviewShowFourierFlag())
arg << "-f";
// start with averaged data/Fourier?
if (fAdmin->getMusrviewShowAvgFlag())
arg << "-a";
QProcess *proc = new QProcess(this);
// make sure that the system environment variables are properly set
@ -2333,6 +2348,7 @@ void PTextEdit::musrPrefs()
if (dlg->exec() == QDialog::Accepted) {
fAdmin->setMusrviewShowFourierFlag(dlg->getMusrviewShowFourierFlag());
fAdmin->setMusrviewShowAvgFlag(dlg->getMusrviewShowAvgFlag());
fAdmin->setKeepMinuit2OutputFlag(dlg->getKeepMinuit2OutputFlag());
fAdmin->setTitleFromDataFileFlag(dlg->getTitleFromDataFileFlag());
fAdmin->setEnableMusrT0Flag(dlg->getEnableMusrT0Flag());

15
src/musredit_qt5/forms/PPrefsDialog.ui
View File

@ -17,7 +17,7 @@
<string>Preferences</string>
</property>
<property name="windowIcon">
<iconset resource="../musredit.qrc">
<iconset>
<normaloff>:/images/musrfit.xpm</normaloff>:/images/musrfit.xpm</iconset>
</property>
<widget class="QWidget" name="layoutWidget">
@ -175,6 +175,19 @@
<string>start with Fourier</string>
</property>
</widget>
<widget class="QCheckBox" name="fAvg_checkBox">
<property name="geometry">
<rect>
<x>10</x>
<y>40</y>
<width>231</width>
<height>21</height>
</rect>
</property>
<property name="text">
<string>start with averaged data/Fourier</string>
</property>
</widget>
</widget>
<widget class="QWidget" name="fMusrt0_tab">
<attribute name="title">

44
src/musrfit.cpp
View File

@ -104,9 +104,8 @@ void musrfit_syntax()
cout << endl << " -t, --title-from-data-file: will replace the <msr-file> run title by the";
cout << endl << " run title of the FIRST run of the <msr-file> run block, if a run title";
cout << endl << " is present in the data file.";
cout << endl << " -e, --estimateN0: estimate N0 for single histogram fits flag. <flag> can have the values 'yes' or 'no'.";
cout << endl << " -e, --estimateN0: estimate N0 for single histogram fits.";
cout << endl << " -p, --per-run-block-chisq: will write per run block chisq to the msr-file.";
cout << endl << " <flag> can have the values 'yes' or 'no'.";
cout << endl << " --dump <type> is writing a data file with the fit data and the theory";
cout << endl << " <type> can be 'ascii', 'root'";
cout << endl << " --timeout <timeout_tag>: overwrites to predefined timeout of " << timeout << " (sec).";
@ -444,8 +443,7 @@ int main(int argc, char *argv[])
bool timeout_enabled = true;
PStartupOptions startup_options;
startup_options.writeExpectedChisq = false;
startup_options.estimateN0 = true;
startup_options.alphaEstimateN0 = 0.0;
startup_options.estimateN0 = false;
TString dump("");
char filename[1024];
@ -496,39 +494,9 @@ int main(int argc, char *argv[])
break;
}
} else if (!strcmp(argv[i], "-e") || !strcmp(argv[i], "--estimateN0")) {
if (i<argc-1) {
if (!strcmp(argv[i+1], "yes")) {
startup_options.estimateN0 = true;
} else if (!strcmp(argv[i+1], "no")) {
startup_options.estimateN0 = false;
} else {
cerr << endl << "musrfit: **ERROR** option --estimateN0 <flag> with unsupported <flag> = " << argv[i+1] << endl;
show_syntax = true;
break;
}
i++;
} else {
cerr << endl << "musrfit: **ERROR** found option --estimateN0 without <flag>" << endl;
show_syntax = true;
break;
}
startup_options.estimateN0 = true;
} else if (!strcmp(argv[i], "-p") || !strcmp(argv[i], "--per-run-block-chisq")) {
if (i<argc-1) {
if (!strcmp(argv[i+1], "yes")) {
startup_options.writeExpectedChisq = true;
} else if (!strcmp(argv[i+1], "no")) {
startup_options.writeExpectedChisq = false;
} else {
cerr << endl << "musrfit: **ERROR** option --per-run-block-chisq <flag> with unsupported <flag> = " << argv[i+1] << endl;
show_syntax = true;
break;
}
i++;
} else {
cerr << endl << "musrfit: **ERROR** found option --per-run-block-chisq without <flag>" << endl;
show_syntax = true;
break;
}
startup_options.writeExpectedChisq = true;
} else if (!strcmp(argv[i], "--timeout")) {
if (i<argc-1) {
TString str(argv[i+1]);
@ -614,13 +582,11 @@ int main(int argc, char *argv[])
}
}
}
if (startupHandler)
startupHandler->SetStartupOptions(startup_options);
// read msr-file
PMsrHandler *msrHandler = 0;
if (startupHandler)
msrHandler = new PMsrHandler(filename, startupHandler->GetStartupOptions());
msrHandler = new PMsrHandler(filename, &startup_options);
else
msrHandler = new PMsrHandler(filename);
status = msrHandler->ReadMsrFile();

5
src/musrfit_startup.xml
View File

@ -14,11 +14,6 @@
<data_path>/afs/psi.ch/project/bulkmusr/data/alc</data_path>
<data_path>/afs/psi.ch/project/bulkmusr/data/hifi</data_path>
<data_path>/afs/psi.ch/project/bulkmusr/data/lem</data_path>
<options>
<write_per_run_block_chisq>n</write_per_run_block_chisq>
<estimate_n0>yes</estimate_n0>
<alpha_estimate_n0>0.0</alpha_estimate_n0>
</options>
<fourier_settings>
<units>Gauss</units>
<fourier_power>0</fourier_power>

8
src/musrview.cpp
View File

@ -63,6 +63,7 @@ void musrview_syntax()
cout << endl << " --help : display this help and exit.";
cout << endl << " --version : output version information and exit.";
cout << endl << " -f, --fourier: will directly present the Fourier transform of the <msr-file>.";
cout << endl << " -a, --avg: will directly present the averaged data/Fourier of the <msr-file>.";
cout << endl << " --<graphic-format-extension>: ";
cout << endl << " will produce a graphics-output-file without starting a root session.";
cout << endl << " the name is based on the <msr-file>, e.g. 3310.msr -> 3310_0.png";
@ -102,6 +103,7 @@ int main(int argc, char *argv[])
bool success = true;
char fileName[128];
bool fourier = false;
bool avg = false;
bool graphicsOutput = false;
bool asciiOutput = false;
char graphicsExtension[128];
@ -135,6 +137,8 @@ int main(int argc, char *argv[])
break;
} else if (!strcmp(argv[i], "-f") || !strcmp(argv[i], "--fourier")) {
fourier = true;
} else if (!strcmp(argv[i], "-a") || !strcmp(argv[i], "--avg")) {
avg = true;
} else if (!strcmp(argv[i], "--eps") || !strcmp(argv[i], "--pdf") || !strcmp(argv[i], "--gif") ||
!strcmp(argv[i], "--jpg") || !strcmp(argv[i], "--png") || !strcmp(argv[i], "--svg") ||
!strcmp(argv[i], "--xpm") || !strcmp(argv[i], "--root")) {
@ -308,12 +312,12 @@ int main(int argc, char *argv[])
startupHandler->GetMarkerList(),
startupHandler->GetColorList(),
graphicsOutput||asciiOutput,
fourier);
fourier, avg);
else
musrCanvas = new PMusrCanvas(i, msrHandler->GetMsrTitle()->Data(),
10+i*100, 10+i*100, 800, 600,
graphicsOutput||asciiOutput,
fourier);
fourier, avg);
if (!musrCanvas->IsValid()) {
cerr << endl << ">> musrview **SEVERE ERROR** Couldn't invoke all necessary objects, will quit.";