increased musrfit patch number.

Master

Approved-by: Andreas Suter

CMakeLists.txt

@@ -1,7 +1,7 @@
 # - musrfit
 cmake_minimum_required(VERSION 3.17)
 
-project(musrfit VERSION 1.9.1 LANGUAGES C CXX)
+project(musrfit VERSION 1.9.3 LANGUAGES C CXX)
 
 #--- musrfit specific options -------------------------------------------------
 option(nexus "build optional NeXus support. Needed for ISIS" OFF)
@@ -222,6 +222,29 @@ else ()
   set(IS_GIT_REPO 0)
 endif ()
 
+#--- rpath related things -----------------------------------------------------
+# use, i.e. don't skip the full RPATH for the build tree
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+
+# when building, don't use the install RPATH already
+# (but later on when installing)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+
+set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+
+# add the automatically determined parts of the RPATH
+# which point to directories outside the build tree to the install RPATH
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+
+# the RPATH to be used when installing, but only if it's not a system directory
+list(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir)
+if("${isSystemDir}" STREQUAL "-1")
+    set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
+endif("${isSystemDir}" STREQUAL "-1")
+set(rpath ${CMAKE_INSTALL_RPATH})
+string(APPEND rpath ";/usr/local/lib")
+set(CMAKE_INSTALL_RPATH "${rpath}")
+
 #--- propagate to the sub-directories -----------------------------------------
 add_subdirectory(src)
 

ChangeLog

@@ -12,6 +12,11 @@ or
 
 https://bitbucket.org/muonspin/musrfit/commits/all
 
+Release of V1.9.2, 2023/10/25
+=============================
+
+switch over to smart pointers wherever possible.
+
 Release of V1.9.1, 2023/05/16
 =============================
 

README.md

@@ -32,7 +32,6 @@ For a more exhaustive user documentation see:
 
 <andreas.suter@psi.ch>
 
-For the beta-NMR related parts, please contact
-
+For the beta-NMR related parts, please contact Zaher Salman
 <zaher.salman@psi.ch>
 

doc/examples/UserFcn/PUserFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

doc/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: ea8ddbeaec87fd554dad49f5d0917959
+config: b18a215470778ea2da02b3cad4d0e07c
 tags: 645f666f9bcd5a90fca523b33c5a78b7

doc/html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.9.0',
+    VERSION: '1.9.1',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

doc/html/acknowledgement.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Acknowledgements &mdash; musrfit 1.9.0 documentation</title>
+  <title>Acknowledgements &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -94,6 +94,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -198,7 +199,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -220,7 +221,7 @@ extremely competent way to deal with his projects as well as to deal with the ch
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/any2many.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>any2many - a Universal μSR-file-format converter &mdash; musrfit 1.9.0 documentation</title>
+  <title>any2many - a Universal μSR-file-format converter &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -29,7 +29,7 @@
   <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" />
+    <link rel="next" title="Short description and references to the supported file-formats" href="file-formats.html" />
     <link rel="prev" title="msr2data - A Program for Automatically Processing Multiple musrfit msr Files" href="msr2data.html" /> 
 
   
@@ -94,6 +94,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -175,7 +176,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
   
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
       
-        <a href="musr-root.html" class="btn btn-neutral float-right" title="MusrRoot - an Extensible Open File Format for μSR" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+        <a href="file-formats.html" class="btn btn-neutral float-right" title="Short description and references to the supported file-formats" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
       
       
         <a href="msr2data.html" class="btn btn-neutral" title="msr2data - A Program for Automatically Processing Multiple musrfit msr Files" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
@@ -188,7 +189,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -210,7 +211,7 @@ For a detailed description see <a class="reference internal" href="user-manual.h
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/bugtracking.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Bugtracking &mdash; musrfit 1.9.0 documentation</title>
+  <title>Bugtracking &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -93,6 +93,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Bugtracking</a></li>
@@ -186,7 +187,7 @@ or send an e-mail to A. Suter at PSI.</p>
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -208,7 +209,7 @@ or send an e-mail to A. Suter at PSI.</p>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/cite.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>How to Cite musrfit? &mdash; musrfit 1.9.0 documentation</title>
+  <title>How to Cite musrfit? &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -94,6 +94,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -200,7 +201,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -222,7 +223,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/file-formats.html

@@ -0,0 +1,553 @@
+
+
+<!DOCTYPE html>
+<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
+<!--[if gt IE 8]><!--> <html class="no-js" lang="en" > <!--<![endif]-->
+<head>
+  <meta charset="utf-8">
+  
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  
+  <title>Short description and references to the supported file-formats &mdash; musrfit 1.9.1 documentation</title>
+  
+
+  
+  
+  
+  
+
+  
+
+  
+  
+    
+
+  
+
+  
+    <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+    <link rel="next" title="MusrRoot - an Extensible Open File Format for μSR" href="musr-root.html" />
+    <link rel="prev" title="any2many - a Universal μSR-file-format converter" href="any2many.html" /> 
+
+  
+  <script src="_static/js/modernizr.min.js"></script>
+
+</head>
+
+<body class="wy-body-for-nav">
+
+   
+  <div class="wy-grid-for-nav">
+
+    
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search">
+          
+
+          
+            <a href="index.html" class="icon icon-home"> musrfit
+          
+
+          
+          </a>
+
+          
+            
+            
+              <div class="version">
+                1.9
+              </div>
+            
+          
+
+          
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
+          
+        </div>
+
+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+          
+            
+            
+              
+            
+            
+              <ul class="current">
+<li class="toctree-l1"><a class="reference internal" href="cite.html">How to Cite <code class="docutils literal notranslate"><span class="pre">musrfit</span></code>?</a></li>
+<li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial for <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="user-manual.html">User manual</a></li>
+<li class="toctree-l1"><a class="reference internal" href="user-libs.html">Documentation of user libs (user functions)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="setup-standard.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> on Different Platforms</a></li>
+<li class="toctree-l1"><a class="reference internal" href="setup-dks.html">Setting up <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> / <code class="docutils literal notranslate"><span class="pre">DKS</span></code>: High Speed Fitting with GPU’s</a></li>
+<li class="toctree-l1"><a class="reference internal" href="musredit.html"><code class="docutils literal notranslate"><span class="pre">musredit</span></code>: the GUI Based Interface to <code class="docutils literal notranslate"><span class="pre">musrfit</span></code></a></li>
+<li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
+<li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">Short description and references to the supported file-formats</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#ascii-file-format-for-non-mgrsr">ASCII file format for non-μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#db-file-format-for-non-mgrsr">DB file format for non-μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#dat-csv-like-file-format-for-non-mgrsr">DAT: CSV like file format for non-μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#mdu-file-format-psi-for-mgrsr">MDU file format (psi) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#mud-file-format-triumf-for-mgrsr">MUD file format (triumf) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#musrroot-file-format-psi-for-mgrsr">MusrRoot file format (PSI) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#nexus-file-format-isis-for-mgrsr">NeXus file format (isis) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#psi-bin-file-format-psi-for-mgrsr">PSI-BIN file format (psi) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#root-file-format-psi-lem-before-2012-for-mgrsr">ROOT file format (psi/lem before 2012) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#wkm-file-format-for-mgrsr">WKM file format for μSR</a></li>
+</ul>
+</li>
+<li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
+<li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
+</ul>
+
+            
+          
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+      
+      <nav class="wy-nav-top" aria-label="top navigation">
+        
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="index.html">musrfit</a>
+        
+      </nav>
+
+
+      <div class="wy-nav-content">
+        
+        <div class="rst-content">
+        
+          
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+<div role="navigation" aria-label="breadcrumbs navigation">
+
+  <ul class="wy-breadcrumbs">
+    
+      <li><a href="index.html">Docs</a> &raquo;</li>
+        
+      <li>Short description and references to the supported file-formats</li>
+    
+    
+      <li class="wy-breadcrumbs-aside">
+        
+            
+            <a href="_sources/file-formats.rst.txt" rel="nofollow"> View page source</a>
+          
+        
+      </li>
+    
+  </ul>
+
+  
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+            
+  <div class="section" id="short-description-and-references-to-the-supported-file-formats">
+<span id="file-formats"></span><span id="index-0"></span><h1>Short description and references to the supported file-formats<a class="headerlink" href="#short-description-and-references-to-the-supported-file-formats" title="Permalink to this headline">¶</a></h1>
+<p>Currently the following μSR and non-μSR file formats are supported (in alphabetic order):</p>
+<ul class="simple">
+<li>ascii (non-μSR): <a class="reference internal" href="#ascii-file-format"><span class="std std-ref">ASCII file format for non-uSR</span></a></li>
+<li>db (non-μSR): <a class="reference internal" href="#db-file-format"><span class="std std-ref">DB (triumf)</span></a></li>
+<li>dat (non-μSR): <a class="reference internal" href="#dat-file-format"><span class="std std-ref">DAT: CSV like data file</span></a></li>
+<li>mdu (μSR): <a class="reference internal" href="#mdu-file-format"><span class="std std-ref">MDU file format (PSI)</span></a></li>
+<li>mud (μSR): <a class="reference internal" href="#mud-file-format"><span class="std std-ref">MUon Data access file format (TRIUMF)</span></a></li>
+<li>musr-root (μSR): <a class="reference internal" href="musr-root.html#musrroot"><span class="std std-ref">MusrRoot - an Extensible Open File Format for uSR</span></a></li>
+<li>nexus (μSR): used to read NeXus files from ISIS (HDF4 and HDF5): <a class="reference internal" href="#nexus-file-format"><span class="std std-ref">NeXus</span></a></li>
+<li>psi-bin (μSR): <a class="reference internal" href="#psi-bin-file-format"><span class="std std-ref">PSI-BIN file format (PSI)</span></a></li>
+<li>root (μSR): specific version for LEM before 2012 <a class="reference internal" href="#root-file-format"><span class="std std-ref">LEM ROOT file format</span></a></li>
+<li>wkm (μSR): special ascii file format used in the past by the TU Braunschweig (outdated): <a class="reference internal" href="#wkm-file-format"><span class="std std-ref">WKM</span></a></li>
+</ul>
+<div class="section" id="ascii-file-format-for-non-mgrsr">
+<span id="ascii-file-format"></span><span id="index-1"></span><h2>ASCII file format for non-μSR<a class="headerlink" href="#ascii-file-format-for-non-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>This for instance can be used to fit <span class="math notranslate nohighlight">\(1/\lambda^2 ~ \mathrm{vs} ~ T\)</span> to study gap properties of superconductors.
+Details about the gap-intergrals can be found in the memo <em>GapIntegrals.pdf</em> which can be found in the source code of musrfit
+under &lt;musrfit-home-dir&gt;/src/external/libGapIntegrals.</p>
+<p>This primitive file format has the following structure:</p>
+<p>Comment lines start with a ‘#’ or ‘%’ character.
+The file can start with some header info. The header is optional, as all its tags, but
+if present it has the following format:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">HEADER</span>
+<span class="n">TITLE</span><span class="p">:</span>  <span class="n">title</span>
+<span class="n">X</span><span class="o">-</span><span class="n">AXIS</span><span class="o">-</span><span class="n">TITLE</span><span class="p">:</span> <span class="n">x</span><span class="o">-</span><span class="n">axis</span> <span class="n">title</span>
+<span class="n">Y</span><span class="o">-</span><span class="n">AXIS</span><span class="o">-</span><span class="n">TITLE</span><span class="p">:</span> <span class="n">y</span><span class="o">-</span><span class="n">axis</span> <span class="n">title</span>
+<span class="n">SETUP</span><span class="p">:</span>  <span class="n">setup</span>
+<span class="n">FIELD</span><span class="p">:</span>  <span class="n">field</span>
+<span class="n">TEMP</span><span class="p">:</span>   <span class="n">temperature</span>
+<span class="n">ENERGY</span><span class="p">:</span> <span class="n">energy</span>
+</pre></div>
+</div>
+<p>Field has to be given in (G), temperature in (K) and energy in (keV).</p>
+<p>The data are read column like and start with the data tag DATA, followed by the
+data columns, i.e.:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">DATA</span>
+<span class="n">x</span><span class="p">,</span> <span class="n">y</span> <span class="p">[,</span> <span class="n">error</span> <span class="n">y</span><span class="p">]</span>
+</pre></div>
+</div>
+<p>where spaces, column, are a tab are possible separations.
+If no error in y is present, the weighting in the fit will be equal.</p>
+<p>A full example might look like this:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># libGapIntegrals-test.dat</span>
+<span class="c1"># This is a comment</span>
+<span class="o">%</span> <span class="n">This</span> <span class="k">as</span> <span class="n">well</span>
+<span class="n">HEADER</span>
+<span class="n">TITLE</span><span class="p">:</span> <span class="n">Test</span> <span class="n">superconductor</span> <span class="n">data</span>
+<span class="n">X</span><span class="o">-</span><span class="n">AXIS</span><span class="o">-</span><span class="n">TITLE</span><span class="p">:</span> <span class="n">T</span> <span class="p">(</span><span class="n">K</span><span class="p">)</span>
+<span class="n">Y</span><span class="o">-</span><span class="n">AXIS</span><span class="o">-</span><span class="n">TITLE</span><span class="p">:</span> <span class="c1">#lambda^{-2} (#mum^{-2})</span>
+<span class="n">SETUP</span><span class="p">:</span> <span class="n">H</span> <span class="c1">#parallel c</span>
+<span class="n">FIELD</span><span class="p">:</span> <span class="mi">100</span>
+<span class="n">TEMP</span><span class="p">:</span> <span class="mf">0.0</span>
+<span class="n">ENERGY</span><span class="p">:</span> <span class="mi">4200</span>
+<span class="c1"># here the data will follow</span>
+<span class="n">DATA</span>
+<span class="c1"># x, y, error y</span>
+<span class="mf">0.0318411</span><span class="p">,</span> <span class="mf">7.77455</span><span class="p">,</span> <span class="mf">0.2</span>
+<span class="mf">0.0629929</span><span class="p">,</span> <span class="mf">7.9869</span><span class="p">,</span> <span class="mf">0.15</span>
+<span class="mf">0.113914</span><span class="p">,</span> <span class="mf">7.64209</span><span class="p">,</span> <span class="mf">0.15</span>
+<span class="mf">0.202492</span><span class="p">,</span> <span class="mf">7.37699</span><span class="p">,</span> <span class="mf">0.15</span>
+<span class="mf">0.302725</span><span class="p">,</span> <span class="mf">7.70893</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">0.447456</span><span class="p">,</span> <span class="mf">7.77565</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">0.611685</span><span class="p">,</span> <span class="mf">7.45768</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">0.813613</span><span class="p">,</span> <span class="mf">7.19287</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">1.00822</span><span class="p">,</span> <span class="mf">7.57813</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">1.24793</span><span class="p">,</span> <span class="mf">7.31343</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">1.50635</span><span class="p">,</span> <span class="mf">7.16818</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">1.74591</span><span class="p">,</span> <span class="mf">6.99634</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">1.99795</span><span class="p">,</span> <span class="mf">6.90414</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">2.25061</span><span class="p">,</span> <span class="mf">6.41393</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">2.4958</span><span class="p">,</span> <span class="mf">6.66666</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">2.75514</span><span class="p">,</span> <span class="mf">5.93766</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">3.00753</span><span class="p">,</span> <span class="mf">5.61992</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">3.26056</span><span class="p">,</span> <span class="mf">4.89091</span><span class="p">,</span> <span class="mf">0.12</span>
+<span class="mf">3.49414</span><span class="p">,</span> <span class="mf">4.52005</span><span class="p">,</span> <span class="mf">0.08</span>
+<span class="mf">3.75356</span><span class="p">,</span> <span class="mf">3.73799</span><span class="p">,</span> <span class="mf">0.08</span>
+<span class="mf">3.99425</span><span class="p">,</span> <span class="mf">2.84974</span><span class="p">,</span> <span class="mf">0.08</span>
+<span class="mf">4.30518</span><span class="p">,</span> <span class="mf">1.35139</span><span class="p">,</span> <span class="mf">0.08</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="db-file-format-for-non-mgrsr">
+<span id="db-file-format"></span><span id="index-2"></span><h2>DB file format for non-μSR<a class="headerlink" href="#db-file-format-for-non-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>The DB file format is an <em>archaic</em> ascii file format from TRIUMF which is intended to be used to collect parameter summaries of various runs, which can be read directly by <a class="reference internal" href="mupp.html#mupp"><span class="std std-ref">mupp</span></a>.</p>
+<p>The DB file is organized in a couple of tags defining various properties, followed by the parameter data with its errors.
+Tags and is content are always separated by an empty line.
+The first tag is the <strong>TITLE</strong>. Followed by the title in the next line</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">TITLE</span>
+<span class="n">This</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">best</span> <span class="n">data</span> <span class="n">ever</span>
+</pre></div>
+</div>
+<p>The next tag is the <strong>ABSTRACT</strong>, followed a potentially multi-line abstract, e.g.</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">ABSTRACT</span>
+<span class="n">Here</span> <span class="n">comes</span> <span class="n">the</span> <span class="n">detailed</span> <span class="n">description</span> <span class="o">...</span>
+</pre></div>
+</div>
+<p>The next tag, <strong>LABELS</strong>, are used to define human readable names for the data parameters to be followed:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">LABELS</span>
+<span class="n">T</span> <span class="p">(</span><span class="n">K</span><span class="p">)</span>
+<span class="n">B</span> <span class="p">(</span><span class="n">G</span><span class="p">)</span>
+<span class="o">...</span>
+</pre></div>
+</div>
+<p>The number of labels have to fit the number of parameters present!</p>
+<p>The next tag is <strong>DATA</strong>, which is a list of the parameter names as found in you msr-file.
+Unlike the other tags, here the list of names follow directly after the <strong>DATA</strong> tag</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">DATA</span> <span class="n">dataT</span> <span class="n">dataB</span> <span class="n">dataE</span> <span class="n">dataTr</span> <span class="o">...</span>
+</pre></div>
+</div>
+<p>Next there will be a line with the tag <strong>\-e</strong>, followed by</p>
+<p>The parameters are afterwards listed as</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">param</span><span class="o">-</span><span class="n">name</span> <span class="o">=</span> <span class="n">val</span><span class="p">,</span> <span class="n">pos</span><span class="o">-</span><span class="n">err</span><span class="p">,</span> <span class="n">neg</span><span class="o">-</span><span class="n">err</span><span class="p">,</span>\
+</pre></div>
+</div>
+<p>After all the parameters listed of a specific run, the <strong>run number</strong> with the run title ends a run data set.
+This might look like this (be aware of the comma!):</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="mi">11231</span><span class="p">,,,</span> <span class="n">AgPlate</span> <span class="mi">250</span><span class="n">nm</span> <span class="p">(</span><span class="n">T5034</span><span class="p">),</span> <span class="n">T</span><span class="o">=</span><span class="mf">200.00</span> <span class="n">K</span><span class="p">,</span> <span class="n">E</span><span class="o">=</span><span class="mf">12.99</span> <span class="n">keV</span><span class="p">,</span> <span class="n">B</span><span class="o">=~</span><span class="mi">50</span><span class="p">(</span><span class="n">G</span><span class="p">)</span><span class="o">/</span><span class="mf">8.65</span><span class="p">(</span><span class="n">A</span><span class="p">),</span> <span class="n">Tr</span><span class="o">/</span><span class="n">Sa</span><span class="o">=</span><span class="mf">12.00</span><span class="o">/-</span><span class="mf">1.80</span> <span class="n">kV</span><span class="p">,</span> <span class="n">SR</span><span class="o">=-</span><span class="mf">10.00</span>
+</pre></div>
+</div>
+<p>A full example might look like this:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">TITLE</span>
+<span class="n">Ag</span> <span class="n">Plate</span> <span class="mi">2023</span> <span class="n">runs</span><span class="p">,</span> <span class="n">Tr12kV</span><span class="p">,</span> <span class="n">E</span><span class="o">=</span><span class="mi">13</span><span class="n">keV</span><span class="p">,</span> <span class="n">TF</span> <span class="n">B</span><span class="o">=</span><span class="mi">50</span><span class="n">G</span>
+
+<span class="n">Abstract</span>
+<span class="n">Summary</span> <span class="n">of</span> <span class="n">the</span>
+
+<span class="n">LABELS</span>
+<span class="n">T</span> <span class="p">(</span><span class="n">K</span><span class="p">)</span>
+<span class="n">B</span> <span class="p">(</span><span class="n">G</span><span class="p">)</span>
+<span class="n">Implantation</span> <span class="n">Energy</span> <span class="p">(</span><span class="n">keV</span><span class="p">)</span>
+<span class="n">Transport</span> <span class="p">(</span><span class="n">kV</span><span class="p">)</span>
+<span class="n">RAL</span><span class="o">-</span><span class="n">RAR</span> <span class="p">(</span><span class="n">kV</span><span class="p">)</span>
+<span class="n">RAT</span><span class="o">-</span><span class="n">RAB</span> <span class="p">(</span><span class="n">kV</span><span class="p">)</span>
+<span class="n">Spin</span> <span class="n">Rotation</span> <span class="n">Angle</span> <span class="p">(</span><span class="n">degree</span><span class="p">)</span>
+<span class="n">Asy</span>
+<span class="n">Lambda</span>
+<span class="n">Ph</span>
+<span class="n">Field</span>
+<span class="n">RelPh_L</span>
+<span class="n">N0_L</span>
+<span class="n">N_bkg_L</span>
+<span class="n">RelPh_T</span>
+<span class="n">N0_T</span>
+<span class="n">N_bkg_T</span>
+<span class="n">RelPh_R</span>
+<span class="n">alpha_LR</span>
+<span class="n">N_bkg_R</span>
+<span class="n">RelPh_B</span>
+<span class="n">alpha_TB</span>
+<span class="n">N_bkg_B</span>
+<span class="n">maxLH</span>
+<span class="n">NDF</span>
+<span class="n">maxLHred</span>
+<span class="n">RUN</span>
+
+<span class="n">Data</span> <span class="n">dataT</span> <span class="n">dataB</span> <span class="n">dataE</span> <span class="n">dataTr</span> <span class="n">dataRALRAR</span> <span class="n">dataRATRAB</span> <span class="n">dataSpinRot</span> <span class="n">Asy</span> <span class="n">Lambda</span> <span class="n">Ph</span> <span class="n">Field</span> <span class="n">RelPh_L</span> <span class="n">N0_L</span> <span class="n">N_bkg_L</span> <span class="n">RelPh_T</span> <span class="n">N0_T</span> <span class="n">N_bkg_T</span> <span class="n">RelPh_R</span> <span class="n">alpha_LR</span> <span class="n">N_bkg_R</span> <span class="n">RelPh_B</span> <span class="n">alpha_TB</span> <span class="n">N_bkg_B</span> <span class="n">maxLH</span> <span class="n">NDF</span> <span class="n">maxLHred</span> <span class="n">RUN</span>
+\<span class="o">-</span><span class="n">e</span>
+<span class="n">dataT</span> <span class="o">=</span> <span class="mf">200.001</span><span class="p">,</span> <span class="mf">0.0009</span><span class="p">,</span> <span class="mf">0.0009</span><span class="p">,</span>\
+<span class="n">dataB</span> <span class="o">=</span> <span class="mf">49.49</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataE</span> <span class="o">=</span> <span class="mf">12.9952</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataTr</span> <span class="o">=</span> <span class="mf">11.9993</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataRALRAR</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.008</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataRATRAB</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.009</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataSpinRot</span> <span class="o">=</span> <span class="o">-</span><span class="mi">10</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">Asy</span> <span class="o">=</span> <span class="mf">0.22466</span><span class="p">,</span> <span class="mf">0.00084</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.00084</span><span class="p">,</span>\
+<span class="n">Lambda</span> <span class="o">=</span> <span class="mf">0.0081</span><span class="p">,</span> <span class="mf">0.0014</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.0014</span><span class="p">,</span>\
+<span class="n">Ph</span> <span class="o">=</span> <span class="mf">12.14</span><span class="p">,</span> <span class="mf">0.32</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.32</span><span class="p">,</span>\
+<span class="n">Field</span> <span class="o">=</span> <span class="mf">50.837</span><span class="p">,</span> <span class="mf">0.017</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.017</span><span class="p">,</span>\
+<span class="n">RelPh_L</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">N0_L</span> <span class="o">=</span> <span class="mf">430.67</span><span class="p">,</span> <span class="mf">0.39</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.39</span><span class="p">,</span>\
+<span class="n">N_bkg_L</span> <span class="o">=</span> <span class="mf">6.81</span><span class="p">,</span> <span class="mf">0.048</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.048</span><span class="p">,</span>\
+<span class="n">RelPh_T</span> <span class="o">=</span> <span class="o">-</span><span class="mf">89.95</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span>\
+<span class="n">N0_T</span> <span class="o">=</span> <span class="mf">422.6</span><span class="p">,</span> <span class="mf">0.37</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.37</span><span class="p">,</span>\
+<span class="n">N_bkg_T</span> <span class="o">=</span> <span class="mf">7.125</span><span class="p">,</span> <span class="mf">0.047</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.048</span><span class="p">,</span>\
+<span class="n">RelPh_R</span> <span class="o">=</span> <span class="o">-</span><span class="mf">178.55</span><span class="p">,</span> <span class="mf">0.39</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.39</span><span class="p">,</span>\
+<span class="n">alpha_LR</span> <span class="o">=</span> <span class="mf">0.9729</span><span class="p">,</span> <span class="mf">0.0012</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.0012</span><span class="p">,</span>\
+<span class="n">N_bkg_R</span> <span class="o">=</span> <span class="mf">7.375</span><span class="p">,</span> <span class="mf">0.048</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.048</span><span class="p">,</span>\
+<span class="n">RelPh_B</span> <span class="o">=</span> <span class="mf">90.38</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span>\
+<span class="n">alpha_TB</span> <span class="o">=</span> <span class="mf">0.9522</span><span class="p">,</span> <span class="mf">0.0012</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.0012</span><span class="p">,</span>\
+<span class="n">N_bkg_B</span> <span class="o">=</span> <span class="mf">6.546</span><span class="p">,</span> <span class="mf">0.047</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.047</span><span class="p">,</span>\
+<span class="n">maxLH</span> <span class="o">=</span> <span class="mf">20303.3</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">NDF</span> <span class="o">=</span> <span class="mi">20361</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">maxLHred</span> <span class="o">=</span> <span class="mf">0.997166</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="mi">11231</span><span class="p">,,,</span> <span class="n">AgPlate</span> <span class="mi">250</span><span class="n">nm</span> <span class="p">(</span><span class="n">T5034</span><span class="p">),</span> <span class="n">T</span><span class="o">=</span><span class="mf">200.00</span> <span class="n">K</span><span class="p">,</span> <span class="n">E</span><span class="o">=</span><span class="mf">12.99</span> <span class="n">keV</span><span class="p">,</span> <span class="n">B</span><span class="o">=~</span><span class="mi">50</span><span class="p">(</span><span class="n">G</span><span class="p">)</span><span class="o">/</span><span class="mf">8.65</span><span class="p">(</span><span class="n">A</span><span class="p">),</span> <span class="n">Tr</span><span class="o">/</span><span class="n">Sa</span><span class="o">=</span><span class="mf">12.00</span><span class="o">/-</span><span class="mf">1.80</span> <span class="n">kV</span><span class="p">,</span> <span class="n">SR</span><span class="o">=-</span><span class="mf">10.00</span>
+<span class="n">dataT</span> <span class="o">=</span> <span class="mi">153</span><span class="p">,</span> <span class="mf">0.7</span><span class="p">,</span> <span class="mf">0.7</span><span class="p">,</span>\
+<span class="n">dataB</span> <span class="o">=</span> <span class="mf">49.49</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataE</span> <span class="o">=</span> <span class="mf">12.9952</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataTr</span> <span class="o">=</span> <span class="mf">11.9993</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataRALRAR</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.008</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataRATRAB</span> <span class="o">=</span> <span class="o">-</span><span class="mf">0.009</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">dataSpinRot</span> <span class="o">=</span> <span class="o">-</span><span class="mi">10</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">Asy</span> <span class="o">=</span> <span class="mf">0.22253</span><span class="p">,</span> <span class="mf">0.00084</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.00083</span><span class="p">,</span>\
+<span class="n">Lambda</span> <span class="o">=</span> <span class="mf">0.0055</span><span class="p">,</span> <span class="mf">0.0014</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.0014</span><span class="p">,</span>\
+<span class="n">Ph</span> <span class="o">=</span> <span class="mf">11.53</span><span class="p">,</span> <span class="mf">0.32</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.32</span><span class="p">,</span>\
+<span class="n">Field</span> <span class="o">=</span> <span class="mf">51.026</span><span class="p">,</span> <span class="mf">0.017</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.017</span><span class="p">,</span>\
+<span class="n">RelPh_L</span> <span class="o">=</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">N0_L</span> <span class="o">=</span> <span class="mf">430.31</span><span class="p">,</span> <span class="mf">0.39</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.39</span><span class="p">,</span>\
+<span class="n">N_bkg_L</span> <span class="o">=</span> <span class="mf">6.762</span><span class="p">,</span> <span class="mf">0.048</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.048</span><span class="p">,</span>\
+<span class="n">RelPh_T</span> <span class="o">=</span> <span class="o">-</span><span class="mf">89.3</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span>\
+<span class="n">N0_T</span> <span class="o">=</span> <span class="mf">422.31</span><span class="p">,</span> <span class="mf">0.37</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.37</span><span class="p">,</span>\
+<span class="n">N_bkg_T</span> <span class="o">=</span> <span class="mf">6.96</span><span class="p">,</span> <span class="mf">0.047</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.047</span><span class="p">,</span>\
+<span class="n">RelPh_R</span> <span class="o">=</span> <span class="o">-</span><span class="mf">178.61</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span>\
+<span class="n">alpha_LR</span> <span class="o">=</span> <span class="mf">0.975</span><span class="p">,</span> <span class="mf">0.0013</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.0012</span><span class="p">,</span>\
+<span class="n">N_bkg_R</span> <span class="o">=</span> <span class="mf">7.361</span><span class="p">,</span> <span class="mf">0.048</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.048</span><span class="p">,</span>\
+<span class="n">RelPh_B</span> <span class="o">=</span> <span class="mf">90.24</span><span class="p">,</span> <span class="mf">0.4</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.4</span><span class="p">,</span>\
+<span class="n">alpha_TB</span> <span class="o">=</span> <span class="mf">0.9605</span><span class="p">,</span> <span class="mf">0.0012</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.0012</span><span class="p">,</span>\
+<span class="n">N_bkg_B</span> <span class="o">=</span> <span class="mf">6.623</span><span class="p">,</span> <span class="mf">0.047</span><span class="p">,</span> <span class="o">-</span><span class="mf">0.047</span><span class="p">,</span>\
+<span class="n">maxLH</span> <span class="o">=</span> <span class="mf">20435.6</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">NDF</span> <span class="o">=</span> <span class="mi">20361</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="n">maxLHred</span> <span class="o">=</span> <span class="mf">1.00366</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span>\
+<span class="mi">11235</span><span class="p">,,,</span> <span class="n">AgPlate</span> <span class="mi">250</span><span class="n">nm</span> <span class="p">(</span><span class="n">T5034</span><span class="p">),</span> <span class="n">T</span><span class="o">=</span><span class="mf">151.72</span> <span class="n">K</span><span class="p">,</span> <span class="n">E</span><span class="o">=</span><span class="mf">13.00</span> <span class="n">keV</span><span class="p">,</span> <span class="n">B</span><span class="o">=~</span><span class="mi">50</span><span class="p">(</span><span class="n">G</span><span class="p">)</span><span class="o">/</span><span class="mf">8.65</span><span class="p">(</span><span class="n">A</span><span class="p">),</span> <span class="n">Tr</span><span class="o">/</span><span class="n">Sa</span><span class="o">=</span><span class="mf">12.00</span><span class="o">/-</span><span class="mf">1.80</span> <span class="n">kV</span><span class="p">,</span> <span class="n">SR</span><span class="o">=-</span><span class="mf">10.00</span>
+<span class="o">&gt;&gt;</span> <span class="n">here</span> <span class="n">many</span> <span class="n">more</span> <span class="n">run</span> <span class="n">data</span> <span class="n">would</span> <span class="n">follow</span> <span class="o">...</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="dat-csv-like-file-format-for-non-mgrsr">
+<span id="dat-file-format"></span><span id="index-3"></span><h2>DAT: CSV like file format for non-μSR<a class="headerlink" href="#dat-csv-like-file-format-for-non-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>This is typically used when exporting the parameter data from <strong>msr2data</strong> to be used in <strong>mupp</strong>, gnuplot, origin, or whatever parameter plotter you might use.
+The first line defines the parameter tags separated by spaces or tabs. If errors are available there are labeled be the ending <em>Err</em>.
+This is followed by the parameter values and its errors if present. A fill example looks like this:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">dataT</span>        <span class="n">dataTErr</span>        <span class="n">dataB</span>        <span class="n">dataE</span>        <span class="n">dataTr</span>       <span class="n">dataRALRAR</span>   <span class="n">dataRATRAB</span>   <span class="n">dataSpinRot</span>  <span class="n">Asy</span>          <span class="n">AsyPosErr</span>          <span class="n">AsyNegErr</span>          <span class="n">Lambda</span>       <span class="n">LambdaPosErr</span>       <span class="n">LambdaNegErr</span>       <span class="n">Ph</span>           <span class="n">PhPosErr</span>           <span class="n">PhNegErr</span>           <span class="n">Field</span>        <span class="n">FieldPosErr</span>        <span class="n">FieldNegErr</span>        <span class="n">RelPh_L</span>      <span class="n">RelPh_LPosErr</span>      <span class="n">RelPh_LNegErr</span>      <span class="n">N0_L</span>         <span class="n">N0_LPosErr</span>         <span class="n">N0_LNegErr</span>         <span class="n">N_bkg_L</span>      <span class="n">N_bkg_LPosErr</span>      <span class="n">N_bkg_LNegErr</span>      <span class="n">RelPh_T</span>      <span class="n">RelPh_TPosErr</span>      <span class="n">RelPh_TNegErr</span>      <span class="n">N0_T</span>         <span class="n">N0_TPosErr</span>         <span class="n">N0_TNegErr</span>         <span class="n">N_bkg_T</span>      <span class="n">N_bkg_TPosErr</span>      <span class="n">N_bkg_TNegErr</span>      <span class="n">RelPh_R</span>      <span class="n">RelPh_RPosErr</span>      <span class="n">RelPh_RNegErr</span>      <span class="n">alpha_LR</span>     <span class="n">alpha_LRPosErr</span>     <span class="n">alpha_LRNegErr</span>     <span class="n">N_bkg_R</span>      <span class="n">N_bkg_RPosErr</span>      <span class="n">N_bkg_RNegErr</span>      <span class="n">RelPh_B</span>      <span class="n">RelPh_BPosErr</span>      <span class="n">RelPh_BNegErr</span>      <span class="n">alpha_TB</span>     <span class="n">alpha_TBPosErr</span>     <span class="n">alpha_TBNegErr</span>     <span class="n">N_bkg_B</span>      <span class="n">N_bkg_BPosErr</span>      <span class="n">N_bkg_BNegErr</span>      <span class="n">maxLH</span>        <span class="n">NDF</span>          <span class="n">maxLHred</span>     <span class="n">RUN</span>
+<span class="mi">200</span>          <span class="mf">0.007</span>           <span class="mf">99.48</span>        <span class="mf">1.11754</span>      <span class="mf">10.001</span>       <span class="o">-</span><span class="mf">0.008</span>       <span class="o">-</span><span class="mf">0.008</span>       <span class="o">-</span><span class="mi">10</span>          <span class="mf">0.1587</span>        <span class="mf">0.0012</span>        <span class="mf">0.0012</span>        <span class="mf">0.0263</span>        <span class="mf">0.003</span>         <span class="mf">0.003</span>         <span class="mf">29.85</span>         <span class="mf">0.64</span>          <span class="mf">0.64</span>          <span class="mf">101.179</span>       <span class="mf">0.035</span>         <span class="mf">0.035</span>         <span class="mi">0</span>             <span class="mi">0</span>             <span class="mi">0</span>             <span class="mf">219.27</span>        <span class="mf">0.27</span>          <span class="mf">0.27</span>          <span class="mf">2.676</span>         <span class="mf">0.033</span>         <span class="mf">0.033</span>         <span class="o">-</span><span class="mf">89.79</span>        <span class="mf">0.81</span>          <span class="mf">0.81</span>          <span class="mf">210.42</span>        <span class="mf">0.26</span>          <span class="mf">0.26</span>          <span class="mf">2.723</span>         <span class="mf">0.032</span>         <span class="mf">0.032</span>         <span class="o">-</span><span class="mf">179.73</span>       <span class="mf">0.81</span>          <span class="mf">0.81</span>          <span class="mf">0.9808</span>        <span class="mf">0.0017</span>        <span class="mf">0.0017</span>        <span class="mf">2.993</span>         <span class="mf">0.033</span>         <span class="mf">0.033</span>         <span class="mf">90.05</span>         <span class="mf">0.82</span>          <span class="mf">0.82</span>          <span class="mf">0.9755</span>        <span class="mf">0.0017</span>        <span class="mf">0.0017</span>        <span class="mf">2.501</span>         <span class="mf">0.032</span>         <span class="mf">0.032</span>         <span class="mf">20444.8</span>      <span class="mi">20361</span>        <span class="mf">1.00412</span>      <span class="mi">11400</span>
+<span class="mi">200</span>          <span class="mf">0.009</span>           <span class="mf">99.49</span>        <span class="mf">2.11668</span>      <span class="mf">10.001</span>       <span class="o">-</span><span class="mf">0.008</span>       <span class="o">-</span><span class="mf">0.008</span>       <span class="o">-</span><span class="mi">10</span>          <span class="mf">0.1732</span>        <span class="mf">0.0012</span>        <span class="mf">0.0012</span>        <span class="mf">0.0096</span>        <span class="mf">0.0025</span>        <span class="mf">0.0026</span>        <span class="mf">28.88</span>         <span class="mf">0.57</span>          <span class="mf">0.57</span>          <span class="mf">101.231</span>       <span class="mf">0.03</span>          <span class="mf">0.03</span>          <span class="mi">0</span>             <span class="mi">0</span>             <span class="mi">0</span>             <span class="mf">219.86</span>        <span class="mf">0.27</span>          <span class="mf">0.27</span>          <span class="mf">2.749</span>         <span class="mf">0.033</span>         <span class="mf">0.033</span>         <span class="o">-</span><span class="mf">88.87</span>        <span class="mf">0.71</span>          <span class="mf">0.71</span>          <span class="mf">211.47</span>        <span class="mf">0.26</span>          <span class="mf">0.26</span>          <span class="mf">2.791</span>         <span class="mf">0.032</span>         <span class="mf">0.032</span>         <span class="o">-</span><span class="mf">178.48</span>       <span class="mf">0.72</span>          <span class="mf">0.71</span>          <span class="mf">0.9678</span>        <span class="mf">0.0017</span>        <span class="mf">0.0017</span>        <span class="mf">2.969</span>         <span class="mf">0.033</span>         <span class="mf">0.033</span>         <span class="mf">90.94</span>         <span class="mf">0.73</span>          <span class="mf">0.73</span>          <span class="mf">0.9608</span>        <span class="mf">0.0017</span>        <span class="mf">0.0017</span>        <span class="mf">2.653</span>         <span class="mf">0.032</span>         <span class="mf">0.032</span>         <span class="mf">20182.5</span>      <span class="mi">20361</span>        <span class="mf">0.991233</span>     <span class="mi">11401</span>
+</pre></div>
+</div>
+</div>
+<div class="section" id="mdu-file-format-psi-for-mgrsr">
+<span id="mdu-file-format"></span><span id="index-4"></span><h2>MDU file format (psi) for μSR<a class="headerlink" href="#mdu-file-format-psi-for-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>For details about the PSI-BIN/MDU file format from PSI see <a class="reference external" href="http://lmu.web.psi.ch/docu/manuals/bulk_manuals/software/Class_MuSR_PSI/index.html">Class_MuSR_PSI</a></p>
+</div>
+<div class="section" id="mud-file-format-triumf-for-mgrsr">
+<span id="mud-file-format"></span><span id="index-5"></span><h2>MUD file format (triumf) for μSR<a class="headerlink" href="#mud-file-format-triumf-for-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>For details about the MUD file format from triumf see <a class="reference external" href="https://cmms.triumf.ca/mud/">MUon Data access</a> .</p>
+</div>
+<div class="section" id="musrroot-file-format-psi-for-mgrsr">
+<span id="musr-root-file-format"></span><h2>MusrRoot file format (PSI) for μSR<a class="headerlink" href="#musrroot-file-format-psi-for-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>For details see <a class="reference internal" href="musr-root.html#musrroot"><span class="std std-ref">MusrRoot - an Extensible Open File Format for uSR</span></a>.</p>
+</div>
+<div class="section" id="nexus-file-format-isis-for-mgrsr">
+<span id="nexus-file-format"></span><span id="index-6"></span><h2>NeXus file format (isis) for μSR<a class="headerlink" href="#nexus-file-format-isis-for-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>For details about the NeXus file format from ISIS (UK) see <a class="reference external" href="https://doi.org/10.1016/S0921-4526(02)01613-7">The application of the NeXus data format to ISIS muon data</a> . For a detailed list of available meta information and data see <a class="reference external" href="https://www.isis.stfc.ac.uk/Pages/nexus-definition-v27924.pdf">NeXus Instrument Definitions for ISIS muon Data</a> .</p>
+</div>
+<div class="section" id="psi-bin-file-format-psi-for-mgrsr">
+<span id="psi-bin-file-format"></span><span id="index-7"></span><h2>PSI-BIN file format (psi) for μSR<a class="headerlink" href="#psi-bin-file-format-psi-for-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>For details about the PSI-BIN/MDU file format from PSI see <a class="reference external" href="http://lmu.web.psi.ch/docu/manuals/bulk_manuals/software/Class_MuSR_PSI/index.html">Class_MuSR_PSI</a>.</p>
+</div>
+<div class="section" id="root-file-format-psi-lem-before-2012-for-mgrsr">
+<span id="root-file-format"></span><span id="index-8"></span><h2>ROOT file format (psi/lem before 2012) for μSR<a class="headerlink" href="#root-file-format-psi-lem-before-2012-for-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>For details about the API of ROOT files can be here: <a class="reference external" href="https://root.cern/manual/root_files/">ROOT files</a>.
+The structure of the ROOT files (LEM, before 2012) looks like this:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">ROOT</span><span class="o">-</span><span class="n">file</span> <span class="o">--|</span>
+            <span class="o">|--</span> <span class="n">histos</span> <span class="o">---|</span>
+            <span class="o">|</span>             <span class="o">|--</span> <span class="n">DecayAnaModule</span>
+            <span class="o">|</span>             <span class="o">|--</span> <span class="n">PileUpAnaModule</span>
+            <span class="o">|</span>             <span class="o">|--</span> <span class="n">ScalerSumRate</span>
+            <span class="o">|</span>             <span class="o">|--</span> <span class="n">SCAnaModule</span>
+            <span class="o">|</span>
+            <span class="o">|--</span> <span class="n">RunInfo</span> <span class="o">--|</span>
+                          <span class="o">|--</span> <span class="n">RunSummary</span>
+</pre></div>
+</div>
+<p><code class="docutils literal notranslate"><span class="pre">histos</span></code>, <code class="docutils literal notranslate"><span class="pre">RunInfo</span></code>, <code class="docutils literal notranslate"><span class="pre">DecayAnaModule</span></code>, <code class="docutils literal notranslate"><span class="pre">PileUpAnaModule</span></code>, <code class="docutils literal notranslate"><span class="pre">ScalerSumRate</span></code>, <code class="docutils literal notranslate"><span class="pre">SCAnaModule</span></code> are <strong>TFolder</strong> objects.</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">DecayAnaModule</span></code> object holds the positron spectra</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">DecayAnaModule</span> <span class="o">--|</span>
+                 <span class="o">|--</span> <span class="n">hDecay00</span>
+                 <span class="o">|--</span> <span class="n">hDecay01</span>
+                 <span class="o">|--</span> <span class="n">hDecay02</span>
+                 <span class="o">|--</span> <span class="n">hDecay03</span>
+                 <span class="o">|--</span> <span class="n">hDecay20</span>
+                 <span class="o">|--</span> <span class="n">hDecay21</span>
+                 <span class="o">|--</span> <span class="n">hDecay22</span>
+                 <span class="o">|--</span> <span class="n">hDecay23</span>
+</pre></div>
+</div>
+<p>The <code class="docutils literal notranslate"><span class="pre">hDecayXX</span></code> files or <strong>TH1F</strong> objects containing the positron spectra of the LEM detectors.</p>
+<p>The detectors (00, 01, 02, and 03) are the detectors (Left, Top, Right, Bottom). These are non-post-pileup (NPP) histograms.</p>
+<p>The detectors (20, 21, 22, and 23) are the detectors (Left, Top, Right, Bottom). These are post-pileup-corrected (PPC) histograms.</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">SCAnaModule</span></code> contains various <strong>TF1H</strong> objects of slow control data of the run.</p>
+<p>The <code class="docutils literal notranslate"><span class="pre">RunSummary</span></code> is essentially an ascii dump, with summary information of the run.</p>
+</div>
+<div class="section" id="wkm-file-format-for-mgrsr">
+<span id="wkm-file-format"></span><span id="index-9"></span><h2>WKM file format for μSR<a class="headerlink" href="#wkm-file-format-for-mgrsr" title="Permalink to this headline">¶</a></h2>
+<p>WKM is an obsolete ascii file format, originally introduced by people from the TU Braunschweig.
+It starts with a header which shows like this:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="o">-</span> <span class="n">WKM</span> <span class="n">data</span> <span class="n">file</span> <span class="n">converted</span> <span class="k">with</span> <span class="n">any2many</span>
+<span class="n">NEMU_Run</span><span class="p">:</span>            <span class="mi">2466</span>
+<span class="n">nemu_Run</span><span class="p">:</span>            <span class="o">./</span><span class="mf">2466.</span><span class="n">wkm</span>
+<span class="n">Date</span><span class="p">:</span>                <span class="mi">13</span><span class="p">:</span><span class="mi">22</span><span class="p">:</span><span class="mi">00</span> <span class="mi">2012</span><span class="o">-</span><span class="mi">06</span><span class="o">-</span><span class="mi">03</span> <span class="o">/</span> <span class="mi">14</span><span class="p">:</span><span class="mi">04</span><span class="p">:</span><span class="mi">38</span> <span class="mi">2012</span><span class="o">-</span><span class="mi">06</span><span class="o">-</span><span class="mi">03</span>
+<span class="n">Title</span><span class="p">:</span>               <span class="n">LSCO</span> <span class="n">x</span><span class="o">=</span><span class="mf">0.02</span> <span class="p">(</span><span class="mi">224</span><span class="o">-</span><span class="mi">227</span><span class="p">),</span> <span class="n">T</span><span class="o">=</span><span class="mf">12.00</span> <span class="p">(</span><span class="n">K</span><span class="p">),</span> <span class="n">E</span><span class="o">=</span><span class="mf">5.57</span> <span class="n">keV</span><span class="p">,</span> <span class="n">WEW</span> <span class="n">B</span><span class="o">=~</span><span class="mi">49</span><span class="p">(</span><span class="n">G</span><span class="p">)</span><span class="o">/</span><span class="mf">8.62</span><span class="p">(</span><span class="n">A</span><span class="p">),</span> <span class="n">Tr</span><span class="o">=</span><span class="mf">15.02</span> <span class="p">(</span><span class="n">kV</span><span class="p">),</span> <span class="n">Sample</span><span class="o">=</span><span class="mf">8.70</span> <span class="p">(</span><span class="n">kV</span><span class="p">),</span> <span class="n">SpinRot</span> <span class="o">-</span><span class="mi">10</span>
+<span class="n">Field</span><span class="p">:</span>               <span class="mf">49.11</span>
+<span class="n">Setup</span><span class="p">:</span>               <span class="n">Sample</span><span class="p">,</span> <span class="n">WEW</span><span class="p">,</span> <span class="n">LowTemp</span><span class="o">-</span><span class="mi">2</span>
+<span class="n">Temp</span><span class="p">:</span>                <span class="mf">11.999</span>
+<span class="n">TOF</span><span class="p">(</span><span class="n">M3S1</span><span class="p">):</span>           <span class="n">nocut</span>
+<span class="n">Groups</span><span class="p">:</span>              <span class="mi">8</span>
+<span class="n">Channels</span><span class="p">:</span>            <span class="mi">66601</span>
+<span class="n">Resolution</span><span class="p">:</span>          <span class="mf">0.0001953125</span>
+</pre></div>
+</div>
+<p>The header ends with an empty line.</p>
+<p>The data are stored as following: there are always 10 bin-counts per line.
+Between detectors, there will be an empty line.</p>
+</div>
+</div>
+
+
+           </div>
+           
+          </div>
+          <footer>
+  
+    <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
+      
+        <a href="musr-root.html" class="btn btn-neutral float-right" title="MusrRoot - an Extensible Open File Format for μSR" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
+      
+      
+        <a href="any2many.html" class="btn btn-neutral" title="any2many - a Universal μSR-file-format converter" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+      
+    </div>
+  
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &copy; Copyright 2023, Andreas Suter.
+      Last updated on Aug 24, 2023.
+
+    </p>
+  </div>
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+
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+
+    <script type="text/javascript">
+        var DOCUMENTATION_OPTIONS = {
+            URL_ROOT:'./',
+            VERSION:'1.9.1',
+            LANGUAGE:'None',
+            COLLAPSE_INDEX:false,
+            FILE_SUFFIX:'.html',
+            HAS_SOURCE:  true,
+            SOURCELINK_SUFFIX: '.txt'
+        };
+    </script>
+      <script type="text/javascript" src="_static/jquery.js"></script>
+      <script type="text/javascript" src="_static/underscore.js"></script>
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+      jQuery(function () {
+          SphinxRtdTheme.Navigation.enable(true);
+      });
+  </script> 
+
+</body>
+</html>

doc/html/genindex.html

@@ -9,7 +9,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Index &mdash; musrfit 1.9.0 documentation</title>
+  <title>Index &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -93,6 +93,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -183,6 +184,7 @@
  | <a href="#T"><strong>T</strong></a>
  | <a href="#U"><strong>U</strong></a>
  | <a href="#V"><strong>V</strong></a>
+ | <a href="#W"><strong>W</strong></a>
  | <a href="#X"><strong>X</strong></a>
  
 </div>
@@ -205,13 +207,15 @@
 </li>
       <li><a href="user-manual.html#index-37">addt0-asymmetry</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="user-manual.html#index-36">addt0-single-histo</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="user-manual.html#index-22">alpha-beta</a>
 </li>
       <li><a href="any2many.html#index-0">any2many</a>, <a href="user-manual.html#index-8">[1]</a>
+</li>
+      <li><a href="file-formats.html#index-1">ascii-file-format</a>
 </li>
       <li><a href="user-manual.html#index-71">asymmetry-fit</a>
 </li>
@@ -263,18 +267,22 @@
 <h2 id="D">D</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="file-formats.html#index-3">dat-file-format</a>
+</li>
       <li><a href="user-manual.html#index-33">data-asymmetry</a>
 </li>
       <li><a href="user-manual.html#index-32">data-single-histo</a>
+</li>
+      <li><a href="file-formats.html#index-2">db-file-format</a>
 </li>
       <li><a href="user-libs.html#index-15">DepthProf-lib</a>
 </li>
       <li><a href="setup-dks.html#index-0">dks</a>
-</li>
-      <li><a href="user-manual.html#index-43">dks-command-overview</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="user-manual.html#index-43">dks-command-overview</a>
+</li>
       <li><a href="setup-dks.html#index-3">dks-install</a>
 </li>
       <li><a href="setup-dks.html#index-5">dks-opencl-macOS</a>
@@ -300,6 +308,8 @@
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="setup-standard.html#index-4">fftw</a>
+</li>
+      <li><a href="file-formats.html#index-0">file-formats</a>
 </li>
       <li><a href="user-manual.html#index-39">fit</a>
 </li>
@@ -310,11 +320,11 @@
       <li><a href="user-manual.html#index-27">forward</a>
 </li>
       <li><a href="user-manual.html#index-28">forward-backward</a>
-</li>
-      <li><a href="user-manual.html#index-50">fourier-block-apodization</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="user-manual.html#index-50">fourier-block-apodization</a>
+</li>
       <li><a href="user-manual.html#index-49">fourier-block-dc-corrected</a>
 </li>
       <li><a href="user-manual.html#index-48">fourier-block-fourier_power</a>
@@ -406,6 +416,8 @@
       <li><a href="setup-standard.html#index-21">macports</a>
 </li>
       <li><a href="user-manual.html#index-26">map</a>
+</li>
+      <li><a href="file-formats.html#index-4">mdu-file-format</a>
 </li>
       <li><a href="user-manual.html#index-17">meta-information</a>
 </li>
@@ -469,10 +481,12 @@
 </li>
       <li><a href="user-manual.html#index-7">msr2msr</a>
 </li>
-      <li><a href="mupp.html#index-0">mupp</a>
+      <li><a href="file-formats.html#index-5">mud-file-format</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="mupp.html#index-0">mupp</a>
+</li>
       <li><a href="mupp.html#index-1">mupp-gui</a>
 </li>
       <li><a href="mupp.html#index-2">mupp-scripting</a>
@@ -558,6 +572,8 @@
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="setup-standard.html#index-22">nexus-build-macports</a>
+</li>
+      <li><a href="file-formats.html#index-6">nexus-file-format</a>
 </li>
       <li><a href="user-manual.html#index-75">non-musr-fit</a>
 </li>
@@ -583,13 +599,15 @@
 </li>
       <li><a href="user-libs.html#index-32">PowderLineAsymGss</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="user-libs.html#index-31">PowderLineAsymLor</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="user-libs.html#index-30">PowderLineAxialGss</a>
 </li>
       <li><a href="user-libs.html#index-29">PowderLineAxialLor</a>
+</li>
+      <li><a href="file-formats.html#index-7">psi-bin-file-format</a>
 </li>
   </ul></td>
 </tr></table>
@@ -609,13 +627,15 @@
 </li>
       <li><a href="setup-standard.html#index-26">root-build-homebrew</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="setup-standard.html#index-16">root-build-linux</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="setup-standard.html#index-23">root-build-macports</a>
 </li>
       <li><a href="setup-standard.html#index-5">root-cern</a>
+</li>
+      <li><a href="file-formats.html#index-8">root-file-format</a>
 </li>
   </ul></td>
 </tr></table>
@@ -700,6 +720,14 @@
   </ul></td>
 </tr></table>
 
+<h2 id="W">W</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="file-formats.html#index-9">wkm-file-format</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="X">X</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -721,7 +749,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 24, 2023.
 
     </p>
   </div>
@@ -743,7 +771,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/index.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Welcome to the musrfit documentation! &mdash; musrfit 1.9.0 documentation</title>
+  <title>Welcome to the musrfit documentation! &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -93,6 +93,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -223,6 +224,19 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#ascii-file-format-for-non-mgrsr">ASCII file format for non-μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#db-file-format-for-non-mgrsr">DB file format for non-μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#dat-csv-like-file-format-for-non-mgrsr">DAT: CSV like file format for non-μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#mdu-file-format-psi-for-mgrsr">MDU file format (psi) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#mud-file-format-triumf-for-mgrsr">MUD file format (triumf) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#musrroot-file-format-psi-for-mgrsr">MusrRoot file format (PSI) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#nexus-file-format-isis-for-mgrsr">NeXus file format (isis) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#psi-bin-file-format-psi-for-mgrsr">PSI-BIN file format (psi) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#root-file-format-psi-lem-before-2012-for-mgrsr">ROOT file format (psi/lem before 2012) for μSR</a></li>
+<li class="toctree-l2"><a class="reference internal" href="file-formats.html#wkm-file-format-for-mgrsr">WKM file format for μSR</a></li>
+</ul>
+</li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="musr-root.html#some-basics-concerning-root-files">Some Basics Concerning ROOT Files</a></li>
 <li class="toctree-l2"><a class="reference internal" href="musr-root.html#id1">MusrRoot an Extensible Open File Format for μSR</a></li>
@@ -268,7 +282,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 24, 2023.
 
     </p>
   </div>
@@ -290,7 +304,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/msr2data.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &mdash; musrfit 1.9.0 documentation</title>
+  <title>msr2data - A Program for Automatically Processing Multiple musrfit msr Files &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -109,6 +109,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -515,7 +516,7 @@ fit serves as template for the second and so on. The template field stays empty
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -537,7 +538,7 @@ fit serves as template for the second and so on. The template field stays empty
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/mupp.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>mupp - μSR Parameter Plotter &mdash; musrfit 1.9.0 documentation</title>
+  <title>mupp - μSR Parameter Plotter &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -102,6 +102,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -405,7 +406,7 @@ SCRIPT COMMANDS:
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -427,7 +428,7 @@ SCRIPT COMMANDS:
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/musr-root.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>MusrRoot - an Extensible Open File Format for μSR &mdash; musrfit 1.9.0 documentation</title>
+  <title>MusrRoot - an Extensible Open File Format for μSR &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -30,7 +30,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Acknowledgements" href="acknowledgement.html" />
-    <link rel="prev" title="any2many - a Universal μSR-file-format converter" href="any2many.html" /> 
+    <link rel="prev" title="Short description and references to the supported file-formats" href="file-formats.html" /> 
 
   
   <script src="_static/js/modernizr.min.js"></script>
@@ -94,6 +94,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">MusrRoot - an Extensible Open File Format for μSR</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#some-basics-concerning-root-files">Some Basics Concerning ROOT Files</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#id1">MusrRoot an Extensible Open File Format for μSR</a><ul>
@@ -994,7 +995,7 @@ the entry has been added. The last token, <code class="docutils literal notransl
         <a href="acknowledgement.html" class="btn btn-neutral float-right" title="Acknowledgements" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
       
       
-        <a href="any2many.html" class="btn btn-neutral" title="any2many - a Universal μSR-file-format converter" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
+        <a href="file-formats.html" class="btn btn-neutral" title="Short description and references to the supported file-formats" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
       
     </div>
   
@@ -1004,7 +1005,7 @@ the entry has been added. The last token, <code class="docutils literal notransl
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -1026,7 +1027,7 @@ the entry has been added. The last token, <code class="docutils literal notransl
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/musredit.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>musredit: the GUI Based Interface to musrfit &mdash; musrfit 1.9.0 documentation</title>
+  <title>musredit: the GUI Based Interface to musrfit &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -114,6 +114,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -631,7 +632,7 @@ the corresponding fit parameter value, except the phases where the step will be
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -653,7 +654,7 @@ the corresponding fit parameter value, except the phases where the step will be
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/search.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Search &mdash; musrfit 1.9.0 documentation</title>
+  <title>Search &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -92,6 +92,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -182,7 +183,7 @@
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 24, 2023.
 
     </p>
   </div>
@@ -204,7 +205,7 @@
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/setup-dks.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Setting up musrfit / DKS: High Speed Fitting with GPU’s &mdash; musrfit 1.9.0 documentation</title>
+  <title>Setting up musrfit / DKS: High Speed Fitting with GPU’s &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -113,6 +113,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -405,7 +406,7 @@ The only thing you need <code class="docutils literal notranslate"><span class="
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -427,7 +428,7 @@ The only thing you need <code class="docutils literal notranslate"><span class="
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/setup-standard.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Setting up musrfit on Different Platforms &mdash; musrfit 1.9.0 documentation</title>
+  <title>Setting up musrfit on Different Platforms &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -138,6 +138,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -1092,7 +1093,7 @@ $ musrview test-histo-ROOT-NPP.msr
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -1114,7 +1115,7 @@ $ musrview test-histo-ROOT-NPP.msr
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/tutorial.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Tutorial for musrfit &mdash; musrfit 1.9.0 documentation</title>
+  <title>Tutorial for musrfit &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -106,6 +106,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -524,7 +525,7 @@ For a complete description please refer to the manuals of <a class="reference in
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -546,7 +547,7 @@ For a complete description please refer to the manuals of <a class="reference in
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/user-libs.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>Documentation of user libs (user functions) &mdash; musrfit 1.9.0 documentation</title>
+  <title>Documentation of user libs (user functions) &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -119,6 +119,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -865,7 +866,7 @@ K(m)&amp;=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -887,7 +888,7 @@ K(m)&amp;=\int_0^{\pi/2}\frac{\mathrm d\varphi}{\sqrt{1-m^2\sin^2{\varphi}}},\en
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/html/user-manual.html

@@ -8,7 +8,7 @@
   
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
   
-  <title>User manual &mdash; musrfit 1.9.0 documentation</title>
+  <title>User manual &mdash; musrfit 1.9.1 documentation</title>
   
 
   
@@ -157,6 +157,7 @@
 <li class="toctree-l1"><a class="reference internal" href="mupp.html">mupp - μSR Parameter Plotter</a></li>
 <li class="toctree-l1"><a class="reference internal" href="msr2data.html">msr2data - A Program for Automatically Processing Multiple <code class="docutils literal notranslate"><span class="pre">musrfit</span></code> msr Files</a></li>
 <li class="toctree-l1"><a class="reference internal" href="any2many.html">any2many - a Universal μSR-file-format converter</a></li>
+<li class="toctree-l1"><a class="reference internal" href="file-formats.html">Short description and references to the supported file-formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="musr-root.html">MusrRoot - an Extensible Open File Format for μSR</a></li>
 <li class="toctree-l1"><a class="reference internal" href="acknowledgement.html">Acknowledgements</a></li>
 <li class="toctree-l1"><a class="reference internal" href="bugtracking.html">Bugtracking</a></li>
@@ -2871,7 +2872,7 @@ The syntax here is attribute driven</li>
   <div role="contentinfo">
     <p>
         &copy; Copyright 2023, Andreas Suter.
-      Last updated on Feb 17, 2023.
+      Last updated on Aug 17, 2023.
 
     </p>
   </div>
@@ -2893,7 +2894,7 @@ The syntax here is attribute driven</li>
     <script type="text/javascript">
         var DOCUMENTATION_OPTIONS = {
             URL_ROOT:'./',
-            VERSION:'1.9.0',
+            VERSION:'1.9.1',
             LANGUAGE:'None',
             COLLAPSE_INDEX:false,
             FILE_SUFFIX:'.html',

doc/mupp_dox.cfg

@@ -38,7 +38,7 @@ PROJECT_NAME           = "mupp"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.0.0
+PROJECT_NUMBER         = 1.1.0
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

doc/musrfit.dox

@@ -12,8 +12,7 @@
 
 \mainpage musrfit - a framework to analyse muSR data.
 
-<p>This pages here are meant to explain the software structure of the musrfit framework. Only the core-classes 
-are described, *i.e.* not the Qt GUI related stuff.
+<p>This pages here are meant to explain the software structure of the musrfit framework. 
 
 <p>People merely interested in the handling of the programs should check this link:
 \htmlonly
@@ -64,13 +63,9 @@ under Linux, Mac OS X, and (with some more work) under Windows. The musrfit fram
 
 \section roadmap Road map and missing features
 
-<p>Support for NeXus files is fully available from early 2012 on. 
-
 <p>The following features should eventually be implemented, but are still missing:
 - non-muSR: The plan is to add an option to fit/plot \f$f(x_1,\ldots,x_n)\f$ versus \f$g(x_1,\ldots,x_n)\f$, where \f$x_i\f$ is a given data set element.
-- as soon as ROOT will properly support MS Windows platforms, some better support for MS Windows will be added. Currently only the cygwin version will be supported.
 - add an interface to maxent
-- we will provide rpm's for various linux flavors.
 
 \section shortComings Short comings of the current musrfit design
 

doc/musrfit_dox.cfg

@@ -38,7 +38,7 @@ PROJECT_NAME           = musrfit
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 1.6.0
+PROJECT_NUMBER         = 1.9.2
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

src/addRun.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -37,6 +37,7 @@
 
 #include <iostream>
 #include <fstream>
+#include <memory>
 
 #include <boost/algorithm/string.hpp>
 #include <boost/filesystem.hpp>
@@ -535,40 +536,22 @@ int main(int argc, char *argv[])
 
   // read startup file
   char startup_path_name[128];
-  TSAXParser *saxParser = new TSAXParser();
-  PStartupHandler *startupHandler = new PStartupHandler();
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<PStartupHandler> startupHandler = std::make_unique<PStartupHandler>();
   if (!startupHandler->StartupFileFound()) {
     std::cerr << std::endl << ">> addRun **WARNING** couldn't find " << startupHandler->GetStartupFilePath().Data();
     std::cerr << std::endl;
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = nullptr;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = nullptr;
-    }
   } else {
     strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
-    saxParser->ConnectToHandler("PStartupHandler", startupHandler);
+    saxParser->ConnectToHandler("PStartupHandler", startupHandler.get());
     //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)
-    status = parseXmlFile(saxParser, startup_path_name);
+    status = parseXmlFile(saxParser.get(), startup_path_name);
     // check for parse errors
     if (status) { // error
       std::cerr << std::endl << ">> addRun **WARNING** Reading/parsing musrfit_startup.xml failed.";
       std::cerr << std::endl;
-      // clean up
-      if (saxParser) {
-        delete saxParser;
-        saxParser = nullptr;
-      }
-      if (startupHandler) {
-        delete startupHandler;
-        startupHandler = nullptr;
-      }
     } else {
       startupHandler->CheckLists();
     }
@@ -639,19 +622,12 @@ int main(int argc, char *argv[])
   }
 
   // load the files
-  std::vector<PRunDataHandler*> runDataHandler;
+  std::vector< std::unique_ptr<PRunDataHandler> > runDataHandler;
   runDataHandler.resize(addRunInfo.size());
   Bool_t isGood{true};
   for (UInt_t i=0; i<runDataHandler.size(); i++) {
     if (startupHandler != nullptr) {
-      runDataHandler[i] = new PRunDataHandler(addRunInfo[i].fPathFileName, addRunInfo[i].fFileFormat, startupHandler->GetDataPathList());
-      if (runDataHandler[i] == nullptr) {
-        isGood = false;
-        std::cerr << std::endl;
-        std::cerr << "**ERROR** couldn't invoke PRunDataHandler (i=" << i << ")." << std::endl;
-        std::cerr << std::endl;
-        break;
-      }
+      runDataHandler[i] = std::make_unique<PRunDataHandler>(addRunInfo[i].fPathFileName, addRunInfo[i].fFileFormat, startupHandler->GetDataPathList());
       runDataHandler[i]->ReadData();
       if (!runDataHandler[i]->IsAllDataAvailable()) {
         isGood = false;
@@ -661,14 +637,7 @@ int main(int argc, char *argv[])
         break;
       }
     } else {
-      runDataHandler[i] = new PRunDataHandler(addRunInfo[i].fPathFileName, addRunInfo[i].fFileFormat);
-      if (runDataHandler[i] == nullptr) {
-        isGood = false;
-        std::cerr << std::endl;
-        std::cerr << "**ERROR** couldn't invoke PRunDataHandler (i=" << i << ")." << std::endl;
-        std::cerr << std::endl;
-        break;
-      }
+      runDataHandler[i] = std::make_unique<PRunDataHandler>(addRunInfo[i].fPathFileName, addRunInfo[i].fFileFormat);
       runDataHandler[i]->ReadData();
       if (!runDataHandler[i]->IsAllDataAvailable()) {
         isGood = false;
@@ -683,8 +652,8 @@ int main(int argc, char *argv[])
   // make sure that the number of provided t0's are matching the number of histos from the run-file
 
   // 1st make sure all the runs have the same number run data (==1 here)
-  PAny2ManyInfo *info{nullptr};
-  PRunDataHandler *dataOut{nullptr};
+  std::unique_ptr<PAny2ManyInfo> info;
+  std::unique_ptr<PRunDataHandler> dataOut;
   if (isGood) {
     for (UInt_t i=1; i<runDataHandler.size(); i++) {
       if (runDataHandler[0]->GetNoOfRunData() != runDataHandler[i]->GetNoOfRunData()) {
@@ -695,13 +664,7 @@ int main(int argc, char *argv[])
         break;
       }
     }
-    info = new PAny2ManyInfo();
-    if (info == nullptr) {
-      std::cerr << std::endl;
-      std::cerr << "**ERROR** couldn't invoke PAny2ManyInfo." << std::endl;
-      std::cerr << std::endl;
-      isGood = false;
-    }
+    info = std::make_unique<PAny2ManyInfo>();
   }
 
   if (isGood) {
@@ -709,13 +672,7 @@ int main(int argc, char *argv[])
     info->outFormat = format;
     info->year = year;
     info->outFileName = flnOut;
-    dataOut = new PRunDataHandler(info);
-    if (dataOut == nullptr) {
-      std::cerr << std::endl;
-      std::cerr << "**ERROR** couldn't invoke PRunDataHandler for the output file." << std::endl;
-      std::cerr << std::endl;
-      isGood = false;
-    }
+    dataOut = std::make_unique<PRunDataHandler>(info.get());
   }
 
   if (isGood) {
@@ -812,8 +769,12 @@ int main(int argc, char *argv[])
     }
 
     // feed all the necessary information for the data file
-    PRawRunData *rawRunData = new PRawRunData();
+    PRawRunData *rawRunData = nullptr;
     rawRunData = runDataHandler[0]->GetRunData(); // copy all
+    if (rawRunData == nullptr) {
+      std::cerr << ">> addRun: **ERROR** couldn't obtain PRawRunData object." << std::endl;
+      return PMUSR_MSR_ALLOCATION_ERROR;
+    }
     rawRunData->SetGenerator("addRun");
     // overwrite the t0 values with the new ones
     for (UInt_t i=0; i<rawRunData->GetNoOfHistos(); i++) {
@@ -831,21 +792,5 @@ int main(int argc, char *argv[])
     }
   }
 
-  // clean up
-  if (startupHandler) {
-    delete startupHandler;
-  }
-  if (info) {
-    delete info;
-  }
-  if (dataOut) {
-    delete dataOut;
-  }
-  for (int i=0; i<runDataHandler.size(); i++) {
-    if (runDataHandler[i])
-      delete runDataHandler[i];
-  }
-  runDataHandler.clear();  
-
   return PMUSR_SUCCESS;
 }

src/any2many.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -37,6 +37,7 @@
 
 #include <iostream>
 #include <fstream>
+#include <memory>
 
 #include <TString.h>
 #include <TSAXParser.h>
@@ -493,49 +494,31 @@ int main(int argc, char *argv[])
 
   // read startup file
   char startup_path_name[128];
-  TSAXParser *saxParser = new TSAXParser();
-  PStartupHandler *startupHandler = new PStartupHandler();
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<PStartupHandler> startupHandler = std::make_unique<PStartupHandler>();
   if (!startupHandler->StartupFileFound()) {
     std::cerr << std::endl << ">> any2many **WARNING** couldn't find " << startupHandler->GetStartupFilePath().Data();
     std::cerr << std::endl;
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = nullptr;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = nullptr;
-    }
   } else {
     strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
-    saxParser->ConnectToHandler("PStartupHandler", startupHandler);
+    saxParser->ConnectToHandler("PStartupHandler", startupHandler.get());
     //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)
-    status = parseXmlFile(saxParser, startup_path_name);
+    status = parseXmlFile(saxParser.get(), startup_path_name);
     // check for parse errors
     if (status) { // error
       std::cerr << std::endl << ">> any2many **WARNING** Reading/parsing musrfit_startup.xml failed.";
       std::cerr << std::endl;
-      // clean up
-      if (saxParser) {
-        delete saxParser;
-        saxParser = nullptr;
-      }
-      if (startupHandler) {
-        delete startupHandler;
-        startupHandler = nullptr;
-      }
     }
   }
 
   // read all the necessary runs (raw data)
-  PRunDataHandler *dataHandler;
+  std::unique_ptr<PRunDataHandler> dataHandler;
   if (startupHandler)
-    dataHandler = new PRunDataHandler(&info, startupHandler->GetDataPathList());
+    dataHandler = std::make_unique<PRunDataHandler>(&info, startupHandler->GetDataPathList());
   else
-    dataHandler = new PRunDataHandler(&info);
+    dataHandler = std::make_unique<PRunDataHandler>(&info);
 
   // read and convert all data
   dataHandler->ConvertData();
@@ -546,21 +529,6 @@ int main(int argc, char *argv[])
     std::cerr << std::endl << ">> any2many **ERROR** Couldn't read all data files, will quit ..." << std::endl;
   }
 
-  // clean up
-  info.runList.clear();
-  if (saxParser) {
-    delete saxParser;
-    saxParser = nullptr;
-  }
-  if (startupHandler) {
-    delete startupHandler;
-    startupHandler = nullptr;
-  }
-  if (dataHandler) {
-    delete dataHandler;
-    dataHandler = nullptr;
-  }
-
   return PMUSR_SUCCESS;
 }
 

src/classes/CMakeLists.txt

@@ -73,7 +73,7 @@ set(prefix "${CMAKE_INSTALL_PREFIX}")
 set(exec_prefix "\$\{prefix\}")
 set(libdir "\$\{exec_prefix\}/lib")
 set(includedir "\$\{prefix\}/include")   
-set(MUSR_VERSION "1.3.0")
+set(MUSR_VERSION "1.4.0")
 set(MUSR_LIBRARY_NAME "PMusr")
 configure_file("PMusr.pc.in" "PMusr.pc" @ONLY)
 set(USERFCN_LIBRARY_NAME "PUserFcnBase")

src/classes/PFindRun.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -54,8 +54,10 @@ PFindRun::PFindRun(const PStringVector path, const PRunNameTemplateList runNameT
  * @param run
  */
 PFindRun::PFindRun(const PStringVector path, const PRunNameTemplateList runNameTemplateList,
-                   const TString &instrument, const UInt_t year, const UInt_t run) :
-  fPath(path), fRunNameTemplateList(runNameTemplateList), fInstrument(instrument), fYear(year), fRun(run)
+                   const TString &instrument, const UInt_t year, const UInt_t run,
+                   const TString file_format) :
+  fPath(path), fRunNameTemplateList(runNameTemplateList), fInstrument(instrument),
+  fYear(year), fRun(run), fFileFormat(file_format)
 {
   // nothing to be done here
 }
@@ -130,6 +132,23 @@ TString PFindRun::CreatePathName(const TString path, const TString runNameTempla
  */
 Bool_t PFindRun::FoundPathName()
 {
+  // if file format is given, get proper extension
+  TString ext("");
+  if (fFileFormat.Length() != 0) {
+    if (!fFileFormat.CompareTo("MusrRoot") || !fFileFormat.CompareTo("ROOT"))
+      ext = ".root";
+    else if (!fFileFormat.CompareTo("NeXus"))
+      ext = ".nxs";
+    else if (!fFileFormat.CompareTo("PSI-BIN"))
+      ext = ".bin";
+    else if (!fFileFormat.CompareTo("PSI-MDU"))
+      ext = ".mdu";
+    else if (!fFileFormat.CompareTo("MUD"))
+      ext = ".mud";
+    else if (!fFileFormat.CompareTo("WKM"))
+      ext = ".wkm";
+  }
+
   // find instrument name in path list
   TString pathName{""};
   for (Int_t i=0; i<fPath.size(); i++) {
@@ -137,6 +156,10 @@ Bool_t PFindRun::FoundPathName()
       for (Int_t j=0; j<fRunNameTemplateList.size(); j++) {
         if (fRunNameTemplateList[j].instrument == fInstrument) {
           pathName = CreatePathName(fPath[i], fRunNameTemplateList[j].runNameTemplate);
+          if (fFileFormat.Length() != 0) {
+            if (!pathName.Contains(ext, TString::kIgnoreCase))
+              continue;
+          }
           if (boost::filesystem::exists(pathName.Data())) {
             fPathName = pathName;
             return true;

src/classes/PFitter.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -280,9 +280,6 @@ PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bo
   fCmdLines = *runInfo->GetMsrCommands();
 
   // init class variables
-  fFitterFcn = nullptr;
-  fFcnMin = nullptr;
-
   fScanAll = true;
   fScanParameter[0] = 0;
   fScanParameter[1] = 0;
@@ -317,11 +314,7 @@ PFitter::PFitter(PMsrHandler *runInfo, PRunListCollection *runListCollection, Bo
   GetPhaseParams();
 
   // create fit function object
-  fFitterFcn = new PFitterFcn(runListCollection, fUseChi2);
-  if (!fFitterFcn) {
-    fIsValid = false;
-    return;
-  }
+  fFitterFcn = std::make_unique<PFitterFcn>(runListCollection, fUseChi2);
 }
 
 //--------------------------------------------------------------------------
@@ -337,16 +330,6 @@ PFitter::~PFitter()
   fScanData.clear();
 
   fElapsedTime.clear();
-
-  if (fFcnMin) {
-    delete fFcnMin;
-    fFcnMin = nullptr;
-  }
-
-  if (fFitterFcn) {
-    delete fFitterFcn;
-    fFitterFcn = nullptr;
-  }
 }
 
 //--------------------------------------------------------------------------
@@ -1802,11 +1785,7 @@ Bool_t PFitter::ExecuteMigrad()
   }
 
   // keep FunctionMinimum object
-  if (fFcnMin) { // fFcnMin exist hence clean up first
-    delete fFcnMin;
-    fFcnMin = nullptr;
-  }
-  fFcnMin = new ROOT::Minuit2::FunctionMinimum(min);
+  fFcnMin.reset(new ROOT::Minuit2::FunctionMinimum(min));
 
   // keep user parameters
   if (fFcnMin)
@@ -1883,11 +1862,7 @@ Bool_t PFitter::ExecuteMinimize()
   }
 
   // keep FunctionMinimum object
-  if (fFcnMin) { // fFcnMin exist hence clean up first
-    delete fFcnMin;
-    fFcnMin = nullptr;
-  }
-  fFcnMin = new ROOT::Minuit2::FunctionMinimum(min);
+  fFcnMin.reset(new ROOT::Minuit2::FunctionMinimum(min));
 
   // keep user parameters
   if (fFcnMin)
@@ -2435,8 +2410,8 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
       title += fRunInfo->GetFileName();
       title += " - ";
       title += dt.AsSQLString();
-      TCanvas *ccorr = new TCanvas("ccorr", "title", 500, 500);
-      TH2D *hcorr = new TH2D("hcorr", title, cov.Nrow(), 0.0, cov.Nrow(), cov.Nrow(), 0.0, cov.Nrow());
+      std::unique_ptr<TCanvas> ccorr = std::make_unique<TCanvas>("ccorr", "title", 500, 500);
+      std::unique_ptr<TH2D> hcorr = std::make_unique<TH2D>("hcorr", title, cov.Nrow(), 0.0, cov.Nrow(), cov.Nrow(), 0.0, cov.Nrow());
       Double_t dval;
       for (UInt_t i=0; i<cov.Nrow(); i++) {
         // parameter number
@@ -2498,15 +2473,6 @@ Bool_t PFitter::ExecuteSave(Bool_t firstSave)
       ccorr->Write("ccorr", TObject::kOverwrite, sizeof(ccorr));
       hcorr->Write("hcorr", TObject::kOverwrite, sizeof(hcorr));
       ff.Close();
-      // clean up
-      if (ccorr) {
-        delete ccorr;
-        ccorr = nullptr;
-      }
-      if (hcorr) {
-        delete hcorr;
-        hcorr = nullptr;
-      }
     }
     parNo.clear(); // clean up
   } else {
@@ -2596,11 +2562,7 @@ Bool_t PFitter::ExecuteSimplex()
   }
 
   // keep FunctionMinimum object
-  if (fFcnMin) { // fFcnMin exist hence clean up first
-    delete fFcnMin;
-    fFcnMin = nullptr;
-  }
-  fFcnMin = new ROOT::Minuit2::FunctionMinimum(min);
+  fFcnMin.reset(new ROOT::Minuit2::FunctionMinimum(min));
 
   // keep user parameters
   if (fFcnMin)

src/classes/PFitterFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PFourier.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PFourierCanvas.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -55,7 +55,6 @@ ClassImpQ(PFourierCanvas)
 PFourierCanvas::PFourierCanvas()
 {
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
 
   fBatchMode = false;
   fValid = false;
@@ -69,18 +68,10 @@ PFourierCanvas::PFourierCanvas()
   fXaxisTitle = TString("");
 
   fCurrentFourierPhase = 0.0;
-  fCurrentFourierPhaseText = nullptr;
 
-  fStyle = nullptr;
   fImp = nullptr;
   fBar = nullptr;
   fPopupMain = nullptr;
-  fPopupFourier = nullptr;
-
-  fMainCanvas = nullptr;
-  fTitlePad = nullptr;
-  fFourierPad = nullptr;
-  fInfoPad = nullptr;
 }
 
 //---------------------------------------------------------------------------
@@ -112,12 +103,9 @@ PFourierCanvas::PFourierCanvas(std::vector<PFourier*> &fourier, PIntVector dataS
   fInitialXRange[1] = fourierXrange[1];
 
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
 
   fValid = false;
 
-  fCurrentFourierPhaseText = nullptr;
-
   // generate fMarkerList and fColorList, since they are not provided
   TRandom rand;
   Int_t style, color;
@@ -168,12 +156,9 @@ PFourierCanvas::PFourierCanvas(std::vector<PFourier*> &fourier, PIntVector dataS
   fInitialXRange[1] = fourierXrange[1];
 
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
 
   fValid = false;
 
-  fCurrentFourierPhaseText = nullptr;
-
   // generate fMarkerList and fColorList, since they are not provided
   TRandom rand;
   Int_t style, color;
@@ -196,70 +181,6 @@ PFourierCanvas::PFourierCanvas(std::vector<PFourier*> &fourier, PIntVector dataS
   gStyle->SetHistMinimumZero(kTRUE); // needed to enforce proper bar option handling
 }
 
-//---------------------------------------------------------------------------
-/**
- * <p>Destructor
- */
-PFourierCanvas::~PFourierCanvas()
-{
-  if (fTimeoutTimer)
-    delete fTimeoutTimer;
-
-  if (fCurrentFourierPhaseText)
-    delete fCurrentFourierPhaseText;
-
-/*
-  if (fStyle) {
-    delete fStyle;
-    fStyle = 0;
-  }
-*/
-  if (fTitlePad) {
-    fTitlePad->Clear();
-    delete fTitlePad;
-    fTitlePad = nullptr;
-  }
-
-  if (fFourierHistos.size() > 0) {
-    for (UInt_t i=0; i<fFourierHistos.size(); i++) {
-      delete fFourierHistos[i].dataFourierRe;
-      delete fFourierHistos[i].dataFourierIm;
-      delete fFourierHistos[i].dataFourierPwr;
-      delete fFourierHistos[i].dataFourierPhase;
-      delete fFourierHistos[i].dataFourierPhaseOptReal;
-    }
-    fFourierHistos.clear();
-  }
-
-  CleanupAverage();
-
-/*
-  if (fFourierPad) {
-    fFourierPad->Clear();
-    delete fFourierPad;
-    fFourierPad = 0;
-  }
-*/
-  if (fInfoPad) {
-    fInfoPad->Clear();
-    delete fInfoPad;
-    fInfoPad = nullptr;
-  }
-
-  if (fLegAvgPerDataSet) {
-    fLegAvgPerDataSet->Clear();
-    delete fLegAvgPerDataSet;
-    fLegAvgPerDataSet = nullptr;
-  }
-
-/*
-  if (fMainCanvas) {
-    delete fMainCanvas;
-    fMainCanvas = nullptr;
-  }
-*/
-}
-
 //--------------------------------------------------------------------------
 // Done (SIGNAL)
 //--------------------------------------------------------------------------
@@ -563,11 +484,7 @@ void PFourierCanvas::SetTimeout(Int_t timeout)
   if (fTimeout <= 0)
     return;
 
-  if (fTimeoutTimer) {
-    delete fTimeoutTimer;
-    fTimeoutTimer = nullptr;
-  }
-  fTimeoutTimer = new TTimer();
+  fTimeoutTimer.reset(new TTimer());
 
   fTimeoutTimer->Connect("Timeout()", "PFourierCanvas", this, "Done()");
 
@@ -831,7 +748,7 @@ void PFourierCanvas::CreateXaxisTitle()
 void PFourierCanvas::CreateStyle()
 {
   TString musrFTStyle("musrFTStyle");
-  fStyle = new TStyle(musrFTStyle, musrFTStyle);
+  fStyle = std::make_unique<TStyle>(musrFTStyle, musrFTStyle);
   fStyle->SetOptStat(0);  // no statistics options
   fStyle->SetOptTitle(0); // no title
   fStyle->cd();
@@ -990,21 +907,10 @@ void PFourierCanvas::InitFourierCanvas(const Char_t* title, Int_t wtopx, Int_t w
   fImp   = nullptr;
   fBar   = nullptr;
   fPopupMain    = nullptr;
-  fPopupFourier = nullptr;
-
-  fMainCanvas  = nullptr;
-  fTitlePad    = nullptr;
-  fFourierPad  = nullptr;
-  fInfoPad     = nullptr;
 
   // invoke canvas
   TString canvasName = TString("fMainCanvas");
-  fMainCanvas = new TCanvas(canvasName.Data(), title, wtopx, wtopy, ww, wh);
-  if (fMainCanvas == nullptr) {
-    std::cerr << std::endl << "PFourierCanvas::PFourierCanvas: **PANIC ERROR**: Couldn't invoke " << canvasName.Data();
-    std::cerr << std::endl;
-    return;
-  }
+  fMainCanvas = std::make_unique<TCanvas>(canvasName.Data(), title, wtopx, wtopy, ww, wh);
 
   // add canvas menu if not in batch mode
   if (!fBatchMode) {
@@ -1012,9 +918,9 @@ void PFourierCanvas::InitFourierCanvas(const Char_t* title, Int_t wtopx, Int_t w
     fBar = fImp->GetMenuBar();
     fPopupMain = fBar->AddPopup("MusrFT");
 
-    fPopupFourier = new TGPopupMenu();
+    fPopupFourier = std::make_unique<TGPopupMenu>();
 
-    fPopupMain->AddPopup("&Fourier", fPopupFourier);
+    fPopupMain->AddPopup("&Fourier", fPopupFourier.get());
     fPopupFourier->AddEntry("Show Real", P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_REAL);
     fPopupFourier->AddEntry("Show Imag", P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_IMAG);
     fPopupFourier->AddEntry("Show Real+Imag", P_MENU_ID_FOURIER+P_MENU_ID_FOURIER_REAL_AND_IMAG);
@@ -1067,39 +973,25 @@ void PFourierCanvas::InitFourierCanvas(const Char_t* title, Int_t wtopx, Int_t w
 
   // divide the canvas into sub pads
   // title pad
-  fTitlePad = new TPaveText(0.0, YTITLE, 1.0, 1.0, "NDC");
-  if (fTitlePad == nullptr) {
-    std::cerr << std::endl << "PFourierCanvas::PFourierCanvas: **PANIC ERROR**: Couldn't invoke fTitlePad";
-    std::cerr << std::endl;
-    return;
-  }
+  fTitlePad = std::make_unique<TPaveText>(0.0, YTITLE, 1.0, 1.0, "NDC");
+
   fTitlePad->SetFillColor(TColor::GetColor(255,255,255));
   fTitlePad->SetTextAlign(12); // middle, left
   fTitlePad->AddText(title);
   fTitlePad->Draw();
 
   // fourier pad
-  fFourierPad = new TPad("fFourierPad", "fFourierPad", 0.0, YINFO, 1.0, YTITLE);
-  if (fFourierPad == nullptr) {
-    std::cerr << std::endl << "PFourierCanvas::PFourierCanvas: **PANIC ERROR**: Couldn't invoke fFourierPad";
-    std::cerr << std::endl;
-    return;
-  }
+  fFourierPad = std::make_unique<TPad>("fFourierPad", "fFourierPad", 0.0, YINFO, 1.0, YTITLE);
+
   fFourierPad->SetFillColor(TColor::GetColor(255,255,255));
   fFourierPad->Draw();
 
   // info pad
-  fInfoPad = new TLegend(0.0, 0.0, 1.0, YINFO, "NDC");
-  if (fInfoPad == nullptr) {
-    std::cerr << std::endl << "PFourierCanvas::PFourierCanvas: **PANIC ERROR**: Couldn't invoke fInfoPad";
-    std::cerr << std::endl;
-    return;
-  }
+  fInfoPad = std::make_unique<TLegend>(0.0, 0.0, 1.0, YINFO, "NDC");
+
   fInfoPad->SetFillColor(TColor::GetColor(255,255,255));
   fInfoPad->SetTextAlign(12); // middle, left
 
-  fLegAvgPerDataSet = nullptr;
-
   fValid = true;
 
   if ((fFourier.size() != fDataSetTag.size()) && fAveragedViewPerDataSet) {
@@ -1629,12 +1521,6 @@ void PFourierCanvas::PlotFourier()
  */
 void PFourierCanvas::PlotFourierPhaseValue()
 {
-  // check if phase TLatex object is present
-  if (fCurrentFourierPhaseText) {
-    delete fCurrentFourierPhaseText;
-    fCurrentFourierPhaseText = nullptr;
-  }
-
   Double_t x, y;
   TString str;
 
@@ -1643,7 +1529,7 @@ void PFourierCanvas::PlotFourierPhaseValue()
   str += fCurrentFourierPhase;
   x = 0.7;
   y = 0.85;
-  fCurrentFourierPhaseText = new TLatex();
+  fCurrentFourierPhaseText.reset(new TLatex());
   fCurrentFourierPhaseText->SetNDC(kTRUE);
   fCurrentFourierPhaseText->SetText(x, y, str.Data());
   fCurrentFourierPhaseText->SetTextFont(62);
@@ -1675,10 +1561,8 @@ void PFourierCanvas::PlotAverage()
   xmax = fInitialXRange[1];
   Double_t ymin=0.0, ymax=0.0;
 
-  if (fLegAvgPerDataSet) {
+  if (fLegAvgPerDataSet.get()) {
     fLegAvgPerDataSet->Clear();
-    delete fLegAvgPerDataSet;
-    fLegAvgPerDataSet = nullptr;
   }
 
   switch (fCurrentPlotView) {
@@ -1799,7 +1683,7 @@ void PFourierCanvas::PlotAverage()
   }
 
   if (fAveragedViewPerDataSet) { // plot all the rest
-    fLegAvgPerDataSet = new TLegend(0.55, 0.4, 0.85, 0.6);
+    fLegAvgPerDataSet = std::make_unique<TLegend>(0.55, 0.4, 0.85, 0.6);
     TString str = GetDataSetName(fFourierAverage[0].dataFourierPwr->GetTitle());
     TString label = TString::Format("<%s>", str.Data());
     fLegAvgPerDataSet->AddEntry(fFourierAverage[0].dataFourierPwr, label.Data());

src/classes/PFunction.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -655,7 +655,9 @@ void PFunction::EvalTreeForStringExpression(iter_t const& i)
       assert(i->children.size() == 2);
       EvalTreeForStringExpression(i->children.begin());
       fFuncString += " / ";
+      fFuncString += "(";
       EvalTreeForStringExpression(i->children.begin()+1);
+      fFuncString += ")";
     } else {
       assert(0);
     }

src/classes/PFunctionHandler.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PMsr2Data.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Bastian M. Wojek / Andreas Suter           *
+ *   Copyright (C) 2009-2024 by Bastian M. Wojek / Andreas Suter           *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -38,6 +38,7 @@
 #include <iomanip>
 #include <algorithm>
 #include <limits>
+#include <memory>
 
 #include <boost/algorithm/string/trim.hpp>  // for stripping leading whitespace in std::string 
 #include <boost/algorithm/string/case_conv.hpp> // for to_lower() in std::string
@@ -58,7 +59,6 @@ PMsr2Data::PMsr2Data(const std::string &ext) : fFileExtension(ext), fRunListFile
 {
   fRunVector.clear();
   fRunVectorIter = fRunVector.end();
-  fRunListFileStream = nullptr;
   fSaxParser = nullptr;
   fStartupHandler = nullptr;
   fDataHandler = nullptr;
@@ -74,28 +74,6 @@ PMsr2Data::~PMsr2Data()
   fRunVector.clear();
   fRunVectorIter = fRunVector.end();
   fIndVar.clear();
-
-  if (fRunListFileStream) {
-    fRunListFileStream->close();
-    delete fRunListFileStream;
-    fRunListFileStream = nullptr;
-  }
-  if (fSaxParser) {
-    delete fSaxParser;
-    fSaxParser = nullptr;
-  }
-  if (fStartupHandler) {
-    delete fStartupHandler;
-    fStartupHandler = nullptr;
-  }
-  if (fDataHandler) {
-    delete fDataHandler;
-    fDataHandler = nullptr;
-  }
-  if (fMsrHandler) {
-    delete fMsrHandler;
-    fMsrHandler = nullptr;
-  }
 }
 
 //-------------------------------------------------------------
@@ -118,19 +96,17 @@ int PMsr2Data::DetermineRunNumberDigits(unsigned int runNo, bool normalMode) con
 {
   std::ostringstream strInfile;
   strInfile << runNo << fFileExtension << ".msr";
-  std::ifstream *in = new std::ifstream(strInfile.str().c_str());
+  std::unique_ptr<std::ifstream> in = std::make_unique<std::ifstream>(strInfile.str().c_str());
   if (!in->is_open()) {
-    delete in;
     if (!normalMode && (runNo == *fRunVectorIter)) {
       std::string fileNameCopy(strInfile.str());
       strInfile.clear();
       strInfile.str("");
       strInfile << runNo << "+global" << fFileExtension << ".msr";
-      in = new std::ifstream(strInfile.str().c_str());
+      in.reset(new std::ifstream(strInfile.str().c_str()));
       if (!in->is_open()) {
         std::cerr << std::endl << ">> msr2data: **ERROR** Neither the file " << fileNameCopy << " nor the file " << strInfile.str() << " can be opened! Please check!";
         std::cerr << std::endl;
-        delete in;
         return -1;
       }
     } else if (runNo == *fRunVectorIter) { // the first run of the runlist was given - if it did not exist, try the rest of the runlist
@@ -176,8 +152,6 @@ int PMsr2Data::DetermineRunNumberDigits(unsigned int runNo, bool normalMode) con
           }
         }
         in->close();
-        delete in;
-        in = nullptr;
         fRunVectorIter = fRunVector.begin(); // set back the runlist-iterator which might have changed during the search for the correct file
         return 0;
       } else {
@@ -187,8 +161,6 @@ int PMsr2Data::DetermineRunNumberDigits(unsigned int runNo, bool normalMode) con
          std::cerr << std::endl << ">> msr2data: **ERROR** this is either some template or the first existing file from the run list.";
          std::cerr << std::endl;
          in->close();
-         delete in;
-         in = nullptr;
          return -2;
       }
     }
@@ -198,8 +170,7 @@ int PMsr2Data::DetermineRunNumberDigits(unsigned int runNo, bool normalMode) con
   std::cerr << std::endl << ">> msr2data: **ERROR** Obviously it contains no RUN block...";
   std::cerr << std::endl;
   in->close();
-  delete in;
-  in = nullptr;
+
   return -3;
 }
 
@@ -387,7 +358,8 @@ int PMsr2Data::SetRunNumbers(const std::string &runListFile)
   in.close();
   fRunVectorIter = fRunVector.begin();
   fRunListFile = true;
-  fRunListFileStream = new std::ifstream(runListFile.c_str());
+  fRunListFileStream = std::make_unique<std::ifstream>(runListFile.c_str());
+
   return 0;
 }
 
@@ -402,26 +374,17 @@ int PMsr2Data::SetRunNumbers(const std::string &runListFile)
 int PMsr2Data::ParseXmlStartupFile()
 {
   int status;
-  fSaxParser = new TSAXParser();
-  fStartupHandler = new PStartupHandler();
+  fSaxParser = std::make_unique<TSAXParser>();
+  fStartupHandler = std::make_unique<PStartupHandler>();
   std::string startup_path_name(fStartupHandler->GetStartupFilePath().Data());
-  fSaxParser->ConnectToHandler("PStartupHandler", fStartupHandler);
+  fSaxParser->ConnectToHandler("PStartupHandler", fStartupHandler.get());
   //status = fSaxParser->ParseFile(startup_path_name.c_str());
   // parsing the file as above seems to lead to problems in certain environments;
   // use the parseXmlFile function instead (see PStartupHandler.cpp for the definition)
-  status = parseXmlFile(fSaxParser, startup_path_name.c_str());
+  status = parseXmlFile(fSaxParser.get(), startup_path_name.c_str());
   // check for parse errors
   if (status) { // error
     std::cerr << std::endl << ">> msr2data: **WARNING** Reading/parsing musrfit_startup.xml failed." << std::endl;
-    // clean up
-    if (fSaxParser) {
-      delete fSaxParser;
-      fSaxParser = nullptr;
-    }
-    if (fStartupHandler) {
-      delete fStartupHandler;
-      fStartupHandler = nullptr;
-    }
   }
   return status;
 }
@@ -439,7 +402,7 @@ int PMsr2Data::ParseXmlStartupFile()
 int PMsr2Data::ReadMsrFile(const std::string &infile) const
 {
   int status;
-  fMsrHandler = new PMsrHandler(infile.c_str());
+  fMsrHandler = std::make_unique<PMsrHandler>(infile.c_str());
   status = fMsrHandler->ReadMsrFile();
   if (status != PMUSR_SUCCESS) {
     switch (status) {
@@ -487,6 +450,7 @@ PMsrHandler* PMsr2Data::GetSingleRunMsrFile() const
     }
     return nullptr;
   }
+
   return singleRunMsrFile;
 }
 
@@ -501,19 +465,18 @@ PMsrHandler* PMsr2Data::GetSingleRunMsrFile() const
 int PMsr2Data::ReadRunDataFile()
 {
   if (fStartupHandler)
-    fDataHandler = new PRunDataHandler(fMsrHandler, fStartupHandler->GetDataPathList());
+    fDataHandler = std::make_unique<PRunDataHandler>(fMsrHandler.get(), fStartupHandler->GetDataPathList());
   else
-    fDataHandler = new PRunDataHandler(fMsrHandler);
+    fDataHandler = std::make_unique<PRunDataHandler>(fMsrHandler.get());
 
   fDataHandler->ReadData();
 
   bool success = fDataHandler->IsAllDataAvailable();
   if (!success) {
     std::cerr << std::endl << ">> msr2data: **WARNING** Could not read all data files, will continue without the data file information..." << std::endl;
-    delete fDataHandler;
-    fDataHandler = nullptr;
     return 1;
   }
+
   return 0;
 }
 
@@ -1339,8 +1302,11 @@ bool PMsr2Data::PrepareGlobalInputFile(unsigned int tempRun, const std::string &
 
   if (newRunNumber.str().compare(tempRunNumber.str())) { // first run number does not match the template run number
     // in global+ mode, read in the single run msr-file of the corresponding run
-    if (globalPlus)
+    if (globalPlus) {
       singleRunMsrFile = GetSingleRunMsrFile();
+      if (singleRunMsrFile == nullptr)
+        return false;
+    }
 
     // substitute the template run-numbers in the parameter names
     for (unsigned int l(fNumGlobalParam); l < msrParamList->size(); ++l) {
@@ -1417,8 +1383,11 @@ bool PMsr2Data::PrepareGlobalInputFile(unsigned int tempRun, const std::string &
     newRunNumber << *fRunVectorIter;
 
     // in global+ mode, read in the single run msr-file
-    if (globalPlus)
+    if (globalPlus) {
       singleRunMsrFile = GetSingleRunMsrFile();
+      if (singleRunMsrFile == nullptr)
+        return false;
+    }
 
     // add parameters for each run
     for (unsigned int l(0); l < fNumSpecParam; ++l) {
@@ -1945,14 +1914,6 @@ int PMsr2Data::WriteOutput(const std::string &outfile, const std::vector<unsigne
     std::cerr << std::endl;
     fRunVectorIter++;
 
-    delete fMsrHandler;
-    fMsrHandler = nullptr;
-
-    if (fDataHandler) {
-      delete fDataHandler;
-      fDataHandler = nullptr;
-    }
-
 // clean up some vectors
     dataParamNames.clear();
     dataParamLabels.clear();
@@ -2454,13 +2415,7 @@ int PMsr2Data::WriteOutput(const std::string &outfile, const std::vector<unsigne
   outFile.close();
 
   if (!global || (fRunVectorIter == fRunVector.end())) {
-    delete fMsrHandler;
-    fMsrHandler = nullptr;
-
-    if (fDataHandler) {
-      delete fDataHandler;
-      fDataHandler = nullptr;
-    }
+    fDataHandler.reset();
   }
 
   msrParamList = nullptr;

src/classes/PMsrHandler.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -66,8 +66,6 @@ PMsrHandler::PMsrHandler(const Char_t *fileName, PStartupOptions *startupOptions
   fStatistic.fMinExpectedPerHisto.clear();
   fStatistic.fNdfPerHisto.clear();
 
-  fFuncHandler = nullptr;
-
   // check if the file name given is a path-file-name, and if yes, split it into path and file name.
   if (fFileName.Contains("/")) {
     Int_t idx = -1;
@@ -99,11 +97,6 @@ PMsrHandler::~PMsrHandler()
   fStatistic.fMinExpectedPerHisto.clear();
   fStatistic.fNdfPerHisto.clear();
   fParamInUse.clear();
-
-  if (fFuncHandler) {
-    delete fFuncHandler;
-    fFuncHandler = nullptr;
-  }
 }
 
 //--------------------------------------------------------------------------
@@ -2697,10 +2690,6 @@ Int_t PMsrHandler::ParameterInUse(UInt_t paramNo)
  */
 Bool_t PMsrHandler::HandleFitParameterEntry(PMsrLines &lines)
 {
-  // If msr-file is used for musrFT only, nothing needs to be done here.
-  if (fFourierOnly)
-    return true;
-
   PMsrParamStructure param;
   Bool_t    error = false;
 
@@ -2945,11 +2934,7 @@ Bool_t PMsrHandler::HandleFunctionsEntry(PMsrLines &lines)
   fFunctions = lines;
 
   // create function handler
-  fFuncHandler = new PFunctionHandler(fFunctions);
-  if (fFuncHandler == nullptr) {
-    std::cerr << std::endl << ">> PMsrHandler::HandleFunctionsEntry: **ERROR** Couldn't invoke PFunctionHandler." << std::endl;
-    return false;
-  }
+  fFuncHandler = std::make_unique<PFunctionHandler>(fFunctions);
 
   // do the parsing
   if (!fFuncHandler->DoParse()) {
@@ -3549,7 +3534,7 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
       } else {
         PUIntVector group;
         str = iter->fLine;
-        PStringNumberList *rl = new PStringNumberList(str.Data());
+        std::unique_ptr<PStringNumberList> rl = std::make_unique<PStringNumberList>(str.Data());
         std::string errorMsg("");
         if (rl->Parse(errorMsg, true)) {
           group = rl->GetList();
@@ -3559,7 +3544,6 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
         } else {
           error = true;
         }
-        delete rl;
         group.clear();
       }
     }
@@ -3574,7 +3558,7 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
       } else {
         PUIntVector group;
         str = iter->fLine;
-        PStringNumberList *rl = new PStringNumberList(str.Data());
+        std::unique_ptr<PStringNumberList> rl = std::make_unique<PStringNumberList>(str.Data());
         std::string errorMsg("");
         if (rl->Parse(errorMsg, true)) {
           group = rl->GetList();
@@ -3584,7 +3568,6 @@ Bool_t PMsrHandler::HandleRunEntry(PMsrLines &lines)
         } else {
           error = true;
         }
-        delete rl;
         group.clear();
       }
     }
@@ -4638,7 +4621,7 @@ Bool_t PMsrHandler::HandlePlotEntry(PMsrLines &lines)
         param.fLifeTimeCorrection = true;
       } else if (line.Contains("runs", TString::kIgnoreCase)) { // handle plot runs
         TComplex run;
-        PStringNumberList *rl;
+        std::unique_ptr<PStringNumberList> rl;
         std::string errorMsg;
         PUIntVector runList;
         switch (param.fPlotType) {
@@ -4652,7 +4635,7 @@ Bool_t PMsrHandler::HandlePlotEntry(PMsrLines &lines)
           case MSR_PLOT_ASYM_RRF:
           case MSR_PLOT_NON_MUSR:
           case MSR_PLOT_MU_MINUS:
-            rl = new PStringNumberList(line.Data());
+            rl = std::make_unique<PStringNumberList>(line.Data());
             if (!rl->Parse(errorMsg, true)) {
               std::cerr << std::endl << ">> PMsrHandler::HandlePlotEntry: **SEVERE ERROR** Couldn't tokenize PLOT in line " << iter1->fLineNo;
               std::cerr << std::endl << ">>   Error Message: " << errorMsg;
@@ -4666,7 +4649,6 @@ Bool_t PMsrHandler::HandlePlotEntry(PMsrLines &lines)
             }
             // clean up
             runList.clear();
-            delete rl;
             break;
           default:
             error = true;

src/classes/PMusr.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PMusrCanvas.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -119,7 +119,6 @@ ClassImpQ(PMusrCanvas)
 PMusrCanvas::PMusrCanvas()
 {
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
 
   fScaleN0AndBkg = true;
   fValid = false;
@@ -134,16 +133,6 @@ PMusrCanvas::PMusrCanvas()
   fImp   = nullptr;
   fBar   = nullptr;
   fPopupMain    = nullptr;
-  fPopupFourier = nullptr;
-
-  fStyle            = nullptr;
-  fMainCanvas       = nullptr;
-  fTitlePad         = nullptr;
-  fDataTheoryPad    = nullptr;
-  fParameterPad     = nullptr;
-  fTheoryPad        = nullptr;
-  fInfoPad          = nullptr;
-  fMultiGraphLegend = nullptr;
 
   fHistoFrame     = nullptr;
 
@@ -153,11 +142,6 @@ PMusrCanvas::PMusrCanvas()
   InitFourier();
   InitAverage();
 
-  fCurrentFourierPhaseText = nullptr;
-
-  fRRFText      = nullptr;
-  fRRFLatexText = nullptr;
-
   fXRangePresent = false;
   fYRangePresent = false;
   fXmin = 0.0;
@@ -193,7 +177,6 @@ PMusrCanvas::PMusrCanvas(const Int_t number, const Char_t* title,
     fBatchMode(batch), fPlotNumber(number)
 {
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
   fAveragedView = false;
 
   fMultiGraphData = nullptr;
@@ -206,11 +189,6 @@ PMusrCanvas::PMusrCanvas(const Int_t number, const Char_t* title,
   CreateStyle();
   InitMusrCanvas(title, wtopx, wtopy, ww, wh);
 
-  fCurrentFourierPhaseText = nullptr;
-
-  fRRFText      = nullptr;
-  fRRFLatexText = nullptr;
-
   fXRangePresent = false;
   fYRangePresent = false;
   fXmin = 0.0;
@@ -252,7 +230,6 @@ PMusrCanvas::PMusrCanvas(const Int_t number, const Char_t* title,
      fMarkerList(markerList), fColorList(colorList)
 {
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
 
   fMultiGraphData = nullptr;
   fMultiGraphDiff = nullptr;
@@ -263,11 +240,6 @@ PMusrCanvas::PMusrCanvas(const Int_t number, const Char_t* title,
   CreateStyle();
   InitMusrCanvas(title, wtopx, wtopy, ww, wh);
 
-  fCurrentFourierPhaseText = nullptr;
-
-  fRRFText      = nullptr;
-  fRRFLatexText = nullptr;
-
   fXRangePresent = false;
   fYRangePresent = false;
   fXmin = 0.0;
@@ -287,31 +259,6 @@ PMusrCanvas::PMusrCanvas(const Int_t number, const Char_t* title,
 PMusrCanvas::~PMusrCanvas()
 {
   // cleanup
-  if (fTimeoutTimer) {
-    delete fTimeoutTimer;
-    fTimeoutTimer = nullptr;
-  }
-  if (fCurrentFourierPhaseText) {
-    delete fCurrentFourierPhaseText;
-    fCurrentFourierPhaseText = nullptr;
-  }
-  if (fRRFLatexText) {
-    delete fRRFLatexText;
-    fRRFLatexText = nullptr;
-  }
-  if (fRRFText) {
-    delete fRRFText;
-    fRRFText = nullptr;
-  }
-  if (fStyle) {
-    delete fStyle;
-    fStyle = nullptr;
-  }
-  if (fTitlePad) {
-    fTitlePad->Clear();
-    delete fTitlePad;
-    fTitlePad = nullptr;
-  }
   if (fData.size() > 0) {
     for (UInt_t i=0; i<fData.size(); i++)
       CleanupDataSet(fData[i]);
@@ -322,11 +269,6 @@ PMusrCanvas::~PMusrCanvas()
       CleanupDataSet(fNonMusrData[i]);
     fNonMusrData.clear();
   }
-  if (fMultiGraphLegend) {
-    fMultiGraphLegend->Clear();
-    delete fMultiGraphLegend;
-    fMultiGraphLegend = nullptr;
-  }
   if (fMultiGraphData) {
     delete fMultiGraphData;
     fMultiGraphData = nullptr;
@@ -335,29 +277,6 @@ PMusrCanvas::~PMusrCanvas()
     delete fMultiGraphDiff;
     fMultiGraphDiff = nullptr;
   }
-  if (fDataTheoryPad) {
-    delete fDataTheoryPad;
-    fDataTheoryPad = nullptr;
-  }
-  if (fParameterPad) {
-    fParameterPad->Clear();
-    delete fParameterPad;
-    fParameterPad = nullptr;
-  }
-  if (fTheoryPad) {
-    fTheoryPad->Clear();
-    delete fTheoryPad;
-    fTheoryPad = nullptr;
-  }
-  if (fInfoPad) {
-    fInfoPad->Clear();
-    delete fInfoPad;
-    fInfoPad = nullptr;
-  }
-  if (fMainCanvas) {
-    delete fMainCanvas;
-    fMainCanvas = nullptr;
-  }
 }
 
 //--------------------------------------------------------------------------
@@ -409,7 +328,7 @@ void PMusrCanvas::SetMsrHandler(PMsrHandler *msrHandler)
       (fMsrHandler->GetMsrPlotList()->at(0).fRRFFreq != 0.0)) ||
       (fMsrHandler->GetMsrGlobal()->GetRRFPacking() > 0 &&
        fMsrHandler->GetMsrGlobal()->GetRRFUnit().CompareTo("??"))) {
-    fRRFLatexText = new TLatex();
+    fRRFLatexText = std::make_unique<TLatex>();
     fRRFLatexText->SetNDC(kTRUE);
     fRRFLatexText->SetTextFont(62);
     fRRFLatexText->SetTextSize(0.03);
@@ -417,7 +336,7 @@ void PMusrCanvas::SetMsrHandler(PMsrHandler *msrHandler)
     Int_t rrfUnitTag = -1;
     Double_t rrfFreq = 0.0;
     if (fMsrHandler->GetMsrPlotList()->at(0).fRRFPacking > 0) { // RRF single histo PLOT
-      fRRFText = new TString("RRF: ");
+      fRRFText = std::make_unique<TString>("RRF: ");
       rrfUnitTag = fMsrHandler->GetMsrPlotList()->at(0).fRRFUnit;
       rrfFreq = fMsrHandler->GetMsrPlotList()->at(0).fRRFFreq;
       TString rrfFreqStr("");
@@ -446,7 +365,7 @@ void PMusrCanvas::SetMsrHandler(PMsrHandler *msrHandler)
       *fRRFText += TString(", RRF packing = ");
       *fRRFText += fMsrHandler->GetMsrPlotList()->at(0).fRRFPacking;
     } else { // RRF single histo FIT
-      fRRFText = new TString("RRF: ");
+      fRRFText = std::make_unique<TString>("RRF: ");
       rrfUnitTag = fMsrHandler->GetMsrGlobal()->GetRRFUnitTag();
       rrfFreq = fMsrHandler->GetMsrGlobal()->GetRRFFreq(fMsrHandler->GetMsrGlobal()->GetRRFUnit().Data());
       TString rrfFreqStr("");
@@ -493,11 +412,7 @@ void PMusrCanvas::SetTimeout(Int_t timeout)
   if (fTimeout <= 0)
     return;
 
-  if (fTimeoutTimer) {
-    delete fTimeoutTimer;
-    fTimeoutTimer = nullptr;
-  }
-  fTimeoutTimer = new TTimer();
+  fTimeoutTimer.reset(new TTimer());
 
   fTimeoutTimer->Connect("Timeout()", "PMusrCanvas", this, "Done()");
 
@@ -1542,7 +1457,7 @@ void PMusrCanvas::LastCanvasClosed()
 void PMusrCanvas::WindowClosed()
 {
 //  std::cerr << ">> fMainCanvas->GetName()=" << fMainCanvas->GetName() << std::endl;
-  gROOT->GetListOfCanvases()->Remove(fMainCanvas);
+  gROOT->GetListOfCanvases()->Remove(fMainCanvas.get());
   LastCanvasClosed();
 }
 
@@ -2323,7 +2238,7 @@ void PMusrCanvas::CreateStyle()
 {
   TString musrStyle("musrStyle");
   musrStyle += fPlotNumber;
-  fStyle = new TStyle(musrStyle, musrStyle);
+  fStyle = std::make_unique<TStyle>(musrStyle, musrStyle);
   fStyle->SetOptStat(0);  // no statistics options
   fStyle->SetOptTitle(0); // no title
   fStyle->cd();
@@ -2407,25 +2322,11 @@ void PMusrCanvas::InitMusrCanvas(const Char_t* title, Int_t wtopx, Int_t wtopy,
   fImp   = nullptr;
   fBar   = nullptr;
   fPopupMain    = nullptr;
-  fPopupFourier = nullptr;
-
-  fMainCanvas          = nullptr;
-  fTitlePad            = nullptr;
-  fDataTheoryPad       = nullptr;
-  fParameterPad        = nullptr;
-  fTheoryPad           = nullptr;
-  fInfoPad             = nullptr;
-  fMultiGraphLegend    = nullptr;
 
   // invoke canvas
   TString canvasName = TString("fMainCanvas");
   canvasName += fPlotNumber;
-  fMainCanvas = new TCanvas(canvasName.Data(), title, wtopx, wtopy, ww, wh);
-  if (fMainCanvas == nullptr) {
-    std::cerr << std::endl << ">> PMusrCanvas::PMusrCanvas(): **PANIC ERROR** Couldn't invoke " << canvasName.Data();
-    std::cerr << std::endl;
-    return;
-  }
+  fMainCanvas = std::make_unique<TCanvas>(canvasName.Data(), title, wtopx, wtopy, ww, wh);
 
   fMainCanvas->Connect("Closed()", "PMusrCanvas", this, "LastCanvasClosed()");
 
@@ -2436,11 +2337,11 @@ void PMusrCanvas::InitMusrCanvas(const Char_t* title, Int_t wtopx, Int_t wtopy,
     fBar = fImp->GetMenuBar();
     fPopupMain = fBar->AddPopup("&Musrfit");
 
-    fPopupFourier = new TGPopupMenu();
+    fPopupFourier = std::make_unique<TGPopupMenu>();
     fPopupMain->AddEntry("&Data", P_MENU_ID_DATA+P_MENU_PLOT_OFFSET*fPlotNumber);
     fPopupMain->AddSeparator();
 
-    fPopupMain->AddPopup("&Fourier", fPopupFourier);
+    fPopupMain->AddPopup("&Fourier", fPopupFourier.get());
     fPopupFourier->AddEntry("Show Real", P_MENU_ID_FOURIER+P_MENU_PLOT_OFFSET*fPlotNumber+P_MENU_ID_FOURIER_REAL);
     fPopupFourier->AddEntry("Show Imag", P_MENU_ID_FOURIER+P_MENU_PLOT_OFFSET*fPlotNumber+P_MENU_ID_FOURIER_IMAG);
     fPopupFourier->AddEntry("Show Real+Imag", P_MENU_ID_FOURIER+P_MENU_PLOT_OFFSET*fPlotNumber+P_MENU_ID_FOURIER_REAL_AND_IMAG);
@@ -2470,57 +2371,32 @@ void PMusrCanvas::InitMusrCanvas(const Char_t* title, Int_t wtopx, Int_t wtopy,
 
   // divide the canvas into 4 pads
   // title pad
-  fTitlePad = new TPaveText(0.0, YTITLE, 1.0, 1.0, "NDC");
-  if (fTitlePad == nullptr) {
-    std::cerr << std::endl << ">> PMusrCanvas::PMusrCanvas(): **PANIC ERROR** Couldn't invoke fTitlePad";
-    std::cerr << std::endl;
-    return;
-  }
+  fTitlePad = std::make_unique<TPaveText>(0.0, YTITLE, 1.0, 1.0, "NDC");
   fTitlePad->SetFillColor(TColor::GetColor(255,255,255));
   fTitlePad->SetTextAlign(12); // middle, left
   fTitlePad->AddText(title);
   fTitlePad->Draw();
 
   // data/theory pad
-  fDataTheoryPad = new TPad("dataTheoryPad", "dataTheoryPad", 0.0, YINFO, XTHEO, YTITLE);
-  if (fDataTheoryPad == nullptr) {
-    std::cerr << std::endl << ">> PMusrCanvas::PMusrCanvas(): **PANIC ERROR** Couldn't invoke fDataTheoryPad";
-    std::cerr << std::endl;
-    return;
-  }
+  fDataTheoryPad = std::make_unique<TPad>("dataTheoryPad", "dataTheoryPad", 0.0, YINFO, XTHEO, YTITLE);
   fDataTheoryPad->SetFillColor(TColor::GetColor(255,255,255));
   fDataTheoryPad->Draw();
 
   // parameter pad
-  fParameterPad = new TPaveText(XTHEO, 0.5, 1.0, YTITLE, "NDC");
-  if (fParameterPad == nullptr) {
-    std::cerr << std::endl << ">> PMusrCanvas::PMusrCanvas(): **PANIC ERROR** Couldn't invoke fParameterPad";
-    std::cerr << std::endl;
-    return;
-  }
+  fParameterPad = std::make_unique<TPaveText>(XTHEO, 0.5, 1.0, YTITLE, "NDC");
   fParameterPad->SetFillColor(TColor::GetColor(255,255,255));
   fParameterPad->SetTextAlign(13); // top, left
   fParameterPad->SetTextFont(102); // courier bold, scalable so that greek parameters will be plotted properly
 
   // theory pad
-  fTheoryPad = new TPaveText(XTHEO, 0.1, 1.0, 0.5, "NDC");
-  if (fTheoryPad == nullptr) {
-    std::cerr << std::endl << ">> PMusrCanvas::PMusrCanvas(): **PANIC ERROR** Couldn't invoke fTheoryPad";
-    std::cerr << std::endl;
-    return;
-  }
+  fTheoryPad = std::make_unique<TPaveText>(XTHEO, 0.1, 1.0, 0.5, "NDC");
   fTheoryPad->SetFillColor(TColor::GetColor(255,255,255));
   fTheoryPad->SetTextAlign(13); // top, left
   fTheoryPad->SetTextFont(102); // courier bold, scalable so that greek parameters will be plotted properly
 
 
   // info pad
-  fInfoPad = new TLegend(0.0, 0.0, 1.0, YINFO, "NDC");
-  if (fInfoPad == nullptr) {
-    std::cerr << std::endl << ">> PMusrCanvas::PMusrCanvas(): **PANIC ERROR** Couldn't invoke fInfoPad";
-    std::cerr << std::endl;
-    return;
-  }
+  fInfoPad = std::make_unique<TLegend>(0.0, 0.0, 1.0, YINFO, "NDC");
   fInfoPad->SetFillColor(TColor::GetColor(255,255,255));
   fInfoPad->SetTextAlign(12); // middle, left
 
@@ -4913,11 +4789,7 @@ void PMusrCanvas::PlotData(Bool_t unzoom)
         // set y-axis label
         fMultiGraphData->GetYaxis()->SetTitle(yAxisTitle.Data());
       } else { // more than one data set present, hence add a legend
-        if (fMultiGraphLegend) {
-          delete fMultiGraphLegend;
-        }
-        fMultiGraphLegend = new TLegend(0.8, 0.8, 1.0, 1.0);
-        assert(fMultiGraphLegend != nullptr);
+        fMultiGraphLegend.reset(new TLegend(0.8, 0.8, 1.0, 1.0));
         PStringVector legendLabel;
         for (UInt_t i=0; i<plotInfo.fRuns.size(); i++) {
            runNo = (UInt_t)plotInfo.fRuns[i]-1;
@@ -6110,12 +5982,6 @@ void PMusrCanvas::PlotFourierDifference(Bool_t unzoom)
  */
 void PMusrCanvas::PlotFourierPhaseValue(Bool_t unzoom)
 {
-  // check if phase TLatex object is present
-  if (fCurrentFourierPhaseText) {
-    delete fCurrentFourierPhaseText;
-    fCurrentFourierPhaseText = nullptr;
-  }
-
   double x, y;
   TString str;
 
@@ -6127,7 +5993,7 @@ void PMusrCanvas::PlotFourierPhaseValue(Bool_t unzoom)
   }
   x = 0.7;
   y = 0.85;
-  fCurrentFourierPhaseText = new TLatex();
+  fCurrentFourierPhaseText.reset(new TLatex());
   fCurrentFourierPhaseText->SetNDC(kTRUE);
   fCurrentFourierPhaseText->SetText(x, y, str.Data());
   fCurrentFourierPhaseText->SetTextFont(62);

src/classes/PMusrT0.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -245,20 +245,11 @@ ClassImpQ(PMusrT0)
 PMusrT0::PMusrT0()
 {
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
 
   fValid = false;
 
   fStatus = 0; // default is quit locally
 
-  fMainCanvas = nullptr;
-
-  fHisto = nullptr;
-  fData  = nullptr;
-  fBkg   = nullptr;
-
-  fToDoInfo = nullptr;
-
   fDataAndBkgEnabled = false;
   fT0Enabled         = false;
   fShowT0DataChannel = false;
@@ -267,13 +258,6 @@ PMusrT0::PMusrT0()
   fDataRange[1] = 0;
   fBkgRange[0]  = 0;
   fBkgRange[1]  = 0;
-
-  fT0Line        = nullptr;
-  fT0DataLine    = nullptr;
-  fFirstBkgLine  = nullptr;
-  fLastBkgLine   = nullptr;
-  fFirstDataLine = nullptr;
-  fLastDataLine  = nullptr;
 }
 
 //--------------------------------------------------------------------------
@@ -287,20 +271,11 @@ PMusrT0::PMusrT0()
 PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
 {
   fTimeout = 0;
-  fTimeoutTimer = nullptr;
 
   fValid = true;
 
   fStatus = 0; // default is quit locally
 
-  fMainCanvas = nullptr;
-
-  fHisto = nullptr;
-  fData  = nullptr;
-  fBkg   = nullptr;
-
-  fToDoInfo = nullptr;
-
   fDataAndBkgEnabled = false;
   fT0Enabled         = false;
   fShowT0DataChannel = false;
@@ -310,13 +285,6 @@ PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
   fBkgRange[0]  = 0;
   fBkgRange[1]  = 0;
 
-  fT0Line        = nullptr;
-  fT0DataLine    = nullptr;
-  fFirstBkgLine  = nullptr;
-  fLastBkgLine   = nullptr;
-  fFirstDataLine = nullptr;
-  fLastDataLine  = nullptr;
-
   // feed necessary objects
   TString str;
 
@@ -347,7 +315,7 @@ PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
     Int_t noOfBins = rawRunData->GetDataBin(histoNo)->size();
     Double_t start = -0.5;
     Double_t end   = noOfBins - 0.5; // -0.5 is correct since the data start at 0.0
-    fHisto = new TH1F("fHisto", str.Data(), noOfBins, start, end);
+    fHisto = std::make_unique<TH1F>("fHisto", str.Data(), noOfBins, start, end);
     fHisto->SetMarkerStyle(21);
     fHisto->SetMarkerSize(0.5);
     fHisto->SetMarkerColor(TColor::GetColor(0,0,0)); // black
@@ -382,7 +350,7 @@ PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
     Int_t noOfBins = rawRunData->GetDataBin(histoNo)->size();
     Double_t start = -0.5;
     Double_t end   = noOfBins - 0.5; // -0.5 is correct since the data start at 0.0
-    fHisto = new TH1F("fHisto", str.Data(), noOfBins, start, end);
+    fHisto = std::make_unique<TH1F>("fHisto", str.Data(), noOfBins, start, end);
     fHisto->SetMarkerStyle(21);
     fHisto->SetMarkerSize(0.5);
     fHisto->SetMarkerColor(TColor::GetColor(0,0,0)); // black
@@ -517,7 +485,7 @@ PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
   }
 
   // generate canvas etc
-  fMainCanvas = new TCanvas("fMainCanvas", str);
+  fMainCanvas = std::make_unique<TCanvas>("fMainCanvas", str);
   fMainCanvas->SetFillColor(TColor::GetColor(255,255,255));
 
 
@@ -545,7 +513,7 @@ PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
 
   if (fMusrT0Data.GetCmdTag() == PMUSRT0_GET_T0) {
     str = "please set t0 bin only.";
-    fToDoInfo = new TLatex();
+    fToDoInfo = std::make_unique<TLatex>();
     fToDoInfo->SetTextFont(51);
     fToDoInfo->SetTextSize(0.030);
     fToDoInfo->SetLineWidth(2);
@@ -554,7 +522,7 @@ PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
   }
   if (fMusrT0Data.GetCmdTag() == PMUSRT0_GET_DATA_AND_BKG_RANGE) {
     str = "please set data and bkg range.";
-    fToDoInfo = new TLatex();
+    fToDoInfo = std::make_unique<TLatex>();
     fToDoInfo->SetTextFont(51);
     fToDoInfo->SetTextSize(0.030);
     fToDoInfo->SetLineWidth(2);
@@ -563,64 +531,6 @@ PMusrT0::PMusrT0(PMusrT0Data &data) : fMusrT0Data(data)
   }
 }
 
-//--------------------------------------------------------------------------
-// Destructor
-//--------------------------------------------------------------------------
-/**
- * <p>Destructor.
- */
-PMusrT0::~PMusrT0()
-{
-  if (fTimeoutTimer) {
-    delete fTimeoutTimer;
-    fTimeoutTimer = nullptr;
-  }
-  if (fHisto) {
-    delete fHisto;
-    fHisto = nullptr;
-  }
-  if (fData) {
-    delete fData;
-    fData = nullptr;
-  }
-  if (fBkg) {
-    delete fBkg;
-    fBkg = nullptr;
-  }
-  if (fToDoInfo) {
-    delete fToDoInfo;
-    fToDoInfo = nullptr;
-  }
-  if (fT0Line) {
-    delete fT0Line;
-    fT0Line = nullptr;
-  }
-  if (fT0DataLine) {
-    delete fT0DataLine;
-    fT0DataLine = nullptr;
-  }
-  if (fFirstBkgLine) {
-    delete fFirstBkgLine;
-    fFirstBkgLine = nullptr;
-  }
-  if (fLastBkgLine) {
-    delete fLastBkgLine;
-    fLastBkgLine = nullptr;
-  }
-  if (fFirstDataLine) {
-    delete fFirstDataLine;
-    fFirstDataLine = nullptr;
-  }
-  if (fLastDataLine) {
-    delete fLastDataLine;
-    fLastDataLine = nullptr;
-  }
-  if (fMainCanvas && (fStatus != 2)) {
-    delete fMainCanvas;
-    fMainCanvas = nullptr;
-  }
-}
-
 //--------------------------------------------------------------------------
 // Done (SIGNAL)
 //--------------------------------------------------------------------------
@@ -724,11 +634,7 @@ void PMusrT0::SetTimeout(Int_t timeout)
   if (fTimeout <= 0)
     return;
 
-  if (fTimeoutTimer) {
-    delete fTimeoutTimer;
-    fTimeoutTimer = nullptr;
-  }
-  fTimeoutTimer = new TTimer();
+  fTimeoutTimer.reset(new TTimer());
 
   fTimeoutTimer->Connect("Timeout()", "PMusrT0", this, "Quit()");
 
@@ -782,7 +688,7 @@ void PMusrT0::InitT0()
   }
   Double_t max = fHisto->GetMaximum();
 
-  fT0Line = new TLine((Double_t)t0Bin, 0.0, (Double_t)t0Bin, max);
+  fT0Line = std::make_unique<TLine>((Double_t)t0Bin, 0.0, (Double_t)t0Bin, max);
   fT0Line->SetLineStyle(1); // solid
   fT0Line->SetLineColor(TColor::GetColor(0,255,0)); // green
   fT0Line->SetLineWidth(2);
@@ -815,7 +721,7 @@ void PMusrT0::InitDataAndBkg()
   Int_t noOfBins = fDataRange[1]-fDataRange[0]+1;
   Double_t start = fDataRange[0] - 0.5;
   Double_t end   = fDataRange[1] + 0.5;
-  fData = new TH1F("fData", "fData", noOfBins, start, end);
+  fData = std::make_unique<TH1F>("fData", "fData", noOfBins, start, end);
   fData->SetMarkerStyle(21);
   fData->SetMarkerSize(0.5);
   fData->SetMarkerColor(TColor::GetColor(0,0,255)); // blue
@@ -843,7 +749,7 @@ void PMusrT0::InitDataAndBkg()
   noOfBins = fBkgRange[1]-fBkgRange[0]+1;
   start = fBkgRange[0] - 0.5;
   end   = fBkgRange[1] + 0.5;
-  fBkg = new TH1F("fBkg", "fBkg", noOfBins, start, end);
+  fBkg = std::make_unique<TH1F>("fBkg", "fBkg", noOfBins, start, end);
   fBkg->SetMarkerStyle(21);
   fBkg->SetMarkerSize(0.5);
   fBkg->SetMarkerColor(TColor::GetColor(255,0,0)); // red
@@ -857,26 +763,26 @@ void PMusrT0::InitDataAndBkg()
   Double_t max = fHisto->GetMaximum();
 
   // data lines
-  fFirstDataLine = new TLine(static_cast<Double_t>(fDataRange[0]), 0.0, static_cast<Double_t>(fDataRange[0]), max);
+  fFirstDataLine = std::make_unique<TLine>(static_cast<Double_t>(fDataRange[0]), 0.0, static_cast<Double_t>(fDataRange[0]), max);
   fFirstDataLine->SetLineStyle(3); // doted
   fFirstDataLine->SetLineColor(TColor::GetColor(0,0,255)); // blue
   fFirstDataLine->SetLineWidth(2);
   fFirstDataLine->Draw();
 
-  fLastDataLine = new TLine(static_cast<Double_t>(fDataRange[1]), 0.0, static_cast<Double_t>(fDataRange[1]), max);
+  fLastDataLine = std::make_unique<TLine>(static_cast<Double_t>(fDataRange[1]), 0.0, static_cast<Double_t>(fDataRange[1]), max);
   fLastDataLine->SetLineStyle(3); // doted
   fLastDataLine->SetLineColor(TColor::GetColor(0,0,255)); // blue
   fLastDataLine->SetLineWidth(2);
   fLastDataLine->Draw();
 
   // bkg lines
-  fFirstBkgLine = new TLine(static_cast<Double_t>(fBkgRange[0]), 0.0, static_cast<Double_t>(fBkgRange[0]), max);
+  fFirstBkgLine = std::make_unique<TLine>(static_cast<Double_t>(fBkgRange[0]), 0.0, static_cast<Double_t>(fBkgRange[0]), max);
   fFirstBkgLine->SetLineStyle(6); // _..._...
   fFirstBkgLine->SetLineColor(TColor::GetColor(255,0,0)); // red
   fFirstBkgLine->SetLineWidth(2);
   fFirstBkgLine->Draw();
 
-  fLastBkgLine = new TLine(static_cast<Double_t>(fBkgRange[1]), 0.0, static_cast<Double_t>(fBkgRange[1]), max);
+  fLastBkgLine = std::make_unique<TLine>(static_cast<Double_t>(fBkgRange[1]), 0.0, static_cast<Double_t>(fBkgRange[1]), max);
   fLastBkgLine->SetLineStyle(6); // _..._...
   fLastBkgLine->SetLineColor(TColor::GetColor(255,0,0)); // red
   fLastBkgLine->SetLineWidth(2);
@@ -898,7 +804,7 @@ void PMusrT0::ShowDataFileT0Channel()
   Double_t max = fHisto->GetMaximum();
 
   if (!fT0DataLine) {
-    fT0DataLine = new TLine(static_cast<Double_t>(t0Bin), 0.0, static_cast<Double_t>(t0Bin), max);
+    fT0DataLine = std::make_unique<TLine>(static_cast<Double_t>(t0Bin), 0.0, static_cast<Double_t>(t0Bin), max);
     fT0DataLine->SetLineStyle(1); // solid
     fT0DataLine->SetLineColor(kOrange-3);
     fT0DataLine->SetLineWidth(2);
@@ -917,8 +823,7 @@ void PMusrT0::ShowDataFileT0Channel()
 void PMusrT0::HideDataFileT0Channel()
 {
   if (fT0DataLine) {
-    delete fT0DataLine;
-    fT0DataLine = nullptr;
+    fT0DataLine.reset();
   }
   fMainCanvas->Update();
 }
@@ -1036,15 +941,11 @@ void PMusrT0::SetDataFirstChannel()
   fFirstDataLine->SetX1(x);
   fFirstDataLine->SetX2(x);
 
-  // recreate data histo
-  delete fData;
-  fData = nullptr;
-
   // refill data histo
   Int_t noOfBins = fDataRange[1]-fDataRange[0]+1;
   Double_t start = fDataRange[0] - 0.5;
   Double_t end   = fDataRange[1] + 0.5;
-  fData = new TH1F("fData", "fData", noOfBins, start, end);
+  fData.reset(new TH1F("fData", "fData", noOfBins, start, end));
   fData->SetMarkerStyle(21);
   fData->SetMarkerSize(0.5);
   fData->SetMarkerColor(TColor::GetColor(0,0,255)); // blue
@@ -1086,15 +987,11 @@ void PMusrT0::SetDataLastChannel()
   fLastDataLine->SetX1(x);
   fLastDataLine->SetX2(x);
 
-  // recreate data histo
-  delete fData;
-  fData = nullptr;
-
   // refill data histo
   Int_t noOfBins = fDataRange[1]-fDataRange[0]+1;
   Double_t start = fDataRange[0] - 0.5;
   Double_t end   = fDataRange[1] + 0.5;
-  fData = new TH1F("fData", "fData", noOfBins, start, end);
+  fData.reset(new TH1F("fData", "fData", noOfBins, start, end));
   fData->SetMarkerStyle(21);
   fData->SetMarkerSize(0.5);
   fData->SetMarkerColor(TColor::GetColor(0,0,255)); // blue
@@ -1136,15 +1033,11 @@ void PMusrT0::SetBkgFirstChannel()
   fFirstBkgLine->SetX1(x);
   fFirstBkgLine->SetX2(x);
 
-  // recreate data histo
-  delete fBkg;
-  fBkg = nullptr;
-
   // refill data histo
   Int_t noOfBins = fBkgRange[1]-fBkgRange[0]+1;
   Double_t start = fBkgRange[0] - 0.5;
   Double_t end   = fBkgRange[1] + 0.5;
-  fBkg = new TH1F("fBkg", "fBkg", noOfBins, start, end);
+  fBkg.reset(new TH1F("fBkg", "fBkg", noOfBins, start, end));
   fBkg->SetMarkerStyle(21);
   fBkg->SetMarkerSize(0.5);
   fBkg->SetMarkerColor(TColor::GetColor(255,0,0)); // red
@@ -1186,15 +1079,11 @@ void PMusrT0::SetBkgLastChannel()
   fLastBkgLine->SetX1(x);
   fLastBkgLine->SetX2(x);
 
-  // recreate data histo
-  delete fBkg;
-  fBkg = nullptr;
-
   // refill data histo
   Int_t noOfBins = fBkgRange[1]-fBkgRange[0]+1;
   Double_t start = fBkgRange[0] - 0.5;
   Double_t end   = fBkgRange[1] + 0.5;
-  fBkg = new TH1F("fBkg", "fBkg", noOfBins, start, end);
+  fBkg.reset(new TH1F("fBkg", "fBkg", noOfBins, start, end));
   fBkg->SetMarkerStyle(21);
   fBkg->SetMarkerSize(0.5);
   fBkg->SetMarkerColor(TColor::GetColor(255,0,0)); // red

src/classes/PPrepFourier.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRgeHandler.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -31,6 +31,7 @@
 #include <iostream>
 #include <vector>
 #include <string>
+#include <memory>
 
 #include <boost/filesystem.hpp>
 #include <boost/algorithm/string.hpp>
@@ -345,7 +346,7 @@ PRgeHandler::PRgeHandler(const std::string fln)
   }
 
   // create the rge xml handler
-  PXmlRgeHandler *xmlRge = new PXmlRgeHandler();
+  std::unique_ptr<PXmlRgeHandler> xmlRge = std::make_unique<PXmlRgeHandler>();
   if (xmlRge == nullptr) {
     std::cerr << std::endl;
     std::cerr << "**ERROR** couldn't invoke PXmlRgeHandler." << std::endl;
@@ -355,7 +356,7 @@ PRgeHandler::PRgeHandler(const std::string fln)
   }
 
   // create the SAX parser
-  TSAXParser *saxParser = new TSAXParser();
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
   if (saxParser == nullptr) {
     std::cerr << std::endl;
     std::cerr << "**ERROR** couldn't invoke TSAXParser." << std::endl;
@@ -366,7 +367,7 @@ PRgeHandler::PRgeHandler(const std::string fln)
   saxParser->SetStopOnError();
 
   // connect SAX parser and rge handler
-  saxParser->ConnectToHandler("PXmlRgeHandler", xmlRge);
+  saxParser->ConnectToHandler("PXmlRgeHandler", xmlRge.get());
   int status = saxParser->ParseFile(fln.c_str());
   if (status != 0) {
     std::cerr << std::endl;
@@ -433,9 +434,6 @@ PRgeHandler::PRgeHandler(const std::string fln)
       fData.push_back(dataSet);
     }
   }
-
-  delete saxParser;
-  delete xmlRge;
 }
 
 //--------------------------------------------------------------------------

src/classes/PRunAsymmetry.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRunAsymmetryBNMR.cpp

@@ -9,7 +9,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2018-2023 by Zaher Salman                              *
+ *   Copyright (C) 2018-2024 by Zaher Salman                              *
  *   zaher.salman@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRunAsymmetryRRF.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRunBase.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -99,7 +99,7 @@ PRunBase::PRunBase(PMsrHandler *msrInfo, PRunDataHandler *rawData, UInt_t runNo,
     fFuncValues.push_back(0.0);
 
   // generate theory
-  fTheory = new PTheory(fMsrInfo, runNo);
+  fTheory = std::make_unique<PTheory>(fMsrInfo, runNo);
   if (fTheory == nullptr) {
     std::cerr << std::endl << "**SEVERE ERROR** PRunBase::PRunBase: Couldn't create an instance of PTheory :-(, will quit" << std::endl;
     exit(0);
@@ -181,10 +181,7 @@ void PRunBase::SetFitRange(PDoublePairVector fitRange)
  */
 void PRunBase::CleanUp()
 {
-  if (fTheory) {
-    delete fTheory;
-    fTheory = nullptr;
-  }
+  fTheory.reset();
 }
 
 //--------------------------------------------------------------------------

src/classes/PRunDataHandler.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -41,6 +41,7 @@
 #include <fstream>
 #include <string>
 #include <sstream>
+#include <memory>
 
 #include <TROOT.h>
 #include <TSystem.h>
@@ -1713,7 +1714,7 @@ Bool_t PRunDataHandler::ReadRootFile()
     }
   } else { // MusrRoot file
     // invoke the MusrRoot header object
-    TMusrRunHeader *header = new TMusrRunHeader(true); // read quite
+    std::unique_ptr<TMusrRunHeader> header = std::make_unique<TMusrRunHeader>(true); // read quiet
     if (header == nullptr) {
       std::cerr << std::endl << ">> PRunDataHandler::ReadRootFile: **ERROR** Couldn't invoke MusrRoot RunHeader in file:" << fRunPathName;
       std::cerr << std::endl;
@@ -2080,12 +2081,6 @@ Bool_t PRunDataHandler::ReadRootFile()
         histoData.clear();
       }
     }
-
-    // clean up
-    if (header) {
-      delete header;
-      header=nullptr;
-    }
   }
 
   f.Close();
@@ -2122,7 +2117,7 @@ Bool_t PRunDataHandler::ReadNexusFile()
   Double_t dval;
   bool ok;
 
-  PNeXus *nxs_file = new PNeXus(fRunPathName.Data());
+  std::unique_ptr<PNeXus> nxs_file = std::make_unique<PNeXus>(fRunPathName.Data());
   if (!nxs_file->IsValid()) {
     std::cerr << std::endl << ">> PRunDataHandler::ReadNexusFile(): Not a valid NeXus file.";
     std::cerr << std::endl << ">> Error Message: " << nxs_file->GetErrorMsg().data() << std::endl;
@@ -2454,12 +2449,6 @@ Bool_t PRunDataHandler::ReadNexusFile()
   } else {
     std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): IDF version " << nxs_file->GetIdfVersion() << ", not implemented." << std::endl;
   }
-
-  // clean up
-  if (nxs_file) {
-    delete nxs_file;
-    nxs_file = nullptr;
-  }
 #else
   std::cout << std::endl << ">> PRunDataHandler::ReadNexusFile(): Sorry, not enabled at configuration level, i.e. --enable-NeXus when executing configure" << std::endl << std::endl;
 #endif
@@ -4531,7 +4520,7 @@ Bool_t PRunDataHandler::WriteMusrRootFile(TString fln)
 
   runHeader = gROOT->GetRootFolder()->AddFolder("RunHeader", "MusrRoot Run Header Info");
   gROOT->GetListOfBrowsables()->Add(runHeader, "RunHeader");
-  TMusrRunHeader *header = new TMusrRunHeader(true);
+  std::unique_ptr<TMusrRunHeader> header = std::make_unique<TMusrRunHeader>(true);
   gROOT->GetListOfBrowsables()->Add(runHeader, "RunHeader");
 
   // feed header info
@@ -4647,9 +4636,13 @@ Bool_t PRunDataHandler::WriteMusrRootFile(TString fln)
       str.Form("hDecay%03d", dataSet->GetHistoNo());
       length = dataSet->GetData()->size();
       histo = new TH1F(str.Data(), str.Data(), length+1, -0.5, static_cast<Double_t>(length)+0.5);
+      Int_t sum=0, entries=0;
       for (UInt_t j=0; j<length; j++) {
-        histo->SetBinContent(j+1, dataSet->GetData()->at(j));
+        entries = dataSet->GetData()->at(j);
+        histo->SetBinContent(j+1, entries);
+        sum += entries;
       }
+      histo->SetEntries(sum);
       histos.push_back(histo);
     }
   } else { // rebin > 1
@@ -4666,14 +4659,18 @@ Bool_t PRunDataHandler::WriteMusrRootFile(TString fln)
       length = dataSet->GetData()->size();
       histo = new TH1F(str.Data(), str.Data(), static_cast<Int_t>(length/fAny2ManyInfo->rebin)+1, -0.5, static_cast<Double_t>(static_cast<Int_t>(length/fAny2ManyInfo->rebin))+0.5);
       dataCount = 0;
+      Int_t sum=0, entries=0;
       for (UInt_t j=0; j<length; j++) {
         if ((j > 0) && (j % fAny2ManyInfo->rebin == 0)) {
           dataCount++;
           histo->SetBinContent(dataCount, dataRebin);
           dataRebin = 0;
         }
-        dataRebin += static_cast<UInt_t>(dataSet->GetData()->at(j));
+        entries = dataSet->GetData()->at(j);
+        sum += entries;
+        dataRebin += static_cast<UInt_t>(entries);
       }
+      histo->SetEntries(sum);
       histos.push_back(histo);
     }
   }
@@ -4683,7 +4680,7 @@ Bool_t PRunDataHandler::WriteMusrRootFile(TString fln)
     decayAnaModule->Add(histos[i]);
 
   // write file
-  TFile *fout = new TFile(fln, "RECREATE", fln);
+  std::unique_ptr<TFile> fout = std::make_unique<TFile>(fln, "RECREATE", fln);
   if (fout == nullptr) {
     std::cerr << std::endl << "PRunDataHandler::WriteMusrRootFile(): **ERROR** Couldn't create ROOT file '" << fln << "'" << std::endl;
     return false;
@@ -4695,6 +4692,12 @@ Bool_t PRunDataHandler::WriteMusrRootFile(TString fln)
   histosFolder->Write();
   fout->Close();
 
+  // cleanup
+  for (UInt_t i=0; i<histos.size(); i++) {
+    if (histos[i])
+      delete histos[i];
+  }
+
   // check if root file shall be streamed to stdout
   if (fAny2ManyInfo->useStandardOutput && (fAny2ManyInfo->compressionTag == 0)) {
     // stream file to stdout
@@ -4774,7 +4777,7 @@ Bool_t PRunDataHandler::WriteRootFile(TString fln)
 
   runInfo = gROOT->GetRootFolder()->AddFolder("RunInfo", "LEM RunInfo");
   gROOT->GetListOfBrowsables()->Add(runInfo, "RunInfo");
-  TLemRunHeader *header = new TLemRunHeader();
+  std::unique_ptr<TLemRunHeader> header = std::make_unique<TLemRunHeader>();
   gROOT->GetListOfBrowsables()->Add(runInfo, "RunInfo");
 
   // feed header info
@@ -4813,7 +4816,7 @@ Bool_t PRunDataHandler::WriteRootFile(TString fln)
     tt0[i] = dataSet->GetTimeZeroBin()/fAny2ManyInfo->rebin;
   }
   header->SetTimeZero(tt0);
-  runInfo->Add(header); // add header to RunInfo folder
+  runInfo->Add(header.get()); // add header to RunInfo folder
 
   // feed histos
   std::vector<TH1F*> histos;
@@ -4867,7 +4870,7 @@ Bool_t PRunDataHandler::WriteRootFile(TString fln)
     decayAnaModule->Add(histos[i]);
 
   // write file
-  TFile *fout = new TFile(fln, "RECREATE", fln);
+  std::unique_ptr<TFile> fout = std::make_unique<TFile>(fln, "RECREATE", fln);
   if (fout == nullptr) {
     std::cerr << std::endl << "PRunDataHandler::WriteRootFile(): **ERROR** Couldn't create ROOT file '" << fln << "'" << std::endl;
     return false;
@@ -4883,9 +4886,7 @@ Bool_t PRunDataHandler::WriteRootFile(TString fln)
     delete histos[i];
   }
   histos.clear();
-  delete fout;
   delete [] tt0;
-  delete header;
 
   // check if root file shall be streamed to stdout
   if (fAny2ManyInfo->useStandardOutput && (fAny2ManyInfo->compressionTag == 0)) {
@@ -4956,7 +4957,7 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
     std::cout << std::endl << ">> PRunDataHandler::WriteNexusFile(): writing a NeXus data file (" << fln.Data() << ") ... " << std::endl;
 
   // create NeXus object
-  PNeXus *nxs = new PNeXus();
+  std::unique_ptr<PNeXus> nxs = std::make_unique<PNeXus>();
   if (nxs == nullptr) {
     std::cerr << std::endl << ">> PRunDataHandler::WriteNexusFile(): **ERROR** couldn't invoke the NeXus object." << std::endl;
     return false;
@@ -5236,11 +5237,6 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
     if (fgb) delete [] fgb;
     if (lgb) delete [] lgb;
   } else {
-    // clean up
-    if (nxs != 0) {
-      delete nxs;
-      nxs = nullptr;
-    }
     return false;
   }
 
@@ -5256,20 +5252,11 @@ Bool_t PRunDataHandler::WriteNexusFile(TString fln)
   else {
     std::cerr << std::endl << ">> PRunDataHandler::WriteNexusFile(): **ERROR** undefined output NeXus format " << fAny2ManyInfo->outFormat.Data() << " found.";
     std::cerr << std::endl << ">>   Allowed are: hdf4, hdf5, xml" << std::endl;
-    if (nxs != 0) {
-      delete nxs;
-      nxs = nullptr;
-    }
     return false;
   }
 
   // write file
   nxs->WriteFile(fln, fileType, fAny2ManyInfo->idf);
-
-  if (nxs != 0) {
-    delete nxs;
-    nxs = nullptr;
-  }
 #else
   std::cout << std::endl << ">> PRunDataHandler::WriteNexusFile(): Sorry, not enabled at configuration level, i.e. --enable-NeXus when executing configure" << std::endl << std::endl;
 #endif

src/classes/PRunListCollection.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRunMuMinus.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRunNonMusr.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRunSingleHisto.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PRunSingleHistoRRF.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -38,6 +38,7 @@
 #include <cmath>
 #include <iostream>
 #include <fstream>
+#include <memory>
 
 #include <TString.h>
 #include <TObjArray.h>
@@ -1068,13 +1069,13 @@ Double_t PRunSingleHistoRRF::GetMainFrequency(PDoubleVector &data)
   // create histo
   Double_t startTime = (fGoodBins[0]-fT0s[0]) * fTimeResolution;
   Int_t noOfBins = fGoodBins[1]-fGoodBins[0]+1;
-  TH1F *histo = new TH1F("data", "data", noOfBins, startTime-fTimeResolution/2.0, startTime+fTimeResolution/2.0+noOfBins*fTimeResolution);
+  std::unique_ptr<TH1F> histo = std::make_unique<TH1F>("data", "data", noOfBins, startTime-fTimeResolution/2.0, startTime+fTimeResolution/2.0+noOfBins*fTimeResolution);
   for (Int_t i=fGoodBins[0]; i<=fGoodBins[1]; i++) {
     histo->SetBinContent(i-fGoodBins[0]+1, data[i]);
   }
 
   // Fourier transform
-  PFourier *ft = new PFourier(histo, FOURIER_UNIT_FREQ);
+  std::unique_ptr<PFourier> ft = std::make_unique<PFourier>(histo.get(), FOURIER_UNIT_FREQ);
   ft->Transform(F_APODIZATION_STRONG);
 
   // find frequency maximum
@@ -1099,10 +1100,6 @@ Double_t PRunSingleHistoRRF::GetMainFrequency(PDoubleVector &data)
   // clean up
   if (power)
     delete power;
-  if (ft)
-    delete ft;
-  if (histo)
-    delete histo;
 
   return freqMax;
 }

src/classes/PStartupHandler.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -91,7 +91,7 @@ int parseXmlFile(TSAXParser *saxParser, const char *startup_path_name)
 /**
  * <p>Constructor. Check if the musrfit_startup.xml file is found in some standard search paths
  */
-PStartupHandler::PStartupHandler()
+PStartupHandler::PStartupHandler(bool reset_startup_file)
 {
   fStartupFileFound = false;
   fStartupFilePath = "";
@@ -145,6 +145,17 @@ PStartupHandler::PStartupHandler()
     }
   }
 
+  // musrfit_startup.xml found. Check if it should be rewritten
+  if (fStartupFileFound && reset_startup_file) {
+    std::cout << std::endl;
+    std::cout << ">> Will only reset the file: '" << fStartupFilePath.Data() << "'."<< std::endl;
+    std::cout << std::endl;
+    if (!WriteDefaultStartupFile(reset_startup_file)) {
+      std::cerr << std::endl << "**ERROR** couldn't re-write " << fStartupFilePath.Data() << "." << std::endl;
+      return;
+    }
+  }
+
   // if musrfit_startup.xml is still not found, will create a default one
   if (!fStartupFileFound) {
     std::cout << std::endl << "**INFO** no musrfit_startup.xml file found, will write a default one." << std::endl;
@@ -606,33 +617,37 @@ Bool_t PStartupHandler::StartupFileExists(Char_t *fln)
 //--------------------------------------------------------------------------
 // WriteDefaultStartupFile
 //--------------------------------------------------------------------------
-Bool_t PStartupHandler::WriteDefaultStartupFile()
+Bool_t PStartupHandler::WriteDefaultStartupFile(bool reset_startup_file)
 {
-  // get home
   Char_t startup_path_name[256];
-  Char_t *home = nullptr;
-  home = getenv("HOME");
-  if (home == nullptr) {
-    std::cerr << std::endl << "**ERROR** couldn't obtain $HOME." << std::endl;
-    return false;
-  }
-
-  // first check that $HOME/.musrfit exists and if NOT create it
-  struct stat info;
-
-  snprintf(startup_path_name, sizeof(startup_path_name), "%s/.musrfit", home);
-  if (!stat(startup_path_name, &info)) {
-    if (!(info.st_mode & S_IFDIR))
-      return false;
-  } else {
-    if (mkdir(startup_path_name, 0777)) {
-      std::cerr << std::endl << "**ERROR** couldn't create '" << startup_path_name << "'" << std::endl;
+  if (reset_startup_file) { // reset the found
+    snprintf(startup_path_name, sizeof(startup_path_name), "%s", fStartupFilePath.Data());
+  } else { // no musrfit_startup.xml found, hence write default under $HOME/.musrfit
+    // get home
+    Char_t *home = nullptr;
+    home = getenv("HOME");
+    if (home == nullptr) {
+      std::cerr << std::endl << "**ERROR** couldn't obtain $HOME." << std::endl;
       return false;
     }
-  }
 
-  // set path-name for musrfit_startup.xml
-  snprintf(startup_path_name, sizeof(startup_path_name), "%s/.musrfit/musrfit_startup.xml", home);
+    // first check that $HOME/.musrfit exists and if NOT create it
+    struct stat info;
+
+    snprintf(startup_path_name, sizeof(startup_path_name), "%s/.musrfit", home);
+    if (!stat(startup_path_name, &info)) {
+      if (!(info.st_mode & S_IFDIR))
+        return false;
+    } else {
+      if (mkdir(startup_path_name, 0777)) {
+        std::cerr << std::endl << "**ERROR** couldn't create '" << startup_path_name << "'" << std::endl;
+        return false;
+      }
+    }
+
+    // set path-name for musrfit_startup.xml
+    snprintf(startup_path_name, sizeof(startup_path_name), "%s/.musrfit/musrfit_startup.xml", home);
+  }
 
   std::ofstream fout(startup_path_name, std::ofstream::out);
   if (!fout.is_open()) {
@@ -648,25 +663,36 @@ Bool_t PStartupHandler::WriteDefaultStartupFile()
   fout << "    </comment>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/nemu/data/his</data_path>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/nemu/data/wkm</data_path>" << std::endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/misc</data_path>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/gps</data_path>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/dolly</data_path>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/gpd</data_path>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/ltf</data_path>" << std::endl;
-  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/alc</data_path>" << std::endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/alc/td</data_path>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/hifi</data_path>" << std::endl;
   fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/lem</data_path>" << std::endl;
+  fout << "    <data_path>/afs/psi.ch/project/bulkmusr/data/flame</data_path>" << std::endl;
+  fout << "    <!-- MISC/PSI 1985 - 1990 -->" << std::endl;
+  fout << "    <run_name_template inst=\"misc\">d%yyyy%/deltat_misc_%rrrr%.bin</run_name_template>" << std::endl;
+  fout << "    <!-- ALC TD/PSI -->" << std::endl;
+  fout << "    <run_name_template inst=\"alc\">d%yyyy%/deltat_zh_chem_%rrrr%.bin</run_name_template>" << std:: endl;
+  fout << "    <run_name_template inst=\"alc\">d%yyyy%/deltat_tdc_alc_%rrrr%.bin</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"alc\">d%yyyy%/tdc/deltat_tdc_alc_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <!-- Dolly/PSI -->" << std::endl;
+  fout << "    <run_name_template inst=\"dolly\">d%yyyy%/tdc/root/deltat_tdc_dolly_%yyyy%_%rrrr%.root</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"dolly\">d%yyyy%/pie1/deltat_flc_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"dolly\">d%yyyy%/pie3/deltat_flc_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"dolly\">d%yyyy%/deltat_flc_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"dolly\">d%yyyy%/deltat_pta_dolly_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"dolly\">d%yyyy%/pta/deltat_pta_dolly_%rrrr%.bin</run_name_template>" << std::endl;
-  fout << "    <run_name_template inst=\"dolly\">d%yyyy%/pta/deltat_pta_dolly_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"dolly\">d%yyyy%/tdc/deltat_tdc_dolly_%rrrr%.bin</run_name_template>" << std::endl;
-  fout << "    <run_name_template inst=\"dolly\">d%yyyy%/tdc/root/deltat_tdc_dolly_%rrrr%.root</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"dolly\">d%yyyy%/tdc/mdu/deltat_tdc_dolly_%rrrr%.mdu</run_name_template>" << std::endl;
   fout << "    <!-- Flame/PSI -->" << std::endl;
-  fout << "    <run_name_template inst=\"flame\">d%yyyy%/tdc/root/deltat_tdc_flame_%yyyy%_%rrrr%.bin</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"flame\">d%yyyy%/tdc/root/deltat_tdc_flame_%yyyy%_%rrrr%.root</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"flame\">d%yyyy%/tdc/deltat_tdc_flame_%rrrr%.bin</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"flame\">d%yyyy%/tdc/mdu/deltat_tdc_flame_%yyyy%_%rrrr%.mdu</run_name_template>" << std::endl;
   fout << "    <!-- GPD/PSI -->" << std::endl;
+  fout << "    <run_name_template inst=\"gpd\">d%yyyy%/tdc/root/deltat_tdc_gpd_%yyyy%_%rrrr%.root</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gpd\">d%yyyy%/deltat_mue1_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gpd\">d%yyyy%/deltat_fq_si_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gpd\">d%yyyy%/deltat_strobo_%rrrr%.bin</run_name_template>" << std::endl;
@@ -677,9 +703,11 @@ Bool_t PStartupHandler::WriteDefaultStartupFile()
   fout << "    <run_name_template inst=\"gpd\">d%yyyy%/deltat_janis_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gpd\">d%yyyy%/deltat_janis_gpd_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gpd\">d%yyyy%/deltat_pta_gpd_%rrrr%.bin</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"gpd\">d%yyyy%/pta/deltat_pta_gpd_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gpd\">d%yyyy%/tdc/deltat_tdc_gpd_%rrrr%.bin</run_name_template>" << std::endl;
-  fout << "    <run_name_template inst=\"gpd\">d%yyyy%/tdc/root/deltat_tdc_gpd_%rrrr%.root</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"gpd\">d%yyyy%/tdc/mdu/deltat_tdc_gpd_%rrrr%.mdu</run_name_template>" << std::endl;
   fout << "    <!-- GPS/PSI -->" << std::endl;
+  fout << "    <run_name_template inst=\"gps\">d%yyyy%/tdc/root/deltat_tdc_gps_%yyyy%_%rrrr%.root</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gps\">d%yyyy%/deltat_ccr_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gps\">d%yyyy%/deltat_he3_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gps\">d%yyyy%/deltat_stutt_%rrrr%.bin</run_name_template>" << std::endl;
@@ -690,13 +718,15 @@ Bool_t PStartupHandler::WriteDefaultStartupFile()
   fout << "    <run_name_template inst=\"gps\">d%yyyy%/deltat_oven2_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gps\">d%yyyy%/deltat_pta_gps_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"gps\">d%yyyy%/tdc/deltat_tdc_gps_%rrrr%.bin</run_name_template>" << std::endl;
-  fout << "    <run_name_template inst=\"gps\">d%yyyy%/tdc/root/deltat_tdc_gps_%yyyy%_%rrrr%.root</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"gps\">d%yyyy%/tdc/mdu/deltat_tdc_gps_%yyyy%_%rrrr%.mdu</run_name_template>" << std::endl;
   fout << "    <!-- HAL-9500/PSI == HIFI/PSI -->" << std::endl;
+  fout << "    <run_name_template inst=\"hifi\">d%yyyy%/tdc/root/deltat_tdc_hifi_%yyyy%_%rrrr%.root</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"hifi\">d%yyyy%/tdc/deltat_hifi_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"hifi\">d%yyyy%/tdc/tdc_hifi_%yyyy%_%rrrrr%.mdu</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"hifi\">d%yyyy%/tdc/root/deltat_tdc_hifi_%yyyy%_%rrrr%.mdu</run_name_template>" << std::endl;
   fout << "    <!-- LTF/PSI -->" << std::endl;
   fout << "    <run_name_template inst=\"ltf\">d%yyyy%/deltat_ltf_%rrrr%.bin</run_name_template>" << std::endl;
+  fout << "    <run_name_template inst=\"ltf\">d%yyyy%/deltat_ltf2_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"ltf\">d%yyyy%/deltat_pta_ltf_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"ltf\">d%yyyy%/pta/deltat_pta_ltf_%rrrr%.bin</run_name_template>" << std::endl;
   fout << "    <run_name_template inst=\"ltf\">d%yyyy%/tdc/deltat_tdc_ltf_%rrrr%.bin</run_name_template>" << std::endl;

src/classes/PTheory.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PUserFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/classes/PUserFcnBase.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/dump_header.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -43,6 +43,7 @@
 #include <sstream>
 #include <string>
 #include <vector>
+#include <memory>
 
 #include <boost/algorithm/string.hpp>
 
@@ -99,7 +100,7 @@ void dump_header_syntax()
   std::cout << std::endl << "       -s, --summary : this option is used for LE-uSR data sets only. It will, additionally";
   std::cout << std::endl << "                     to the header information, print the summary file content.";
   std::cout << std::endl << "       -i, --instrument <inst> : where <inst> is the requested instrument:";
-  std::cout << std::endl << "                     lem (default) | gps | ltf | dolly | gpd | hifi.";
+  std::cout << std::endl << "                     lem (default) | gps | ltf | dolly | gpd | hifi | flame.";
   std::cout << std::endl << "       -c, --counts  : will show detector counts as well.";
   std::cout << std::endl << "       -h, --help    : will show this help";
   std::cout << std::endl << "       -v, --version : will show the current version.";
@@ -145,12 +146,16 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
     fileType = DH_LEM_ROOT;
   }
 
+  std::unique_ptr<TMusrRunHeader> header;
+  bool ok;
+  Int_t ival;
+
   if (fileType == DH_LEM_ROOT) { // ROOT (LEM)
     // read header and check if some missing run info need to be fed
-    TLemRunHeader *runHeader = dynamic_cast<TLemRunHeader*>(folder->FindObjectAny("TLemRunHeader"));
+    TLemRunHeader* runHeader = dynamic_cast<TLemRunHeader*>(folder->FindObjectAny("TLemRunHeader"));
 
     // check if run header is valid
-    if (!runHeader) {
+    if (runHeader == nullptr) {
       std::cerr << std::endl << "**ERROR** Couldn't obtain run header info from ROOT file " << fileName << std::endl;
       f.Close();
       return 1;
@@ -193,17 +198,9 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
     std::cout << std::endl << "First Good Bin     : " << timeZero[0];
     std::cout << std::endl << "Last Good Bin      : " << runHeader->GetNChannels()-1;
     std::cout << std::endl << "-------------------" << std::endl << std::endl;
-
-    delete runHeader;
   } else { // MusrRoot
     // invoke the MusrRoot header object
-    TMusrRunHeader *header = new TMusrRunHeader(fileName.c_str(), true); // read quite
-    if (header == 0) {
-      std::cerr << std::endl << "**ERROR** Couldn't invoke MusrRoot RunHeader in file:" << fileName;
-      std::cerr << std::endl;
-      f.Close();
-      return 1;
-    }
+    header = std::make_unique<TMusrRunHeader>(fileName.c_str(), true); // read quite
 
     // try to populate the MusrRoot header object
     if (!header->ExtractAll(folder)) {
@@ -216,8 +213,6 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
     header->DumpHeader();
 
     if (counts) {
-      bool ok;
-      Int_t ival;
       PIntVector ivec;
       header->Get("RunInfo/No of Histos", ival, ok);
       if (ok)
@@ -226,8 +221,6 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
       if (ok)
         redGreenOffset = ivec;
     }
-
-    delete header;
   }
 
   // summary as well?
@@ -248,33 +241,54 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
       tstr = static_cast<TObjString*>(runSum->At(i));
       str = tstr->String();
       std::cout << str;
+      if (!str.Contains("\r") && !str.Contains("\n"))
+        std::cout << std::endl;
     }
   }
 
   // detector counts as well?
   if (counts && (fileType == DH_MUSR_ROOT)) {
     // dump the detector counts
-    std::cout << "Detector counts" << std::endl;
+    std::cout << "Detector counts (all, between fgb and lgb)" << std::endl;
     f.GetObject("histos", folder);
-    if (folder != nullptr) {
+    if ((folder != nullptr) && (header != nullptr)) {
       char detectorLabel[64];
       TH1F *histo{nullptr};
-      UInt_t total{0};
+      UInt_t total{0}, total_good{0}, ta, tg;
+      Int_t fgb, lgb;
       for (UInt_t i=0; i<redGreenOffset.size(); i++) {
         std::cout << "  Group " << i+1 << " (Offset=" << redGreenOffset[i] << ") : " << std::endl;
         total = 0;
+        total_good = 0;
         for (UInt_t j=0; j<noOfHistos; j++) {
+          // get fgb, lgb
+          fgb = -1;
+          snprintf(detectorLabel, sizeof(detectorLabel), "DetectorInfo/Detector%03d/First Good Bin", redGreenOffset[i]+j+1);
+          header->Get(detectorLabel, ival, ok);
+          if (ok) {
+            fgb = ival;
+          }
+          lgb = -1;
+          snprintf(detectorLabel, sizeof(detectorLabel), "DetectorInfo/Detector%03d/Last Good Bin", redGreenOffset[i]+j+1);
+          header->Get(detectorLabel, ival, ok);
+          if (ok) {
+            lgb = ival;
+          }
+          // get histo info
           snprintf(detectorLabel, sizeof(detectorLabel), "hDecay%03d", redGreenOffset[i]+j+1);
           histo = (TH1F*) folder->FindObjectAny(detectorLabel);
           if (histo != nullptr) {
-            std::cout << "    " << histo->GetTitle() << ":\t " << histo->GetEntries() << std::endl;
-            total += histo->GetEntries();
+            ta = histo->Integral(0, histo->GetNbinsX()+1);
+            tg = histo->Integral(fgb, lgb);
+            std::cout << "    " << histo->GetTitle() << ":\t " << ta << ", " << tg << std::endl;
+            total += ta;
+            total_good += tg;
           }
         }
         if (i % 2 == 0)
-          std::cout << "    total counts of group " << i+1 << ":\t\t\t " << total << std::endl;
+          std::cout << "    total counts of group " << i+1 << ":\t\t\t " << total << ", " << total_good << std::endl;
         else
-          std::cout << "    total counts of group " << i+1 << ":\t\t\t\t\t " << total << std::endl;
+          std::cout << "    total counts of group " << i+1 << ":\t\t\t\t\t " << total << ", " << total_good << std::endl;
       }
     } else {
       std::cout << "Sorry, no histos folder found" << std::endl;
@@ -293,32 +307,23 @@ int dump_header_root(const std::string fileName, const bool summary, const bool
  * <p>dumps the header information of a NeXus file.
  *
  * @param fileName file name of the NeXus file.
+ * @param counts bool, if true dump detector counts
  *
  * @return  0 on success, 1 otherwise
  */
-int dump_header_nexus(const std::string fileName) {
+int dump_header_nexus(const std::string fileName, const bool counts) {
 
 #ifdef PNEXUS_ENABLED
-  PNeXus *nxs_file = new PNeXus(fileName.c_str());
-
-  if (nxs_file == nullptr) {
-    std::cerr << std::endl;
-    std::cerr << "**ERROR** couldn't invoke NeXus file object." << std::endl;
-    std::cerr << std::endl;
-    return 1;
-  }
+  std::unique_ptr<PNeXus> nxs_file = std::make_unique<PNeXus>(fileName.c_str());
 
   if (nxs_file->IsValid(false)) {
-    nxs_file->Dump();
+    nxs_file->Dump(counts);
   } else {
     std::cerr << std::endl;
     std::cerr << "**ERROR** found invalid NeXus file." << std::endl;
     std::cerr << std::endl;
     return 1;
   }
-
-  if (nxs_file)
-    delete nxs_file;
 #else
   std::cout << std::endl << "NeXus not enabled, hence the header information cannot be dumped." << std::endl << std::endl;
 #endif
@@ -395,10 +400,11 @@ std::vector<std::string> dump_header_instrument_info(std::string fileName)
  *
  * @param fileName file name of the PSI-BIN
  * @param fileFormat either PSI-BIN or PSI-MDU
+ * @param counts bool, if true dump detector counts
  *
  * @return 0 on success, 1 otherwise
  */
-int dump_header_psi_bin(const std::string fileName, const std::string fileFormat)
+int dump_header_psi_bin(const std::string fileName, const std::string fileFormat, const bool counts)
 {
   MuSR_td_PSI_bin psiBin;
   int status;
@@ -490,7 +496,8 @@ int dump_header_psi_bin(const std::string fileName, const std::string fileFormat
     std::cout << std::endl << "Time Zero Bin      : " << psiBin.GetT0Int(i);
     std::cout << std::endl << "First Good Bin     : " << psiBin.GetFirstGoodInt(i);
     std::cout << std::endl << "Last Good Bin      : " << psiBin.GetLastGoodInt(i);
-    std::cout << std::endl << "No of Events       : " << psiBin.GetEventsHistoLong(i);
+    if (counts)
+      std::cout << std::endl << "No of Events       : " << psiBin.GetEventsHistoLong(i);
   }
   std::cout << std::endl << "-------------------" << std::endl << std::endl;
 
@@ -501,10 +508,11 @@ int dump_header_psi_bin(const std::string fileName, const std::string fileFormat
 /**
  * <p>dump the header information of a MUD file.
  * @param fileName file name of the MUD file
+ * @param counts bool, if true dump detector counts
  *
  * @return 0 on success, 1 otherwise
  */
-int dump_header_mud(const std::string fileName)
+int dump_header_mud(const std::string fileName, const bool counts)
 {
   int    fh;
   UINT32 type, val;
@@ -669,6 +677,12 @@ int dump_header_mud(const std::string fileName)
       std::cout << std::endl << "Last Good Bin  : " << val;
     else
       std::cout << std::endl << "Last Good Bin  : ???";
+    if (counts) {
+      success = MUD_getHistNumEvents( fh, i+1, &val );
+      if (success) {
+        std::cout << std::endl << "#Events        : " << val;
+      }
+    }
   }
 
   std::cout << std::endl << "-------------------" << std::endl << std::endl;
@@ -873,7 +887,8 @@ int main(int argc, char *argv[])
         return 1;
       }
       if (strcmp(argv[i+1], "lem") && strcmp(argv[i+1], "gps") && strcmp(argv[i+1], "ltf") &&
-          strcmp(argv[i+1], "dolly") && strcmp(argv[i+1], "gpd") && strcmp(argv[i+1], "hifi")) {
+          strcmp(argv[i+1], "dolly") && strcmp(argv[i+1], "gpd") && strcmp(argv[i+1], "hifi") &&
+          strcmp(argv[i+1], "flame")) {
         std::cerr << std::endl << "**ERROR** found --instrument with unkown instrument name: '" << argv[i+1] << "'!" << std::endl;
         dump_header_syntax();
         return 1;
@@ -902,40 +917,22 @@ int main(int argc, char *argv[])
   // 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();
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<PStartupHandler> startupHandler = std::make_unique<PStartupHandler>();
   if (!startupHandler->StartupFileFound()) {
     std::cerr << std::endl << ">> musrfit **WARNING** couldn't find " << startupHandler->GetStartupFilePath().Data();
     std::cerr << std::endl;
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = nullptr;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = nullptr;
-    }
   } else {
     strcpy(startup_path_name, startupHandler->GetStartupFilePath().Data());
-    saxParser->ConnectToHandler("PStartupHandler", startupHandler);
+    saxParser->ConnectToHandler("PStartupHandler", startupHandler.get());
     //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);
+    int status = parseXmlFile(saxParser.get(), startup_path_name);
     // check for parse errors
     if (status) { // error
       std::cerr << std::endl << ">> musrfit **WARNING** Reading/parsing musrfit_startup.xml failed.";
       std::cerr << std::endl;
-      // clean up
-      if (saxParser) {
-        delete saxParser;
-        saxParser = nullptr;
-      }
-      if (startupHandler) {
-        delete startupHandler;
-        startupHandler = nullptr;
-      }
     }
   }
 
@@ -944,7 +941,8 @@ int main(int argc, char *argv[])
   if (fileName == "") { // only look for runs if the file name is not explicitly given
     int yy = static_cast<int>(strtod(year.c_str(), static_cast<char**>(nullptr)));
     int run = static_cast<int>(strtod(runNo.c_str(), static_cast<char**>(nullptr)));
-    PFindRun findRun(startupHandler->GetDataPathList(), startupHandler->GetRunNameTemplateList(), instrument, yy, run);
+    PFindRun findRun(startupHandler->GetDataPathList(), startupHandler->GetRunNameTemplateList(),
+                     instrument, yy, run, fileFormat);
     if (findRun.FoundPathName()) {
       pathFln = findRun.GetPathName().Data();
     } else {
@@ -986,27 +984,17 @@ int main(int argc, char *argv[])
     dump_header_root(pathFln, summary, counts);
   } else if (boost::iequals(fileFormat, "NeXus")) {
 #ifdef PNEXUS_ENABLED
-    dump_header_nexus(pathFln);
+    dump_header_nexus(pathFln, counts);
 #else
     std::cout << std::endl << "Sorry, NeXus is not enabled, hence I cannot help you." << std::endl;
 #endif
   } else if (boost::iequals(fileFormat, "PSI-BIN") || boost::iequals(fileFormat, "PSI-MDU")) {
-    dump_header_psi_bin(pathFln, fileFormat);
+    dump_header_psi_bin(pathFln, fileFormat, counts);
   } else if (boost::iequals(fileFormat, "MUD")) {
-    dump_header_mud(pathFln);
+    dump_header_mud(pathFln, counts);
   } else if (boost::iequals(fileFormat, "WKM")) {
     dump_header_wkm(pathFln);
   }
 
-  // cleanup
-  if (saxParser) {
-    delete saxParser;
-    saxParser = nullptr;
-  }
-  if (startupHandler) {
-    delete startupHandler;
-    startupHandler = nullptr;
-  }
-
   return 0;
 }

src/external/BMWtools/BMWIntegrator.h

@@ -35,6 +35,7 @@
 
 #include <cmath>
 #include <vector>
+#include <memory>
 
 //-----------------------------------------------------------------------------
 /**
@@ -88,10 +89,8 @@ inline double T2Integrator::IntegrateFunc(double x1, double x2, const std::vecto
   ptrPair.first = (this);
   ptrPair.second = &par;
 
-  ROOT::Math::GSLIntegrator *integrator = new ROOT::Math::GSLIntegrator(ROOT::Math::Integration::kADAPTIVE,ROOT::Math::Integration::kGAUSS31);
+  std::unique_ptr<ROOT::Math::GSLIntegrator> integrator = std::make_unique<ROOT::Math::GSLIntegrator>(ROOT::Math::Integration::kADAPTIVE,ROOT::Math::Integration::kGAUSS31);
   double value(integrator->Integral(&T2Integrator::FuncAtXgsl, static_cast<void*>(&ptrPair), x1, x2));
-  delete integrator;
-  integrator = nullptr;
 
   return value;
 }
@@ -115,7 +114,7 @@ class TIntegrator {
 
   private:
     static double FuncAtXgsl(double, void *);
-    ROOT::Math::GSLIntegrator *fIntegrator; ///< pointer to the GSL integrator
+    std::unique_ptr<ROOT::Math::GSLIntegrator> fIntegrator; ///< pointer to the GSL integrator
     mutable double (*fFunc)(double, void *); ///< pointer to the integrand function
 };
 
@@ -125,7 +124,7 @@ class TIntegrator {
  *    Allocation of memory for an integration using the adaptive 31 point Gauss-Kronrod rule
  */
 inline TIntegrator::TIntegrator() : fFunc(0) {
-  fIntegrator = new ROOT::Math::GSLIntegrator(ROOT::Math::Integration::kADAPTIVE,ROOT::Math::Integration::kGAUSS31);
+  fIntegrator = std::make_unique<ROOT::Math::GSLIntegrator>(ROOT::Math::Integration::kADAPTIVE,ROOT::Math::Integration::kGAUSS31);
 }
 
 //-----------------------------------------------------------------------------
@@ -135,8 +134,6 @@ inline TIntegrator::TIntegrator() : fFunc(0) {
  */
 inline TIntegrator::~TIntegrator(){
   fPar.clear();
-  delete fIntegrator;
-  fIntegrator=nullptr;
   fFunc=0;
 }
 
@@ -190,7 +187,7 @@ class TMCIntegrator {
 
   private:
     static double FuncAtXgsl(double *, size_t, void *);
-    ROOT::Math::GSLMCIntegrator *fMCIntegrator; ///< pointer to the GSL integrator
+    std::unique_ptr<ROOT::Math::GSLMCIntegrator> fMCIntegrator; ///< pointer to the GSL integrator
     mutable double (*fFunc)(double *, size_t, void *); ///< pointer to the integrand function
 };
 
@@ -200,7 +197,7 @@ class TMCIntegrator {
  *    Allocation of memory for an integration using the MISER algorithm of Press and Farrar
  */
 inline TMCIntegrator::TMCIntegrator() : fFunc(0) {
-  fMCIntegrator = new ROOT::Math::GSLMCIntegrator(ROOT::Math::MCIntegration::kMISER, 1.E-6, 1.E-4, 500000);
+  fMCIntegrator = std::make_unique<ROOT::Math::GSLMCIntegrator>(ROOT::Math::MCIntegration::kMISER, 1.E-6, 1.E-4, 500000);
 }
 
 //-----------------------------------------------------------------------------
@@ -210,8 +207,6 @@ inline TMCIntegrator::TMCIntegrator() : fFunc(0) {
  */
 inline TMCIntegrator::~TMCIntegrator(){
   fPar.clear();
-  delete fMCIntegrator;
-  fMCIntegrator=nullptr;
   fFunc=0;
 }
 

src/external/BMWtools/BMWStartupHandler.cpp

@@ -11,7 +11,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter, Bastian M. Wojek            *
+ *   Copyright (C) 2007-2024 by Andreas Suter, Bastian M. Wojek            *
  *                                                                         *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/BMWtools/BMWStartupHandler.h

@@ -11,7 +11,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter, Bastian M. Wojek            *
+ *   Copyright (C) 2007-2024 by Andreas Suter, Bastian M. Wojek            *
  *                                                                         *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/BMWtools/TTrimSPDataHandler.cpp

@@ -33,37 +33,33 @@
 #include <cmath>
 #include <cassert>
 #include <algorithm>
-
-using namespace std;
+#include <memory>
 
 //--------------------
 // Constructor of the TrimSPData class -- reading all available trim.SP-rge-files with a given name into std::vectors
 //--------------------
 
-TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool debug, unsigned int highRes) {
+TTrimSPData::TTrimSPData(const std::string &path, std::map<double, std::string> &energies, bool debug, unsigned int highRes) {
 
   // sort the energies in ascending order - this might be useful for later applications (energy-interpolations etc.)
   // after the change from the vector to the map this is not necessary any more - since maps are always ordered!
   // sort(energies.begin(), energies.end());
 
   double zz(0.0), nzz(0.0);
-  vector<double> vzz, vnzz;
-  string word, energyStr;
+  std::vector<double> vzz, vnzz;
+  std::string word, energyStr;
   bool goodFile(false);
 
-  for ( map<double, string>::const_iterator iter(energies.begin()); iter != energies.end(); ++iter ) {
+  for ( std::map<double, std::string>::const_iterator iter(energies.begin()); iter != energies.end(); ++iter ) {
 
     energyStr = path + iter->second + ".rge";
 
-    ifstream *rgeFile = new ifstream(energyStr.c_str());
-    if(! *rgeFile) {
-      cerr << "TTrimSPData::TTrimSPData: file " << energyStr << " not found! Try next energy..." << endl;
-      delete rgeFile;
-      rgeFile = 0;
+    std::unique_ptr<std::ifstream> rgeFile = std::make_unique<std::ifstream>(energyStr.c_str());
+    if (rgeFile == nullptr) {
+      std::cerr << "TTrimSPData::TTrimSPData: file " << energyStr << " not found! Try next energy..." << std::endl;
     } else {
-
-      while(*rgeFile >> word) {
-        if(word == "PARTICLES") {
+      while (*rgeFile >> word) {
+        if (word == "PARTICLES") {
           goodFile = true;
           break;
         }
@@ -73,7 +69,7 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool
 
         fEnergy.push_back(iter->first);
 
-        while(!rgeFile->eof()) {
+        while (!rgeFile->eof()) {
           *rgeFile >> zz >> nzz;
           vzz.push_back(zz);
           vnzz.push_back(nzz);
@@ -92,8 +88,6 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool
 
 
         rgeFile->close();
-        delete rgeFile;
-        rgeFile = 0;
 
         vzz.clear();
         vnzz.clear();
@@ -106,14 +100,14 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool
         }
 
       } else {
-        cerr << "TTrimSPData::TTrimSPData: " << energyStr << " does not seem to be a valid unmodified TRIM.SP output file!" << endl;
+        std::cerr << "TTrimSPData::TTrimSPData: " << energyStr << " does not seem to be a valid unmodified TRIM.SP output file!" << std::endl;
         continue;
       }
     }
   }
 
   if (debug)
-    cout << "TTrimSPData::TTrimSPData: Read in " << fDataNZ.size() << " implantation profiles in total." << endl;
+    std::cout << "TTrimSPData::TTrimSPData: Read in " << fDataNZ.size() << " implantation profiles in total." << std::endl;
 
   fOrigDataNZ = fDataNZ;
 
@@ -126,8 +120,8 @@ TTrimSPData::TTrimSPData(const string &path, map<double, string> &energies, bool
 // If it is not found the energy iterator will point to the end() of the energy vector.
 
 void TTrimSPData::FindEnergy(double e) const {
-  for(fEnergyIter = fEnergy.begin(); fEnergyIter != fEnergy.end(); ++fEnergyIter) {
-    if(fabs(*fEnergyIter - e) < 0.05)
+  for (fEnergyIter = fEnergy.begin(); fEnergyIter != fEnergy.end(); ++fEnergyIter) {
+    if (fabs(*fEnergyIter - e) < 0.05)
       return;
   }
   return;
@@ -137,11 +131,11 @@ void TTrimSPData::UseHighResolution(double e) {
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
-    vector<double> vecZ;
-    vector<double> vecNZ;
-    for(double zz(1.); zz<2100.; zz+=1.) {
+    std::vector<double> vecZ;
+    std::vector<double> vecNZ;
+    for (double zz(1.); zz<2100.; zz+=1.) {
       vecZ.push_back(zz);
       vecNZ.push_back(GetNofZ(zz/10.0, e));
     }
@@ -153,7 +147,7 @@ void TTrimSPData::UseHighResolution(double e) {
     return;
   }
 
-  cout << "TTrimSPData::DataZ: No implantation profile available for the specified energy... Nothing happens." << endl;
+  std::cout << "TTrimSPData::DataZ: No implantation profile available for the specified energy... Nothing happens." << std::endl;
   return;
 }
 
@@ -161,16 +155,16 @@ void TTrimSPData::UseHighResolution(double e) {
 // Method returning z-vector calculated by trim.SP for given energy[keV]
 //---------------------
 
-vector<double> TTrimSPData::DataZ(double e) const {
+std::vector<double> TTrimSPData::DataZ(double e) const {
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     return fDataZ[i];
   }
   // default
-  cout << "TTrimSPData::DataZ: No implantation profile available for the specified energy... You get back the first one." << endl;
+  std::cout << "TTrimSPData::DataZ: No implantation profile available for the specified energy... You get back the first one." << std::endl;
   return fDataZ[0];
 }
 
@@ -179,50 +173,50 @@ vector<double> TTrimSPData::DataZ(double e) const {
 // potentially altered by the WeightLayers- or the Normalize-method for given energy[keV]
 //---------------------
 
-vector<double> TTrimSPData::DataNZ(double e) const {
+std::vector<double> TTrimSPData::DataNZ(double e) const {
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     return fDataNZ[i];
   }
   // default
-  cout << "TTrimSPData::DataNZ: No implantation profile available for the specified energy... You get back the first one." << endl;
-  return fDataNZ[0];
+  std::cout << "TTrimSPData::DataNZ: No implantation profile available for the specified energy... You get back the first one." << std::endl;
 
+  return fDataNZ[0];
 }
 
 //---------------------
 // Method returning original n(z)-vector calculated by trim.SP for given energy[keV]
 //---------------------
 
-vector<double> TTrimSPData::OrigDataNZ(double e) const {
+std::vector<double> TTrimSPData::OrigDataNZ(double e) const {
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     return fOrigDataNZ[i];
   }
   // default
-  cout << "TTrimSPData::OrigDataNZ: No implantation profile available for the specified energy... You get back the first one." << endl;
-  return fOrigDataNZ[0];
+  std::cout << "TTrimSPData::OrigDataNZ: No implantation profile available for the specified energy... You get back the first one." << std::endl;
 
+  return fOrigDataNZ[0];
 }
 
 double TTrimSPData::DataDZ(double e) const {
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     return fDZ[i];
   }
   // default
-  cout << "TTrimSPData::DataDZ: No implantation profile available for the specified energy... The resolution will be zero!" << endl;
-  return 0.0;
+  std::cout << "TTrimSPData::DataDZ: No implantation profile available for the specified energy... The resolution will be zero!" << std::endl;
 
+  return 0.0;
 }
 
 //---------------------
@@ -230,10 +224,10 @@ double TTrimSPData::DataDZ(double e) const {
 // Parameters: Energy[keV], LayerNumber[1], Interfaces[nm]
 //---------------------
 
-double TTrimSPData::LayerFraction(double e, unsigned int layno, const vector<double>& interface) const {
+double TTrimSPData::LayerFraction(double e, unsigned int layno, const std::vector<double>& interface) const {
 
-  if(layno < 1 && layno > (interface.size()+1)) {
-    cout << "TTrimSPData::LayerFraction: No such layer available according to your specified interfaces... Returning 0.0!" << endl;
+  if (layno < 1 && layno > (interface.size()+1)) {
+    std::cout << "TTrimSPData::LayerFraction: No such layer available according to your specified interfaces... Returning 0.0!" << std::endl;
     return 0.0;
   }
 
@@ -244,21 +238,21 @@ double TTrimSPData::LayerFraction(double e, unsigned int layno, const vector<dou
     // Because we do not know if the implantation profile is normalized or not, do not care about this and calculate the fraction from the beginning
     // Total "number of muons"
     double totalNumber(0.0);
-    for(unsigned int j(0); j<fDataZ[i].size(); j++)
+    for (unsigned int j(0); j<fDataZ[i].size(); j++)
       totalNumber += fDataNZ[i][j];
     // "number of muons" in layer layno
     double layerNumber(0.0);
-    if(!(layno-1)){
-      for(unsigned int j(0); j<fDataZ[i].size(); j++)
-        if(fDataZ[i][j] < interface[0]*10.0)
+    if (!(layno-1)){
+      for (unsigned int j(0); j<fDataZ[i].size(); j++)
+        if (fDataZ[i][j] < interface[0]*10.0)
           layerNumber += fDataNZ[i][j];
-    } else if(!(layno-interface.size()-1)){
-      for(unsigned int j(0); j<fDataZ[i].size(); j++)
-        if(fDataZ[i][j] >= *(interface.end()-1)*10.0)
+    } else if (!(layno-interface.size()-1)) {
+      for (unsigned int j(0); j<fDataZ[i].size(); j++)
+        if (fDataZ[i][j] >= *(interface.end()-1)*10.0)
           layerNumber += fDataNZ[i][j];
     } else {
-      for(unsigned int j(0); j<fDataZ[i].size(); j++)
-        if(fDataZ[i][j] >= interface[layno-2]*10.0 && fDataZ[i][j] < interface[layno-1]*10.0)
+      for (unsigned int j(0); j<fDataZ[i].size(); j++)
+        if (fDataZ[i][j] >= interface[layno-2]*10.0 && fDataZ[i][j] < interface[layno-1]*10.0)
           layerNumber += fDataNZ[i][j];
     }
     // fraction of muons in layer layno
@@ -267,9 +261,9 @@ double TTrimSPData::LayerFraction(double e, unsigned int layno, const vector<dou
   }
 
   // default
-  cout << "TTrimSPData::LayerFraction: No implantation profile available for the specified energy " << e << " keV... Returning 0.0" << endl;
-  return 0.0;
+  std::cout << "TTrimSPData::LayerFraction: No implantation profile available for the specified energy " << e << " keV... Returning 0.0" << std::endl;
 
+  return 0.0;
 }
 
 //---------------------
@@ -280,30 +274,30 @@ double TTrimSPData::LayerFraction(double e, unsigned int layno, const vector<dou
 //          the first and last layers get the full n(z), where only one third of the muons in the second layer will be taken into account
 //---------------------
 
-void TTrimSPData::WeightLayers(double e, const vector<double>& interface, const vector<double>& weight) const {
+void TTrimSPData::WeightLayers(double e, const std::vector<double>& interface, const std::vector<double>& weight) const {
 
-  if(weight.size()-interface.size()-1) {
-    cout << "TTrimSPData::WeightLayers: For the weighting the number of interfaces has to be one less than the number of weights!" << endl;
-    cout << "TTrimSPData::WeightLayers: No weighting of the implantation profile will be done unless you take care of that!" << endl;
+  if (weight.size()-interface.size()-1) {
+    std::cout << "TTrimSPData::WeightLayers: For the weighting the number of interfaces has to be one less than the number of weights!" << std::endl;
+    std::cout << "TTrimSPData::WeightLayers: No weighting of the implantation profile will be done unless you take care of that!" << std::endl;
     return;
   }
 
-  for(unsigned int i(0); i<interface.size(); i++) {
+  for (unsigned int i(0); i<interface.size(); i++) {
     if (interface[i]<0.0) {
-      cout << "TTrimSPData::WeightLayers: One of your layer interfaces has a negative coordinate! - No weighting will be done!" << endl;
+      std::cout << "TTrimSPData::WeightLayers: One of your layer interfaces has a negative coordinate! - No weighting will be done!" << std::endl;
       return;
     }
     else if (i>1) {
       if (interface[i]<interface[i-1]) {
-        cout << "TTrimSPData::WeightLayers: The specified interfaces appear to be not in ascending order! - No weighting will be done!" << endl;
+        std::cout << "TTrimSPData::WeightLayers: The specified interfaces appear to be not in ascending order! - No weighting will be done!" << std::endl;
         return;
       }
     }
   }
 
-  for(unsigned int i(0); i<weight.size(); i++) {
+  for (unsigned int i(0); i<weight.size(); i++) {
     if (weight[i]>1.0 || weight[i]<0.0) {
-      cout << "TTrimSPData::WeightLayers: At least one of the specified weights is out of range - no weighting will be done!" << endl;
+      std::cout << "TTrimSPData::WeightLayers: At least one of the specified weights is out of range - no weighting will be done!" << std::endl;
       return;
     }
   }
@@ -311,11 +305,11 @@ void TTrimSPData::WeightLayers(double e, const vector<double>& interface, const
   FindEnergy(e);
 
   // If all weights are equal to one, use the original n(z) vector
-  for(unsigned int i(0); i<weight.size(); i++) {
-    if(weight[i]-1.0)
+  for (unsigned int i(0); i<weight.size(); i++) {
+    if (weight[i]-1.0)
       break;
-    if(i == weight.size() - 1) {
-      if(fEnergyIter != fEnergy.end()) {
+    if (i == weight.size() - 1) {
+      if (fEnergyIter != fEnergy.end()) {
         unsigned int j(fEnergyIter - fEnergy.begin());
         fDataNZ[j] = fOrigDataNZ[j];
         fIsNormalized[j] = false;
@@ -324,12 +318,12 @@ void TTrimSPData::WeightLayers(double e, const vector<double>& interface, const
     }
   }
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     unsigned int k(0);
-    for(unsigned int j(0); j<fDataZ[i].size(); j++) {
-      if(k<interface.size()) {
-        if(fDataZ[i][j] < interface[k]*10.0)
+    for (unsigned int j(0); j<fDataZ[i].size(); j++) {
+      if (k<interface.size()) {
+        if (fDataZ[i][j] < interface[k]*10.0)
           fDataNZ[i][j] = fOrigDataNZ[i][j]*weight[k];
         else {
           k++;
@@ -339,11 +333,11 @@ void TTrimSPData::WeightLayers(double e, const vector<double>& interface, const
       else
         fDataNZ[i][j] = fOrigDataNZ[i][j]*weight[k];
     }
-  fIsNormalized[i] = false;
-  return;
+    fIsNormalized[i] = false;
+    return;
   }
 
-  cout << "TTrimSPData::WeightLayers: No implantation profile available for the specified energy... No weighting done." << endl;
+  std::cout << "TTrimSPData::WeightLayers: No implantation profile available for the specified energy... No weighting done." << std::endl;
   return;
 }
 
@@ -353,20 +347,20 @@ void TTrimSPData::WeightLayers(double e, const vector<double>& interface, const
 
 double TTrimSPData::GetNofZ(double zz, double e) const {
 
-  vector<double> z, nz;
+  std::vector<double> z, nz;
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     z = fDataZ[i];
     nz = fDataNZ[i];
   } else {
-      cout << "TTrimSPData::GetNofZ: No implantation profile available for the specified energy " << e << " keV... Quitting!" << endl;
+      std::cout << "TTrimSPData::GetNofZ: No implantation profile available for the specified energy " << e << " keV... Quitting!" << std::endl;
       exit(-1);
   }
 
-  if(zz < 0)
+  if (zz < 0)
     return 0.0;
 
   bool found = false;
@@ -395,7 +389,7 @@ void TTrimSPData::Normalize(double e) const {
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     double nZsum = 0.0;
     for (unsigned int j(0); j<fDataZ[i].size(); j++)
@@ -408,9 +402,9 @@ void TTrimSPData::Normalize(double e) const {
     return;
   }
   // default
-  cout << "TTrimSPData::Normalize: No implantation profile available for the specified energy... No normalization done." << endl;
-  return;
+  std::cout << "TTrimSPData::Normalize: No implantation profile available for the specified energy... No normalization done." << std::endl;
 
+  return;
 }
 
 //---------------------
@@ -420,12 +414,12 @@ void TTrimSPData::Normalize(double e) const {
 bool TTrimSPData::IsNormalized(double e) const {
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     return fIsNormalized[i];
   }
 
-  cout << "TTrimSPData::IsNormalized: No implantation profile available for the specified energy... Returning false! Check your code!" << endl;
+  std::cout << "TTrimSPData::IsNormalized: No implantation profile available for the specified energy... Returning false! Check your code!" << std::endl;
   return false;
 }
 
@@ -436,19 +430,19 @@ bool TTrimSPData::IsNormalized(double e) const {
 double TTrimSPData::MeanRange(double e) const {
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     if (!fIsNormalized[i])
       Normalize(e);
     double mean(0.0);
-    for(unsigned int j(0); j<fDataNZ[i].size(); j++){
+    for (unsigned int j(0); j<fDataNZ[i].size(); j++){
       mean += fDataNZ[i][j]*fDataZ[i][j];
     }
     mean *= fDZ[i]/10.0;
     return mean;
   }
 
-  cout << "TTrimSPData::MeanRange: No implantation profile available for the specified energy... Returning -1! Check your code!" << endl;
+  std::cout << "TTrimSPData::MeanRange: No implantation profile available for the specified energy... Returning -1! Check your code!" << std::endl;
   return -1.;
 }
 
@@ -460,21 +454,21 @@ double TTrimSPData::PeakRange(double e) const {
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
 
-    vector<double>::const_iterator nziter;
+    std::vector<double>::const_iterator nziter;
     nziter = max_element(fDataNZ[i].begin(),fDataNZ[i].end());
 
-    if(nziter != fDataNZ[i].end()){
+    if (nziter != fDataNZ[i].end()){
       unsigned int j(nziter - fDataNZ[i].begin());
       return fDataZ[i][j]/10.0;
     }
-    cout << "TTrimSPData::PeakRange: No maximum found in the implantation profile... Returning -1! Please check the profile!" << endl;
+    std::cout << "TTrimSPData::PeakRange: No maximum found in the implantation profile... Returning -1! Please check the profile!" << std::endl;
     return -1.;
   }
 
-  cout << "TTrimSPData::PeakRange: No implantation profile available for the specified energy... Returning -1! Check your code!" << endl;
+  std::cout << "TTrimSPData::PeakRange: No implantation profile available for the specified energy... Returning -1! Check your code!" << std::endl;
   return -1.;
 }
 
@@ -484,26 +478,26 @@ double TTrimSPData::PeakRange(double e) const {
 //---------------------
 
 void TTrimSPData::ConvolveGss(double w, double e) const {
-  if(!w)
+  if (!w)
     return;
 
-  vector<double> z, nz, gss;
+  std::vector<double> z, nz, gss;
   double nn;
 
   FindEnergy(e);
 
-  if(fEnergyIter != fEnergy.end()) {
+  if (fEnergyIter != fEnergy.end()) {
     unsigned int i(fEnergyIter - fEnergy.begin());
     z = fDataZ[i];
     nz = fDataNZ[i];
 
-    for(unsigned int k(0); k<z.size(); k++) {
+    for (unsigned int k(0); k<z.size(); k++) {
       gss.push_back(exp(-z[k]*z[k]/200.0/w/w));
     }
 
-    for(unsigned int k(0); k<nz.size(); k++) {
+    for (unsigned int k(0); k<nz.size(); k++) {
       nn = 0.0;
-      for(unsigned int j(0); j<nz.size(); j++) {
+      for (unsigned int j(0); j<nz.size(); j++) {
         nn += nz[j]*gss[abs(int(k)-int(j))];
       }
       fDataNZ[i][k] = nn;
@@ -514,6 +508,6 @@ void TTrimSPData::ConvolveGss(double w, double e) const {
     return;
   }
 
-  cout << "TTrimSPData::ConvolveGss: No implantation profile available for the specified energy... No convolution done!" << endl;
+  std::cout << "TTrimSPData::ConvolveGss: No implantation profile available for the specified energy... No convolution done!" << std::endl;
   return;
 }

src/external/BMWtools/TTrimSPDataHandler.h

@@ -32,7 +32,6 @@
 #include <vector>
 #include <string>
 #include <map>
-using namespace std;
 
 /**
  * <p>Class used to handle a set of low energy muon implantation profiles
@@ -41,7 +40,7 @@ class TTrimSPData {
 
 public:
 
-  TTrimSPData(const string&, map<double, string>&, bool debug = false, unsigned int highRes = 0);
+  TTrimSPData(const std::string&, std::map<double, std::string>&, bool debug = false, unsigned int highRes = 0);
 
   ~TTrimSPData() {
     fDataZ.clear();
@@ -52,15 +51,15 @@ public:
     fIsNormalized.clear();
   }
 
-  vector<double> Energy() const {return fEnergy;}
-  vector<double> DataZ(double) const;
-  vector<double> DataNZ(double) const;
-  vector<double> OrigDataNZ(double) const;
+  std::vector<double> Energy() const {return fEnergy;}
+  std::vector<double> DataZ(double) const;
+  std::vector<double> DataNZ(double) const;
+  std::vector<double> OrigDataNZ(double) const;
   double DataDZ(double) const;
   void UseHighResolution(double);
   void SetOriginal() {fOrigDataNZ = fDataNZ;}
-  void WeightLayers(double, const vector<double>&, const vector<double>&) const;
-  double LayerFraction(double, unsigned int, const vector<double>&) const;
+  void WeightLayers(double, const std::vector<double>&, const std::vector<double>&) const;
+  double LayerFraction(double, unsigned int, const std::vector<double>&) const;
   double GetNofZ(double, double) const;
   void Normalize(double) const;
   bool IsNormalized(double) const;
@@ -71,13 +70,13 @@ public:
 private:
   void FindEnergy(double) const;
 
-  vector<double> fEnergy; ///< vector holding all available muon energies
-  vector<double> fDZ; ///< vector holding the spatial resolution of the TRIM.SP output for all energies
-  vector< vector<double> > fDataZ; ///< discrete points in real space for which n(z) has been calculated for all energies
-  mutable vector< vector<double> > fDataNZ; ///< n(z) for all energies
-  vector< vector<double> > fOrigDataNZ; ///< original (unmodified) implantation profiles for all energies as read in from rge-files
-  mutable vector<bool> fIsNormalized; ///< tag indicating if the implantation profiles are normalized (for each energy separately)
-  mutable vector<double>::const_iterator fEnergyIter; ///< iterator traversing the vector of available energies
+  std::vector<double> fEnergy; ///< vector holding all available muon energies
+  std::vector<double> fDZ; ///< vector holding the spatial resolution of the TRIM.SP output for all energies
+  std::vector< std::vector<double> > fDataZ; ///< discrete points in real space for which n(z) has been calculated for all energies
+  mutable std::vector< std::vector<double> > fDataNZ; ///< n(z) for all energies
+  std::vector< std::vector<double> > fOrigDataNZ; ///< original (unmodified) implantation profiles for all energies as read in from rge-files
+  mutable std::vector<bool> fIsNormalized; ///< tag indicating if the implantation profiles are normalized (for each energy separately)
+  mutable std::vector<double>::const_iterator fEnergyIter; ///< iterator traversing the vector of available energies
 };
 
 #endif // _TTrimSPDataHandler_H_

src/external/DepthProfile/inc/PDepthProfile.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2013-2023 by Andreas Suter                              *
+ *   Copyright (C) 2013-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/DepthProfile/inc/PDepthProfileLinkDef.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2013-2023 by Andreas Suter                              *
+ *   Copyright (C) 2013-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/DepthProfile/src/PDepthProfile.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/DummyUserFcn/inc/PDummyUserFcn.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2013-2023 by Andreas Suter                              *
+ *   Copyright (C) 2013-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/DummyUserFcn/inc/PDummyUserFcnLinkDef.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2013-2023 by Andreas Suter                              *
+ *   Copyright (C) 2013-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/DummyUserFcn/src/PDummyUserFcn.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MagProximity/PMPStartupHandler.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2011-2023 by Andreas Suter                              *
+ *   Copyright (C) 2011-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MagProximity/PMPStartupHandler.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2011-2023 by Andreas Suter                              *
+ *   Copyright (C) 2011-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MagProximity/PMPStartupHandlerLinkDef.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2011-2023 by Andreas Suter                              *
+ *   Copyright (C) 2011-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MagProximity/PMagProximity.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2011-2023 by Andreas Suter                              *
+ *   Copyright (C) 2011-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MagProximity/PMagProximityFitter.cpp

@@ -10,7 +10,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2011-2023 by Andreas Suter                              *
+ *   Copyright (C) 2011-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -59,14 +59,14 @@ PMagProximityFitterGlobal::PMagProximityFitterGlobal()
 
   // read XML startup file
   char startup_path_name[128];
-  TSAXParser *saxParser = new TSAXParser();
-  PMPStartupHandler *fStartupHandler = new PMPStartupHandler();
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  fStartupHandler = std::make_unique<PMPStartupHandler>();
   strcpy(startup_path_name, fStartupHandler->GetStartupFilePath().Data());
-  saxParser->ConnectToHandler("PMPStartupHandler", fStartupHandler);
+  saxParser->ConnectToHandler("PMPStartupHandler", fStartupHandler.get());
   //Int_t 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 PUserFcnBase.cpp for the definition)
-  Int_t status = parseXmlFile(saxParser, startup_path_name);
+  Int_t status = parseXmlFile(saxParser.get(), startup_path_name);
   // check for parse errors
   if (status) { // error
     std::cout << std::endl << ">> PMagProximityFitterGlobal::PMagProximityFitterGlobal: **WARNING** Reading/parsing mag_proximity_startup.xml failed.";
@@ -74,12 +74,6 @@ PMagProximityFitterGlobal::PMagProximityFitterGlobal()
     fValid = false;
   }
 
-  // clean up
-  if (saxParser) {
-    delete saxParser;
-    saxParser = 0;
-  }
-
   // check if everything went fine with the startup handler
   if (!fStartupHandler->IsValid()) {
     std::cout << std::endl << ">> PMagProximityFitterGlobal::PMagProximityFitterGlobal **PANIC ERROR**";
@@ -89,7 +83,7 @@ PMagProximityFitterGlobal::PMagProximityFitterGlobal()
   }
 
   // load all the TRIM.SP rge-files
-  fRgeHandler = new PRgeHandler();
+  fRgeHandler = std::make_unique<PRgeHandler>();
   if (!fRgeHandler->IsValid()) {
     std::cout << std::endl << ">> PMagProximityFitterGlobal::PMagProximityFitterGlobal **PANIC ERROR**";
     std::cout << std::endl << ">>  rge data handler too unhappy. Will terminate unfriendly, sorry.";
@@ -109,15 +103,6 @@ PMagProximityFitterGlobal::~PMagProximityFitterGlobal()
   fPreviousParam.clear();
 
   fField.clear();
-
-  if (fRgeHandler) {
-    delete fRgeHandler;
-    fRgeHandler = nullptr;
-  }
-  if (fStartupHandler) {
-    delete fStartupHandler;
-    fStartupHandler = nullptr;
-  }
 }
 
 //--------------------------------------------------------------------------

src/external/MagProximity/PMagProximityFitter.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -30,6 +30,8 @@
 #ifndef _PMAGPROXIMITYFITTER_H_
 #define _PMAGPROXIMITYFITTER_H_
 
+#include <memory>
+
 #include "PUserFcnBase.h"
 #include "PMPStartupHandler.h"
 #include "PRgeHandler.h"
@@ -49,8 +51,8 @@ class PMagProximityFitterGlobal
   private:
     Bool_t fValid;
 
-    PMPStartupHandler *fStartupHandler;
-    PRgeHandler *fRgeHandler;
+    std::unique_ptr<PMPStartupHandler> fStartupHandler;
+    std::unique_ptr<PRgeHandler> fRgeHandler;
 
     mutable std::vector<Double_t> fPreviousParam;
 

src/external/MagProximity/PMagProximityFitterLinkDef.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2011-2023 by Andreas Suter                              *
+ *   Copyright (C) 2011-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MusrRoot/TMusrRunHeader.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -31,6 +31,7 @@
 #include <ctime>
 #include <iostream>
 #include <iomanip>
+#include <memory>
 
 #include "TMusrRunHeader.h"
 
@@ -1075,7 +1076,7 @@ Bool_t TMusrRunHeader::ExtractHeaderInformation(TObjArray *headerInfo, TString r
         }
         for (Int_t i=0; i<tokens->GetEntries(); i++) {
           ostr = dynamic_cast<TObjString*>(tokens->At(i));
-          dvec.push_back(ostr->GetString().Atoi());
+          dvec.push_back(ostr->GetString().Atof());
         }
         if (tokens) {
           delete tokens;
@@ -1234,7 +1235,7 @@ void TMusrRunHeader::DumpHeader()
           str += subStr;
           str += "; ";
         }
-        subStr.Form(fmt, dvec.size()-1);
+        subStr.Form(fmt, dvec[dvec.size()-1]);
         str += subStr;
         str += " -@";
         str += MRH_DOUBLE_VECTOR;
@@ -1254,13 +1255,13 @@ void TMusrRunHeader::DumpHeader()
  */
 void TMusrRunHeader::DrawHeader()
 {
-  TPaveText *pt;
-  TCanvas *ca;
+  std::unique_ptr<TPaveText> pt;
+  std::unique_ptr<TCanvas> ca;
 
-  ca = new TCanvas("MusrRoot RunHeader","MusrRoot RunHeader", 147,37,699,527);
+  ca = std::make_unique<TCanvas>("MusrRoot RunHeader","MusrRoot RunHeader", 147,37,699,527);
   ca->Range(0., 0., 100., 100.);
 
-  pt = new TPaveText(10.,10.,90.,90.,"br");
+  pt = std::make_unique<TPaveText>(10.,10.,90.,90.,"br");
   pt->SetFillColor(19);
   pt->SetTextAlign(12);
 
@@ -1506,7 +1507,7 @@ bool TMusrRunHeader::UpdateFolder(TObject *treeObj, TString path)
 
   if (!obj) { // required object not present, create it
     TObjArray *oarray = new TObjArray();
-    if (!oarray) {
+    if (oarray == nullptr) {
       std::cerr << std::endl << ">> TMusrRunHeader::UpdateFolder(): **ERROR** couldn't create header structure!!" << std::endl;
       return false;
     }

src/external/MusrRoot/TMusrRunHeader.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MusrRoot/TMusrRunHeaderLinkDef.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2007-2023 by Andreas Suter                              *
+ *   Copyright (C) 2007-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/MusrRoot/doc/MusrRootDefinition.tex

@@ -274,7 +274,7 @@ An example program \verb!write_musrRoot_runHeader! which is writing a full run h
 
 \begin{shaded}
 \begin{verbatim}  
-TMusrRunHeader *header = new TMusrRunHeader();
+std::unique_ptr<TMusrRunHeader> header = std::make_unique<TMusrRunHeader>();
 TMusrRunPhysicalQuantity prop;
 \end{verbatim}
 \end{shaded}
@@ -318,14 +318,15 @@ header->Set("DetectorInfo/Detector001/Time Zero Bin", 3419.0);
 
 \begin{shaded}
 \begin{verbatim}  
-TFile *f = new TFile(fileName, "RECREATE", "write_musrRoot_runHeader");
+std::unique_ptr<TFile> f = std::make_unique<TFile>(fileName, "RECREATE",
+                                                   "write_musrRoot_runHeader");
 if (f->IsZombie()) {
-  delete f;
   return -1;
 }
 
 // create the needed TFolder object
-TFolder *runHeader = new TFolder("RunHeader", "MusrRoot Run Header Info");
+std::unique_ptr<TFolder> runHeader = std::make_unique<TFolder>("RunHeader",
+                                                    "MusrRoot Run Header Info");
 
 // create the "directory" structure
 if (header->FillFolder(runHeader)) {
@@ -343,21 +344,22 @@ The following code snippet shows how the extract the full run header from the \m
 
 \begin{shaded}
 \begin{verbatim}  
-TFile *f = new TFile(fileName, "READ", "read_musrRoot_runHeader");
+std::unique_ptr<TFile> f = std::make_unique<TFile>(fileName, "READ",
+                                                   "read_musrRoot_runHeader");
 if (f->IsZombie()) {
-  delete f;
   return -1;
 }
 
-TFolder *runHeader = 0;
+TFolder *runHeader = nullptr;
 f->GetObject("RunHeader", runHeader);
-if (runHeader == 0) {
+if (runHeader == nullptr) {
   cerr << endl << ">> **ERROR** Couldn't get top folder RunHeader";
   closeFile(f);
   return -1;
 }
 
-TMusrRunHeader *header = new TMusrRunHeader(fileName);
+std::unique_ptr<TMusrRunHeader> header =
+               std::make_unique<TMusrRunHeader>(fileName);
 
 if (!header->ExtractAll(runHeader)) {
   cerr << endl << ">> **ERROR** couldn't extract all RunHeader information";
@@ -366,7 +368,6 @@ if (!header->ExtractAll(runHeader)) {
 }
 
 f->Close();
-delete f;
 \end{verbatim}
 \end{shaded}
 

src/external/Nonlocal/PNL_PippardFitter.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -31,6 +31,7 @@
 #include <cmath>
 
 #include <iostream>
+#include <memory>
 
 #include <TSAXParser.h>
 #include <TMath.h>
@@ -52,14 +53,14 @@ PNL_PippardFitterGlobal::PNL_PippardFitterGlobal()
 {
   // read XML startup file
   char startup_path_name[128];
-  TSAXParser *saxParser = new TSAXParser();
-  PNL_StartupHandler *fStartupHandler = new PNL_StartupHandler();
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  fStartupHandler = std::make_unique<PNL_StartupHandler>();
   strcpy(startup_path_name, fStartupHandler->GetStartupFilePath().Data());
-  saxParser->ConnectToHandler("PNL_StartupHandler", fStartupHandler);
+  saxParser->ConnectToHandler("PNL_StartupHandler", fStartupHandler.get());
   //Int_t 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 PUserFcnBase.cpp for the definition)
-  Int_t status = parseXmlFile(saxParser, startup_path_name);
+  Int_t status = parseXmlFile(saxParser.get(), startup_path_name);
   // check for parse errors
   if (status) { // error
     std::cout << std::endl << ">> PNL_PippardFitterGlobal::PNL_PippardFitterGlobal: **WARNING** Reading/parsing nonlocal_startup.xml failed.";
@@ -67,14 +68,8 @@ PNL_PippardFitterGlobal::PNL_PippardFitterGlobal()
     fValid = false;
   }
 
-  // clean up
-  if (saxParser) {
-    delete saxParser;
-    saxParser = 0;
-  }
-
   // check if everything went fine with the startup handler
-  if (!fStartupHandler->IsValid()) {
+  if (!fStartupHandler->IsValid() && fValid) {
     std::cout << std::endl << ">> PNL_PippardFitterGlobal::PNL_PippardFitterGlobal **PANIC ERROR**";
     std::cout << std::endl << ">>   startup handler too unhappy. Will terminate unfriendly, sorry.";
     std::cout << std::endl;
@@ -84,12 +79,14 @@ PNL_PippardFitterGlobal::PNL_PippardFitterGlobal()
   fFourierPoints = fStartupHandler->GetFourierPoints();
 
   // load all the TRIM.SP rge-files
-  fRgeHandler = new PRgeHandler("./nonlocal_startup.xml");
-  if (!fRgeHandler->IsValid()) {
-    std::cout << std::endl << ">> PNL_PippardFitterGlobal::PNL_PippardFitterGlobal **PANIC ERROR**";
-    std::cout << std::endl << ">>  rge data handler too unhappy. Will terminate unfriendly, sorry.";
-    std::cout << std::endl;
-    fValid = false;
+  if (fValid) {
+    fRgeHandler = std::make_unique<PRgeHandler>("./nonlocal_startup.xml");
+    if (!fRgeHandler->IsValid()) {
+      std::cout << std::endl << ">> PNL_PippardFitterGlobal::PNL_PippardFitterGlobal **PANIC ERROR**";
+      std::cout << std::endl << ">>  rge data handler too unhappy. Will terminate unfriendly, sorry.";
+      std::cout << std::endl;
+      fValid = false;
+    }
   }
 
   fPlanPresent = false;
@@ -124,15 +121,6 @@ PNL_PippardFitterGlobal::~PNL_PippardFitterGlobal()
     fftw_free(fFieldq);
     fFieldB = 0;
   }
-
-  if (fRgeHandler) {
-    delete fRgeHandler;
-    fRgeHandler = 0;
-  }
-  if (fStartupHandler) {
-    delete fStartupHandler;
-    fStartupHandler = 0;
-  }
 }
 
 //--------------------------------------------------------------------------

src/external/Nonlocal/PNL_PippardFitter.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -36,6 +36,8 @@
 //#endif
 #include <fftw3.h>
 
+#include <memory>
+
 #include "PMusr.h"
 #include "PUserFcnBase.h"
 #include "PNL_StartupHandler.h"
@@ -57,8 +59,8 @@ class PNL_PippardFitterGlobal
   private:
     Bool_t fValid{true};
 
-    PNL_StartupHandler *fStartupHandler{nullptr};
-    PRgeHandler *fRgeHandler{nullptr};
+    std::unique_ptr<PNL_StartupHandler> fStartupHandler;
+    std::unique_ptr<PRgeHandler> fRgeHandler;
 
     mutable std::vector<Double_t> fPreviousParam;
 

src/external/Nonlocal/PNL_PippardFitterLinkDef.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/Nonlocal/PNL_StartupHandler.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/Nonlocal/PNL_StartupHandler.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/Nonlocal/PNL_StartupHandlerLinkDef.h

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *

src/external/Nonlocal/cmake/dnlf_config.h.in

@@ -2,3 +2,7 @@
 
 #define PROJECT_VERSION "@PROJECT_VERSION@"
 
+#define GIT_BRANCH "@GIT_BRANCH@"
+#define GIT_CURRENT_SHA1 @GIT_CURRENT_SHA1@
+
+#define ROOT_VERSION_USED "@ROOT_VERSION_USED@"

src/external/Nonlocal/prog/CMakeLists.txt

@@ -1,23 +1,64 @@
 #--- dump_nonlocal_field ------------------------------------------------------
 
+cmake_minimum_required(VERSION 3.15)
+
 project(dump_nonlocal_field VERSION 1.0.0 LANGUAGES C CXX)
 
+#--- check for git ------------------------------------------------------------
+find_package(Git REQUIRED)
+
+#--- check for ROOT -----------------------------------------------------------
+find_package(ROOT 6.18 REQUIRED COMPONENTS Gui MathMore Minuit2 XMLParser)
+if (ROOT_mathmore_FOUND)
+  execute_process(COMMAND root-config --bindir OUTPUT_VARIABLE ROOT_BINDIR)
+  string(STRIP ${ROOT_BINDIR} ROOT_BINDIR)
+  execute_process(COMMAND root-config --version OUTPUT_VARIABLE ROOT_VERSION_USED)
+  string(STRIP ${ROOT_VERSION_USED} ROOT_VERSION_USED)
+  execute_process(COMMAND root-config --incdir OUTPUT_VARIABLE ROOT_INC)
+  string(STRIP ${ROOT_INC} ROOT_INC)
+  message("-- Found ROOT: ${ROOT_BINDIR} (found version: ${ROOT_VERSION})")
+  #---Define useful ROOT functions and macros (e.g. ROOT_GENERATE_DICTIONARY)
+  include(${ROOT_USE_FILE})
+endif (ROOT_mathmore_FOUND)
+
+#--- check for boost ----------------------------------------------------------
+find_package(Boost REQUIRED
+  COMPONENTS
+    system
+    filesystem
+)
+message(STATUS "Boost libs: ${Boost_LIBRARIES}")
+
+#--- check for fftw3 ----------------------------------------------------------
+#find_package(FFTW3 REQUIRED)
+
+# Get the current working branch
+execute_process(
+  COMMAND git rev-parse --abbrev-ref HEAD
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  OUTPUT_VARIABLE GIT_BRANCH
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+# Get the latest abbreviated commit hash of the working branch
+execute_process(
+  COMMAND git log -1 --pretty="%h, %ci"
+  WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+  OUTPUT_VARIABLE GIT_CURRENT_SHA1
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+
 #--- feed dnlf_config.h -----------------------------------------
 set(HAVE_DNLF_CONFIG_H 1 CACHE INTERNAL "dnlf_config.h is available")
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/../cmake/dnlf_config.h.in ${CMAKE_CURRENT_BINARY_DIR}/dnlf_config.h)
 
-#--- start create git-revision.h ----------------------------------------------
-if (IS_GIT_REPO)
-  set(HAVE_GIT_REV_H "-DHAVE_GIT_REV_H")  
-else (IS_GIT_REPO)
-  set(HAVE_GIT_REV_H "")  
-endif (IS_GIT_REPO)
-
 add_executable(dump_nonlocal_field dump_nonlocal_field.cpp)
 target_compile_options(dump_nonlocal_field BEFORE PRIVATE "-DHAVE_CONFIG_H" "-DHAVE_DNLF_CONFIG_H" "${HAVE_GIT_REV_H}")
 target_include_directories(dump_nonlocal_field 
   BEFORE PRIVATE
     $<BUILD_INTERFACE:${Boost_INCLUDE_DIR}>
+    $<BUILD_INTERFACE:${ROOT_INC}>
     $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}>
     $<BUILD_INTERFACE:${CMAKE_BINARY_DIR}/src>
     $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}>

src/external/Nonlocal/prog/dump_nonlocal_field.cpp

@@ -8,7 +8,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2009-2023 by Andreas Suter                              *
+ *   Copyright (C) 2009-2024 by Andreas Suter                              *
  *   andreas.suter@psi.ch                                                  *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -38,15 +38,9 @@
 
 #include "PNL_PippardFitter.h"
 
-#ifdef HAVE_CONFIG_H
-#include "config.h"
-#endif
 #ifdef HAVE_DNLF_CONFIG_H
 #include "dnlf_config.h"
 #endif
-#ifdef HAVE_GIT_REV_H
-#include "git-revision.h"
-#endif
 
 //-----------------------------------------------------------------------------
 /**
@@ -58,6 +52,7 @@ void dnlf_syntax()
   std::cout << "usage: dump_nonlocal_field [<msr-file> --out <field-dump> [--step <stepVal>] | --version | --help]" << std::endl;
   std::cout << "   <msr-file> : nonlocal msr-file name." << std::endl;
   std::cout << "   --out <field-dump> : ascii field dump output file name." << std::endl;
+  std::cout << "   --range <rangeVal> : this optional parameter (in nm) will overwrite the standard z-range = 5 * lambdaL." << std::endl;
   std::cout << "   --step <stepVal>   : this optional parameters allows to define the z-value step size in (nm)." << std::endl;
   std::cout << "   --version          : dumps the version" << std::endl;
   std::cout << "   --help             : will dump this help" << std::endl;
@@ -190,7 +185,8 @@ int main(int argc, char* argv[])
 {
   std::string msrFileName("");
   std::string outFileName("");
-  double step(0.0);
+  double step{0.0};
+  double range{0.0};
   bool show_syntax(false);
 
   if (argc == 1) {
@@ -202,18 +198,10 @@ int main(int argc, char* argv[])
     if (argv[i][0] != '-') { // must be the msr-file name
       msrFileName = argv[i];
     } else if (!strcmp(argv[i], "--version")) {
-#ifdef HAVE_CONFIG_H
-#ifdef HAVE_GIT_REV_H
-      std::cout << std::endl << "dump_nonlocal_field version: " << PROJECT_VERSION << " (" << PACKAGE_VERSION << "), git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << " (" << BUILD_TYPE << "), ROOT version: " << ROOT_VERSION_USED << std::endl << std::endl;
+#ifdef HAVE_DNLF_CONFIG_H
+      std::cout << std::endl << "dump_nonlocal_field version: " << PROJECT_VERSION << ", git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << ", ROOT version: " << ROOT_VERSION_USED << std::endl << std::endl;
 #else
-      std::cout << std::endl << "dump_nonlocal_field version: " << PROJECT_VERSION << " (" << PACKAGE_VERSION << "/" << BUILD_TYPE << "), ROOT version: " << ROOT_VERSION_USED << std::endl << std::endl;
-#endif
-#else
-#ifdef HAVE_GIT_REV_H
-      std::cout << std::endl << "dump_nonlocal_field git-branch: " << GIT_BRANCH << ", git-rev: " << GIT_CURRENT_SHA1 << std::endl << std::endl;
-#else
-      std::cout << std::endl << "dump_nonlocal_field version: unknown" << std::endl << std::endl;
-#endif
+      std::cout << std::endl << "dump_nonlocal_field version: " << PROJECT_VERSION << ", ROOT version: " << ROOT_VERSION_USED << std::endl << std::endl;
 #endif
       return 0;
     } else if (!strcmp(argv[i], "--help")) {
@@ -228,6 +216,22 @@ int main(int argc, char* argv[])
         show_syntax = true;
         break;
       }
+    } else if (!strcmp(argv[i], "--range")) {
+      if (i < argc-1) {
+        try {
+          range = std::stod(argv[i+1]);
+        }
+        catch(std::exception& e) {
+          std::cout << "dump_nonlocal_field: **ERROR** <rangeVal> '" << argv[i+1] << "' seems not to be a double." << std::endl;
+          show_syntax = true;
+          break;
+        }
+        i++;
+      } else {
+        std::cerr << std::endl << "dump_nonlocal_field: **ERROR** found option --range without <rangeVal>" << std::endl;
+        show_syntax = true;
+        break;
+      }
     } else if (!strcmp(argv[i], "--step")) {
       if (i < argc-1) {
         try {
@@ -260,14 +264,17 @@ int main(int argc, char* argv[])
 
   // calculate field and write it to file
   PNL_PippardFitterGlobal pip;
-  pip.CalculateField(param);
+  if (pip.IsValid())
+    pip.CalculateField(param);
+  else
+    return -3;
 
   std::ofstream fout(outFileName.c_str(), std::ofstream::out);
   if (!fout.is_open()) {
     std::cout << std::endl;
     std::cerr << "**ERROR** can not write to file '" << outFileName << "'." << std::endl;
     std::cout << std::endl;
-    return -3;
+    return -4;
   }
   // write header
   fout << "% z (nm), field (G)" << std::endl;
@@ -280,13 +287,15 @@ int main(int argc, char* argv[])
   bool done(false);
   double deadLayer = param[8];
   double b0 = param[6];
+  if (range == 0.0)
+    range = 5.0*param[5]; // 5*lambda
   do {
     if (z < deadLayer) {
       fout << z << ", " << b0 << std::endl;
     } else {
       field = pip.GetMagneticField(z-deadLayer);
       fout << z << ", " << b0*field << std::endl;
-      if (fabs(prevField-field) < 1.0e-10)
+      if ((fabs(prevField-field) < 1.0e-10) && (z >= range))
         done = true;
       prevField = field;
     }

src/external/libBNMR/libLineProfile/LineProfile.cpp

@@ -23,6 +23,8 @@
 #include "LineProfile.h"
 #include <iostream> //for testing purposes
 
+#include <boost/math/special_functions/ellint_1.hpp>
+
 //Implement helperfunctions
 
 Double_t GaussianShape(Double_t x, Double_t position, Double_t width) {

src/external/libBNMR/libLineProfile/LineProfile.h

@@ -25,8 +25,6 @@
 #include <cmath>
 #include <vector>
 #include <algorithm>
-#include <boost/math/special_functions/ellint_1.hpp>
-
 
 #ifndef PI
 #define PI           3.14159265358979323846  /* pi */

src/external/libCalcMeanFieldsLEM/TCalcMeanFieldsLEM.cpp

@@ -50,33 +50,22 @@ TMeanFieldsForScHalfSpace::TMeanFieldsForScHalfSpace() {
   // read startup file
   std::string startup_path_name("BMW_startup.xml");
 
-  TSAXParser *saxParser = new TSAXParser();
-  BMWStartupHandler *startupHandler = new BMWStartupHandler();
-  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
   int status (saxParser->ParseFile(startup_path_name.c_str()));
   // check for parse errors
   if (status) { // error
-    cerr << endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
-         << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-         << endl;
+    std::cerr << std::endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
+         << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+         << std::endl;
     assert(false);
   }
 
   std::string rge_path(startupHandler->GetDataPath());
-  map<double, std::string> energy_vec(startupHandler->GetEnergies());
-
-  fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
-
-  // clean up
-  if (saxParser) {
-    delete saxParser;
-    saxParser = 0;
-  }
-  if (startupHandler) {
-    delete startupHandler;
-    startupHandler = 0;
-  }
+  std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
+  fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 }
 
 // Operator-method that returns the mean field for a given implantation energy
@@ -141,33 +130,22 @@ TMeanFieldsForScSingleLayer::TMeanFieldsForScSingleLayer() {
   // read startup file
   std::string startup_path_name("BMW_startup.xml");
 
-  TSAXParser *saxParser = new TSAXParser();
-  BMWStartupHandler *startupHandler = new BMWStartupHandler();
-  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
   int status (saxParser->ParseFile(startup_path_name.c_str()));
   // check for parse errors
   if (status) { // error
-    cerr << endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
-         << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-         << endl;
+    std::cerr << std::endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
+         << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+         << std::endl;
     assert(false);
   }
 
   std::string rge_path(startupHandler->GetDataPath());
-  map<double, std::string> energy_vec(startupHandler->GetEnergies());
-
-  fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
-
-  // clean up
-  if (saxParser) {
-    delete saxParser;
-    saxParser = 0;
-  }
-  if (startupHandler) {
-    delete startupHandler;
-    startupHandler = 0;
-  }
+  std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
+  fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 }
 
 // Operator-method that returns the mean field for a given implantation energy
@@ -240,33 +218,22 @@ TMeanFieldsForScBilayer::TMeanFieldsForScBilayer() {
   // read startup file
   std::string startup_path_name("BMW_startup.xml");
 
-  TSAXParser *saxParser = new TSAXParser();
-  BMWStartupHandler *startupHandler = new BMWStartupHandler();
-  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
   int status (saxParser->ParseFile(startup_path_name.c_str()));
   // check for parse errors
   if (status) { // error
-    cerr << endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
-         << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-         << endl;
+    std::cerr << std::endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
+         << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+         << std::endl;
     assert(false);
   }
 
   std::string rge_path(startupHandler->GetDataPath());
-  map<double, std::string> energy_vec(startupHandler->GetEnergies());
-
-  fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug(), 1);
-
-  // clean up
-  if (saxParser) {
-    delete saxParser;
-    saxParser = 0;
-  }
-  if (startupHandler) {
-    delete startupHandler;
-    startupHandler = 0;
-  }
+  std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
+  fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug(), 1);
 }
 
 // Operator-method that returns the mean field for a given implantation energy
@@ -335,10 +302,10 @@ double TMeanFieldsForScBilayer::CalcMeanB (double E, const std::vector<double>&
     std::vector<double> nz(fImpProfile->DataNZ(E));
     double dz(fImpProfile->DataDZ(E));
 
-  if (E==20.0){
-  ofstream of("Implantation-profile-normal.dat");
+  if (E==20.0) {
+  std::ofstream of("Implantation-profile-normal.dat");
   for (unsigned int i(0); i<z.size(); i++) {
-    of << z[i] << " " << nz[i] << endl;
+    of << z[i] << " " << nz[i] << std::endl;
   }
   of.close();
  }
@@ -359,33 +326,22 @@ TMeanFieldsForScTrilayer::TMeanFieldsForScTrilayer() {
   // read startup file
   std::string startup_path_name("BMW_startup.xml");
 
-  TSAXParser *saxParser = new TSAXParser();
-  BMWStartupHandler *startupHandler = new BMWStartupHandler();
-  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
   int status (saxParser->ParseFile(startup_path_name.c_str()));
   // check for parse errors
   if (status) { // error
-    cerr << endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
-         << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-         << endl;
+    std::cerr << std::endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
+         << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+         << std::endl;
     assert(false);
   }
 
   std::string rge_path(startupHandler->GetDataPath());
-  map<double, std::string> energy_vec(startupHandler->GetEnergies());
-
-  fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
-
-  // clean up
-  if (saxParser) {
-    delete saxParser;
-    saxParser = 0;
-  }
-  if (startupHandler) {
-    delete startupHandler;
-    startupHandler = 0;
-  }
+  std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
+  fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 }
 
 // Operator-method that returns the mean field for a given implantation energy
@@ -464,33 +420,22 @@ TMeanFieldsForScTrilayerWithInsulator::TMeanFieldsForScTrilayerWithInsulator() {
   // read startup file
   std::string startup_path_name("BMW_startup.xml");
 
-  TSAXParser *saxParser = new TSAXParser();
-  BMWStartupHandler *startupHandler = new BMWStartupHandler();
-  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+  std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+  std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+  saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
   int status (saxParser->ParseFile(startup_path_name.c_str()));
   // check for parse errors
   if (status) { // error
-    cerr << endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
-         << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-         << endl;
+    std::cerr << std::endl << "**ERROR** reading/parsing " << startup_path_name << " failed." \
+         << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+         << std::endl;
     assert(false);
   }
 
   std::string rge_path(startupHandler->GetDataPath());
-  map<double, std::string> energy_vec(startupHandler->GetEnergies());
-
-  fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
-
-  // clean up
-  if (saxParser) {
-    delete saxParser;
-    saxParser = 0;
-  }
-  if (startupHandler) {
-    delete startupHandler;
-    startupHandler = 0;
-  }
+  std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
+  fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 }
 
 // Operator-method that returns the mean field for a given implantation energy

src/external/libCalcMeanFieldsLEM/TCalcMeanFieldsLEM.h

@@ -29,6 +29,8 @@
 #ifndef _TCalcMeanFieldsLEM_H_
 #define _TCalcMeanFieldsLEM_H_
 
+#include <memory>
+
 #include "TLondon1D.h"
 
 class TMeanFieldsForScHalfSpace : public PUserFcnBase {
@@ -36,13 +38,12 @@ class TMeanFieldsForScHalfSpace : public PUserFcnBase {
 public:
   // default constructor
   TMeanFieldsForScHalfSpace();
-  ~TMeanFieldsForScHalfSpace() {delete fImpProfile; fImpProfile = 0;}
 
   double operator()(double, const std::vector<double>&) const;
   double CalcMeanB (double, const TLondon1D_HS&) const;
 
 private:
-  TTrimSPData *fImpProfile;
+  std::unique_ptr<TTrimSPData> fImpProfile;
 
   ClassDef(TMeanFieldsForScHalfSpace,1)
 };
@@ -52,13 +53,12 @@ class TMeanFieldsForScSingleLayer : public PUserFcnBase {
 public:
   // default constructor
   TMeanFieldsForScSingleLayer();
-  ~TMeanFieldsForScSingleLayer() {delete fImpProfile; fImpProfile = 0;}
 
   double operator()(double, const std::vector<double>&) const;
   double CalcMeanB (double, const std::vector<double>&, const std::vector<double>&, const TLondon1D_1L&) const;
 
 private:
-  TTrimSPData *fImpProfile;
+  std::unique_ptr<TTrimSPData> fImpProfile;
 
   ClassDef(TMeanFieldsForScSingleLayer,1)
 };
@@ -68,13 +68,12 @@ class TMeanFieldsForScBilayer : public PUserFcnBase {
 public:
   // default constructor
   TMeanFieldsForScBilayer();
-  ~TMeanFieldsForScBilayer() {delete fImpProfile; fImpProfile = 0;}
 
   double operator()(double, const std::vector<double>&) const;
   double CalcMeanB (double, const std::vector<double>&, const std::vector<double>&, const TLondon1D_2L&, double) const;
 
 private:
-  TTrimSPData *fImpProfile;
+  std::unique_ptr<TTrimSPData> fImpProfile;
 
   ClassDef(TMeanFieldsForScBilayer,1)
 };
@@ -84,13 +83,12 @@ class TMeanFieldsForScTrilayer : public PUserFcnBase {
 public:
   // default constructor
   TMeanFieldsForScTrilayer();
-  ~TMeanFieldsForScTrilayer() {delete fImpProfile; fImpProfile = 0;}
 
   double operator()(double, const std::vector<double>&) const;
   double CalcMeanB (double, const std::vector<double>&, const std::vector<double>&, const TLondon1D_3L&) const;
 
 private:
-  TTrimSPData *fImpProfile;
+  std::unique_ptr<TTrimSPData> fImpProfile;
 
   ClassDef(TMeanFieldsForScTrilayer,1)
 };
@@ -100,13 +98,12 @@ class TMeanFieldsForScTrilayerWithInsulator : public PUserFcnBase {
 public:
   // default constructor
   TMeanFieldsForScTrilayerWithInsulator();
-  ~TMeanFieldsForScTrilayerWithInsulator() {delete fImpProfile; fImpProfile = 0;}
 
   double operator()(double, const std::vector<double>&) const;
   double CalcMeanB (double, const std::vector<double>&, const std::vector<double>&, const TLondon1D_3LwInsulator&) const;
 
 private:
-  TTrimSPData *fImpProfile;
+  std::unique_ptr<TTrimSPData> fImpProfile;
 
   ClassDef(TMeanFieldsForScTrilayerWithInsulator,1)
 };

src/external/libFitPofB/classes/TLondon1D.cpp

@@ -30,6 +30,7 @@
 
 #include "TLondon1D.h"
 #include <iostream>
+#include <memory>
 #include <cassert>
 #include <cmath>
 
@@ -55,12 +56,6 @@ TLondon1DHS::~TLondon1DHS() {
     fParForBofZ.clear();
     fParForPofB.clear();
     fParForPofT.clear();
-    delete fImpProfile;
-    fImpProfile = 0;
-    delete fPofB;
-    fPofB = 0;
-    delete fPofT;
-    fPofT = 0;
 }
 
 TLondon1D1L::~TLondon1D1L() {
@@ -68,12 +63,6 @@ TLondon1D1L::~TLondon1D1L() {
     fParForBofZ.clear();
     fParForPofB.clear();
     fParForPofT.clear();
-    delete fImpProfile;
-    fImpProfile = 0;
-    delete fPofB;
-    fPofB = 0;
-    delete fPofT;
-    fPofT = 0;
 }
 
 TLondon1D2L::~TLondon1D2L() {
@@ -81,12 +70,6 @@ TLondon1D2L::~TLondon1D2L() {
     fParForBofZ.clear();
     fParForPofB.clear();
     fParForPofT.clear();
-    delete fImpProfile;
-    fImpProfile = 0;
-    delete fPofB;
-    fPofB = 0;
-    delete fPofT;
-    fPofT = 0;
 }
 
 TProximity1D1LHS::~TProximity1D1LHS() {
@@ -94,12 +77,6 @@ TProximity1D1LHS::~TProximity1D1LHS() {
     fParForBofZ.clear();
     fParForPofB.clear();
     fParForPofT.clear();
-    delete fImpProfile;
-    fImpProfile = 0;
-    delete fPofB;
-    fPofB = 0;
-    delete fPofT;
-    fPofT = 0;
 }
 
 TLondon1D3L::~TLondon1D3L() {
@@ -107,12 +84,6 @@ TLondon1D3L::~TLondon1D3L() {
     fParForBofZ.clear();
     fParForPofB.clear();
     fParForPofT.clear();
-    delete fImpProfile;
-    fImpProfile = 0;
-    delete fPofB;
-    fPofB = 0;
-    delete fPofT;
-    fPofT = 0;
 }
 
 TLondon1D3LS::~TLondon1D3LS() {
@@ -120,12 +91,6 @@ TLondon1D3LS::~TLondon1D3LS() {
     fParForBofZ.clear();
     fParForPofB.clear();
     fParForPofT.clear();
-    delete fImpProfile;
-    fImpProfile = 0;
-    delete fPofB;
-    fPofB = 0;
-    delete fPofT;
-    fPofT = 0;
 }
 
 // TLondon1D4L::~TLondon1D4L() {
@@ -133,10 +98,6 @@ TLondon1D3LS::~TLondon1D3LS() {
 //     fParForBofZ.clear();
 //     fParForPofB.clear();
 //     fParForPofT.clear();
-//     delete fImpProfile;
-//     fImpProfile = 0;
-//     delete fPofT;
-//     fPofT = 0;
 // }
 
 //------------------
@@ -147,27 +108,27 @@ TLondon1D3LS::~TLondon1D3LS() {
 TLondon1DHS::TLondon1DHS() : fCalcNeeded(true), fFirstCall(true) {
 
     // read startup file
-    string startup_path_name("BMW_startup.xml");
+    std::string startup_path_name("BMW_startup.xml");
 
-    TSAXParser *saxParser = new TSAXParser();
-    BMWStartupHandler *startupHandler = new BMWStartupHandler();
-    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+    std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+    std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
     //int status (saxParser->ParseFile(startup_path_name.c_str()));
     // parsing the file as above seems to lead to problems in certain environments;
     // use the parseXmlFile function instead (see PUserFcnBase.cpp for the definition)
-    int status = parseXmlFile(saxParser, startup_path_name.c_str());
+    int status = parseXmlFile(saxParser.get(), startup_path_name.c_str());
     // check for parse errors
     if (status) { // error
-      cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
-           << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-           << endl;
+      std::cerr << std::endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
+           << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+           << std::endl;
       assert(false);
     }
 
     fNSteps = startupHandler->GetNSteps();
     fWisdom = startupHandler->GetWisdomFile();
-    string rge_path(startupHandler->GetDataPath());
-    map<double, string> energy_vec(startupHandler->GetEnergies());
+    std::string rge_path(startupHandler->GetDataPath());
+    std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
     fParForPofT.push_back(0.0); // phase
     fParForPofT.push_back(startupHandler->GetDeltat());
@@ -180,21 +141,11 @@ TLondon1DHS::TLondon1DHS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
+    fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 
-    fPofB = new TPofBCalc(fParForPofB);
+    fPofB = std::make_unique<TPofBCalc>(fParForPofB);
 
-    fPofT = new TPofTCalc(fPofB, fWisdom, fParForPofT);
-
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = 0;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = 0;
-    }
+    fPofT = std::make_unique<TPofTCalc>(fPofB.get(), fWisdom, fParForPofT);
 }
 
 //------------------
@@ -203,18 +154,18 @@ TLondon1DHS::TLondon1DHS() : fCalcNeeded(true), fFirstCall(true) {
 // Parameters: all the parameters for the function to be fitted through TLondon1DHS
 //------------------
 
-double TLondon1DHS::operator()(double t, const vector<double> &par) const {
+double TLondon1DHS::operator()(double t, const std::vector<double> &par) const {
 
   assert(par.size() == 5);
 
-  if(t<0.0)
+  if (t<0.0)
     return cos(par[0]*0.017453293);
 
   bool dead_layer_changed(false);
 
   // check if the function is called the first time and if yes, read in parameters
 
-  if(fFirstCall){
+  if (fFirstCall) {
     fPar = par;
 
     for (unsigned int i(2); i<fPar.size(); i++){
@@ -230,7 +181,7 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
   bool only_phase_changed(false);
 
   for (unsigned int i(0); i<fPar.size(); i++) {
-    if( fPar[i]-par[i] ) {
+    if ( fPar[i]-par[i] ) {
       fPar[i] = par[i];
       par_changed = true;
       if (i == 0) {
@@ -253,7 +204,7 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
 
     fParForPofT[0] = par[0]; // phase
 
-    if(!only_phase_changed) {
+    if (!only_phase_changed) {
 
 //      std::cout << " Parameters have changed, (re-)calculating p(B) and P(t) now..." << std::endl;
 
@@ -264,8 +215,8 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
       fParForPofB[3] = par[2]; // Bkg-Field
       //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
 
-      if(dead_layer_changed){
-        vector<double> interfaces;
+      if (dead_layer_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]);// dead layer
         fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces); // Fraction of muons in the deadlayer
         interfaces.clear();
@@ -273,7 +224,7 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
 
       TLondon1D_HS BofZ(fParForBofZ);
       fPofB->UnsetPBExists();
-      fPofB->Calculate(&BofZ, fImpProfile, fParForPofB);
+      fPofB->Calculate(&BofZ, fImpProfile.get(), fParForPofB);
       fPofT->DoFFT();
 
     }/* else {
@@ -286,7 +237,6 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
   }
 
   return fPofT->Eval(t);
-
 }
 
 
@@ -298,27 +248,27 @@ double TLondon1DHS::operator()(double t, const vector<double> &par) const {
 TLondon1D1L::TLondon1D1L() : fCalcNeeded(true), fFirstCall(true) {
 
     // read startup file
-    string startup_path_name("BMW_startup.xml");
+    std::string startup_path_name("BMW_startup.xml");
 
-    TSAXParser *saxParser = new TSAXParser();
-    BMWStartupHandler *startupHandler = new BMWStartupHandler();
-    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+    std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+    std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
     //int status (saxParser->ParseFile(startup_path_name.c_str()));
     // parsing the file as above seems to lead to problems in certain environments;
     // use the parseXmlFile function instead (see PUserFcnBase.cpp for the definition)
-    int status = parseXmlFile(saxParser, startup_path_name.c_str());
+    int status = parseXmlFile(saxParser.get(), startup_path_name.c_str());
     // check for parse errors
     if (status) { // error
-      cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
-           << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-           << endl;
+      std::cerr << std::endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
+           << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+           << std::endl;
       assert(false);
     }
 
     fNSteps = startupHandler->GetNSteps();
     fWisdom = startupHandler->GetWisdomFile();
-    string rge_path(startupHandler->GetDataPath());
-    map<double, string> energy_vec(startupHandler->GetEnergies());
+    std::string rge_path(startupHandler->GetDataPath());
+    std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
     fParForPofT.push_back(0.0);
     fParForPofT.push_back(startupHandler->GetDeltat());
@@ -331,21 +281,11 @@ TLondon1D1L::TLondon1D1L() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
+    fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 
-    fPofB = new TPofBCalc(fParForPofB);
+    fPofB = std::make_unique<TPofBCalc>(fParForPofB);
 
-    fPofT = new TPofTCalc(fPofB, fWisdom, fParForPofT);
-
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = 0;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = 0;
-    }
+    fPofT = std::make_unique<TPofTCalc>(fPofB.get(), fWisdom, fParForPofT);
 }
 
 //------------------
@@ -354,7 +294,7 @@ TLondon1D1L::TLondon1D1L() : fCalcNeeded(true), fFirstCall(true) {
 // Parameters: all the parameters for the function to be fitted through TLondon1D1L
 //------------------
 
-double TLondon1D1L::operator()(double t, const vector<double> &par) const {
+double TLondon1D1L::operator()(double t, const std::vector<double> &par) const {
 
   assert(par.size() == 6 || par.size() == 8);
 
@@ -362,7 +302,7 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
   // Count the number of function calls
   //  fCallCounter++;
 
-  if(t<0.0)
+  if (t<0.0)
     return cos(par[0]*0.017453293);
 
   bool bkg_fraction_changed(false);
@@ -370,7 +310,7 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
 
   // check if the function is called the first time and if yes, read in parameters
 
-  if(fFirstCall){
+  if (fFirstCall) {
     fPar = par;
 
     for (unsigned int i(2); i<fPar.size(); i++){
@@ -389,7 +329,7 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
   bool only_phase_changed(false);
 
   for (unsigned int i(0); i<fPar.size(); i++) {
-    if( fPar[i]-par[i] ) {
+    if ( fPar[i]-par[i] ) {
       fPar[i] = par[i];
       par_changed = true;
       if (i == 0) {
@@ -413,7 +353,7 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
 
     fParForPofT[0] = par[0]; // phase
 
-    if(!only_phase_changed) {
+    if (!only_phase_changed) {
 
 //      std::cout << " Parameters have changed, (re-)calculating p(B) and P(t) now..." << std::endl;
 
@@ -424,12 +364,12 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
       fParForPofB[3] = par[2]; // Bkg-Field
       //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
 
-      if(weights_changed) {
-        vector<double> interfaces;
+      if (weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]+par[4]);
 
-        vector<double> weights;
-        for(unsigned int i(6); i<8; i++)
+        std::vector<double> weights;
+        for (unsigned int i(6); i<8; i++)
           weights.push_back(par[i]);
 
 //        std::cout << "Weighting has changed, re-calculating n(z) now..." << std::endl;
@@ -439,8 +379,8 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
         weights.clear();
       }
 
-      if(bkg_fraction_changed || weights_changed) {
-        vector<double> interfaces;
+      if (bkg_fraction_changed || weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]);// dead layer
         interfaces.push_back(par[3] + par[4]);// dead layer + first layer
         fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces) + // Fraction of muons in the deadlayer
@@ -451,7 +391,7 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
 
       TLondon1D_1L BofZ1(fParForBofZ);
       fPofB->UnsetPBExists();
-      fPofB->Calculate(&BofZ1, fImpProfile, fParForPofB);
+      fPofB->Calculate(&BofZ1, fImpProfile.get(), fParForPofB);
       fPofT->DoFFT();
 
     }/* else {
@@ -484,27 +424,27 @@ double TLondon1D1L::operator()(double t, const vector<double> &par) const {
 
 TLondon1D2L::TLondon1D2L() : fCalcNeeded(true), fFirstCall(true) {
   // read startup file
-    string startup_path_name("BMW_startup.xml");
+    std::string startup_path_name("BMW_startup.xml");
 
-    TSAXParser *saxParser = new TSAXParser();
-    BMWStartupHandler *startupHandler = new BMWStartupHandler();
-    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+    std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+    std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
     //int status (saxParser->ParseFile(startup_path_name.c_str()));
     // parsing the file as above seems to lead to problems in certain environments;
     // use the parseXmlFile function instead (see PUserFcnBase.cpp for the definition)
-    int status = parseXmlFile(saxParser, startup_path_name.c_str());
+    int status = parseXmlFile(saxParser.get(), startup_path_name.c_str());
     // check for parse errors
     if (status) { // error
-      cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
-           << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-           << endl;
+      std::cerr << std::endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
+           << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+           << std::endl;
       assert(false);
     }
 
     fNSteps = startupHandler->GetNSteps();
     fWisdom = startupHandler->GetWisdomFile();
-    string rge_path(startupHandler->GetDataPath());
-    map<double, string> energy_vec(startupHandler->GetEnergies());
+    std::string rge_path(startupHandler->GetDataPath());
+    std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
     fParForPofT.push_back(0.0);
     fParForPofT.push_back(startupHandler->GetDeltat());
@@ -517,21 +457,11 @@ TLondon1D2L::TLondon1D2L() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
+    fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 
-    fPofB = new TPofBCalc(fParForPofB);
+    fPofB = std::make_unique<TPofBCalc>(fParForPofB);
 
-    fPofT = new TPofTCalc(fPofB, fWisdom, fParForPofT);
-
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = 0;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = 0;
-    }
+    fPofT = std::make_unique<TPofTCalc>(fPofB.get(), fWisdom, fParForPofT);
 }
 
 //------------------
@@ -540,11 +470,11 @@ TLondon1D2L::TLondon1D2L() : fCalcNeeded(true), fFirstCall(true) {
 // Parameters: all the parameters for the function to be fitted through TLondon1D2L
 //------------------
 
-double TLondon1D2L::operator()(double t, const vector<double> &par) const {
+double TLondon1D2L::operator()(double t, const std::vector<double> &par) const {
 
   assert(par.size() == 8 || par.size() == 11);
 
-  if(t<0.0)
+  if (t<0.0)
     return cos(par[0]*0.017453293);
 
   bool bkg_fraction_changed(false);
@@ -552,7 +482,7 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
 
   // check if the function is called the first time and if yes, read in parameters
 
-  if(fFirstCall){
+  if (fFirstCall) {
     fPar = par;
 
     for (unsigned int i(2); i<fPar.size(); i++){
@@ -570,7 +500,7 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
   bool only_phase_changed(false);
 
   for (unsigned int i(0); i<fPar.size(); i++) {
-    if( fPar[i]-par[i] ) {
+    if ( fPar[i]-par[i] ) {
       fPar[i] = par[i];
       par_changed = true;
       if (i == 0) {
@@ -594,7 +524,7 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
 
     fParForPofT[0] = par[0]; // phase
 
-    if(!only_phase_changed) {
+    if (!only_phase_changed) {
 
 //      std::cout << " Parameters have changed, (re-)calculating p(B) and P(t) now..." << std::endl;
 
@@ -605,13 +535,13 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
       fParForPofB[3] = par[2]; // Bkg-Field
       //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
 
-      if(weights_changed) {
-        vector<double> interfaces;
+      if (weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]+par[4]);
         interfaces.push_back(par[3]+par[4]+par[5]);
 
-        vector<double> weights;
-        for(unsigned int i(8); i<11; i++)
+        std::vector<double> weights;
+        for (unsigned int i(8); i<11; i++)
           weights.push_back(par[i]);
 
 //        std::cout << "Weighting has changed, re-calculating n(z) now..." << std::endl;
@@ -621,8 +551,8 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
         weights.clear();
       }
 
-      if(bkg_fraction_changed || weights_changed) {
-        vector<double> interfaces;
+      if (bkg_fraction_changed || weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]);// dead layer
         interfaces.push_back(par[3] + par[4] + par[5]);// dead layer + first layer + second layer
         fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces) + // Fraction of muons in the deadlayer
@@ -632,7 +562,7 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
 
       TLondon1D_2L BofZ2(fParForBofZ);
       fPofB->UnsetPBExists();
-      fPofB->Calculate(&BofZ2, fImpProfile, fParForPofB);
+      fPofB->Calculate(&BofZ2, fImpProfile.get(), fParForPofB);
       fPofT->DoFFT();
 
 
@@ -646,7 +576,6 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
   }
 
   return fPofT->Eval(t);
-
 }
 
 //------------------
@@ -657,27 +586,27 @@ double TLondon1D2L::operator()(double t, const vector<double> &par) const {
 TProximity1D1LHS::TProximity1D1LHS() : fCalcNeeded(true), fFirstCall(true) {
 
     // read startup file
-    string startup_path_name("BMW_startup.xml");
+    std::string startup_path_name("BMW_startup.xml");
 
-    TSAXParser *saxParser = new TSAXParser();
-    BMWStartupHandler *startupHandler = new BMWStartupHandler();
-    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+    std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+    std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
     //int status (saxParser->ParseFile(startup_path_name.c_str()));
     // parsing the file as above seems to lead to problems in certain environments;
     // use the parseXmlFile function instead (see PUserFcnBase.cpp for the definition)
-    int status = parseXmlFile(saxParser, startup_path_name.c_str());
+    int status = parseXmlFile(saxParser.get(), startup_path_name.c_str());
     // check for parse errors
     if (status) { // error
-      cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
-           << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-           << endl;
+      std::cerr << std::endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
+           << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+           << std::endl;
       assert(false);
     }
 
     fNSteps = startupHandler->GetNSteps();
     fWisdom = startupHandler->GetWisdomFile();
-    string rge_path(startupHandler->GetDataPath());
-    map<double, string> energy_vec(startupHandler->GetEnergies());
+    std::string rge_path(startupHandler->GetDataPath());
+    std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
     fParForPofT.push_back(0.0);
     fParForPofT.push_back(startupHandler->GetDeltat());
@@ -690,21 +619,11 @@ TProximity1D1LHS::TProximity1D1LHS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.01); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
+    fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 
-    fPofB = new TPofBCalc(fParForPofB);
+    fPofB = std::make_unique<TPofBCalc>(fParForPofB);
 
-    fPofT = new TPofTCalc(fPofB, fWisdom, fParForPofT);
-
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = 0;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = 0;
-    }
+    fPofT = std::make_unique<TPofTCalc>(fPofB.get(), fWisdom, fParForPofT);
 }
 
 //------------------
@@ -713,18 +632,18 @@ TProximity1D1LHS::TProximity1D1LHS() : fCalcNeeded(true), fFirstCall(true) {
 // Parameters: all the parameters for the function to be fitted through TProximity1D1LHS
 //------------------
 
-double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
+double TProximity1D1LHS::operator()(double t, const std::vector<double> &par) const {
 
   assert(par.size() == 7);
 
-  if(t<0.0)
+  if (t<0.0)
     return cos(par[0]*0.017453293);
 
   // check if the function is called the first time and if yes, read in parameters
 
   bool dead_layer_changed(false);
 
-  if(fFirstCall){
+  if (fFirstCall) {
     fPar = par;
 
     for (unsigned int i(2); i<fPar.size(); i++){
@@ -740,14 +659,14 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
   bool only_phase_changed(false);
 
   for (unsigned int i(0); i<fPar.size(); i++) {
-    if( fPar[i]-par[i] ) {
+    if ( fPar[i]-par[i] ) {
       fPar[i] = par[i];
       par_changed = true;
       if (i == 0) {
         only_phase_changed = true;
       } else {
         only_phase_changed = false;
-        if (i == 4){
+        if (i == 4) {
           dead_layer_changed = true;
         }
       }
@@ -763,7 +682,7 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
 
     fParForPofT[0] = par[0]; // phase
 
-    if(!only_phase_changed) {
+    if (!only_phase_changed) {
 
 //      std::cout << " Parameters have changed, (re-)calculating p(B) and P(t) now..." << std::endl;
 
@@ -774,8 +693,8 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
       fParForPofB[3] = par[2]; // Bkg-Field
       //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
 
-      if(dead_layer_changed){
-        vector<double> interfaces;
+      if (dead_layer_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[4]);// dead layer
         fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces); // Fraction of muons in the deadlayer
         interfaces.clear();
@@ -783,7 +702,7 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
 
       TProximity1D_1LHS BofZ(fParForBofZ);
       fPofB->UnsetPBExists();
-      fPofB->Calculate(&BofZ, fImpProfile, fParForPofB);
+      fPofB->Calculate(&BofZ, fImpProfile.get(), fParForPofB);
       fPofT->DoFFT();
 
 
@@ -797,7 +716,6 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
   }
 
   return fPofT->Eval(t);
-
 }
 
 //------------------
@@ -807,27 +725,27 @@ double TProximity1D1LHS::operator()(double t, const vector<double> &par) const {
 
 TLondon1D3L::TLondon1D3L() : fCalcNeeded(true), fFirstCall(true) {
     // read startup file
-    string startup_path_name("BMW_startup.xml");
+    std::string startup_path_name("BMW_startup.xml");
 
-    TSAXParser *saxParser = new TSAXParser();
-    BMWStartupHandler *startupHandler = new BMWStartupHandler();
-    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+    std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+    std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
     //int status (saxParser->ParseFile(startup_path_name.c_str()));
     // parsing the file as above seems to lead to problems in certain environments;
     // use the parseXmlFile function instead (see PUserFcnBase.cpp for the definition)
-    int status = parseXmlFile(saxParser, startup_path_name.c_str());
+    int status = parseXmlFile(saxParser.get(), startup_path_name.c_str());
     // check for parse errors
     if (status) { // error
-      cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
-           << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-           << endl;
+      std::cerr << std::endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
+           << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+           << std::endl;
       assert(false);
     }
 
     fNSteps = startupHandler->GetNSteps();
     fWisdom = startupHandler->GetWisdomFile();
-    string rge_path(startupHandler->GetDataPath());
-    map<double, string> energy_vec(startupHandler->GetEnergies());
+    std::string rge_path(startupHandler->GetDataPath());
+    std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
     fParForPofT.push_back(0.0);
     fParForPofT.push_back(startupHandler->GetDeltat());
@@ -840,21 +758,11 @@ TLondon1D3L::TLondon1D3L() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
+    fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 
-    fPofB = new TPofBCalc(fParForPofB);
+    fPofB = std::make_unique<TPofBCalc>(fParForPofB);
 
-    fPofT = new TPofTCalc(fPofB, fWisdom, fParForPofT);
-
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = 0;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = 0;
-    }
+    fPofT = std::make_unique<TPofTCalc>(fPofB.get(), fWisdom, fParForPofT);
 }
 
 //------------------
@@ -863,11 +771,11 @@ TLondon1D3L::TLondon1D3L() : fCalcNeeded(true), fFirstCall(true) {
 // Parameters: all the parameters for the function to be fitted through TLondon1D3L
 //------------------
 
-double TLondon1D3L::operator()(double t, const vector<double> &par) const {
+double TLondon1D3L::operator()(double t, const std::vector<double> &par) const {
 
   assert(par.size() == 10 || par.size() == 14);
 
-  if(t<0.0)
+  if (t<0.0)
     return cos(par[0]*0.017453293);
 
   bool bkg_fraction_changed(false);
@@ -875,7 +783,7 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
 
   // check if the function is called the first time and if yes, read in parameters
 
-  if(fFirstCall){
+  if (fFirstCall) {
     fPar = par;
 
     for (unsigned int i(2); i<fPar.size(); i++){
@@ -893,7 +801,7 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
   bool only_phase_changed(false);
 
   for (unsigned int i(0); i<fPar.size(); i++) {
-    if( fPar[i]-par[i] ) {
+    if ( fPar[i]-par[i] ) {
       fPar[i] = par[i];
       par_changed = true;
       if (i == 0) {
@@ -917,7 +825,7 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
 
     fParForPofT[0] = par[0]; // phase
 
-    if(!only_phase_changed) {
+    if (!only_phase_changed) {
 
 //      std::cout << " Parameters have changed, (re-)calculating p(B) and P(t) now..." << std::endl;
 
@@ -928,14 +836,14 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
       fParForPofB[3] = par[2]; // Bkg-Field
       //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
 
-      if(weights_changed) {
-        vector<double> interfaces;
+      if (weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]+par[4]);
         interfaces.push_back(par[3]+par[4]+par[5]);
         interfaces.push_back(par[3]+par[4]+par[5]+par[6]);
 
-        vector<double> weights;
-        for(unsigned int i(10); i<14; i++)
+        std::vector<double> weights;
+        for (unsigned int i(10); i<14; i++)
           weights.push_back(par[i]);
 
 //        std::cout << "Weighting has changed, re-calculating n(z) now..." << std::endl;
@@ -945,8 +853,8 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
         weights.clear();
       }
 
-      if(bkg_fraction_changed || weights_changed) {
-        vector<double> interfaces;
+      if (bkg_fraction_changed || weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]);// dead layer
         interfaces.push_back(par[3] + par[4] + par[5] + par[6]);// dead layer + first layer + second layer + third layer
         fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces) + // Fraction of muons in the deadlayer
@@ -956,7 +864,7 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
 
       TLondon1D_3L BofZ3(fParForBofZ);
       fPofB->UnsetPBExists();
-      fPofB->Calculate(&BofZ3, fImpProfile, fParForPofB);
+      fPofB->Calculate(&BofZ3, fImpProfile.get(), fParForPofB);
       fPofT->DoFFT();
 
     }/* else {
@@ -969,7 +877,6 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
   }
 
   return fPofT->Eval(t);
-
 }
 
 //------------------
@@ -979,27 +886,27 @@ double TLondon1D3L::operator()(double t, const vector<double> &par) const {
 
 TLondon1D3LS::TLondon1D3LS() : fCalcNeeded(true), fFirstCall(true) {
     // read startup file
-    string startup_path_name("BMW_startup.xml");
+    std::string startup_path_name("BMW_startup.xml");
 
-    TSAXParser *saxParser = new TSAXParser();
-    BMWStartupHandler *startupHandler = new BMWStartupHandler();
-    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler);
+    std::unique_ptr<TSAXParser> saxParser = std::make_unique<TSAXParser>();
+    std::unique_ptr<BMWStartupHandler> startupHandler = std::make_unique<BMWStartupHandler>();
+    saxParser->ConnectToHandler("BMWStartupHandler", startupHandler.get());
     //int status (saxParser->ParseFile(startup_path_name.c_str()));
     // parsing the file as above seems to lead to problems in certain environments;
     // use the parseXmlFile function instead (see PUserFcnBase.cpp for the definition)
-    int status = parseXmlFile(saxParser, startup_path_name.c_str());
+    int status = parseXmlFile(saxParser.get(), startup_path_name.c_str());
     // check for parse errors
     if (status) { // error
-      cerr << endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
-           << endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
-           << endl;
+      std::cerr << std::endl << "**ERROR** Reading/parsing " << startup_path_name << " failed." \
+           << std::endl << "**ERROR** Please make sure that the file exists in the local directory and it is set up correctly!" \
+           << std::endl;
       assert(false);
     }
 
     fNSteps = startupHandler->GetNSteps();
     fWisdom = startupHandler->GetWisdomFile();
-    string rge_path(startupHandler->GetDataPath());
-    map<double, string> energy_vec(startupHandler->GetEnergies());
+    std::string rge_path(startupHandler->GetDataPath());
+    std::map<double, std::string> energy_vec(startupHandler->GetEnergies());
 
     fParForPofT.push_back(0.0);
     fParForPofT.push_back(startupHandler->GetDeltat());
@@ -1012,21 +919,11 @@ TLondon1D3LS::TLondon1D3LS() : fCalcNeeded(true), fFirstCall(true) {
     fParForPofB.push_back(0.005); // Bkg-width
     fParForPofB.push_back(0.0); // Bkg-weight
 
-    fImpProfile = new TTrimSPData(rge_path, energy_vec, startupHandler->GetDebug());
+    fImpProfile = std::make_unique<TTrimSPData>(rge_path, energy_vec, startupHandler->GetDebug());
 
-    fPofB = new TPofBCalc(fParForPofB);
+    fPofB = std::make_unique<TPofBCalc>(fParForPofB);
 
-    fPofT = new TPofTCalc(fPofB, fWisdom, fParForPofT);
-
-    // clean up
-    if (saxParser) {
-      delete saxParser;
-      saxParser = 0;
-    }
-    if (startupHandler) {
-      delete startupHandler;
-      startupHandler = 0;
-    }
+    fPofT = std::make_unique<TPofTCalc>(fPofB.get(), fWisdom, fParForPofT);
 }
 
 //------------------
@@ -1035,11 +932,11 @@ TLondon1D3LS::TLondon1D3LS() : fCalcNeeded(true), fFirstCall(true) {
 // Parameters: all the parameters for the function to be fitted through TLondon1D3LS
 //------------------
 
-double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
+double TLondon1D3LS::operator()(double t, const std::vector<double> &par) const {
 
   assert(par.size() == 9 || par.size() == 13);
 
-  if(t<0.0)
+  if (t<0.0)
     return cos(par[0]*0.017453293);
 
   bool bkg_fraction_changed(false);
@@ -1047,7 +944,7 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
 
   // check if the function is called the first time and if yes, read in parameters
 
-  if(fFirstCall){
+  if (fFirstCall) {
     fPar = par;
 
     for (unsigned int i(2); i<fPar.size(); i++){
@@ -1065,7 +962,7 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
   bool only_phase_changed(false);
 
   for (unsigned int i(0); i<fPar.size(); i++) {
-    if( fPar[i]-par[i] ) {
+    if ( fPar[i]-par[i] ) {
       fPar[i] = par[i];
       par_changed = true;
       if (i == 0) {
@@ -1089,7 +986,7 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
 
     fParForPofT[0] = par[0]; // phase
 
-    if(!only_phase_changed) {
+    if (!only_phase_changed) {
 
 //      std::cout << " Parameters have changed, (re-)calculating p(B) and P(t) now..." << std::endl;
 
@@ -1100,14 +997,14 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
       fParForPofB[3] = par[2]; // Bkg-Field
       //fParForPofB[4] = 0.005; // Bkg-width (in principle zero)
 
-      if(weights_changed) {
-        vector<double> interfaces;
+      if (weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]+par[4]);
         interfaces.push_back(par[3]+par[4]+par[5]);
         interfaces.push_back(par[3]+par[4]+par[5]+par[6]);
 
-        vector<double> weights;
-        for(unsigned int i(9); i<13; i++)
+        std::vector<double> weights;
+        for (unsigned int i(9); i<13; i++)
           weights.push_back(par[i]);
 
 //        std::cout << "Weighting has changed, re-calculating n(z) now..." << std::endl;
@@ -1117,8 +1014,8 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
         weights.clear();
       }
 
-      if(bkg_fraction_changed || weights_changed) {
-        vector<double> interfaces;
+      if (bkg_fraction_changed || weights_changed) {
+        std::vector<double> interfaces;
         interfaces.push_back(par[3]);// dead layer
         interfaces.push_back(par[3] + par[4] + par[5] + par[6]);// dead layer + first layer + second layer + third layer
         fParForPofB[5] = fImpProfile->LayerFraction(par[1], 1, interfaces) + // Fraction of muons in the deadlayer
@@ -1128,7 +1025,7 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
 
       TLondon1D_3LS BofZ3(fParForBofZ);
       fPofB->UnsetPBExists();
-      fPofB->Calculate(&BofZ3, fImpProfile, fParForPofB);
+      fPofB->Calculate(&BofZ3, fImpProfile.get(), fParForPofB);
       fPofT->DoFFT();
 
     }/* else {
@@ -1141,7 +1038,6 @@ double TLondon1D3LS::operator()(double t, const vector<double> &par) const {
   }
 
   return fPofT->Eval(t);
-
 }
 
 // //------------------

src/external/libFitPofB/classes/TPofBCalc.cpp

@@ -553,7 +553,7 @@ void TPofBCalc::Calculate(const TBulkVortexFieldCalc *vortexLattice, const std::
         if (fill_index < fPBSize) {
           fPB[fill_index] += 1.0;
         } else {
-          cout << "Field over the limit..." << endl;
+          std::cout << "Field over the limit..." << std::endl;
         }
       }
 //      of << endl;

src/external/libFitPofB/classes/TPofTCalc.cpp

@@ -13,7 +13,7 @@
 ***************************************************************************/
 
 /***************************************************************************
- *   Copyright (C) 2008-2023 by Bastian M. Wojek, Andreas Suter            *
+ *   Copyright (C) 2008-2024 by Bastian M. Wojek, Andreas Suter            *
  *                                                                         *
  *                                                                         *
  *   This program is free software; you can redistribute it and/or modify  *
@@ -36,12 +36,14 @@
 #include "config.h"
 #endif
 
-#include "TPofTCalc.h"
-#include "fftw3.h"
 #include <cmath>
-#include <iostream>
 #include <cstdio>
 #include <cstdlib>
+#include <iostream>
+#include <memory>
+
+#include "TPofTCalc.h"
+#include "fftw3.h"
 
 #ifdef HAVE_GOMP
 #include <omp.h>
@@ -217,7 +219,7 @@ double TPofTCalc::Eval(double t) const {
 // Parameters: output filename, par(dt, dB, timeres, channels, asyms, phases, t0s, N0s, bgs) optPar(field, energy)
 //---------------------
 
-void TPofTCalc::FakeData(const string &rootOutputFileName, const std::vector<double> &par, const std::vector<double> *optPar = 0) {
+void TPofTCalc::FakeData(const std::string &rootOutputFileName, const std::vector<double> &par, const std::vector<double> *optPar = 0) {
 
   //determine the number of histograms to be built
   unsigned int numHist(0);
@@ -314,8 +316,8 @@ void TPofTCalc::FakeData(const string &rootOutputFileName, const std::vector<dou
 
   std::cout << "TPofTCalc::FakeData: Adding Poisson noise ..." << std::endl;
 
-  TH1F* theoHisto;
-  TH1F* fakeHisto;
+  std::unique_ptr<TH1F> theoHisto;
+  std::unique_ptr<TH1F> fakeHisto;
   std::vector<TH1F*> histoData;
 
   TString name;
@@ -323,13 +325,13 @@ void TPofTCalc::FakeData(const string &rootOutputFileName, const std::vector<dou
     // create histos
     name   = "theoHisto";
     name  += i;
-    theoHisto = new TH1F(name.Data(), name.Data(), int(par[3]), -par[2]/2.0, (par[3]+0.5)*par[2]);
+    theoHisto = std::make_unique<TH1F>(name.Data(), name.Data(), int(par[3]), -par[2]/2.0, (par[3]+0.5)*par[2]);
     if (i < 10)
       name   = "hDecay0";
     else
       name   = "hDecay";
     name  += i;
-    fakeHisto = new TH1F(name.Data(), name.Data(), int(par[3]), -par[2]/2.0, (par[3]+0.5)*par[2]);
+    fakeHisto = std::make_unique<TH1F>(name.Data(), name.Data(), int(par[3]), -par[2]/2.0, (par[3]+0.5)*par[2]);
     // fill theoHisto
     #ifdef HAVE_GOMP
     #pragma omp parallel for default(shared) private(j) schedule(dynamic,chunk)
@@ -339,24 +341,18 @@ void TPofTCalc::FakeData(const string &rootOutputFileName, const std::vector<dou
 // end omp
 
     // fill fakeHisto
-    fakeHisto->FillRandom(theoHisto, (int)theoHisto->Integral());
+    fakeHisto->FillRandom(theoHisto.get(), (int)theoHisto->Integral());
 
     // keep fake data
-    histoData.push_back(fakeHisto);
-
-    // cleanup
-   if (theoHisto) {
-     delete theoHisto;
-     theoHisto = 0;
-   }
+    histoData.push_back(fakeHisto.get());
   }
 
   std::cout << "TPofTCalc::FakeData: Write histograms and header information to the file ..." << std::endl;
 
   // save the histograms as root files
   // create run info folder and content
-  TFolder *runInfoFolder = new TFolder("RunInfo", "Run Info");
-  TLemRunHeader *runHeader = new TLemRunHeader();
+  std::unique_ptr<TFolder> runInfoFolder = std::make_unique<TFolder>("RunInfo", "Run Info");
+  std::unique_ptr<TLemRunHeader> runHeader = std::make_unique<TLemRunHeader>();
   //snprintf(str, sizeof(str), "Fake Data generated from %s", pBFileName.Data());
   runHeader->SetRunTitle("Fake Data");
   if (optPar && (optPar->size() > 1)) { // set energy and field if they were specified
@@ -375,12 +371,12 @@ void TPofTCalc::FakeData(const string &rootOutputFileName, const std::vector<dou
     delete[] t0array;
     t0array = 0;
   }
-  runInfoFolder->Add(runHeader);
+  runInfoFolder->Add(runHeader.get());
 
   // create decay histo folder and content
-  TFolder *histoFolder = new TFolder("histos", "histos");
-  TFolder *decayAnaModule = new TFolder("DecayAnaModule", "DecayAnaModule");
-  histoFolder->Add(decayAnaModule);
+  std::unique_ptr<TFolder> histoFolder = std::make_unique<TFolder>("histos", "histos");
+  std::unique_ptr<TFolder> decayAnaModule = std::make_unique<TFolder>("DecayAnaModule", "DecayAnaModule");
+  histoFolder->Add(decayAnaModule.get());
   // no post pileup corrected (NPP)
   for (unsigned int i(0); i<histoData.size(); i++)
     decayAnaModule->Add(histoData[i]);
@@ -420,13 +416,9 @@ void TPofTCalc::FakeData(const string &rootOutputFileName, const std::vector<dou
   fakeHisto = 0;
 
   histoFolder->Clear();
-  delete histoFolder; histoFolder = 0;
   decayAnaModule->Clear();
-  delete decayAnaModule; decayAnaModule = 0;
 
   runInfoFolder->Clear();
-  delete runInfoFolder; runInfoFolder = 0;
-  delete runHeader; runHeader = 0;
 
   t0.clear();
   asy0.clear();